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Antimicrobials have been widely used in dairy farms to prevent and control dairy cattle diseases since 1960s. This led to the emergence of antimicrobial resistant bacteria (ARB) that, along with their antimicrobial resistance genes (ARGs), can spread from dairy farms to humans. Therefore, regular antimicrobial resistance (AMR) monitoring is important to implement proper mitigation measures. The objective of this study was to determine the prevalence of AMR and extended-spectrum beta-lactamases (ESBLs)-producing Escherichia coli in dairy cattle. A cross-sectional study was conducted in four dairy cattle farms (A-D) in East Tennessee. A total of 80 samples consisting of 20 samples each of bulk tank milk, feces, dairy cattle manure-amended soil, and prairie soil adjacent to the farms were collected and cultured for the isolation of E. coli . Tetracycline (TET r )-, third-generation cephalosporin (TGC r )- and nalidixic acid (NAL r )-resistant E. coli ( n  = 88) were isolated and identified on agar media supplemented with TET, cefotaxime, and NAL, respectively. TGC r E. coli were tested for ESBLs and other coselected ARGs. TET r (74%, n  = 88) was the most common, followed by TGC r (20%) and NAL r (8%). Farms had significant ( p  < 0.001) differences: the highest prevalence of TGC r (55%) and TET r (100%) were observed in farm D, while all NAL r isolates were from farm C. Over 83% of TGC r isolates ( n  = 18) harbored ESBL gene bla CTX-M . Majority (78%) of the E. coli isolates were multidrug-resistant (MDR), being positive for beta-lactams ( bla CTX-M ), TETs tet ( A ), tet ( B ), tet ( M )), sulfonamides ( sul 2), aminoglycosides ( strA ), and phenicols ( floR ). This study indicated the widespread occurrence of MDR ESBLs- E. coli in dairy cattle farms. AMR surveillance of more dairy farms and identification of farm-level risk factors are important to mitigate the occurrence and spread of ARB of significant public health importance, such as ESBLs- E. coli .

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

Enterobacteria that produce extended-spectrum β-lactamase (ESBL) such as Escherichia coli (E. coli) are common in our environment and known to cause serious health implications in humans and animals. β-lactam antibiotics such as penicillins, cephalosporins and monobactams are the most commonly used anti-bacterials in both humans and animals, however, Gram negative bacteria (such as E. coli) that produces extended-spectrum β-lactamases (ESBLs) have the ability to hydrolyze most β-lactams therefore making them resistant to β-lactam antibiotics. Recent extensive researches on the epidemiology and genetic characteristics of extended-spectrum β-lactamase (ESBL)-producing E. coli reported the existence of ESBL-producing E. coli in humans, companion animals and poultry. Therefore, this experiment was performed to investigate the prevalence and genetic characteristics of β-lactamase producing E. coli isolated from beef cattle farms in the Sichuan-Chongqing circle of China. Phenotypic confirmation of ESBL-producing E. coli was performed using the double disk synergy test. Polymerase Chain Reaction (PCR) was used to detect bla CTX-M , bla SHV and bla TEM gene codes, then after, isolates were divided into different phylogenetic groups and multi-locus sequence typing (MLST). The results showed that out of the 222 E. coli strains isolated from the beef cattle, 102 strains showed ESBL phenotypes. The PCR results showed that bla CTX-M was the predominant ESBL gene identified among the E. coli strains with 21 (9.5%) isolates having this gene, followed by bla SHV which was found in 18 (8.1%) isolates. The majority of these ESBL positive isolates were assigned to phylogroup A (19.8%) followed by phylogroup B1 (13.5%). In addition, from the MLST results on ESBL positive isolates (n = 30) we identified 19 STs, ST398 (ST398cplx) and ST7130 which were the prevalent population (20%). In conclusion, the high prevalence of CTX-M, and SHV in the study confirmed its association with E. coli infection; therefore, this calls for health concerns on ESBL-producing E. coli. As far as we know, this is the first comprehensive research report relating to ESBL-producing E. coli incidence in Chinese beef cattle.

Colistin is a last-resort antimicrobial used to treat infections caused by multidrug-resistant Gram-negative bacilli (MDR-GNB). The emergence of colistin resistance, particularly linked to mobile genetic elements including the mcr genes, is a major threat to the management of MDR-GNB infections. The aim of this study was to assess the presence of mcr genes in a collection of 40 colistin-resistant commensal Escherichia coli isolated from healthy pigs, cattle and poultry in Belgium between 2012 and 2016. All isolates carried at least one mcr gene. The genes mcr-1 to -5 were observed in this collection. Different replicons associated with mcr genes were identified, including IncHI2/IncHI2A associated with mcr-1, IncX4 associated with mcr-1 and mcr-2, and ColE10 associated with mcr-4. While the occurrence of multiple mcr genes in a single isolate has rarely been reported elsewhere, a triple occurrence (mcr-1, -3 and -5) was found in this study. All isolates were MDR and carried between one and nine different replicons. Seventeen different sequence types were observed among the 40 E. coli isolates. In conclusion, this study revealed the presence of a reservoir of mobile colistin resistance genes (mcr-1 to -5) observed during at least 5 years (2012-2016) in the commensal gut flora of pigs, cattle and poultry in Belgium., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: Selection pressure exerted by use of antibiotics in both human and veterinary medicine is responsible for increasing antimicrobial resistance (AMR). The objectives of this study were to better understand antimicrobial use in pigs, beef cattle, and poultry on farms on Guadeloupe, French West Indies, and to acquire data on AMR in Escherichia coli in these food-producing animals. A cross-sectional survey was conducted at 45 farms on Guadeloupe, and practical use of antimicrobials was documented in declarative interviews between March and July 2018. A total of 216 fecal samples were collected between January 2018 and May 2019, comprising 124 from pigs, 75 from beef cattle, and 17 from poultry litter. E. coli isolates were obtained for further testing by isolation and identification from field samples. Antimicrobial susceptibility testing and screening for bla CTX-M , bla TEM , tetA, and tetB resistance genes by polymerase chain reaction on extracted genomic DNA were performed., Results: The study showed rational use of antimicrobials, consisting of occasional use for curative treatment by veterinary prescription. Tetracycline was the most commonly used antimicrobial, but its use was not correlated to E. coli resistance. Extended-spectrum β-lactamase (ESBL) E. coli isolates were detected in 7.3% of pigs, 14.7% of beef cattle, and 35.3% of poultry. bla CTX-M-1 was the predominant gene found in ESBL-E. coli isolates (68.8%), followed by bla CTX-M-15 (31.3%)., Conclusion: Despite rational use of antimicrobials, the rate of ESBL-E. coli in food-producing animals in Guadeloupe, although moderate, is a concern. Further studies are in progress to better define the genetic background of the ESBL-E. coli isolates.

Background: Antimicrobial resistance (AMR) is an increasing global health concern reducing options for therapy of infections and also for perioperative prophylaxis. Many Enterobacteriaceae cannot be treated anymore with third generation cephalosporins (3GC) due to the production of certain 3GC hydrolysing enzymes (extended spectrum beta-lactamases, ESBLs). The role of animals as carriers and vectors of multi-resistant bacteria in different geographical regions is poorly understood. Therefore, we investigated the occurrence and molecular characteristics of ESBL-producing Escherichia coli (E. coli) in wild birds and slaughtered cattle in Ibadan, Nigeria. Cattle faecal samples (n = 250) and wild bird pooled faecal samples (cattle egrets, Bubulcus ibis, n = 28; white-faced whistling duck, Dendrocygna viduata, n = 24) were collected and cultured on cefotaxime-eosin methylene blue agar. Antimicrobial susceptibility was determined by agar diffusion assays and all 3GC resistant isolates were genotypically characterised for AMR genes, virulence associated genes (VAGs) and serotypes using DNA microarray-based assays., Results: All 3GC resistant isolates were E. coli: cattle (n = 53), egrets (n = 87) and whistling duck (n = 4); cultured from 32/250 (12.8%), 26/28 (92.9%), 2/24(8.3%), cattle, egrets and whistling duck faecal samples, respectively. blaCTX-M gene family was prevalent; blaCTX-M15 (83.3%) predominated over blaCTX-M9 (11.8%). All were susceptible to carbapenems. The majority of isolates were resistant to at least one of the other tested antimicrobials; multidrug resistance was highest in the isolates recovered from egrets. The isolates harboured diverse repositories of other AMR genes (including strB and sul2), integrons (predominantly class 1) and VAGs. The isolates recovered from egrets harboured more AMR genes; eight were unique to these isolates including tetG, gepA, and floR. The prevalent VAGs included hemL and iss; while 14 (including sepA) were unique to certain animal isolates. E. coli serotypes O9:H9, O9:H30 and O9:H4 predominated. An identical phenotypic microarray profile was detected in three isolates from egrets and cattle, indicative of a clonal relationship amongst these isolates., Conclusion: Wild birds and cattle harbour diverse ESBL-producing E. coli populations with potential of inter-species dissemination and virulence. Recommended guidelines to balance public health and habitat conservation should be implemented with continuous surveillance.

The commonly used laboratory bacterium Escherichia coli normally does not produce and secrete cellulases due to its complex bilayer membrane structure and poor secretory apparatus. In our previous study, the cellulolytic E. coli strain ZH-4 with extracellular cellulase activity was found in the bovine rumen. In this study, we demonstrate that the secretion of cellulase is a common feature of E. coli isolates from the rumen of animals such as sheep and cattle. Physiological phenotype characterization of these E. coli isolates, together with genome, transcriptome, and comparative genomics analysis, suggests their adaption to the rumen niche. The higher growth rate of the isolated strains under aerobic conditions meets the competitive requirements of the strains in rumen microecosystem, while anaerobic accumulation of reduced H 2 and succinate is hypothesized to be the results of adaptation to the rumen environment. Cellulase secretion increased significantly when the molecular chaperone genes ibpA and ibpB were overexpressed. This was also revealed by the transcriptomic data. A possible mechanism for cellulase secretion by E. coli isolates was proposed based on the transcriptomic data and molecular experiments. IMPORTANCE As an important intestinal microorganism, E. coli is present in the intestinal tract of animals and in many other environments. However, it normally does not produce and secret cellulases due to its complex bilayer membrane structure and poor secretory apparatus. Here, we proved that E. coli is widely present in the rumen of sheep and cattle. Systematic analysis of the isolates indicated that they have adapted to the rumen niche, with phenotypes that include secretion of cellulase and fermentative accumulation of succinate and H 2 The finding that overexpression of small heat shock protein genes ibpA and ibpB could facilitate cellulase BcsZ secretion, which provides a possible insight into the protein secretion mechanism of rumen-colonizing E. coli ., (Copyright © 2020 American Society for Microbiology.)

The aim of this article is to report on antimicrobial resistance (AMR) in commensal Escherichia coli from livestock from several European countries. The relationships with antimicrobial usage (AMU) at country level and harmonized indicators to cover the most relevant AMR aspects for human health in animal production were also investigated. E. coli were isolated in faeces from broilers and fattening pigs (from nine countries), and fattening turkeys and veal calves (from three countries) and screened against a fixed antimicrobial panel. AMU data were collected at farm and average treatment incidences stratified by antimicrobial class, country and livestock species were calculated. Associations between AMR and AMU at country level were analysed. Independent of animal species, the highest resistance was observed for ampicillin, sulphamethoxazole, tetracycline and trimethoprim. E. coli from broilers showed the highest resistance level for (fluoro)quinolones, and multidrug resistance peaked in broilers and fattening turkeys. Colistin resistance was observed at very low levels with the exception of fattening turkeys. High resistance to third- and fourth-generation cephalosporins was detected in broilers and fattening turkeys. The lowest levels of resistance were for meropenem, azithromycin and tigecycline (<1 %). Significant correlations between resistance and usage at country level were detected in broilers for polymyxins and aminoglycosides, and in fattening pigs for cephalosporins, amphenicols, fluoroquinolones and polymyxins. None of the correlations observed between AMR and AMU were statistically significant for fattening turkey and veal calves. The strength of the analysis performed here is the correlation of aggregated data from the same farms at country level for both AMU and AMR within antimicrobial classes.

Introduction: The prevalence of Extended-Spectrum Beta-Lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide and the Agri-Food sector acts as a reservoir of clinically relevant ESBL genes. Our study aimed at detecting and characterizing ESBL-producing Enterobacteriaceae responsible for intestinal colonization of Brazilian bovines., Material and Methods: ESBL-producing E. coli isolates were recovered from fecal samples of healthy cattle in Northwest Brazil. Antimicrobial susceptibility was determined by disk diffusion. Resistance and virulence genes were identified by PCR and amplicons were sequenced, clonality was assessed by PFGE and MLST, and plasmids were characterized by replicon typing, S1-PFGE and Southern blot hybridizations. Transferability of ESBL genes was assessed by conjugation assay., Results: A total of 40 ESBL-producing E. coli were characterized, which originated from 34/191 animals (17.8 %) and 15/22 farms (68.2 %). The bla CTX-M-8 gene was the most frequent ESBL gene (62.5 %), followed by bla SHV-2a (20.0 %), bla CTX-M-2 (10.0 %), and bla CTX-M-15 (7.5 %). The bla CTX-M-8 gene was localized on the IncI1/pST113 plasmid in multiple E. coli sequence types across unrelated animals and farms., Discussion: We report the first characterization and a high prevalence of ESBL-producing E. coli in the beef cattle sector in Brazil, which is mainly supported by the spread of an epidemic IncI1/pST113/bla CTX-M-8 plasmid. Since Brazil is one of the biggest beef meat exporters worldwide, the spread of this ESBL plasmid across other sectors, countries and continents should be considered with attention., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Antimicrobial resistance reported in bacteria of animal origin is considered a major challenge to veterinary public health. In this study, the genotypic and phenotypic characterisation of twelve Escherichia coli isolates of bovine origin is reported. Twelve bacterial isolates of animal origin were selected from a previous study based on their multidrug resistant (MDR) profile. Efflux pump activity was measured using ethidium bromide (EtBr) and the biofilm forming ability of the individual strains was assessed using a number of phenotypic assays. All isolates were resistant to tetracyclines and a number of isolates expressed resistance to fluoroquinolones which was also confirmed in silico by the presence of these resistance markers. Amino acid substitutions in the quinolone resistance-determining regions were identified in all isolates and the presence of several siderophores were also noted. Whole genomesequence (WGS) data showed different STs that were not associated with epidemic STs or virulent clonal complexes. Seven isolates formed biofilms in minimal media with some isolates showing better adaptation at 25 °C while others at 37 °C. The capacity to efflux EtBr was found to be high in 4 isolates and impaired in 4 others. The pathogenicity of three selected isolates was assessed in zebrafish embryo infection models, revealing isolates CFS0355 and CFS0356 as highly pathogenic. These results highlight the application of NGS technologies combined with phenotypic assays in providing a better understanding of E. coli of bovine origin and their adaptation to this niche environment., Competing Interests: Declaration of Competing Interest The authors have nothing to declare., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Antimicrobial resistance is a threat to agricultural production and public health. In this proof-of-concept study, we investigated predicting antimicrobial sensitive/resistant (S/R) phenotypes and host sources of Escherichia coli (n = 128) based on differential fatty acid abundance. Myristic (14:0), pentadecanoic acid (15:0), palmitic (16:0), elaidic (18:1 9 ) and steric acid (18:0) were significantly different (α = 0.05) using a two-way ANOVA for predicting nalidixic acid, ciprofloxacin, aztreonam, cefatoxime, and ceftazidime S/R phenotypes. Additionally, analyses of palmitoleic (16:1), palmitic acid (16:0), methyl palmitate (i-17:0), and cis-9,10-methyleneoctadecanoic acid (19:0 Δ ) showed these markers were significantly different (α = 0.05) between isolates obtained from cattle and raccoons. S/R phenotype prediction for the above antibiotics or host source, based on linear regression models of fatty acid abundance, were made using a replicated-randomized subsampling and modeling approach. This model predicted S/R phenotype with 79% and 81% accuracy for nalidixic acid and ciprofloxacin, respectively. The isolate host source was predicted with 63% accuracy., (Published by Elsevier Inc.)

Using multiplex real-time PCR, 960 fecal samples collected from poultry, cattle, and patients with diarrhea in Bangladesh were screened for diarrheagenic Escherichia coli (DEC). The invasion-related gene virB showed the highest prevalence in human patients (41%) and was shown to be positively correlated first with afaB with regards to diffuse adhesion and second with aggR with regards to aggregative adhesion. These three genes were specific to human patients. In contrast, the Shiga toxin genes stx1 (57%) and stx2 (40%) were prevalent in cattle samples. The eae gene, which is associated with attaching and effacing lesion formation, and the elt and est genes, which are associated with enterotoxins, were detected from all three sample sources. Heat map construction and hierarchical clustering assigned the samples into five different clusters, with the patient samples positive for virB and afaB being placed together in one cluster. Although the detection of virulence genes cannot be a direct indication of the distribution of diarrheagenic organisms, their detection suggests that Shigella spp. or enteroinvasive E. coli are the most prevalent diarrheagenic bacteria in Bangladesh and that diffusely adherent E. coli is concomitantly present with these bacteria. eae-possessing organisms in patients may come from cattle and poultry sources. The small number of stx-positive patients could be explained by the small number of animal samples that were positive for both eae and stx.

In sub-Saharan Africa, many families travel to collect water and store it in their homes for daily use, presenting an opportunity for the introduction of fecal contamination. One stored and one source water sample were each collected from 45 households in rural Kenya. All 90 samples were analyzed for fecal indicator bacteria ( E. coli and enterococci) and species-specific contamination using molecular microbial source tracking assays. Human (HF183), avian (GFD), and ruminant (BacR) contamination were detected in 52, two, and four samples, respectively. Stored water samples had elevated enterococci concentrations ( p < 0.01, Wilcoxon matched pairs test) and more frequent BacR detection (89% versus 27%, p < 0.01, McNemar's exact test) relative to source water samples. fsQCA (fuzzy set qualitative comparative analysis) was conducted on the subset of households with no source water BacR contamination to highlight combinations of factors associated with the introduction of BacR contamination to stored water supplies. Three combinations were identified: (i) ruminants in the compound, safe water extraction methods, and long storage time, (ii) ruminants, unsafe water extraction methods, and no soap at the household handwashing station, and (iii) long storage time and no soap. This suggests that multiple pathways contribute to the transmission of ruminant fecal contamination in this context, which would have been missed if data were analyzed using standard regression techniques.

The objective of our study was to provide a molecular analysis using DNA-microarray based assays of commensal E. coli populations from apparently healthy livestock and their attendants to assess the virulence potential as well as multidrug resistance (MDR) genotypes. We randomly collected 132 fecal samples from seemingly healthy smallholder´s food producing animals [buffalo (n = 32) and cattle (n = 50)] as well as from contacting farmers (n = 50). Bacterial isolation and identification were performed using standard protocols, while E. coli isolates were characterized using a DNA microarray system targeting 60 different virulence and 47 antibiotic resistance genes of clinical importance and allowing assignment to most common H and O types. From the fecal samples examined, 47 E. coli isolates were obtained. The array predicted serotypes for 14 out of the 47 E. coli isolates. Six E. coli isolates were identified as STEC since Shiga toxin genes were detected. In summary, 36 different virulence genes were identified; of which, hemL, lpfA and iss were most prevalent. Thirty-four E. coli isolates were found to carry at least one antimicrobial resistance gene. Of these, 20 did exhibit genes allowing strain classification as MDR. More than half of the isolates contained antimicrobial resistance genes associated with beta lactam resistance 27/47 (57.5 %). The 13 remaining isolates did not contain any resistance gene tested with the array. Our study demonstrated the presence of antimicrobial resistance genes and virulence genotypes among commensal E. coli of human and animal sources., (Copyright © 2019 Elsevier B.V. All rights reserved.)

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., (Copyright © 2020 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

Objective: To determine the prevalence and genetic relatedness of bla CTX-M -type extended spectrum-β-lactamase (ESBL)-producing Escherichia coli at the human-animal interface in Pakistan. Materials and Methods: A total of 150 human, cattle, and poultry fecal samples (50 each) were screened for ESBL-producing E. coli using ESBL CHROMagar ® . Bacterial species confirmation as well as determination of minimum inhibitory concentrations (μg/mL) to different antibiotics was performed using the automated VITEK ® -2 compact system. Phenotypic confirmation of ESBL production was performed according to the Clinical Laboratory Standards Institute (CLSI) guidelines. Genetic analysis of bla CTX-M was carried out by PCR and DNA sequencing. Plasmids and clonal similarity of the E. coli strains were determined by PCR-based replicon typing and pulsed-field gel electrophoresis (PFGE), respectively. Results: Of 150 samples, 29 (19.3%) ESBL-producing E. coli were recovered, and majority of them originated from human ( n  = 16; 55%), followed by cattle ( n  = 9; 31%) and poultry ( n  = 4; 13.7%). bla CTX-M-15 was predominant ESBL genotype ( n  = 25; 86.2%), mainly identified from human ( n  = 15) and cattle ( n  = 9). This is also the first report of the occurrence of CTX-M-15 and CTX-M-55 in cattle and poultry E. coli isolates of Pakistan, respectively. The majority of the ESBL-producing E. coli (96.5%) showed a multidrug resistance phenotype. All isolates carried IncFII or IncFIA plasmids, and the phylogroup B1 was dominant (44.8%) followed by phylogroups A (31%), D (17.2%), and B2 (6.8%). PFGE revealed that isolates from different hosts were genetically unrelated. Conclusion: Presence of CTX-M-15-type ESBL-producing E. coli in different reservoirs is alarming and has the potential to impact both veterinary and human therapeutic treatment options.

Objectives: This study reports the draft genomes of 14 Escherichia coli isolated from contaminated meat samples collected from the Northern Region of Ghana in order to determine the presence of antimicrobial resistance genes (ARGs) and genetic relatedness of the isolates., Methods: The 14 E. coli isolates were of beef (n=3), mutton (n=2), chevon (n=3), local chicken (n=3) and guinea fowl (n=3) origin. Whole-genome sequencing (WGS) was performed using an Illumina MiSeq sequencer. Double-disk synergy test (DDST) was also used to confirm the production of extended-spectrum β-lactamase (ESBL)., Results: WGS confirmed the identity of all of the E. coli isolates. All of the isolates contained at least one ARG and 57.1% (8/14) of them were multidrug-resistant (MDR). The mdf(A) gene was most common ARG, found in all 14 isolates. DDST confirmed the production of an ESBL in a MDR E. coli of guinea fowl origin. The sequence types (STs) varied among the E. coli isolates, with the exception of three isolates of ST155. Similarly, the serotypes of the E. coli isolates from meat sample were genetically diverse. Eleven different plasmid sequences were detected in ten of the isolates., Conclusion: E. coli from contaminated meat sources in Ghana possessed multiple ARGs and were genetically diverse. To the best of our knowledge, this is the first work on WGS of E. coli isolated from various meat samples in the study area. The sequence data add to data base for epidemiological studies., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: To explore the dynamics of faecal ESBL/AmpC shedding in dairy cattle and farmers, a study was conducted to examine changes in shedding by individual animals, as well as environmental exposure, and to study the association between antimicrobial use (AMU) and ESBL/AmpC shedding., Methods: The study comprised a cross-sectional survey of 20 farms and a 1 year follow-up of 10 farms. Faecal samples were cultured by both direct inoculation on MacConkey agar + 1 mg/L cefotaxime (MC+) and enrichment in LB-broth + 1 mg/L cefotaxime with subsequent inoculation on MC+. Dust samples were collected using electrostatic dustfall collectors (EDCs). Human faecal samples were collected by the farmers. Presence of ESBL/AmpC genes was screened for by PCR and sequencing. Using mixed effects logistic regression, ORs were determined and population-attributable fractions (PAFs) calculated subsequently., Results: In Phase 1, 8/20 farms were positive for ESBL/AmpC and, with 2 negative farms, were selected for Phase 2. Transient shedding of dominant allele variants was observed in the animals. EDCs and human faecal samples did not reflect what was observed in the animals. AMU was related to shedding of ESBLs in the next sampling moment [OR 14.6 (95% CI 3.0-80.0)] and the PAF of AMU was 0.36 (95% CI 0.08-0.77). Calves fed with colostrum from cows on dry-off therapy was not a risk factor [OR 1.7 (95% CI 0.7-4.9, P = 0.28)]., Conclusions: The presence of ESBL/AmpC could only be partly explained by AMU. No link was shown between shedding in cattle and humans or the environment. Interventions should focus on prevention of introduction., (© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.)

Objectives: This study aimed to isolate and characterise extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) isolates from animals and wastewater in Tunisia., Methods: ESBL-E from wastewater (n=123 samples), faeces of healthy animals (poultry, sheep, goats and calves) (n=140) and raw milk from healthy cows (n=42) and goats (n=20) were investigated. Antimicrobial susceptibility was determined according to CLSI recommendations. The bla TEM , bla SHV , bla CTX-M and bla OXA-48 genes were analysed by PCR and sequencing. Phylogenetic groups were determined by PCR for Escherichia coli isolates. The clonality of E. coli and Klebsiella pneumoniae isolates was determined by XbaI-PFGE and MLST., Results: A total of 81 E. coli, 20 K. pneumoniae, 4 Enterobacter cloacae, 1 Citrobacter freundii and 1 Citrobacter braakii were isolated. The bla CTX-M-1 and bla CTX-M-15 genes were predominant in E. coli and K. pneumoniae isolates. E. cloacae and C. braakii isolates harboured the bla SHV-12 gene. The C. freundii isolated from wastewater carried bla CTX-M-15 , bla TEM-1 and bla OXA-204 . E. coli isolates belonged to phylogroups A (37), B1 (25), B2 (7) and D (12). Seventy-eight E. coli isolates were typeable by PFGE and were classified into 34 pulsotypes. The K. pneumoniae isolates belonged to 11 pulsotypes. The E. coli isolates belonged to sequence types ST131, ST224, ST162, ST845, ST5204, ST69, ST141 and ST10. The K. pneumoniae isolates belonged to ST405, ST147, ST564, ST307, ST152, ST45, ST661 and ST1564., Conclusion: This is the first report of O25b-B2 3 -CTX-M-27-ST131 E. coli isolates and of C. freundii carrying bla CTX-M-15 , bla TEM-1 and bla OXA-204 in Tunisia., (Copyright © 2019 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Historically, extended-spectrum cephalosporin resistance in bacteria from animals in Canada has been attributed to the SHV and CMY β-lactamase families. This pattern is beginning to change with the emergence of the bla CTX-M gene family among Escherichia coli recovered from various animal species. Here we analyze and compare whole genome sequences of bla CTX-M -positive E. coli isolates (n = 173) from dogs, chicken, swine, horses and beef cattle in Canada. Ten bla CTX-M variants were identified with bla CTX-M-1,-14, -15, -27 and bla CTX-M-55 being identified in most animal species. These variants occurred across many sequence types, suggesting that mobile genetic elements mediate the spread of bla CTX-M . The variants bla CTX-M-14, -15, -27 and bla CTX-M-55 are associated with the global spread of bla CTX-M in human clinical isolates and their presence could be indicative of transfer between humans and animals. These variants were also the principal variants identified among sequence type 131 isolates, which were not associated with any other species than dogs. These isolates carried the same bla CTX-M variants as E. coli isolates found in humans. Close contact may promote the transmission of these isolates between humans and companion animals., (Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.)

The objectives of this study were to describe the frequency of antimicrobial resistance (AMR) in Escherichia coli and Campylobacter spp. isolates in fecal samples from beef cow-calf herds and to examine the associations between herd management practices, reported antimicrobial use, and AMR. Baseline prevalence data are needed to evaluate the effectiveness of antimicrobial stewardship programs. A pooled fecal sample, representing 20 cows, was collected from each of 107 herds during pregnancy testing. In the 305 recovered E. coli isolates (maximum 3 per herd), resistance to ≥ 1 antimicrobial was identified in 12 isolates [4%, 95% confidence interval (CI): 2% to 7%] from 105 herds (11%, 95% CI: 7% to 19%). The most common resistances identified in E. coli isolates were to tetracycline (3%) and to both streptomycin and sulfisoxazole (3%). Only 1 E. coli isolate was resistant to an antimicrobial of very high importance to human health - amoxicillin/clavulanic acid. However, 2 E. coli isolates had intermediate susceptibility to ciprofloxacin. Resistance to 1 antimicrobial was identified in 16 of 87 Campylobacter spp. isolates (18%, 95% CI: 11% to 28%) from 87 herds. Resistance to tetracycline was reported in 15% of Campylobacter spp. isolates and to nalidixic acid in 3.4%. Herds in which cows were treated with florfenicol were more likely to have E. coli resistance to ≥ 2 antimicrobials (OR 7.1, 95% CI: 1.1 to 57, P = 0.03). Herds with calf mortality of > 5% were more likely to have E. coli with resistance to streptomycin and sulfisoxazole [odds ratio (OR): 7.8, P = 0.03]. The results of this study are consistent with previous reports from western Canada and provide a starting point for designing an ongoing antimicrobial surveillance program.

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.

The global dissemination of colistin resistance has received a great deal of attention. Recently, the plasmid-mediated colistin resistance encoded by mcr genes in Escherichia coli (E. coli) strains from animals, food, and patients in China has been reported frequently. To investigate the colistin resistance and mcr-1 and mcr-2 genes spread in domestic animals in Jiangsu Province, we collected fecael swabs from pigs, chicken and cattle at different ages distributed in intensive feeding farms. The selective chromogenic agar and mcr-PCR were used to screen the colistin resistance and mcr gene carriage. Colistin resistant E. coli colonies were identified in 54.25% (440/811), 35.96% (443/1232), and 26.92% (42/156) faecal swabs from pigs, chickens, and cattle, respectively. The prevalence of mcr-1 in colistin resistant E. coli isolates from pigs, chickens and cattle was 68.86% (303/440), 87.58% (388/443), and 71.43% (30/42), respectively, compared to mcr-2 which was present in 46.82% (206/440), 14.90% (66/443), and 19.05% (8/42) of the colistin-resistant E. coli isolated from pigs, chickens and cattle, respectively. Co-occurrence of mcr-1 and mcr-2 was identified in 20% (88/440) in pigs, 7.22% (32/443) in chickens, and 9.52% (4/42) in cattle. Interventions and alternative options are necessary to minimise further dissemination of mcr between food-producing animals and human., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Objectives: To investigate the prevalence and molecular characteristics of ESBL-producing Escherichia coli (ESBL-EC) in faecal samples from dairy cows in China., Methods: In total, 651 faecal samples were collected from cows distributed among the 10 provinces of China. Potential ESBL-EC isolates were cultured on selective medium. The clonal relatedness of the ESBL-EC isolates was assessed using MLST. WGS was conducted on 3 mcr-positive isolates and 14 additional randomly selected ESBL-EC isolates. Southern blot, S1-PFGE and conjugation were performed for mcr-1-carrying isolates. The genetic environment of the pMCR-JLF4 plasmid was also analysed., Results: In total, 290 unique ESBL-EC isolates were detected from 284 cows (43.6%). Alleles of CTX-M were observed in 94.1% (273/290) of all isolates. The most prevalent genotypes observed in this study were blaCTX-M-14, blaCTX-M-15, blaCTX-M-17 and blaCTX-M-55. Differentiation of 79 STs with a polyclonal structure was accomplished using MLST. Clonal complex 10 was the most prevalent major complex detected here. Furthermore, the mcr-1 gene was detected in three isolates. The complete sequence of the mcr-1-containing pMCR-JLF4 was determined. The plasmid was 66.7 kb in length, with a genetic structure of nikA-nikB-mcr-1-pap2. Conjugation analysis confirmed that the mcr-1 gene in pMCR-JLF4 was transferable without the assistance of the ISApl1 gene., Conclusions: The data presented here suggest high prevalence of ESBL-EC in Chinese cow farms. Furthermore, it was clearly demonstrated that commensal E. coli strains can be reservoirs of blaCTX-M genes, potentially contributing to the dissemination and transfer of the mcr-1 gene to pathogenic bacteria among cows.

Antibiotic resistance mediated by bacterial production of extended-spectrum beta-lactamase (ESBL) is a global threat to public health. ESBL resistance is most commonly hospital-acquired; however, infections acquired outside of hospital settings have raised concerns over the role of livestock and wildlife in the zoonotic spread of ESBL-producing bacteria. Only limited data are available on the circulation of ESBL-producing bacteria in animals. Here, we report ESBL-producing Escherichia coli in wild common vampire bats Desmodus rotundus and livestock near Lima, Peru. Molecular analyses revealed that most of this resistance resulted from the expression of bla CTX-M-15 genes carried by plasmids, which are disseminating worldwide in hospital settings and have also been observed in healthy children of Peru. Multilocus sequence typing showed a diverse pool of E. coli strains carrying this resistance that were not always host species-specific, suggesting sharing of strains between species or infection from a common source. This study shows widespread ESBL resistance in wild and domestic animals, supporting animal communities as a potential source of resistance. Future work is needed to elucidate the role of bats in the dissemination of antibiotic-resistant strains of public health importance and to understand the origin of the observed resistance., (© 2018 Blackwell Verlag GmbH.)

Foodborne disease (FBD) is a global public health concern, and foods from animal sources have been associated with outbreaks of food-related illness. In this study, animal carcasses from the two abattoirs (HT1 and HT2) in the formal meat sector (FMS) and slaughter points in the informal meat sector (INMS) were examined at two stages of slaughter (before washing and after washing) for aerobic colony counts (ACC) and total viable count (TCC), as well as Escherichia coli and Staphylococcus aureus count. At each stage, carcasses were sampled by swabbing at the neck, brisket, flank, and rump. ACC for beef, mutton, and pork carcasses at HT1 and HT2 before washing were between 2.5⁻5.8, 2.2⁻4.7, and 2.7⁻3.7 mean log CFU/cm², respectively, and TCC count before washing was highest on the neck of cattle (6.3 &plusmn; 2.4) and after washing was highest on the perineal of sheep (5.7 &plusmn; 6.9). In the INMS, TCC count was highest on the brisket (6.9 &plusmn; 3.2) and in the neck (5.5 &plusmn; 2.4). Higher ACC values of 6.2⁻6.7 mean log CFU/cm² were obtained in the INMS. The highest count for E. coli (4.2 mean log CFU/cm²) after washing was in the neck, while the highest count for S. aureus (4.0 mean log CFU/cm²) was in the flank. All bacteria count in the INMS exceeded acceptable limits, and washing did not significantly reduce microbial load in meat in the FMS and INMS. Bacteria count in the FMS and INMS exceeded acceptable standards. However, meat processed in the INMS poses a more significant risk of FBD to consumers.

To assess phenotypic bacterial antimicrobial resistance (AMR) in different strata (e.g., host populations, environmental areas, manure, or sewage effluents) for epidemiological purposes, isolates of target bacteria can be obtained from a stratum using various sample types. Also, different sample processing methods can be applied. The MIC of each target antimicrobial drug for each isolate is measured. Statistical equivalence testing of the MIC data for the isolates allows evaluation of whether different sample types or sample processing methods yield equivalent estimates of the bacterial antimicrobial susceptibility in the stratum. We demonstrate this approach on the antimicrobial susceptibility estimates for (i) nontyphoidal Salmonella spp. from ground or trimmed meat versus cecal content samples of cattle in processing plants in 2013-2014 and (ii) nontyphoidal Salmonella spp. from urine, fecal, and blood human samples in 2015 (U.S. National Antimicrobial Resistance Monitoring System data). We found that the sample types for cattle yielded nonequivalent susceptibility estimates for several antimicrobial drug classes and thus may gauge distinct subpopulations of salmonellae. The quinolone and fluoroquinolone susceptibility estimates for nontyphoidal salmonellae from human blood are nonequivalent to those from urine or feces, conjecturally due to the fluoroquinolone (ciprofloxacin) use to treat infections caused by nontyphoidal salmonellae. We also demonstrate statistical equivalence testing for comparing sample processing methods for fecal samples (culturing one versus multiple aliquots per sample) to assess AMR in fecal Escherichia coli These methods yield equivalent results, except for tetracyclines. Importantly, statistical equivalence testing provides the MIC difference at which the data from two sample types or sample processing methods differ statistically. Data users (e.g., microbiologists and epidemiologists) may then interpret practical relevance of the difference. IMPORTANCE Bacterial antimicrobial resistance (AMR) needs to be assessed in different populations or strata for the purposes of surveillance and determination of the efficacy of interventions to halt AMR dissemination. To assess phenotypic antimicrobial susceptibility, isolates of target bacteria can be obtained from a stratum using different sample types or employing different sample processing methods in the laboratory. The MIC of each target antimicrobial drug for each of the isolates is measured, yielding the MIC distribution across the isolates from each sample type or sample processing method. We describe statistical equivalence testing for the MIC data for evaluating whether two sample types or sample processing methods yield equivalent estimates of the bacterial phenotypic antimicrobial susceptibility in the stratum. This includes estimating the MIC difference at which the data from the two approaches differ statistically. Data users (e.g., microbiologists, epidemiologists, and public health professionals) can then interpret whether that present difference is practically relevant., (Copyright © 2018 Shakeri et al.)

The objective of this study was to investigate the prevalence of the cfr gene in Escherichia coli isolates from domestic animals in Northeast China and to characterize the cfr-containing plasmids. Between June 2015 and April 2016, 370 E. coli isolates were collected from pigs, chickens, and dairy cows in Northeast China. Among these, 111 were florfenicol resistant, including 109 isolates carrying the floR gene and 6 positives for cfr. The prevalence of cfr in E. coli isolates from the four northeast provinces in China was 1.6% (6/370), which was higher than that previously reported (0.08% and 0.5%). All six cfr-containing E. coli isolates were highly resistant to florfenicol (100%), cefotaxime (100%), and fosfomycin (100%). Complete sequence analysis of two cfr-carrying plasmids revealed high homology of the IncX4-type pEC14cfr plasmid with two other cfr-harboring plasmids, pSD11 and pGXEC6, found in swine E. coli isolates from southern China. pEC14cfr-like plasmids have been isolated in five provinces in southern and northern China. The isolation sites were up to 2700 kilometers apart, implying that pEC14cfr-like plasmids are likely to be national epidemic cfr-carrying plasmids that mediate the dissemination of cfr in China. Moreover, the genetic structure (IS26-IS26-cfr-rec-pre/mob-ramA-IS26) of the second cfr-carrying plasmid, IncF14:A-:B- pEC295cfr, represents a novel genetic environment for cfr identified for the first time in the present study. Sequence homology analysis indicated that the cfr-carrying element was most likely introduced into a cfr-negative pEC12 plasmid backbone, which evolved into the cfr-carrying vector, pEC295cfr. Moreover, isolation of the IncF14:A-:B- pEC295cfr plasmid harboring cfr suggests that IncFII plasmids maybe have become additional effective vehicles for cfr dissemination. These results highlight the importance of surveying the prevalence of IncX4 and IncFII plasmids in gram-negative bacteria, especially in swine E. coli isolates., (Copyright © 2018 Elsevier B.V. All rights reserved.)

The aim of this study was to describe and compare the occurrence of quinolone resistant Escherichia coli (QREC) in various animal species in relation to human population density. Data from the Norwegian monitoring programme for antimicrobial resistance in feed, food and animals from 2006 to 2016 was compiled and analysed. In total, 4568 E. coli isolates were included in this study. The isolates originated from broilers, layers, cattle, turkeys, dogs, wild birds, red foxes, reindeer, sheep, horses and pigs. Data regarding the geographical location of sampling was obtained for 4050 of these isolates and used to categorize the isolates depending on the human population density of the area. In total, 1.4% of the isolates were categorized as quinolone resistant. Compared to most European countries, there was an overall low occurrence of QREC in various animal species in Norway, though with an interspecies variation with the highest occurrence in broilers and wild birds (p < 0.05). Human population density was not associated with the occurrence of QREC. Since fluoroquinolones are not used prophylactically and in almost negligent amounts in various species in Norway, the interspecies variation in the occurrence of QREC suggests that other factors than fluoroquinolone use may be important in the development of QREC., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Escherichia coli (E. coli) is one of the most relevant opportunistic pathogenic bacteria as it may cause severe morbidity and mortality in yaks (poephagus grunniens). In recent years, several kinds of antibiotics have been widely used in Tibetan areas to treat the bacterial diseases, resulting in serious repercussions on the bacterial antibiotic resistance in yaks. This investigation was conducted in order to determine the prevalence of antimicrobial resistance and integron gene cassettes in E. coli isolated from yaks in Aba Tibetan Autonomous Prefecture (Aba TAP), China., Methods: A total of 278 non-duplicated fresh samples were collected from the yaks in Aba TAP for the isolation and identification of E. coli isolates. Antimicrobial susceptibility testing is performed by using the disc diffusion method according to the Clinical and Laboratory Standards Institute guidelines (CLSI, 2013). Various antibiotic resistance genes and integron gene cassettes were detected by polymerase chain reaction (PCR) and sequencing., Results: Overall, a total of 228 E. coli bacteria were isolated from the fresh faeces of yaks in four different geographical regions. 58% of those isolates showed multi-drug resistance capabilities (MDR) in our study. These isolated bacteria showed a high resistance rate to streptomycin (84%), cefotaxime (79%), amikacin (61%) and trimethoprim-sulfamethoxazole (54%). The most common antimicrobial resistance genes in the isolates were bla CTX-M , sul1, aph (3')-IIa, aac (3)-IIa, aac (6')-Ib, tetB, with respective detection rates of 65%, 46%, 35%, 13%, 11%, and 10%. Furthermore, 66% and 6% of the strains carried Class 1 and 2 integrons, respectively. However, the class 3 integron was not detected. Gene cassette arrays in the class 1 integron included aadA1, aadA7, aadA5, aadA17, dfrA1, dfrA5, dfrA1-aadA1, dfrA12-aadA2 and dfrA17-aadA5. The most prevalent gene cassette was aadA1 (20%). For the class 2 integron, dfrA1-sat2-aadA1 (6%) and dfrA1-sat1-aadA1 (0.4%) were also detected as part of this research., Conclusion: High multi-drug resistance rates have been discovered, as well as a prevalence of antibiotic resistance genes and integron gene cassettes in the E. coli isolated from the faeces of yak. This might create a potential problem for treatment of the yaks' bacterial infections as well as food hygiene for humans. It is therefore urgently necessary to begin continuous surveillance and analysis of antibiotic resistance and integron cassettes in other bacteria from yaks., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Several factors are known to affect the intestinal microbiota of cattle. However, how these changes occur over time is poorly understood. This study aimed to investigate the consequences of entrance into a feedlot and the effects of virginiamycin used as a growth promoter on the bovine fecal microbiota. Two batches of beef cattle (B1, n=50 and B2, n=36) entering a feedlot operation were randomly divided into two pens: one receiving virginiamycin and one group not receiving antibiotic (control group). Fecal samples were collected at arrival, mid feedlot and at exit to slaughter. The V4 region of 16S rRNA gene was amplified and sequenced. Escherichia coli strains isolated in samples from arrival and exit of B2 were also isolated and used as indicators of antimicrobial susceptibility. Marked changes in membership and structure of fecal microbiota occurred following entrance into the feedlot. At mid feedlot, virginiamycin affected bacterial community membership, but not structure, suggesting that the antibiotic had a stronger effect on the rare, but not on the most abundant species. The use of virginiamycin had no demonstrable effect on antibiotic resistance in E. coli. The differences found between batches are suggestive that variations in study conditions are important and can strongly affect the intestinal microbiota., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Escherichia coli is one of the main etiological agents of neonatal calf diarrhea (NCD). The objective of this study was to assess the presence of virulence genes, genetic diversity, and antibiotic resistance mechanisms in E. coli associated with NCD in Uruguay. PCR was used to assess the presence of intimin, Shiga-like toxin, and stable and labile enterotoxin genes. Resistance to fluoroquinolones and oxyimino-cephalosporins was estimated on Müller-Hinton agar plates. Further antibiotic disc-diffusion tests were performed to assess bacterial multi-resistance. The presence of PMQR, ESBL, MCR-1, and integron genes was evaluated. Isolates were typed using ERIC-PCR, and 20 were selected for MLST, adhesion to Hep-2 cells, in vitro biofilm formation, and eukaryotic cytotoxicity. The prevalence of ETEC genes was lower than 3% in each case (estA and elt). Six isolates were EPEC (eae+) and 2 were EHEC/STEC (eae+/stx1+). The results of a diversity analysis showed high genetic heterogenicity among isolates. Additionally, different sequence types, including ST10, ST21, and ST69, were assigned to selected isolates. Thirty-six percent (96/264) of the isolates were fluoroquinolone-resistant, with 61/96 (63.5%) being multidrug-resistant. Additionally, 6 were oxyimino-cephalosporin-resistant. The qnrB, qnrS1, and bla CTX-M-14 genes were detected, whereas no isolates carried the mcr-1 gene. Isolates had the ability to adhere to Hep-2 cells and form biofilms. Only 1 isolate expressed toxins in vitro. E. coli from NCD cases in Uruguay are very diverse, potentially virulent, and may interact with eukaryotic cells. Zoonotic potential, together with resistance traits and the presence of horizontal transfer mechanisms, may play a significant role in infections caused by these microorganisms.

Escherichia coli is widely considered to not survive for extended periods outside the intestines of warm-blooded animals; however, recent studies demonstrated that E. coli strains maintain populations in soil and water without any known fecal contamination. The objective of this study was to investigate whether the niche partitioning of E. coli occurs between cattle and their pasture. We attempted to clarify whether E. coli from bovine feces differs phenotypically and genotypically from isolates maintaining a population in pasture soil over winter. Soil, bovine fecal, and run-off samples were collected before and after the introduction of cattle to the pasture. Isolates (363) were genotyped by uidA and mutS sequences and phylogrouping, and evaluated for curli formation (Rough, Dry, And Red, or RDAR). Three types of clusters emerged, viz. bovine-associated, clusters devoid of cattle isolates and representing isolates endemic to the pasture environment, and clusters with both. All isolates clustered with strains of E. coli sensu stricto, distinct from the cryptic species Clades I, III, IV, and V. Pasture soil endemic and bovine fecal populations had very different phylogroup distributions, indicating niche partitioning. The soil endemic population was largely comprised of phylogroup B1 and had a higher average RDAR score than other isolates. These results indicate the existence of environmental E. coli strains that are phylogenetically distinct from bovine fecal isolates, and that have the ability to maintain populations in the soil environment.

To enable future comparison of the antimicrobial susceptibility data between bacteria obtained from animals and humans, it is necessary to compare the relationships between minimum inhibitory concentrations (MICs) of veterinary and human medicine. We evaluated the relationship between the MIC of ceftiofur (CTF) and the MICs of other third-generation cephalosporins (TGCs): cefotaxime (CTX), cefpodoxime (CPDX), and ceftazidime (CAZ), determined by the broth microdilution method using 118 cefazolin-resistant Escherichia coli isolates from food-producing animals. Using the Clinical and Laboratory Standards Institute criteria, very major classification errors were observed only in CAZ (17.8%, 21 of 118); major and minor errors were observed in all TGCs (CTX: 0.8% [1 of 118] and 9.3% [11 of 118]; CPDX: 9.3% [11 of 118] and 6.8% [8 of 118]; CAZ: 2.5% [3 of 118] and 9.3% [11 of 118], respectively). The Spearman correlation coefficients between the MICs of CTF and CTX, CPDX, and CAZ were 0.765, 0.731, and 0.306, respectively. The sensitivity and specificity values were 100.0% and 81.8% for CTX, 99.0% and 27.3% for CPDX, and 76.0% and 86.4% for CAZ compared with CTF. The C-statistic was 0.978 for CTF and CTX, 0.953 for CPDX, and 0.798 for CAZ. For the TGCs evaluated in our study, testing for CTX susceptibility results showed the highest correlation with the results given when testing for CTF susceptibility.

Background: Consumption of meat contaminated by E. coli causes a serious illness and even death to affected individuals. Recently the emerging of antibiotic resistant foodborne E. coli poses serious public health risks worldwide. However, little is known about the antibiotic resistance profile of E. coli in Ethiopia. This study aimed to determine the prevalence and Antimicrobial resistance (AMR) status of E. coli isolated from different type of meat., Methods: Overall 292 samples were collected from December 2015 to April 2016 from slaughterhouses to determine the prevalence and AMR of E. coli isolated from raw beef, mutton, chevon and chicken meat from Addis Ababa and Bishoftu, Ethiopia. The isolates were screened for AMR against commonly used antibiotics circulating in the Ethiopian market. Both phenotypic and genotypic approach were employed for AMR detection using disc diffusion test and PCR respectively., Results: The prevalence of E. coli was 63 (21.6%), indicating one sample in every five samples harbors E. coli. Among these, the highest E. coli isolates was observed in chicken meat samples (37.0%; 27), followed by mutton (23.3%; 17), chevon (20.6%; 15) and beef (5.5%; 4). Results of disk diffusion test on the 63 isolates showed that only 4.8% of them were not resistance to all antimicrobials tested. Multiple drug resistance (resistance to ≥3 drugs) was 46.0%. Significantly high resistance to ampicillin (71.4%) and tetracycline (47.6%) was observed. Identification of genes associated with AMR was also done using PCR. The prevalence of E. coli isolates harboring resistance gene responsible for tetracycline (tet(A)), beta lactams (blaCMY) and sulphanamide (sulI) antibiotics were found 65.1, 65.1 and 54.0%, respectively. Twenty-five out of the 63 (39.7% %) E. coli isolates have got antimicrobial resistance gene to three or more classes of drugs. The associations of antimicrobial resistance phenotypes and resistance genes was also determined. The detection of resistance trait against tetracycline, sulphametazole and chloramphenicol measured either phenotypically or genotypically were high., Conclusions: The rising levels of resistance E. coli to multiple antimicrobial dictate the urgent need to regulate and monitor antimicrobial use in both animals and humans.

Colistin resistance genes mcr-3 and mcr-1 have been detected in an Escherichia coli isolate from cattle faeces in a Spanish slaughterhouse in 2015. The sequences of both genes hybridised to same plasmid band of ca 250 kb, although colistin resistance was non-mobilisable. The isolate was producing extended-spectrum beta-lactamases and belonged to serotype O9:H10 and sequence type ST533. Here we report an mcr-3 gene detected in Europe following earlier reports from Asia and the United States., (This article is copyright of The Authors, 2017.)

We investigated the occurrence of integrons in antibiotic-resistant Escherichia coli strains isolated from free-ranging food animals, including yaks, piglets, and chickens, in China, and characterized the gene cassettes harbored within the integrons. We examined 432 E. coli strains that exhibited resistance to at least one class of antibiotics. Integrase genes and associated gene cassettes were characterized by polymerase chain reaction (PCR) analysis, restriction fragment-length polymorphism, DNA sequencing, conjugation experiments, and plasmid analysis. Twenty-nine (6.7%) integrons were amplified from the 432 antimicrobial-resistant (AMR) isolates evaluated. Specifically, class 1 and 2 integrons were detected in 26 (6%) and 3 (0.7%) strains, respectively. Meanwhile, 6 different gene cassettes, dfrA1, dfr12, aadA1, aadA2, sat1, and orfF, were detected within 6 variable regions (VRs), of which the dfrA1 + aadA1 array was the most common, identified in 12 of 26 class 1 integrons (46.1%). Meanwhile, only one class 2 integron contained a cassette, and the remaining two contained undetermined VRs. Finally, a conjugation assay confirmed the transfer of 4 different types of class 1 integrons into recipient strains, with plasmid sizes ranging from 20 to 30 kb. This is the first report examining the baseline AMR characteristics of E. coli within an extensive farming system of livestock animals in China. Given that integrons were detected in >6% of resistant E. coli strains, precautionary measures are required to prevent the spread of mobile genetic resistance determinants in food animals and monitor their emergence., (© 2017 Institute of Food Technologists®.)

The present study has examined the virulence potential of Escherichia coli isolates harboring at least one virulence gene (associated with ExPEC or InPEC pathotype and belonging to different phylogenetic groups: A, B1, B2 or D), isolated from free ranging Tibetan yak feces. The E. coli isolates (n = 87) were characterized for different serogroups and a mouse model of subcutaneous-infection was used to envisage the virulence within these E. coli strains. Of the 87 E. coli isolates examined, 23% of the E. coli isolates caused lethal infections in a mouse model of subcutaneous infection and were classified as killer. Moreover, the majority of the killer strains belonged to phylogroup A (65%) and serogroup O 60 or O 101 (35%). Phylogroup B1, serogroups O 60 and O 101 were statistically associated with the killer status (P < 0.05). However, positive associations (OR >1) were observed between the killer status isolates and all other bacterial virulence traits. This study comprises the first report on the virulence potential of E. coli strains isolated from free-ranging Tibetan yaks feces. Our findings suggest that pathogenic E. coli of free ranging yaks is highly worrisome, as these feces are used as manures by farmers and therewith pose a health risk to humans upon exposure., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

To get insights into the temporal pattern of commensal Escherichia coli populations, we sampled the feces of four healthy cows from the same herd in the Hwange District of Zimbabwe daily over 25 days. The cows had not received antibiotic treatment during the previous 3 months. We performed viable E. coli counts and characterized the 326 isolates originating from the 98 stool samples at a clonal level, screened them for stx and eae genes, and tested them for their antibiotic susceptibilities. We observed that E. coli counts and dominant clones were different among cows, and very few clones were shared. No clone was shared by three or four cows. Clone richness and evenness were not different between cows. Within each host, the variability in the E. coli count was evidenced between days, and no clone was found to be dominant during the entire sampling period, suggesting the existence of clonal interference. Dominant clones tended to persist longer than subdominant ones and were mainly from phylogenetic groups A and B1. Five E. coli clones were found to contain both the stx 1 and stx 2 genes, representing 6.3% of the studied isolates. All cows harbored at least one Shiga toxin-producing E. coli (STEC) strain. Resistance to tetracycline, penicillins, trimethoprim, and sulfonamides was rare and observed in three clones that were shed at low levels in two cows. This study highlights the fact that the commensal E. coli population, including the STEC population, is host specific, is highly dynamic over a short time frame, and rarely carries antibiotic resistance determinants in the absence of antibiotic treatment. IMPORTANCE The literature about the dynamics of commensal Escherichia coli populations is very scarce. Over 25 days, we followed the total E. coli counts daily and characterized the sampled clones in the feces of four cows from the same herd living in the Hwange District of Zimbabwe. This study deals with the day-to-day dynamics of both quantitative and qualitative aspects of E. coli commensal populations, with a focus on both Shiga toxin-producing E. coli and antibiotic-resistant E. coli strains. We show that the structure of these commensal populations was highly specific to the host, even though the cows ate and roamed together, and was highly dynamic between days. Such data are of importance to understand the ecological forces that drive the dynamics of the emergence of E. coli clones of particular interest within the gastrointestinal tract and their transmission between hosts., (Copyright © 2017 American Society for Microbiology.)

Current culture methods to investigate changes in Escherichia coli community structure are often slow and laborious. Genes such as gnd (6-phosphogluconate dehydrogenase) have a highly variable nucleotide sequence and may provide a target for E. coli microbiome analysis using culture-independent methods. Metabarcoded PCR primers were used to generate separate libraries from calf faecal samples for high throughput sequencing. Although a total of 348 separate gnd sequence types (gSTs) were identified, 188 were likely to be due to sequencing errors. Of the remaining 160 gSTs, 92 did not match those in a database of 319 separate gnd sequences. 'Animal' was the main determinant of E. coli diversity with limited impact of sample type or DNA extraction method on intra-host E. coli community variation from faeces and recto-anal mucosal swab samples. This culture-independent study has addressed the difficulties of quantifying bacterial intra-species diversity and revealed that, whilst individual animals may harbour >50 separate E. coli strains, communities are dominated by <10 strains alongside a large pool of subdominant strains present at low abundances. This method will be useful for characterising the diversity and population structure of E. coli in experimental studies designed to assess the impact of interventions on the gut microbiome.

The aims of the present study were to determine (i) the profiles of phylogroup and (ii) the antimicrobial susceptibility of pathogenic Escherichia coli strains isolated from calves, and of Salmonella spp. strains isolated from calves and pigs in Minas Gerais State, Brazil. Sixty-one pathogenic E. coli strains and Salmonella spp. (n = 24) strains isolated from fecal samples of calves and Salmonella spp. (n = 39) strains previously isolated from fecal samples of growing/finishing pigs were tested. The minimum inhibitory concentration (MIC) using the agar dilution method was determined for nalidixic acid, amikacin, amoxicillin, ampicillin, cefoxitin, norfloxacin, gentamicin, tetracycline, and trimethoprim-sulfamethoxazole. All E. coli isolates were susceptible to amikacin. Tetracycline was the antimicrobial that presented the higher frequency of resistance among E. coli strains, followed by ampicillin, trimethoprim-sulfamethoxazole, amoxicillin, nalidixic acid, norfloxacin, gentamicin, and cefoxitin. E. coli (n = 61) strains isolated from calves belonged to different phylogroup namely, phylogroup A (n = 26), phylogroup B1 (n = 31), phylogroup E (n = 3), and phylogroup F (n = 1). Phylogroups B2, C, and D were not identified among the E. coli in the present study. All Salmonella spp. (n = 24) strains isolated from fecal samples of calves were susceptible to amikacin, amoxicillin, ampicillin, norfloxacin, gentamicin, tetracycline, and trimethoprim-sulfamethoxazole. Resistance to nalidixic acid and cefoxitin was detected in 16.66 and 8.33 % of the Salmonella spp. strains, respectively. Among the Salmonella spp. (n = 39) strains isolated from fecal samples of pigs, the higher frequency of resistance was observed to tetracycline, followed by amoxicillin, gentamicin, ampicillin, trimethoprim-sulfamethoxazole, nalidixic acid, cefoxitin, and norfloxacin. All strains were susceptible to amikacin. Forty-eight (78.68 %) of the E. coli strains were classified as multidrug-resistant, whereas among Salmonella spp. strains, the percentage of multidrug resistance was 57.14 %, being all multidrug-resistant strains isolated from pigs (92.30 %). The results from the present study indicate a high frequency of antimicrobial resistance among pathogenic E. coli strains isolated from calves and Salmonella spp. strains isolated from pigs and a high rate of susceptibility to most antimicrobials tested among Salmonella spp. strains isolated from calves. Our study highlights the presence of multidrug-resistant strains of E. coli and Salmonella spp. isolated from food-producing animals in Minas Gerais, Brazil.

Background: This study describes the phenotypic and genotypic characteristics of 78 genetically different Escherichia coli recovered from air and exudate samples of a dairy cattle farm and its surroundings in Spain, in order to gain insight into the flow of antimicrobial resistance through the environment and food supply., Results: Antimicrobial resistance was detected in 21.8% of the 78 E. coli isolates analyzed (resistance for at least one of the 14 agents tested). The highest resistance rates were recorded for ampicillin, nalidixic acid, trimethoprim/sulfamethoxazole and tetracycline. The resistance genes detected were as follows (antibiotic (number of resistant strains), gene (number of strains)): ampicillin (9), bla TEM-1 (6); tetracycline (15), tet(A) (7), tet(B) (4), tet(A) + tet(B) (1); chloramphenicol (5), cmlA (2), floR (2); trimethoprim/sulfamethoxazole (10), sul2 (4), sul1 (3), sul3 (2), sul1 + sul2 (1); gentamicin-tobramycin (1), ant(2″) (1). About 14% of strains showed a multidrug-resistant phenotype and, of them, seven strains carried class 1 integrons containing predominantly the dfrA1-aadA1 array. One multidrug-resistant strain was found in both inside and outside air, suggesting that the airborne spread of multidrug-resistant bacteria from the animal housing facilities to the surroundings is feasible., Conclusions: This study gives a genetic background of the antimicrobial resistance problem in a dairy cattle farm and shows that air can act as a source for dissemination of antimicrobial-resistant bacteria. © 2016 Society of Chemical Industry., (© 2016 Society of Chemical Industry.)

Many people living in rural areas rely on privately owned wells as their primary source of drinking water. These water sources are at risk for fecal contamination of human, wildlife, and livestock origin. While traditional bacteriological testing involves culture-based methods, microbial source tracking (MST) assays present an opportunity to additionally determine the source of fecal contamination. This study investigated the main host sources of contamination in private well water samples with high levels of Escherichia coli (E. coli), using MST with human and multi-species specific markers. Fecal contamination of human origin was detected in approximately 50% of samples, indicating that current contamination prevention strategies require reconsideration. The relationship between cattle density and fecal contamination of bovine origin was investigated using a Bovine Bacteroidales specific MST assay. Regional variations of microbial sources were examined, and may inform local primary prevention strategies. Additionally, in order to assess MST and E. coli quantitative real time polymerase chain reaction (qPCR) assays as indicators of fecal contamination, these were compared to E. coli culture methods. Variation in results was observed across all assay methods investigated, suggesting the most appropriate routine bacteriological testing methodology cannot be determined without comparison to a method that directly detects the presence of fecal contamination.

Wild birds that forage around livestock facilities have been implicated as vectors of antimicrobial resistant organisms. Although antimicrobial resistant bacteria have been isolated from European starlings (Sturnus vulgaris), their role in the dissemination of antimicrobial resistant elements in livestock facilities needs further investigation. To determine whether on-farm starling density and other factors were associated with the presence of cefotaxime and ciprofloxacin resistant E. coli among dairy cows in Ohio, bovine fecal pats from 150 farms were tested for the presence of cefotaxime and ciprofloxacin resistant E. coli. Each farm was visited twice (during the summer and fall of 2007-2009). Multi-level logistic regression models with a random intercept to account for fecal pats collected within a specific visit to a farm were used to assess the associations. The percentage of samples with cefotaxime and ciprofloxacin resistant E. coli was 13.4% and 13.6%, respectively. The percentage of farms having at least one sample testing positive for cefotaxime and ciprofloxacin resistant E. coli was 56.7% and 48.7%, respectively. The odds of detecting cefotaxime and ciprofloxacin resistant E. coli in the samples was significantly higher in 2007 compared to 2008 and 2009, in fall compared to summer, and from farms closer than 60km to starling night roost sites compared to the farms further than 60km. The presence of starlings during the day had a negative association with the likelihood of detecting cefotaxime resistant E. coli. Presence of calves also had a negative association with the likelihood of detecting both cefotaxime and ciprofloxacin resistant E. coli. European starlings might play a role in the dissemination of antimicrobial resistant agents in livestock facilities related to their daily population movements rather than the specific density of birds on farm during the day., (Copyright © 2016 Elsevier B.V. All rights reserved.)

We identified a novel plasmid-mediated colistin-resistance gene in porcine and bovine colistin-resistant Escherichia coli that did not contain mcr-1. The gene, termed mcr-2, a 1,617 bp phosphoethanolamine transferase harboured on an IncX4 plasmid, has 76.7% nucleotide identity to mcr-1. Prevalence of mcr-2 in porcine colistin-resistant E. coli (11/53) in Belgium was higher than that of mcr-1 (7/53). These data call for an immediate introduction of mcr-2 screening in ongoing molecular epidemiological surveillance of colistin-resistant Gram-negative pathogens., (This article is copyright of The Authors, 2016.)

Multi-locus sequence typing (MLST) is a useful system for phylogenetic and epidemiological studies of multidrug-resistant Escherichiacoli. Most studies utilize a seven-locus MLST, but an alternate two-locus typing method (fumC and fimH; CH typing) has been proposed that may offer a similar degree of discrimination at lower cost. Herein, we compare CH typing to the standard seven-locus method for typing commensal E. coli isolates from dairy cattle. In addition, we evaluated alternative combinations of eight loci to identify combinations that maximize discrimination and congruence with standard seven-locus MLST among commensal E. coli while minimizing the cost. We also compared both methods when used for typing uropathogenic E. coli (UPEC). CH typing was less discriminatory for commensal E. coli than the standard seven-locus method (Simpson's Index of Diversity=0.933 [0.902-0.964] and 0.97 [0.96-0.979], respectively). Combining fimH with housekeeping gene loci improved discriminatory power for commensal E. coli from cattle but resulted in poor congruence with MLST. We found that a four-locus typing method including the housekeeping genes adk, purA, gyrB and recA could be used to minimize cost without sacrificing discriminatory power or congruence with Achtman seven-locus MLST when typing commensal E. coli., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Escherichia coli O104:H4, an hybrid pathotype of Shiga toxigenic and enteroaggregative E. coli, involved in a major foodborne outbreak in Germany in 2011, has not been detected in cattle feces. Serogroup O104 with H type other than H4 has been reported to cause human illnesses, but their prevalence and characteristics in cattle have not been reported. Our objectives were to determine the prevalence of E. coli O104 in feces of feedlot cattle, by culture and PCR detection methods, and characterize the isolated strains. Rectal fecal samples from a total of 757 cattle originating from 29 feedlots were collected at a Midwest commercial slaughter plant. Fecal samples, enriched in E. coli broth, were subjected to culture and PCR methods of detection. The culture method involved immunomagnetic separation with O104-specific beads and plating on a selective chromogenic medium, followed by serogroup confirmation of pooled colonies by PCR. If pooled colonies were positive for the wzxO104 gene, then colonies were tested individually to identify wzxO104-positive serogroup and associated genes of the hybrid strains. Extracted DNA from feces were also tested by a multiplex PCR to detect wzxO104-positive serogroup and associated major genes of the O104 hybrid pathotype. Because wzxO104 has been shown to be present in E. coli O8/O9/O9a, wzxO104-positive isolates and extracted DNA from fecal samples were also tested by a PCR targeting wbdDO8/O9/O9a, a gene specific for E. coli O8/O9/O9a serogroups. Model-adjusted prevalence estimates of E. coli O104 (positive for wzxO104 and negative for wbdDO8/O9/O9a) at the feedlot level were 5.7% and 21.2%, and at the sample level were 0.5% and 25.9% by culture and PCR, respectively. The McNemar's test indicated that there was a significant difference (P < 0.01) between the proportions of samples that tested positive for wzxO104 and samples that were positive for wzxO104, but negative for wbdDO8/O9/O9a by PCR and culture methods. A total of 143 isolates, positive for the wzxO104, were obtained in pure culture from 146 positive fecal samples. Ninety-two of the 143 isolates (64.3%) also tested positive for the wbdDO8/O9/O9a, indicating that only 51 (35.7%) isolates truly belonged to the O104 serogroup (positive for wzxO104 and negative for wbdDO8/O9/O9a). All 51 isolates tested negative for eae, and 16 tested positive for stx1 gene of the subtype 1c. Thirteen of the 16 stx1-positive O104 isolates were from one feedlot. The predominant serotype was O104:H7. Pulsed-field gel electrophoresis analysis indicated that stx1-positive O104:H7 isolates had 62.4% homology to the German outbreak strain and 67.9% to 77.5% homology to human diarrheagenic O104:H7 strains. The 13 isolates obtained from the same feedlot were of the same PFGE subtype with 100% Dice similarity. Although cattle do not harbor the O104:H4 pathotype, they do harbor and shed Shiga toxigenic O104 in the feces and the predominant serotype was O104:H7.

Bovine mastitis is a widespread disease in dairy cows, and is often caused by bacterial mammary gland infection. Mastitis causes reduced milk production and leads to excessive use of antibiotics. We present meta-analysis of transcriptional profiles of bovine mastitis from 10 studies and 307 microarrays, allowing identification of much larger sets of affected genes than any individual study. Combining multiple studies provides insight into the molecular effects of Escherichia coli infection in vivo and uncovers differences between the consequences of E. coli vs. Staphylococcus aureus infection of primary mammary epithelial cells (PMECs). In udders, live E. coli elicits inflammatory and immune defenses through numerous cytokines and chemokines. Importantly, E. coli infection causes downregulation of genes encoding lipid biosynthesis enzymes that are involved in milk production. Additionally, host metabolism is generally suppressed. Finally, defensins and bacteria-recognition genes are upregulated, while the expression of the extracellular matrix protein transcripts is silenced. In PMECs, heat-inactivated E. coli elicits expression of ribosomal, cytoskeletal and angiogenic signaling genes, and causes suppression of the cell cycle and energy production genes. We hypothesize that heat-inactivated E. coli may have prophylactic effects against mastitis. Heat-inactivated S. aureus promotes stronger inflammatory and immune defenses than E. coli. Lipopolysaccharide by itself induces MHC antigen presentation components, an effect not seen in response to E. coli bacteria. These results provide the basis for strategies to prevent and treat mastitis and may lead to the reduction in the use of antibiotics.

The prevalence of potentially positive Shiga toxin-producing Escherichia coli (STEC) bovine hides and carcasses in three abattoirs in Costa Rica was estimated. Two export facilities (A and B) and one non-export establishment (C) were visited during the dry and rainy seasons of 2013. Swabs of hides pre-eviscerated and treated (180-220 peroxyacetic acid spray) carcasses were tested for the potential presence of STEC serogroups O26, O45, O103, O111, O121, and O145. The prevalence on hides during the rainy season was 86.7, 96.7 and 96.7% for facilities A, B, and C, respectively. During the dry season, the prevalence on hides was significantly lower in plants A and B (40% and 26.7%, respectively), but was marginally associated with the season in plant C (76.7%, P=0.0523). The prevalence of non-O157 STEC markers on treated carcasses was low (0 to 3.3%), suggesting that all plants were effective in minimizing the target non-O157 STEC in beef destined for export and for domestic consumption., (Copyright © 2015 Elsevier Ltd. All rights reserved.)