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

Impact of zinc supplementation on phenotypic antimicrobial resistance of fecal commensal bacteria from pre-weaned dairy calves

The objective of this study was to evaluate the impact of dietary zinc supplementation in pre-weaned dairy calves on the phenotypic antimicrobial resistance (AMR) of fecal commensal bacteria. A repository of fecal specimens from a random sample of calves block-randomized into placebo (n = 39) and zinc sulfate (n = 28) groups collected over a zinc supplementation clinical trial at the onset of calf diarrhea, calf diarrheal cure, and the last day of 14 cumulative days of zinc or placebo treatment were analyzed. Antimicrobial susceptibility testing was conducted for Enterococcus spp. (n = 167) and E. coli (n = 44), with one representative isolate of each commensal bacteria tested per sample. Parametric survival interval regression models were constructed to evaluate the association between zinc treatment and phenotypic AMR, with exponentiated accelerated failure time (AFT) coefficients adapted for MIC instead of time representing the degree of change in AMR (MIC Ratio, MR). Findings from our study indicated that zinc supplementation did not significantly alter the MIC in Enterococcus spp. for 13 drugs: gentamicin, vancomycin, ciprofloxacin, erythromycin, penicillin, nitrofurantoin, linezolid, quinupristin/dalfopristin, tylosin tartrate, streptomycin, daptomycin, chloramphenicol, and tigecycline (MR = 0.96-2.94, p > 0.05). In E. coli, zinc supplementation was not associated with resistance to azithromycin (MR = 0.80, p > 0.05) and ceftriaxone (MR = 0.95, p > 0.05). However, a significant reduction in E. coli MIC values was observed for ciprofloxacin (MR = 0.17, 95% CI 0.03-0.97) and nalidixic acid (MR = 0.28, 95% CI 0.15-0.53) for zinc-treated compared to placebo-treated calves. Alongside predictions of MIC values generated from these 17 AFT models, findings from this study corroborate the influence of age and antimicrobial exposure on phenotypic AMR.

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

Introduction. Dairy calves, particularly pre-weaned calves have been identified as a common source of multidrug resistant (MDR) Escherichia coli.Gap statement. E. coli strains isolated from dairy calves and the location of their resistance genes (plasmid or chromosomal) have not been well characterised.Aim. To characterise the phenotypic and genotypic features as well as the population structure of antimicrobial-resistant E. coli isolated from calves located on dairy farms that feed waste-milk to their replacement calves.Methodology. Recto-anal swab enrichments from 40 dairy calves (≤ 14 days old) located on four dairy farms were examined for tetracycline, streptomycin, ciprofloxacin, and third-generation cephalosporin resistant E. coli. Whole genome sequencing was performed using both short- and long-read technologies on selected antimicrobial resistant E. coli.Results. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli: 43 % (17/40) harboured tetracycline resistant, and 23 % (9/40) harboured chromosomal mediated AmpC producing E. coli. Whole genome sequencing of 27 isolates revealed five sequence types, with ST88 being the dominant ST (17/27, 63 % of the sequenced isolates) followed by ST1308 (3/27, 11 %), along with the extraintestinal pathogenic E. coli lineages ST69 (3/27, 11 %), ST10 (2/27, 7 %), and ST58 (2/27, 7 %). Additionally, 16 isolates were MDR, harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined.Conclusion. Our study identified a high incidence of tetracycline and streptomycin-resistant E. coli in dairy calves, and highlighted the presence of multidrug-resistant strains, emphasising the need for further investigation into potential associations with farm management practices.

The Diversity of Escherichia coli Pathotypes and Vaccination Strategies against This Versatile Bacterial Pathogen

Escherichia coli (E. coli) is a gram-negative bacillus and resident of the normal intestinal microbiota. However, some E. coli strains can cause diseases in humans, other mammals and birds ranging from intestinal infections, for example, diarrhea and dysentery, to extraintestinal infections, such as urinary tract infections, respiratory tract infections, meningitis, and sepsis. In terms of morbidity and mortality, pathogenic E. coli has a great impact on public health, with an economic cost of several billion dollars annually worldwide. Antibiotics are not usually used as first-line treatment for diarrheal illness caused by E. coli and in the case of bloody diarrhea, antibiotics are avoided due to the increased risk of hemolytic uremic syndrome. On the other hand, extraintestinal infections are treated with various antibiotics depending on the site of infection and susceptibility testing. Several alarming papers concerning the rising antibiotic resistance rates in E. coli strains have been published. The silent pandemic of multidrug-resistant bacteria including pathogenic E. coli that have become more difficult to treat favored prophylactic approaches such as E. coli vaccines. This review provides an overview of the pathogenesis of different pathotypes of E. coli, the virulence factors involved and updates on the major aspects of vaccine development against different E. coli pathotypes.

First Report of OXA-48 and IMP Genes Among Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates from Diarrheic Calves in Tunisia

Antimicrobial resistance is one of the most serious threats to human and animal health. Evidence suggests that the overuse of antimicrobial agents in animal production has led to the emergence and dissemination of multidrug-resistant isolates. The objective of this study was to assess the rate of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in calf feces and to characterize their resistance genes for antibiotics like beta-lactams and colistin, but also to determine their virulence genes. Fecal samples were collected from 100 diarrheic calves in the region of Bizerte, Tunisia. After isolation, E. coli isolates were screened for antimicrobial resistance against 21 antibiotics by the disc diffusion method. Characterization of β-lactamase genes and determination of associated resistance genes were performed by polymerase chain reaction. Among 71 E. coli isolates, 26 (36.6%) strains were ESBL-producing. Most of these isolates were multidrug-resistant (92.3%) and the most prevalent beta-lactamase genes detected were bla_CTX-M (n = 26), bla_SHV (n = 11), and bla_TEM (n = 8), whereas only 1 isolate carried the bla_CMY gene. In addition, resistance to carbapenems was detected in two isolates; one of them harbored both bla_OXA-48 and bla_IMP genes and the other isolate carried only the bla_IMP gene. Several resistance genes were identified for the first time in Tunisia from cases of diarrheic calves. Furthermore, to the best of our knowledge, this is the first report of detection and identification of carbapenem resistance genes and virulence genes from calves in North Africa. A high occurrence of antimicrobial resistance of E. coli recovered from fecal samples of calves with diarrhea was observed, highlighting the need for prudent use of antimicrobial agents in veterinary medicine to decrease the incidence of multidrug-resistant bacteria for both animals and humans.

Virulence potential of faecal <i>Escherichia coli</i> strains isolated from healthy cows and calves on farms in Perm Krai

Cattle are a reservoir of pathogenic and potentially pathogenic Escherichia coli (E. coli) strains, which can pose a threat to human and animal health. The aim of the study was to evaluate the occurrence of 22 virulence-associated genes (VAGs), as well as the prevalence of antimicrobial drug resistance and three different bla-genes among 49 E. coli strains isolated from healthy cattle. The presence of VAGs that are common among diarrheagenic E. coli (DEC) strains and/or extraintestinal pathogenic E. coli (ExPEC) strains was determined by amplifying specific gene sequences by PCR. The following VAGs associated with DEC were found: east1 in 24.5 % of the studied E. coli strains, estI in 10.2 %, ehxA in 8.2 %, stx2 in 6.1 %, eltA in 4.1 %, estII and stx1 in 2.0 % of the studied strains. The prevalence of ExPEC VAGs was: fimH – 91.8 %, afa/draBC – 61.2 %, iutA – 44.9 %, flu – 32.7 %, sfaDE and hlyF – 30.6 %, iroN – 22.4 %, ompT and papC – 20.4 %, kpsMTII and hlyA – 18.4 %, iss – 14.3 %, usp – 2.0 %, cnf1 and iha were not detected among the studied strains. Based on the found co-occurrence of VAGs “classical”, hetero-pathogenic and hybrid-pathogenic E. coli strains were found. E. coli strains isolated from cows had a higher diarrheagenic potential, whereas E. coli strains isolated from calves more frequently contained genes associated with the ExPEC pathotype. Among the studied E. coli strains, 77.6 % were resistant to ampicillin, 49.0 % to tetracycline, 20.4 % to chloramphenicol, 16.3 % to cefoperazone, 16.3 % to ceftriaxone, 16.3 % to aztreonam, 14.3 % to cefepime, 10.2 % to norfloxacin, 10.2 % to ciprofloxacin, 6.1 % to levofloxacin and 2.0 % to gentamicin. All strains were sensitive to meropenem and amikacin. 32.7 % of the studied E. coli strains were found to be multidrug resistant, as they were resistant to at least three groups of antibiotics. With PCR, the blaTEM, blaSHV, and blaCTX-M genes were detected in 100, 31.6, and 26.3 %, respectively, of strains resistant to at least one of the beta-lactam antibiotics. Thus, it was shown that the studied faecal E. coli of healthy cows and calves had a high hetero-pathogenic potential, therefore in the future molecular genetic characterization of these bacteria shall be an important part of the epizootic monitoring.

Multidrug-Resistant Enteropathogenic Escherichia coli Isolated from Diarrhoeic Calves, Milk, and Workers in Dairy Farms: A Potential Public Health Risk

Enteropathogenic Escherichia coli (EPEC) is a leading cause of diarrhoeagenic diseases in humans and cattle worldwide. The emergence of multidrug-resistant (MDR) EPEC from cattle sources is a public health concern. A total of 240 samples (75 diarrhoeic calves, 150 milk samples, and 15 workers) were examined for prevalence of EPEC in three dairy farms in Egypt. Antimicrobial resistance (AMR) traits were determined by antibiogram and polymerase chain reaction (PCR) detection of β-lactamase-encoding genes, plasmid-mediated quinolone resistance genes, and carbapenemase-encoding genes. The genetic relatedness of the isolates was assessed using repetitive extragenic palindromic sequence-based PCR (REP-PCR). EPEC isolates were detected in 22.7% (17/75) of diarrhoeic calves, 5.3% (8/150) of milk samples, and 20% (3/15) of worker samples. The detected serovars were O26 (5%), O111 (3.3%), O124 (1.6%), O126 (0.8%), and O55 (0.8%). AMR-EPEC (harbouring any AMR gene) was detected in 9.2% of samples. Among isolates, bla_TEM was the most detected gene (39.3%), followed by bla_SHV (32.1%) and bla_CTX-M-1 (25%). The qnrA, qnrB, and qnrS genes were detected in 21.4%, 10.7%, and 7.1% of isolates, respectively. The bla_VIM gene was detected in 14.3% of isolates. All EPEC (100%) isolates were MDR. High resistance rates were reported for ampicillin (100%), tetracycline (89.3%), cefazolin (71%), and ciprofloxacin (64.3%). Three O26 isolates and two O111 isolates showed the highest multiple-antibiotic resistance (MAR) indices (0.85–0.92); these isolates harboured bla_SHV-12 and bla_CTX-M-15 genes, respectively. REP-PCR genotyping showed high genetic diversity of EPEC, although isolates belonging to the same serotype or farm were clustered together. Two worker isolates (O111 and O26) showed high genetic similarity (80–95%) with diarrhoeic calf isolates of matched serotypes/farms. This may highlight potential inter-species transmission within the farm. This study highlights the potential high risk of cattle (especially diarrhoeic calves) as disseminators of MDR-EPEC and/or their AMR genes in the study area. Prohibition of non-prescribed use of antibiotics in dairy farms in Egypt is strongly warranted.

The role of Musca domestica and milk in transmitting pathogenic multidrug-resistant Escherichia coli and associated phylogroups to neonatal calves

Escherichia coli, as a global source of antimicrobial resistance, is a serious veterinary and public health concern. The transmission of pathogenic multidrug-resistant (MDR) E. coli within diarrheic calves and its correlation with Musca domestica and milk strains have been investigated. In total, 110, 80, and 26 E. coli strains were obtained from 70 rectal swabs from diarrheic calves, 60 milk samples and 20 M. domestica, respectively. Molecular pathotyping of E. coli revealed the presence of pathogenic E. coli with a higher percentage of shigatoxigenic strains within diarrheic calves and M. domestica at 46.4% and 34.6%, respectively. Phenotypic antimicrobial resistance revealed higher β-lactams resistance except for cefquinome that exhibited low resistance in M.domestica and milk strains at 30.8% and 30%, respectively. The extended-spectrum cephalosporin (ESC) resistant strains were detected within fecal, M. domestica, and milk strains at 69.1%, 73.1%, and 71.3%, respectively. All E. coli strains isolated from M. domestica exhibited MDR, while fecal and milk strains were harboring MDR at 99.1% and 85%, respectively. Molecular detection of resistant genes revealed the predominance of the bla_TEM gene, while none of these strains harbored the bla_OXA gene. The highest percentages for bla_CTXM and bla_CMYII genes were detected in M. domestica strains at 53.8% and 61.5%, respectively. Regarding colistin resistance, the mcr-1 gene was detected only in fecal and milk strains at 35.5% and 15%, respectively. A high frequency of phylogroup B2 was detected within fecal and M. domestica strains, while milk strains were mainly assigned to the B1 phylogroup. Pathogenic E. coli strains with the same phenotypic and genotypic antimicrobial resistance and phylogroups were identified for both diarrheic calves and M. domestica, suggesting that the possible role of M. domestica in disseminating pathogenic strains and antimicrobial resistance in dairy farms.

Identifying Associations in Minimum Inhibitory Concentration Values of Escherichia coli Samples Obtained From Weaned Dairy Heifers in California Using Bayesian Network Analysis

Objective

Many antimicrobial resistance (AMR) studies in both human and veterinary medicine use traditional statistical methods that consider one bacteria and one antibiotic match at a time. A more robust analysis of AMR patterns in groups of animals is needed to improve on traditional methods examining antibiotic resistance profiles, the associations between the patterns of resistance or reduced susceptibility for all isolates in an investigation. The use of Bayesian network analysis can identify associations between distributions; this investigation seeks to add to the growing body of AMR pattern research by using Bayesian networks to identify relationships between susceptibility patterns in Escherichia coli (E. coli) isolates obtained from weaned dairy heifers in California.

Methods

A retrospective data analysis was performed using data from rectal swab samples collected from 341 weaned dairy heifers on six farms in California and selectively cultured for E. coli. Antibiotic susceptibility tests for 281 isolates against 15 antibiotics were included. Bayesian networks were used to identify joint patterns of reduced susceptibility, defined as an increasing trend in the minimum inhibitory concentration (MIC) values. The analysis involved learning the network structure, identifying the best fitting graphical mode, and learning the parameters in the final model to quantify joint probabilities.

Results

The graph identified that as susceptibility to one antibiotic decreases, so does susceptibility to other antibiotics in the same or similar class. The following antibiotics were connected in the final graphical model: ampicillin was connected to ceftiofur; spectinomycin was connected with trimethoprim-sulfamethoxazole, and this association was mediated by farm; florfenicol was connected with tetracycline.

Conclusions

Bayesian network analysis can elucidate complex relationships between MIC patterns. MIC values may be associated within and between drug classes, and some associations may be correlated with farm of sample origin. Treating MICs as discretized variables and testing for joint associations in trends may overcome common research problems surrounding the lack of clinical breakpoints.

Invited Review: Antimicrobial Use and Antimicrobial Resistance in Pathogens Associated with Diarrhea and Pneumonia in Dairy Calves

Antimicrobial use (AMU) is the major driver of antimicrobial resistance (AMR) among bacteria in dairy herds. There have been numerous studies on AMU and AMR in dairy cows; however, studies on AMU and AMR in dairy calves are limited. A comprehensive overview of the current state of knowledge of AMU and AMR among pathogens in dairy calves is important for the development of scientifically supported and applicable measures to curb antimicrobial use and the increasing risk of AMR. Therefore, we performed a systematic review of research on AMU and AMR in dairy calves. A total of 75 publications were included, of which 19 studies reported AMU data for dairy calves and 68 described AMR profiles of the four most prevalent bacteria that are associated with calf diarrhea and calf pneumonia. Large variation in AMU was found among herds across different regions. There seems to be a positive association between exposure to antimicrobials and occurrence of resistance. Most AMU was accounted for by treatment of diseases, while a small proportion of AMU was prophylactic. AMU was more common in treating calf diarrhea than in treating pneumonia, and the resistance rates in bacteria associated with diarrhea were higher than those in pathogens related to pneumonia. Organic farms used significantly fewer antimicrobials to treat calf disease; however, the antimicrobial resistance rates of bacteria associated with calf diarrhea and pneumonia on both types of farms were comparable. Feeding waste or pasteurized milk was associated with a higher risk of AMR in pathogens. Altogether, this review summarizes AMU and AMR data for dairy calves and suggests areas for future research, providing evidence for the design of antimicrobial use stewardship programs in dairy calf farming.

Antimicrobial Susceptibility of Enterotoxigenic Escherichia coli from Diarrhoeic Neonatal Calves in Spain

Simple Summary

Neonatal calf diarrhoea, a worldwide concern for cattle production, can be caused by viral, bacterial and protozoan enteropathogens: the enterotoxigenic Escherichia coli (ETEC) is one of the most important. The use of antimicrobials for treating neonatal calf diarrhoea cases is still a common practice among veterinary surgeons, although its use is only justified in bacterial infections evolving towards a systemic disease. Since the indiscriminate use of antimicrobials for treating diarrhoeic calves increases the risk for the appearance of antimicrobial resistances, restrictions on the use of antimicrobials in veterinary practice were implemented. The aim of this study was to characterize the antimicrobial susceptibility of ETEC strains obtained from diarrhoeic calves. Our results are alarming since all ETEC strains were resistant to three or more families of antimicrobials; in addition, a high number of strains were resistant to most first-line antimicrobials used in veterinary practice. Only ceftiofur, cefoperazone, cefquinome and gentamicin presented efficacy against most ETEC strains. Thus, empirical treatment of calf scours caused by ETEC is usually ineffective. Our results reveal that performing antimicrobial susceptibility tests in each NCD outbreak is needed for establishing an effective treatment and avoiding the emergence of new resistance mechanisms.

Abstract

Enterotoxigenic Escherichia coli (ETEC) is one of the major pathogens involved in neonatal calf diarrhoea (NCD) causing high economic losses in dairy farms. Antibiotic treatment is common in cases of systemic illness caused by NCD, but antimicrobial susceptibility tests (AST) are usually not performed. Thus, the aim of this study was to characterize the antimicrobial susceptibility of ETEC strains obtained from calves with diarrhoea between 2018–2020. Faecal samples (n = 420) were analyzed to detect the typical ETEC virulence factors F5 and STa. Positive samples were cultured to identify and isolate ETEC strains (n = 41) and ASTs were performed. Our results are alarming since ETEC strains resistant to three or more families of antimicrobials were detected in all isolates. Only four antibiotics (ceftiofur, cefoperazone, cefquinome and gentamicin) presented efficacy against more than 90% of the ETEC strains, while the other ten antibiotics were effective against less than 40% of the strains. In addition, a high number of strains were resistant to most first-line antimicrobials used in veterinary practice. For this reason, when ETEC infection is suspected, an AST must always be performed to select the most appropriate antimicrobial in each case and to avoid the emergence of new resistance mechanisms.

Antimicrobial Resistance, Serologic and Molecular Characterization of E. coli Isolated from Calves with Severe or Fatal Enteritis in Bavaria, Germany

Worldwide, enterotoxigenic Escherichia coli (ETEC) cause neonatal diarrhea and high mortality rates in newborn calves, leading to great economic losses. In Bavaria, Germany, no recent facts are available regarding the prevalence of virulence factors or antimicrobial resistance of ETEC in calves. Antimicrobial susceptibility of 8713 E. coli isolates obtained from 7358 samples of diseased or deceased diarrheic calves were investigated between 2015 to 2019. Considerably high rates of 84.2% multidrug-resistant and 15.8% extensively drug-resistant isolates were detected. The resistance situation of the first, second and third line antimicrobials for the treatment, here amoxicillin-clavulanate, enrofloxacin and trimethoprim-sulfamethoxazole, is currently acceptable with mean non-susceptibility rates of 28.1%, 37.9% and 50.0% over the investigated 5-year period. Furthermore, the ETEC serotypes O101:K28, O9:K35, O101:K30, O101:K32, O78:K80, O139:K82, O8:K87, O141:K85 and O147:K89, as well as the virulence factors F17, F41, F5, ST-I and stx1 were identified in a subset of samples collected in 2019 and 2020. The substantially high rates of multi- and extensively drug-resistant isolates underline the necessity of continuous monitoring regarding antimicrobial resistance to provide reliable prognoses and adjust recommendations for the treatment of bacterial infections in animals.

Phenotypic and molecular characterizations of multidrug-resistant diarrheagenic E. coli of calf origin

Escherichia coli has become one of the most important causes of calf diarrhea. The aim of this study is to determine the patterns of antimicrobial resistance of E. coli isolates from six cattle farms and to identify prominent resistance genes and virulence genes among the strains isolated from the diarrhea of calves. Antimicrobial susceptibility tests were performed using the disk diffusion method, and PCR was used to detect resistance and virulence genes. The prevalence of multidrug resistant (MDR) E. coli was 77.8% in dairy cattle and 63.6% in beef cattle. There were high resistance rates to penicillin (100%, 100%) and ampicillin (96.3%, 86.4%) in E. coli from dairy cattle and beef cattle. Interestingly, resistance rate to antimicrobials and distribution of resistance genes in E. coli isolated from dairy cattle were higher than those in beef cattle. Further analysis showed that the most prevalent resistance genes were blaTEM and aadA1 in dairy cattle and beef cattle, respectively. Moreover, seven diarrheagenic virulence genes (irp2, fyuA, Stx1, eaeA, F41, K99 and STa) were present in the isolates from dairy cattle, with a prevalence ranging from 3.7% to 22.22%. Six diarrheagenic virulence genes (irp2, fyuA, Stx1, eaeA, hylA and F41) were identified in the isolates from beef cattle, with a prevalence ranging from 2.27% to 63.64%. Our results provide important evidence for better exploring their interaction mechanism. Further studies are also needed to understand the origin and transmission route of E. coli in cattle to reduce its prevalence.

Molecular Detection, Serotyping, and Antibiotic Resistance of Shiga Toxigenic Escherichia coli Isolated from She-Camels and In-Contact Humans in Egypt

This study aims to determine the prevalence of STEC in she-camels suffering from mastitis in semi-arid regions by using traditional culture methods and then confirming it with Serological and molecular techniques in milk samples, camel feces, as well as human stool samples for human contacts. In addition, an antibiotic susceptibility profile for these isolates was investigation. Mastitic milk samples were taken after California Mastitis Test (CMT) procedure, and fecal samples were taken from she-camels and human stool samples, then cultured using traditional methods to isolate Escherichiacoli. These isolates were initially classified serologically, then an mPCR (Multiplex PCR) was used to determine virulence genes. Finally, both camel and human isolates were tested for antibiotic susceptibility. Out of a total of 180 she-camels, 34 (18.9%) were mastitic (8.3% clinical and 10.6% sub-clinical mastitis), where it was higher in camels bred with other animals. The total presence of E. coli was 21.9, 13.9, and 33.7% in milk, camel feces, and human stool, respectively, whereas the occurrence of STEC from the total E. coli isolates were 36, 16, and 31.4% for milk, camel feces, and stool, respectively. Among the camel isolates, stx₁ was the most frequently detected virulence gene, while hlyA was not detected. The most detected virulence gene in human isolates was stx₂ (45.5%), followed by stx₁. Camel STEC showed resistance to Oxytetracycline only, while human STEC showed multiple drug resistance to Amoxicillin, Gentamycin, and Clindamycin with 81.8, 72.7, and 63.6%, respectively. Breeding camels in semi-arid areas separately from other animals may reduce the risk of infection with some bacteria, including E. coli; in contrast, mixed breeding with other animals contributes a significant risk factor for STEC emergence in camels.

Antimicrobial Resistance of Escherichia coli in Dairy Calves: A 15-Year Retrospective Analysis and Comparison of Treated and Untreated Animals

Simple Summary

In dairy production, antimicrobial resistance (AMR) is both a health and economic issue that may lead to treatment failures and the spread of multidrug-resistant pathogens. Epidemiological and farm data on AMR are instrumental for selecting the appropriate therapy. However, such data are not always available. We investigated the AMR profile of 2612 Escherichia coli strains isolated from cases of calf diarrhea over a 15-year period (2002–2016). Furthermore, the AMR profiles and major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves were examined, with a comparison made between those treated with antimicrobials (n = 406) and not treated (n = 99) as well as between the two age groups to evaluate the potential effects of treatments on AMR and pathogenicity. Resistance to tetracycline was the most common, followed by resistance to sulfamethoxazole/trimethoprim and flumequine. Treated calves showed a higher rate of AMR and virulence genes. These results highlight the risk of the frequent use of antimicrobials on calf microflora in leading to potentially ineffective treatments. A higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol was found in 1-week-old calves, suggesting the environment as a possible AMR source. In conclusion, measures such as improved hygiene in the calving pen, antimicrobial stewardship, and monitoring for resistant pathogens in manure should be promoted to prevent the spread of AMR.

Abstract

The health problem of antimicrobial resistance (AMR) involves several species. AMR surveillance is essential to identify its development and design control strategies; however, available data are still limited in some contexts. The AMR profiles of 2612 E. coli strains isolated over a period of 15 years (2002–2016) from calf enteric cases were analyzed to determine the presence of resistance and their temporal dynamics. Furthermore, the AMR profiles and the presence of the major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves, 406 treated with antimicrobials and 99 untreated, were analyzed and compared to investigate the potential effects of treatment on AMR and strain pathogenicity. Resistance to tetracycline (90.70%) was the most common, followed by resistance to sulfamethoxazole/trimethoprim (77.70%) and flumequine (72.10%). The significantly higher percentage of AMR and virulence gene expression recorded in treated calves, combined with the statistically higher resistance to sulfamethoxazole/trimethoprim in E. coli with K99, corroborates the notion of resistance being induced by the frequent use of antimicrobials, leading to treatments potentially becoming ineffective. The significantly higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol in isolates from 1-week-old calves suggests the role of the environment as a source of contamination that should be investigated further.

The Antibiotic Treatment of Calf Diarrhea in Four European Countries: A Survey

Neonatal calves are commonly affected by diarrhea caused by different pathogens, but not always bacteria. Yet, antibiotics are routinely used as a treatment to an unknown extent. It was our goal to survey antibiotic use for the treatment of neonatal calf diarrhea in different countries and to identify influencing factors. A total of 873 farmers and veterinarians in Austria, Belgium, Portugal, and Scotland participated in a voluntary online survey. The data were analyzed using classification and regression tree analyses and chi² tests. Overall, 52.5% of the participants stated that they use antibiotics when treating neonatal calf diarrhea. Of those, 27% use them always, and 45% use highest priority critically important antibiotics. The most important factor differentiating antibiotic use practices was the country the participants were from, which could be due to regulatory differences between the countries. All antibiotic products stated were licensed for use in cattle, but several were not licensed for the treatment of diarrhea in calves. Our study shows that there is an urgent need for more scientific evidence to define best practices for the treatment of neonatal calf diarrhea. Furthermore, consensual criteria for antibiotic therapy must be defined, and targeted training for farmers and veterinarians must be provided.

Molecular Analysis of Antimicrobial Resistance among Enterobacteriaceae Isolated from Diarrhoeic Calves in Egypt

Simple Summary

Bacterial antimicrobial resistance is a serious global health challenge. This study investigated the occurrence of major antimicrobial resistance genes, including integrons, ß-lactamases, and florfenicol in Enterobacteriaceae that were isolated from diarrhoeic calves in Egypt. From 120 calves, 149 isolates of bacteria were recovered, identified, and screened phenotypically against 12 antimicrobials, and molecularly for the presence of the resistance determinants of integrons, ß-lactamases and florfenicol. The findings revealed that 24.8% of the isolates exhibited multidrug resistance. Escherichia coli was found to be the most prevalent multidrug resistant species. Class 1 integrons, bla_TEM, and floR genes were detected at incidence rates of 18.8%, 24.8%, and 1.3%, respectively, whereas class 2 integrons and bla_CTX-M were not detected in any isolates. The higher incidence of the antimicrobial resistance genes indicate the importance of regular monitoring of the antibiotic susceptibilities of isolated bacteria to minimise the risk of human exposure to pathogens that are resistant to antimicrobials.

Abstract

The present study was designed to investigate the presence of genes that conferred resistance to antimicrobials among Enterobacteriaceae that were isolated from diarrhoeic calves. A total of 120 faecal samples were collected from diarrhoeic calves that were raised in Kafr El-Sheikh governorate, Egypt. The samples were screened for Enterobacteriaceae. A total of 149 isolates of bacteria were recovered and identified; Escherichia coli was found to be the most overwhelming species, followed by Citrobacter diversus, Shigella spp., Serratia spp., Providencia spp., Enterobacter spp., Klebsiella pneumoniae, Proteus spp., Klebsiella oxytoca, and Morganella morganii. All isolates were tested for susceptibility to 12 antimicrobials; resistant and intermediately resistant strains were screened by conventional polymerase chain reaction for the presence of antimicrobial resistance genes. Of the 149 isolates, 37 (24.8%) exhibited multidrug resistant phenotypes. The most prevalent multidrug resistant species were E. coli, C. diversus, Serratia spp., K. pneumoniae, Shigella spp., Providencia spp., and K. oxytoca. Class 1 integrons were detected in 28 (18.8%) isolates. All isolates were negative for class 2 integrons. The bla_TEM gene was identified in 37 (24.8%) isolates, whereas no isolates carried the bla_CTX-M gene_. The florfenicol gene (floR) was detected in two bacterial isolates (1.3%). The findings of this study reveal that calves may act as potential reservoirs of multidrug resistant bacteria that can be easily transmitted to humans.

Characterization of Multidrug-Resistant Biofilm-Producing Escherichia coli and Klebsiella pneumoniae in Healthy Cattle and Cattle with Diarrhea

This study describes comparative occurrence and characterization of multidrug-resistant (MDR) Escherichia coli and Klebsiella pneumoniae (KP) in healthy cattle (HC) and cattle with diarrhea (DC) in India. During 2018-2020, 72 MDR isolates, including 35 E. coli (DC: 27; HC 8) and 37 K. pneumoniae (DC: 34; HC: 3), from 251 rectal swabs (DC: 219; HC: 32) were investigated for extended-spectrum beta-lactamase (ESBL), AmpC type β-lactamase and carbapenemase production, antimicrobial susceptibility profile, biofilm production, and efflux pump activity. Fifty-five MDR isolates were ESBL producers (ESBLPs) (DC: 50; HC: 5) and ESBLPs from DC were coresistant to multiple antibiotics. The blaCTX-M gene (50) was the most frequently detected β-lactamases followed by blaAmpC (22), blaTEM1 (13), blaCMY-6 (6), blaOXA1 (5), blaPER (2), blaDHA, and blaFOX and blaSHV12 (1 each). Plasmid-mediated quinolone resistance determinants qnrB, qnrS, qnrA, and qepA were detected in 18, 16, 2, and 3 isolates, respectively. Twenty three isolates revealed mutation in gyrA and parC genes. Tetracycline-resistance markers tetA, tetB, tetC, and tetE were detected in 33, 10, 3, and 2 isolates, respectively. Only one of the 41 imipenem-resistant isolates harbored blaNDM-5 and two were colistin-resistant. Altogether, 20 MDR isolates were strong biofilm producers and 19 harbored different virulence factors. This is the first ever report from India on the presence of MDR Enterobacteriaceae with resistance to even last-resort antimicrobials in the bovine diarrhea.

Antimicrobial Resistance Profile and ExPEC Virulence Potential in Commensal Escherichia coli of Multiple Sources

We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.

Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however a major challenge since the data is not harmonized. This study performs a comparative analysis of data on resistance combinations in Escherichia coli (E. coli) from different routine surveillance and monitoring systems for human and different animal populations in Germany. Data on E. coli isolates were collected between 2014 and 2017 from human clinical isolates, non-clinical animal isolates from food-producing animals and food, and clinical animal isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Sixteen possible resistance combinations to four antibiotics—ampicillin, cefotaxime, ciprofloxacin and gentamicin–for these populations were used for hierarchical clustering (Euclidian and average distance). All analyses were performed with the software R 3.5.1 (Rstudio 1.1.442). Data of 333,496 E. coli isolates and forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together. They also clustered separately from the human populations. Cluster analysis has been able to demonstrate the linkage among human isolates and isolates from various animal populations based on the resistance combinations. Further analyses based on these findings might support a better one-health approach for AR in Germany.

The Use of Activated Micronized Zeolite Clinoptilolite as a Possible Alternative to Antibiotics and Chestnut Extract for the Control of Undifferentiated Calf Diarrhea: An In Vitro and In Vivo Study

Simple Summary

Today, zeolite has appeared as an interesting alternative for the symptomatic treatment of acute diarrhea. Therefore, this study aimed to investigate the properties of activated micronized (five microns) zeolite clinoptilolite (MZC) from Transylvania, Romania, first by testing it in vitro and then in vivo on calves with diarrhea. To assess the toxic potential of MZC, we performed a cell cytotoxicity assay on cells of bovine origin, while its antimicrobial activity was investigated on Escherichia coli. The uncontrolled in vivo study was carried out over 8 days on a fattening farm, with some 650 calves. Selected calves were randomly assigned to 4 groups of 20 individuals. Several combinations between activated MZC, chestnut extract, and oxytetracycline were tested. At the beginning of the study, all calves had diarrhea, while at the end of the study, the prevalence of diarrhea was significantly lower in all four groups (p < 0.001), including the ones treated with MZC. Due to its low cytotoxicity on the intestinal cells and with regards to the results we obtained in vivo, MZC could represent an alternative method to reducing the amount of antimicrobials needed for the symptomatic treatment of diarrhea in calves, therefore contributing to the reduction of the antimicrobial resistance phenomenon.

Abstract

Today, zeolite appears as an interesting alternative for the symptomatic treatment of acute diarrhea. Therefore, this study aimed to investigate the properties of activated micronized (5 microns) zeolite clinoptilolite (MZC) from Transylvania, Romania, first by testing it in vitro and then in vivo on calves with diarrhea. To assess the toxic potential of the MZC, we performed a cell cytotoxicity assay using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) technique on primary bovine intestinal epithelial cells (BIECs). The antimicrobial activity of MZC was investigated by measuring the minimal inhibitory concentration (MIC) on Escherichia coli (ATCC 25922). The uncontrolled in vivo study was carried out over 8 days on a fattening farm, with some 650 calves. Selected calves were randomly assigned to four groups of 20 individuals. Several combinations between MZC, chestnut extract, and oxytetracycline were tested. At the beginning of the study, all calves had diarrhea, while at the end of the study, the prevalence of diarrhea was significantly lower in all four groups (p < 0.001), including the ones treated with MZC. Due to its low cytotoxicity on the intestinal cells and with regards to the results we obtained in vivo, MZC may be considered an alternative for the symptomatic treatment of undifferentiated diarrhea in calves.

Antimicrobial Resistance Patterns in Organic and Conventional Dairy Herds in Sweden

Monitoring antimicrobial resistance (AMR) and use (AMU) is important for control. We used Escherichia coli from healthy young calves as an indicator to evaluate whether AMR patterns differ between Swedish organic and conventional dairy herds and whether the patterns could be related to AMU data. Samples were taken twice, in 30 organic and 30 conventional dairy herds. Selective culturing for Escherichia coli, without antibiotics and with nalidixic acid or tetracycline, was used to estimate the proportions of resistant isolates. Microdilution was used to determine the minimum inhibitory concentrations (MICs) for thirteen antimicrobial substances. AMU data were based on collection of empty drug packages. Less than 8% of the bacterial growth on non-selective plates was also found on selective plates with tetracycline, and 1% on plates with nalidixic acid. Despite some MIC variations, resistance patterns were largely similar in both periods, and between organic and conventional herds. For most substances, only a few isolates were classified as resistant. The most common resistances were against ampicillin, streptomycin, sulfamethoxazole, and tetracycline. No clear association with AMU could be found. The lack of difference between organic and conventional herds is likely due to a generally good animal health status and consequent low AMU in both categories.

Antimicrobial resistance in ovine bacteria: A sheep in wolf's clothing?

BACKGROUND

To monitor the prevalence of antimicrobial resistance (AMR), methods for interpretation of susceptibility phenotypes of bacteria are needed. Reference limits to declare resistance are generally based on or dominated by data from human bacterial isolates and may not reflect clinical relevance or wild type (WT) populations in livestock or other hosts.

METHODS

We compared the observed prevalence of AMR using standard and bespoke interpretations based on clinical breakpoints or epidemiological cut-offs (ECOFF) using gram positive (Staphylococcus aureus) and gram negative (Escherichia coli) bacteria from sheep as exemplars. Isolates were obtained from a cross-sectional study in three lowland sheep flocks in Scotland, and from a longitudinal study in one flock in Norway. S. aureus (n = 101) was predominantly isolated from milk or mammary glands whilst E. coli (n = 103) was mostly isolated from faecal samples. Disc diffusion testing was used to determine inhibition zone diameters, which were interpreted using either clinical breakpoints or ECOFF, which distinguish the bacterial wild type population from bacteria with acquired or mutational resistance to the compound of interest (non-wild type). Standard ECOFF values were considered as well as sheep-specific values calculated from the data using Normalized Resistance Interpretation (NRI) methodology.

RESULTS

The prevalence of AMR as measured based on clinical breakpoints was low, e.g. 4.0% for penicillin resistance in S. aureus. Estimation of AMR prevalence based on standard ECOFFs was hampered by lack of relevant reference values. In addition, standard ECOFFS, which are predominantly based on human data, bisected the normal distribution of inhibition zone diameters for several compounds in our analysis of sheep isolates. This contravenes recommendations for ECOFF setting based on NRI methodology and may lead to high apparent AMR prevalence. Using bespoke ECOFF values based on NRI, S. aureus showed non-wild type for less than 4% of isolates across 13 compounds, and ca. 13% non-wild type for amoxicillin and ampicillin, while E. coli showed non-wild type for less than 3% of isolates across 12 compounds, and ca. 13% non-wild type for tetracyclines and sulfamethoxazole-trimethoprim.

CONCLUSION

The apparent prevalence of AMR in bacteria isolated from sheep is highly dependent on interpretation criteria. The sheep industry may want to establish bespoke cut-off values for AMR monitoring to avoid the use of cut-offs developed for other host species. The latter could lead to high apparent prevalence of resistance, including to critically important antimicrobial classes such as 4th generation cephalosporins and carbapenems, suggesting an AMR problem that may not actually exist.

Epidemiology of carbapenem-resistant Escherichia coli and first report of blaVIM carbapenemases gene in calves from India

A cross-sectional study on six dairy farms was conducted to ascertain the occurrence of carbapenem-resistant Escherichia coli in calves. Two-hundred and seventy-nine isolates of E. coli were recovered from 90 faecal samples from apparently healthy (45) and diarrhoeal (45) calves. The isolates were screened for phenotypic susceptibility to carbapenems and production of metallo β-lactamase, as well as five carbapenemase resistance genes by PCR, and overexpression of efflux pumps. Eighty-one isolates (29.03%) were resistant to at least one of three carbapenem antibiotics [meropenem (23.30%), imipenem (2.15%) and ertapenem (1.43%)], and one isolate was positive for the blaVIM gene which was located on an Incl1 plasmid of a novel sequence type (ST 297) by multilocus sequence typing. The majority (83.95%) of isolates had an active efflux pump. Calves housed on concrete floors were approximately seven times more likely to acquire meropenem-resistant isolates than those housed on earthen floors (95% CI 1.27–41.54). In India, carbapenem drugs are not used in food animal treatment, hence carbapenem-resistant strains in calves possibly originate from the natural environment or human contact and is of public health importance. To our knowledge, this is the first report of blaVIM carbapenemases gene in calves from India.

Caution at choosing a particular colony-forming unit from faecal Escherichia coli: it may not represent the sample profile

Data about phylogenetic classification of Escherichia coli colonizing calves, lambs and foals are routinely neglected and restricted to outdated methodologies, even in the context of antimicrobial susceptibility (AS) testing. Thus, the aim of this study was to determine the phylogenetic diversity and the AS profile of E. coli colony-forming units (CFUs) from faecal samples of healthy animals. Five CFUs of E. coli were randomly selected from each faecal culture of calves (n = 13), foals (n = 13) and lambs (n = 13), totalizing 195 CFUs phylo-typed by quadruplex PCR. The AS profile of five CFUs from 15 samples (five from each animal species; n = 75 isolates) against nine drugs was determined by agar diffusion test. We found E. coli belonging to all phylo-groups already described, except D group, with the predominance of B1 (65% CFUs; 126/195) in the three-animal species sampled. Most faecal samples of calves (77%; 10/13) and foals (69%; 9/13) harboured both pathogenic and nonpathogenic E. coli. All faecal samples showed CFUs with diverse AS profile, highlighting the ineffectiveness of tetracycline, sulphonamide and ampicillin. As a key point, our data reinforce the importance to select at least four E. coli CFUs for AS testing. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides relevant data about the high phylogenetic and antimicrobial susceptibility diversity observed in Escherichia coli colony-forming units (CFUs) from a bacteriological culture of faeces from healthy calves, foals and lambs. The selection pressure exerted by the herd treatment may directly impact the intestinal microflora of animals that have never been treated. Finally, we emphasize the importance of Clinical Laboratory Standards Institute guidelines and we recommended to analyse at least four E. coli CFUs to determine, in particular, the antimicrobial susceptibility profile of faecal isolates, independent of the animal's health status.

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.

Antimicrobial resistance in E. coli isolated from dairy calves and bedding material

INTRODUCTION

E. coli is a ubiquitous bacterium commonly used as a sentinel in antimicrobial resistance studies. Here, E. coli was isolated from three groups (sick calves, healthy calves and bedding material), to assess the presence of antimicrobial resistance, describe resistance profiles, and compare these resistances among groups.

MATERIAL AND METHODS

Samples were collected from calves and calving pens from 20 dairy farms. Using the disc diffusion method, E. coli isolates were screened for antimicrobial resistance against seven antimicrobials: Amoxicillin, Ceftiofur, Gentamicin, Enrofloxacin, Trimethoprim-sulfamethoxazole, Florfenicol and Oxytetracycline. Isolates resistant to all these seven antimicrobials were tested again against an extended 19 antimicrobial drug panel and for the presence of the most common E. coli pathogenicity genes through PCR.

RESULTS & DISCUSSION

Three hundred forty-nine E. coli isolates were obtained; most isolates were resistant to a single antimicrobial, but 2.3% (8) were resistant to 16 to 19 of the antimicrobials tested. The group with the highest percentage of multiresistant isolates was the calves with diarrhea group. Younger calves provided samples with higher antimicrobial resistance levels.

CONCLUSIONS

There is a high rate of antimicrobial resistance in dairy farms calving pens. These bacteria could not only be a resistance gene reservoir, but also could have the potential to spread these determinants through horizontal gene transfer to other susceptible bacteria. Measures should be taken to protect colonization of younger calves, based on hygienic measures and proper management.

Antibiogram, virulotyping and genetic diversity of Escherichia coli and Salmonella serovars isolated from diarrheic calves and calf handlers

Antimicrobial resistance profile of E. coli and Salmonella serovars isolated from diarrheic calves and handlers in Egypt is unknown due to the absence of monitoring. Therefore, this study aimed to determine the virulence, genetic and antimicrobial resistance profiles of E. coli and Salmonella serovars associated with diarrhea in calves and handlers in intensive dairy farms in Egypt. A total of 36 bacterial strains (20 E. coli and 16 Salmonella) were isolated from fecal samples of 80 diarrheic Holstein dairy calves (10 E. coli and 13 Salmonella) and hand swabs of 35 handlers (10 E. coli and 3 Salmonella) in two intensive dairy farms in Sharkia Governate in Egypt. E. coli strains belonged to six different serogroups and O114:K90 was the most prevalent serogroup (30%). However, Salmonella strains were serotyped into four different serogroups and S. Kiel was the most prevalent serotype (50%). Thirteen (65%) E. coli isolates were harbouring either stx2, eaeA and/or astA virulence-associated genes. However, stn and spvC virulence genes were detected in 2 (12.5%) and 4 (25%) of Salmonella isolates, respectively. E. coli isolates showed marked resistance to ampicillin (75%), while Salmonella strains exhibited high resistance to amikacin (100%), gentamicin (93.75%) and tobramycin (87.5%). Results of the present study showed that E. coli and Salmonella serovars isolated from diarrheic calves and handlers in intensive dairy farms in Egypt exhibited resistance to multiple classes of antimicrobials, which may pose a public health hazard. Thus, the continuous monitoring of antimicrobial resistance is necessary for both humans and veterinary medicine to decrease the economic losses caused by antimicrobial-resistant strains in animals as well as the zoonotic risk.

Longitudinal Shedding Patterns and Characterization of Antibiotic Resistant E. coli in Pastured Goats using a Cohort Study

There is a scarcity of information on antibiotic resistance in goats. To understand shedding of resistant Escherichia coli in pastured goats, we collected fecal samples from a mixed age cohort over a one-year period. No antibiotic had been used on the study animals one year prior to and during the study period. Resistant isolates were detected in all age groups and prevalence in goat kids was significantly higher than adults; 43–48% vs. 8–25% respectively. The proportion of resistant isolates was higher when animals were congregated near handling facility than on pasture. Most isolates were resistant to tetracycline (51%) and streptomycin (30%), but also to antibiotics that had never been used on the farm; ampicillin (19%). TetB, bla_-TEM, (aadA and strpA/strpB) genes were detected in 70%, 43%, (44% and 24%) of tetracycline, ampicillin, and streptomycin resistant isolates respectively. Resistant isolates also harbored virulent genes and some belonged to D and B2 phylogenetic groups. Thus, pastured goats, despite minimal exposure to antibiotics, are reservoirs of resistant E. coli that may contaminate the environment and food chain and spread resistant genes to pathogenic bacteria and some that are potential animal and human pathogens. Environmental sources may play a role in acquisition of resistant bacteria in pastured goats.

Modification of outer membrane permeability and alteration of LPS in veterinary enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) is a worrying cause of diarrhoea in calves and the drug multiresistance phenotype concerning various antibiotic families are of concern. Resistance mechanisms associated with envelope changes (porin expression, efflux pump overexpression, lipolysaccahride (LPS) modification) were studied in 14 ETEC isolates selected for their resistance. We performed determinations of (i) antimicrobials Minimal Inhibitory Concentrations with or without the efflux pump inhibitor phenylalanine arginine β-naphthylamide; (ii) colistin and polymyxin MICs with and without EDTA, (iii) intracellular accumulation of chloramphenicol in presence of an energy uncoupler of pump energy, (iv) and immunodetection of porins and evaluation of porin trimers thermostability. Results indicated that 9 strains presented significant efflux mechanisms overexpression, among them 8 were resistant to colistin and polymyxin B due to a modification of LPS structure as evidenced by EDTA effect and silver staining electrophoresis. The high resistant strains to colistin and polymyxin exhibited identical LPS patterns. Studies of E. coli porins indicated that the majority of strains didn't show modification in their amount, however analysis of porin thermostability showed that porin trimers of some resistant strains were relatively heat-labile, suggesting a misassembly of the functional trimer. The multidrug resistance (MDR) phenotypes detected in these selected ETEC corresponded to association of LPS modifications, abordive assembly of porin trimers and active efflux which drastically alter the antibiotic activity currently used to combat enteric infections caused by this pathogen.

Characterization of intestinal Escherichia coli isolated from calves with diarrhea due to rotavirus and coronavirus

PURPOSE

To address more information about changes in commensal Escherichia coli during virus intestinal infection, we characterized 30 faecal E. coli isolates from calves (21 to 60 days old) with diarrhea due to rotavirus and coronavirus, which received, before diagnosis, tetracycline, gentamicin and enrofloxacin drugs.

METHODOLOGY

Clermont's phylogenetic classification; presence of genes for curli, cellulose, fimbriae (F4, F5, F6, F18, F41); and antimicrobial susceptibility were used to characterize the isolates. Disk diffusion technique and PCR were used as methodologies.

RESULTS

E. coli isolates from calves with diarrhea were phylogenetically classified as B1 (70%, 21/30), B2 (3.33%, 1/30), C (3.33%, 1/30), D (3.33%, 1/30), E (13.33%, 4/30) and unknown (6.7 %; 2/30), whereas E. coli isolates from the control group were classified only as B1 (83.3%, 25/30), E (10 %; 3/30) and unknown (6,7 %; 2/30). E. coli isolates from calves with diarrhea showed a much higher resistance profile with 16 (53.3%) multiresistant isolates. Only isolates (30%-9/30) from diarrheic calves were also positive for fimbriae, specifically 16.7% (5/30) for F5 and 13.3% (4/30) for F18.

CONCLUSION

To sum up, E. coli isolates from calves with diarrhea showed differences in relation to the control group, confirming changes in commensal E. coli during virus intestinal infection. It can be emphasized that some care should be taken to manage diarrheic calves: the pathological agent must be diagnosed prior to treatment; antibacterial treatment should be with antimicrobials with a different mechanism of action; and finally, treated animals should be maintained separately from others because they can carry micro-organisms with a resistant profile.

Evaluation of virulence factors profiles and antimicrobials resistance of Escherichia coli isolated from bulk tank milk and raw milk filters

Data on the presence of pathogenic Escherichia coli in bulk tank milk (BTM) and raw milk filters (RMF) are not available in Italy and there are few studies worldwide. Therefore, a study under field condition was conducted to assess the presence of E.coli pathogenic and commensal (CoEC) strains in BTM and RMF samples and their associated AMR pattern. One hundred forty-nine E.coli isolates were characterized. Among all the isolates, 53 (35.6%) were classified as pathogenic while the other ones were classified as CoEC. Among the pathogenic ones, 23 (54.7%) were classified as enterotoxigenic E.coli (ETEC), 6 (11.3%) as enteroinvasive E.coli (EIEC), 2 (3.8%) as enteroaggregative E.coli (EAEC), 12 (22.6%) harboured virulence factors (VF) common to ETEC+EIEC, and 2 (3.8%) common to ETEC+EAEC. To our knowledge, it is the first time that ETEC isolates harboring VF associated with EAEC or EIEC are observed in raw milk. These data support the presence of transmission of VFs genes among isolates. None of the isolates showed resistance to three or more antimicrobials. The CoEC role as a vector of AMR was confirmed by the presence of 18% ampicillin- and cephalexin-resistant isolates. The presence of AMR in CoEC supports the role of these bacteria as source of resistance genes. Monitoring raw milk by either BTM or RMF analysis, and the relatively cheap procedure applied to identify E.coli pathotypes can be useful to identify hazards related to the spread of enteric diseases and antimicrobial resistance.

Molecular analysis of Shiga toxin-producing Escherichia coli O157:H7 and non-O157 strains isolated from calves

Shiga toxin-producing Escherichia coli (STEC) O157 and non-O157 are food-borne pathogens and contaminants of foods of animal origin. This study was conducted to investigate the presence of virulence and integrase genes in STEC isolates from diarrhoeic calves in Fars Province, Iran. Five hundred and forty diarrheic neonatal calves were randomly selected for sampling. Rectal swabs were collected and cultured for isolation and identification of E. coli following standard methods. The isolates were analysed for the presence of class 1 integrons and bacterial virulence factors using polymerase chain reaction (PCR). Antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion method. Out of 540 diarrhoeic faecal samples, 312 (57.7%) harboured E. coli and 71 (22.7%) of them were identified as STEC: 41(69.5%) carried the stx2 gene, 21 (35.6%) carried the stx1 gene and 3 (5%) carried both. Twenty-six (44%) of the isolates showed the eaegene. Among the STEC isolates examined for susceptibility to eight antimicrobial agents, erythromycin and penicillin (96.8%) resistance were most commonly observed, followed by resistances to ampicillin (71.8%), tetracycline (62.5%) and trimethoprim/sulfamethoxazole (39%). Integrons were detected by PCR in 36% of the STEC tested isolates, 57 (89%) of which showed resistance to at least three antimicrobial agents. Our findings should raise awareness about antibiotic resistance in diarrhoeic calves in Fars Province, Iran. Class 1 integrons facilitate the emergence and dissemination of multidrug-resistance (MDR) among STEC strains recovered from food animals.

Proteomics for Drug Resistance on the Food Chain? Multidrug-Resistant Escherichia coli Proteomes from Slaughtered Pigs

Understanding global drug resistance demands an integrated vision, focusing on both human and veterinary medicine. Omics technologies offer new vistas to decipher mechanisms of drug resistance in the food chain. For example, Escherichia coli resistance to major antibiotics is increasing whereas multidrug resistance (MDR) strains are now commonly found in humans and animals. Little is known about the structural and metabolic changes in the cell that trigger resistance to antimicrobial agents. Proteomics is an emerging field that is used to advance our knowledge in global health and drug resistance in the food chain. In the present proteomic analysis, we offer an overview of the global protein expression of different MDR E. coli strains from fecal samples of pigs slaughtered for human consumption. A full proteomic survey of the drug-resistant strains SU60, SU62, SU76, and SU23, under normal growth conditions, was made by two-dimensional electrophoresis, identifying proteins by MALDI-TOF/MS. The proteomes of these four E. coli strains with different genetic profiles were compared in detail. Identical transport, stress response, or metabolic proteins were discovered in the four strains. Several of the identified proteins are essential in bacterial pathogenesis (GAPDH, LuxS, FKBPs), development of bacterial resistance (Omp's, TolC, GroEL, ClpB, or SOD), and potential antibacterial targets (FBPA, FabB, ACC's, or Fab1). Effective therapies against resistant bacteria are crucial and, to accomplish this, a comprehensive understanding of putative resistance mechanisms is essential. Moving forward, we suggest that multi-omics research will further improve our knowledge about bacterial growth and virulence on the food chain, especially under antibiotic stress.

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.

Prevalence of Salmonella and E. coli in neonatal diarrheic calves

Neonatal calf diarrhea remains one of the most important problems faced by livestock, causing great economic losses. This study investigated the prevalence of Salmonella and Escherichia coli, especially enterotoxigenic E.  coli (ETEC), in diarrheic calves. Fecal samples were collected from 127 diarrheic calves up to 3 months of age at 12 farms from different governorates in Egypt. 119 bacterial isolates (93.7%) were recovered and the prevalences of Salmonella and E.  coli in diarrheic calves were 18.1% and 75.6%, respectively. Serotyping of Salmonella isolates revealed that S. Enteritidis and S. Typhimurium were the most prevalent serotypes, representing 60.9% and 30.4%, respectively, while S. Dublin was 8.7%. Serogrouping of E.  coli isolates showed that 10 O-serogroups were obtained where O₂₆ and O₁₀₃ were the most prevalent (17.7% of each). Salmonella serotypes showed positive results with PCR test using oligonucleotide primer amplifying 521 bp fragment of invA gene of Salmonella while 70% of E.  coli serogroups possessed ETEC virulent gene (K99). The in-vitro antibiotic sensitivity test indicated that Salmonella serotypes showed high sensitivity against enrofloxacin, spectinomycin and neomycin while E.  coli isolates showed high sensitivities against marbofloxacin, spectinomycin and neomycin only.

Effects of selection pressure and genetic association on the relationship between antibiotic resistance and virulence in Escherichia coli

Antibiotic selection pressure and genetic associations may lead to the cooccurrence of resistance and virulence in individual pathogens. However, there is a lack of rigorous epidemiological evidence that demonstrates the cooccurrence of resistance and virulence at the population level. Using samples from a population-based case-control study in 25 villages in rural Ecuador, we characterized resistance to 12 antibiotics among pathogenic (n = 86) and commensal (n = 761) Escherichia coli isolates, classified by the presence or absence of known diarrheagenic virulence factor genes. The prevalences of resistance to single and multiple antibiotics were significantly higher for pathogenic isolates than for commensal isolates. Using a generalized estimating equation, antibiotic resistance was independently associated with virulence factor carriage, case status, and antibiotic use (for these respective factors: odds ratio [OR] = 3.0, with a 95% confidence interval [CI] of 1.7 to 5.1; OR = 2.0, with a 95% CI of 1.3 to 3.0; and OR = 1.5, with a 95% CI of 0.9 to 2.5). Virulence factor carriage was more strongly related to antibiotic resistance than antibiotic use for all antibiotics examined, with the exception of fluoroquinolones, gentamicin, and cefotaxime. This study provides epidemiological evidence that antibiotic resistance and virulence factor carriage are linked in E. coli populations in a community setting. Further, these data suggest that while the cooccurrence of resistance and virulence in E. coli is partially due to antibiotic selection pressure, it is also genetically determined. These findings should be considered in developing strategies for treating infections and controlling for antibiotic resistance.

Synthesis and application of glycoconjugate-functionalized magnetic nanoparticles as potent anti-adhesion agents for reducing enterotoxigenic Escherichia coli infections

Polyethylene oxide stabilized magnetic nanoparticles (PEO-MNPs) bio-functionalized with glycoconjugate (Neu5Ac(α2-3)Gal(β1-4)Glcβ-sp) (GM3-MNPs) are synthesized using click chemistry. Interaction of GM3-MNPs with Enterotoxigenic Escherichia coli (ETEC) strain K99 (EC K99) is investigated using different microscopic techniques. Our results suggest that GM3-MNPs can effectively act as non-antibiotic anti-adhesion agents for treating ETEC infections.

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.

Effect of preweaned dairy calf housing system on antimicrobial resistance in commensal Escherichia coli

Group housing of preweaned dairy calves is a growing practice in the United States. The objective of this practice is to increase the average daily gain of calves in a healthy and humane environment while reducing labor requirements. However, feeding protocols, commingling of calves, and occurrence of disease in different calf-housing systems may affect the prevalence of antimicrobial drug-resistant bacteria. This study evaluated the effect of a group pen-housing system and individual pen-housing system on antimicrobial resistance trends in fecal Escherichia coli of preweaned dairy calves and on the prevalence of environmental Salmonella. Twelve farms from central New York participated in the study: 6 farms using an individual pen-housing system (IP), and 6 farms using a group pen-housing system (GP). A maximum of 3 fecal E. coli isolates per calf was tested for susceptibility to 12 antimicrobial drugs using a Kirby-Bauer disk diffusion assay. Calves in GP had a significantly higher proportion of E. coli resistant to ciprofloxacin and nalidixic acid, whereas calves in IP had a significantly higher proportion of E. coli resistant to ampicillin, ceftiofur, gentamycin, streptomycin, and tetracycline. Calf-housing system had an effect on resistance to individual antimicrobial drugs in E. coli, but no clear-cut advantage to either system was noted with regard to overall resistance frequency. No outstanding difference in the richness and diversity of resistant phenotypes was observed between the 2 calf-housing systems.

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.

Characterization of Escherichia coli virulence genes, pathotypes and antibiotic resistance properties in diarrheic calves in Iran

Background

Calf diarrhea is a major economic concern in bovine industry all around the world. This study was carried out in order to investigate distribution of virulence genes, pathotypes, serogroups and antibiotic resistance properties of Escherichia coli isolated from diarrheic calves.

Results

Totally, 76.45% of 824 diarrheic fecal samples collected from Isfahan, Chaharmahal, Fars and Khuzestan provinces, Iran were positive for E. coli and all of them were also positive for cnf2, hlyA, cdtIII, f17c, lt, st, stx1, eae, ehly, stx2 and cnf1 virulence genes. Chaharmahal had the highest prevalence of STEC (84.61%), while Isfahan had the lowest (71.95%). E. coli serogroups had the highest frequency in 1–7 days old calves and winter season. Distribution of ETEC, EHEC, AEEC and NTEC pathotypes among E. coli isolates were 28.41%, 5.07%, 29.52% and 3.49%, respectively. Statistical analyses were significant for presence of bacteria between various seasons and ages. All isolates had the high resistance to penicillin (100%), streptomycin (98.25%) and tetracycline (98.09%) antibiotics. The most commonly detected resistance genes were aadA1, sul1, aac[3]-IV, CITM, and dfrA1. The most prevalent serogroup among STEC was O26.

Conclusions

Our findings should raise awareness about antibiotic resistance in diarrheic calves in Iran. Clinicians should exercise caution when prescribing antibiotics.

Prevalence, biogenesis, and functionality of the serine protease autotransporter EspP

Enterohemorrhagic E. coli (EHEC) causes severe diseases in humans worldwide. One of its virulence factors is EspP, which belongs to the serine protease autotransporters of Enterobacteriaceae (SPATE) family. In this review we recapitulate the current data on prevalence, biogenesis, structural properties and functionality. EspP has been used to investigate mechanistic details of autotransport, and recent studies indicate that this transport mechanism is not autonomous but rather dependent on additional factors. Currently, five subtypes have been identified (EspPα-EspPε), with EspPα being associated with highly virulent EHEC serotypes and isolates from patients with severe disease. EspPα has been shown to degrade major proteins of the complement cascade, namely C3 and C5 and probably interferes with hemostasis by cleavage of coagulation factor V. Furthermore, EspPα is believed to contribute to biofilm formation perhaps by polymerization to rope-like structures. Together with the proteolytic activity, EspPα might ameliorate host colonization and interfere with host response.

Shiga toxin-producing Escherichia coli isolated from bovine mastitic milk: serogroups, virulence factors, and antibiotic resistance properties

The aim of this study was to detect the virulence factors, serogroups, and antibiotic resistance properties of Shiga toxin-producing Escherichia coli, by using 268 bovine mastitic milk samples which were diagnosed using California Mastitis Test. After E. coli identification, PCR assays were developed for detection of different virulence genes, serogroups, and antibiotic resistance genes of Escherichia coli. The antibiotic resistance pattern was studied using disk diffusion method. Out of 268 samples, 73 (27.23%) were positive for Escherichia coli, and, out of 73 positive samples, 15 (20.54%) were O26 and 11 (15.06%) were O157 so they were the highest while O111 was not detected in any sample so it was the lowest serogroup. Out of 73 STEC strains, 11 (15.06%) and 36 (49.31%) were EHEC and AEEC, respectively. All of the EHEC strains had stx1, eaeA, and ehly, virulence genes, while in AEEC strains stx1 had the highest prevalence (77.77%), followed by eaeA (55.55%). Totally, aadA1 (65.95%) had the highest while blaSHV (6.38%) had the lowest prevalence of antibiotic resistance genes. The disk diffusion method showed that the STEC strains had the highest resistance to penicillin (100%), followed by tetracycline (57.44%), while resistance to cephalothin (6.38%) was the lowest.