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Background Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions. Breeding and deployment of resistant cultivars carrying major resistance (R) genes has been the most effective approach for BB management. However, because of specific interaction of each R gene with the product of the corresponding pathogen avirulence or effector gene, new pathogen strains that can overcome the deployed resistance often emerge rapidly. To deal with ever-evolving Xoo, it is necessary to identify novel R genes and resistance quantitative trait loci (QTL). Results BB resistance of a diverse panel of 340 accessions from the 3000 Rice Genomes Project (3 K RGP) was evaluated by artificial inoculation with four representative Xoo strains, namely Z173 (C4), GD1358 (C5), V from China and PXO339 (P9a) from Philippines. Using the 3 K RG 4.8mio filtered SNP Dataset, a total of 11 QTL associated with BB resistance on chromosomes 4, 5, 11 and 12 were identified through a genome-wide association study (GWAS). Among them, eight resistance loci, which were narrowed down to relatively small genomic intervals, coincided with previously reported QTL or R genes, e.g. xa5, xa25, xa44(t). The other three QTL were putative novel loci associated with BB resistance. Linear regression analysis showed a dependence of BB lesion length on the number of favorable alleles, suggesting that pyramiding QTL using marker-assisted selection would be an effective approach for improving resistance. In addition, the Hap2 allele of LOC_Os11g46250 underlying qC5–11.1 was validated as positively regulating resistance against strain C5. Conclusions Our findings provide valuable information for the genetic improvement of BB resistance and application of germplasm resources in rice breeding programs.

Escherichia coli carrying prophage with genes that encode for Shiga toxins are categorized as Shiga toxin-producing E. coli (STEC) pathotype. Illnesses caused by STEC in humans, which are often foodborne, range from mild to bloody diarrhea with life-threatening complications of renal failure and hemolytic uremic syndrome and even death, particularly in children. As many as 158 of the total 187 serogroups of E. coli are known to carry Shiga toxin genes, which makes STEC a major pathotype of E. coli. Seven STEC serogroups, called top-7, which include O26, O45, O103, O111, O121, O145, and O157, are responsible for the majority of the STEC-associated human illnesses. The STEC serogroups, other than the top-7, called “non-top-7” have also been associated with human illnesses, more often as sporadic infections. Ruminants, particularly cattle, are principal reservoirs of STEC and harbor the organisms in the hindgut and shed in the feces, which serves as a major source of food and water contaminations. A number of studies have reported on the fecal prevalence of top-7 STEC in cattle feces. However, there is paucity of data on the prevalence of non-top-7 STEC serogroups in cattle feces, generally because of lack of validated detection methods. The objective of our study was to develop and validate 14 sets of multiplex PCR (mPCR) assays targeting serogroup-specific genes to detect 137 non-top-7 STEC serogroups previously reported to be present in cattle feces. Each assay included 7–12 serogroups and primers were designed to amplify the target genes with distinct amplicon sizes for each serogroup that can be readily identified within each assay. The assays were validated with 460 strains of known serogroups. The multiplex PCR assays designed in our study can be readily adapted by most laboratories for rapid identification of strains belonging to the non-top-7 STEC serogroups associated with cattle.

Pseudocapacitive lithium storage is an effective way to promote the improvement of electrochemical performance for lithium ion batteries. However, the intrinsically sluggish lithium ionic diffusion and the low electronic conductivity of TiO

Campylobacter spp. can be pathogenic to humans and often harbor antimicrobial resistance genes. Data on resistance in relation to fluoroquinolone use in beef cattle are scarce. This cross-sectional study of preharvest cattle evaluated Campylobacter prevalence and susceptibility to nalidixic acid and ciprofloxacin in feedlots that previously administered a fluoroquinolone as primary treatment for bovine respiratory disease. Twenty fresh fecal samples were collected from each of 10 pens, in each of five feedlots, 1-2 weeks before harvest. Feces were cultured for Campylobacter using selective enrichment and isolation methods. Genus and species were confirmed via PCR. Minimum inhibitory concentrations (MICs) of ciprofloxacin and nalidixic acid were determined using a micro-broth dilution method and human breakpoints. Antimicrobial use within each pen was recorded. Data were analyzed using generalized linear mixed-models (prevalence) and survival analysis (MICs). Overall, sample-level prevalence of Campylobacter was 27.2% (272/1000) and differed significantly among feedlots (p 0.01). Campylobacter coli was the most common species (55.1%; 150/272), followed by Campylobacter hyointestinalis (42.6%; 116/272). Within-pen prevalence was not significantly associated with the number of fluoroquinolone treatments, sex, body weight, or metaphylaxis use, but was associated with the number of days cattle were in the feedlot (p = 0.03). The MICs for the majority of Campylobacter isolates were above the breakpoints for nalidixic acid (68.4%; 175/256) and for ciprofloxacin (65.6%; 168/256). Distributions of MICs for nalidixic acid (p ≤ 0.01) and ciprofloxacin (p ≤ 0.05) were significantly different among feedlots, and by Campylobacter species. However, fluoroquinolone treatments, sex, body weight, days on feed, and metaphylaxis were not significantly associated with MIC distributions within pens. We found no evidence that the number of fluoroquinolone treatments within feedlot pens significantly affected the within-pen fecal prevalence or quinolone susceptibilies of Campylobacter in feedlots that used a fluoroquinolone as primary treatment for bovine respiratory disease.

Shiga toxin-producing E. coli (STEC) are major foodborne pathogens. While many studies have focused on the "top-7 STEC", little is known for minor serogroups. A total of 284 non-top-7 STEC strains isolated from cattle feces were subjected to whole-genome sequencing (WGS) to determine the serotypes, the presence of virulence genes and antimicrobial resistance (AMR) determinants. Nineteen typeable and three non-typeable serotypes with novel O-antigen loci were identified. Twenty-one AMR genes and point mutations in another six genes that conferred resistance to 10 antimicrobial classes were detected, as well as 46 virulence genes. The distribution of 33 virulence genes and 15 AMR determinants exhibited significant differences among serotypes (p 0.05). Among all strains, 81.7% (n = 232) and 14.1% (n = 40) carried stx2 and stx1 only, respectively; only 4.2% (n = 12) carried both. Subtypes stx1a, stx1c, stx2a, stx2c, stx2d, and stx2g were identified. Forty-six strains carried eae and stx2a and therefore had the potential cause severe diseases; 47 strains were genetically related to human clinical strains inferred from a pan-genome phylogenetic tree. We were able to demonstrate the utility of WGS as a surveillance tool to characterize the novel serotypes, as well as AMR and virulence profiles of uncommon STEC that could potentially cause human illness.

Escherichia coli serogroups O157, O26, O45, O103, O111, O121, and O145, when carrying major virulence genes, the Shiga toxin genes stx(1) and stx(2) and the intimin gene eae, are important foodborne pathogens. They are referred to as the “top 7” Shiga toxin-producing E. coli (STEC) serogroups and were declared by the USDA as adulterants to human health. Since top 7 serogroup-positive cattle feces and ground beef can also contain nonadulterant E. coli strains, regular PCR cannot confirm whether the virulence genes are carried by adulterant or nonadulterant E. coli serogroups. Thus, traditional gold-standard STEC detection requires bacterial isolation and characterization, which are not compatible with high-throughput settings and often take a week to obtain a definitive result. In this study, we demonstrated that the partition-based multichannel digital PCR (dPCR) system can be used to detect and associate the E. coli serogroup-specific gene with major virulence genes and developed a single-cell-based dPCR approach for rapid (within 1 day) and accurate detection and confirmation of major STEC serogroups in high-throughput settings. Major virulence genes carried by each of the top 7 STEC serogroups were detected by dPCR with appropriately diluted intact bacterial cells from pure cultures, culture-spiked cattle feces, and culture-spiked ground beef. Furthermore, from 100 randomly collected, naturally shed cattle fecal samples, 3 O103 strains carrying eae and 2 O45 strains carrying stx(1) were identified by this dPCR assay and verified by the traditional isolation method. This novel and rapid dPCR assay is a culture-independent, high-throughput, accurate, and sensitive method for STEC detection and confirmation.

Background To investigate clinical presentation and molecular aspects of five patients suffered from glutaric aciduria type I (GA-I ), a rare neurometabolic disorder caused by glutaryl-CoA dehydrogenase deficiency due to GCDH gene mutations. Methods All five patients were diagnosed by elevated urinary glutaric acid and GCDH gene analysis. Low protein diet supplemented with special formula, GABA analog and L-carnitine were initialed following laboratory confirmation of diagnosis. The clinical and biochemical features were analyzed, and mutational analysis of GCDH was conducted using Sanger sequencing. Results Clinical manifestations of 5 patients varied from macrocephaly to severe encephalopathy, with notably different phenotype between siblings with the same mutations. Three members present complex heterozygous mutations, while two sisters present homozygous mutations. Among them, four mutations in GCDH were identified (c.1133C>T 、c.1244-2A>C 、c.339delT 、c.406G>T). Of these four mutations, c.1244- 2A>C was found in four patients and c.339delT and c.1133C>T has not yet been reported until now. Conclusions In 5 Chinese patients with GA1, two novel mutations of GCDH gene were identified, which may expand the mutation spectrum of GCDH gene. What we found confirm that there is no correlation between clinical phenotype and genotype in GA-I patients, and c.1244-2A>C may be mutation hotspot in Southern China.

Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, referred to as the top six non-O157 serogroups, are responsible for more than 70% of human non-O157 STEC infections in North America. Cattle harbor non-O157 strains in the hindgut and shed them in the feces. The objective of this study was to use the U.S. Food and Drug Administration (FDA) E. coli identification (ECID) DNA microarray to identify the serotype, assess the virulence potential of each, and determine the phylogenetic relationships among five of the six non-O157 E. coli serogroups isolated from feedlot cattle feces. Forty-four strains of STEC, enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), or putative nonpathotype E. coli (NPEC) of cattle origin and five human clinical strains of EHEC were assayed with the FDA-ECID DNA microarray. The cattle strains harbored diverse flagellar genes. The bovine and human strains belonging to serogroups O26, O45, and O103 carried stx

Escherichia coli O145 serogroup is one of the big six non-O157 Shiga toxin producing E. coli (STEC) that causes foodborne illnesses in the United States and other countries. Cattle are a major reservoir of STEC, which harbor them in their hindgut and shed in the feces. Cattle feces is the main source of hide and subsequent carcass contaminations during harvest leading to foodborne illnesses in humans. The objective of our study was to determine the virulence potential of STEC O145 strains isolated from cattle feces and hide samples. A total of 71 STEC O145 strains isolated from cattle feces (n = 16), hide (n = 53), and human clinical samples (n = 2) were used in the study. The strains were subjected to whole genome sequencing using Illumina MiSeq platform. The average draft genome size of the fecal, hide, and human clinical strains were 5.41, 5.28, and 5.29 Mb, respectively. The average number of genes associated with mobile genetic elements was 260, 238, and 259, in cattle fecal, hide, and human clinical strains, respectively. All strains belonged to O145:H28 serotype and carried eae subtype γ. Shiga toxin 1a was the most common Shiga toxin gene subtype among the strains, followed by stx2a and stx2c. The strains also carried genes encoding type III secretory system proteins, nle, and plasmid-encoded virulence genes. Phylogenetic analysis revealed clustering of cattle fecal strains separately from hide strains, and the human clinical strains were more closely related to the hide strains. All the strains belonged to sequence type (ST)-32. The virulence gene profile of STEC O145 strains isolated from cattle sources was similar to that of human clinical strains and were phylogenetically closely related to human clinical strains. The genetic analysis suggests the potential of cattle STEC O145 strains to cause human illnesses. Inclusion of more strains from cattle and their environment in the analysis will help in further elucidation of the genetic diversity and virulence potential of cattle O145 strains.

To detect potential variation in glutaryl-CoA dehydrogenase (GCDH) gene among three Chinese families affected with glutaric acidemia type Ⅰ(GA-1) and correlate the genotypes with phenotypes.Genomic DNA was extracted from peripheral blood samples derived from three patients with GA-1 and their family members. The coding regions of the GCDH gene were amplified with PCR and subjected to Sanger sequencing.The clinical manifestation of the patients varied from macrocephaly to severe encephalopathy, with notable phenotypic difference between siblings carrying the same variation. In pedigrees 1 and 2, the probands have carried compound heterozygous variations c.1133CT(p.Ala378Val) and c.1244-2AC, which were derived their fathers and mothers, respectively. In pedigree 3, the proband has carried compound heterozygous variation c.339delT (p.Tyr113) and c.406GT (p.Gly136Cys). Among these, variations c.339delT and c.1133CT were verified as novel by retrieval of dsSNP, HGMD and 1000 genome database. Bioinformatic analysis suggested that above variations can affect protein function and are probably pathogenic.Above discovery has expanded the mutation spectrum of the GCDH gene. No correlation was found between the clinical phenotype and genotype of GA-1 patients.

Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, called non-O157 STEC, are important foodborne pathogens. Cattle, a major reservoir, harbor the organisms in the hindgut and shed them in the feces. Although limited data exist on fecal shedding, concentrations of non-O157 STEC in feces have not been reported. The objectives of our study were (i) to develop and validate two multiplex quantitative PCR (mqPCR) assays, targeting O-antigen genes of O26, O103, and O111 (mqPCR-1) and O45, O121, and O145 (mqPCR-2); (ii) to utilize the two assays, together with a previously developed four-plex qPCR assay (mqPCR-3) targeting the O157 antigen and three virulence genes (stx1, stx2, and eae), to quantify seven serogroups and three virulence genes in cattle feces; and (iii) to compare the three mqPCR assays to a 10-plex conventional PCR (cPCR) targeting seven serogroups and three virulence genes and culture methods to detect seven E. coli serogroups in cattle feces. The two mqPCR assays (1 and 2) were shown to be specific to the target genes, and the detection limits were 4 and 2 log CFU/g of pure culture-spiked fecal samples, before and after enrichment, respectively. A total of 576 fecal samples collected from a feedlot were enriched in E. coli broth and were subjected to quantification (before enrichment) and detection (after enrichment). Of the 576 fecal samples subjected, before enrichment, to three mqPCR assays for quantification, 175 (30.4%) were quantifiable (≥4 log CFU/g) for at least one of the seven serogroups, with O157 being the most common serogroup. The three mqPCR assays detected higher proportions of postenriched fecal samples (P0.01) as positive for one or more serogroups compared with cPCR and culture methods. This is the first study to assess the applicability of qPCR assays to detect and quantify six non-O157 serogroups in cattle feces and to generate data on fecal concentration of the six serogroups.

Shiga toxin-producing Escherichia coli (STEC) of the serogroups O26, O45, O103, O111, O121, and O145, often called non-O157 STEC, are foodborne pathogens. Cattle are asymptomatic reservoirs for STEC; the organisms reside in the hindgut and are shed in the feces, which serve as the source of food product contaminations. Culture-based detection of non-O157 STEC involves an immunomagnetic separation (IMS) step to capture the specific serogroups in complex matrices, such as feces. The IMS procedure is time consuming and labor intensive because of the need to subject each fecal sample to six individual beads. Therefore, our objective was to evaluate whether pooling of IMS beads affects sensitivity of non-O157 STEC detection compared with using individual IMS beads. The evaluation was done by comparing detection of serogroups in feces spiked with pure cultures (experiments 1 and 2) and from feces (n = 384) of naturally shedding cattle (experiment 3). In spiked fecal samples, detection with pools of three, four, six, or seven beads was similar to, or at times higher than, detection with individual IMS beads. In experiment 3, the proportions of fecal samples that tested positive for the six serogroups as detected by individual or pooled beads were similar. Based on noninferiority tests, detection with pooled beads was not substantially inferior to detection with individual beads (P0.05). In conclusion, the pooling of IMS beads is a better option for detection of STEC serogroups in fecal samples compared with individual beads because the procedure saves time and labor and has the prospect of a higher throughput.

Poor cycling performance of SnS2 induced by the initial structural transformation and subsequent volumetric expansion during lithiating process hinders the widespread application of SnS2 in lithium ion batteries despite its high theoretic capacity. A simple approach promoting the performance of SnS2 is proposed here via strategically introducing rGO/g-C3N4 hybrid to form a robust framework in the designed SnS2 composite. Nano-composite of rGO/g-C3N4@SnS2 where hollow SnS2 spheres with ultra-thin walls are combined with rGO/g-C3N4. The prepared rGO/g-C3N4@SnS2 possesses excellent lithium storage and high rate performance with a recovered capacity of 864.93 mAh/g at the current density of 800 mA/g.

Red phosphorus, a promising anode candidate for lithium ion batteries, draws wide attention owing to its high theoretical capacity, high abundance in earth as well as environmental benignity. However, its poor electrical conductivity and large volumetric changes during the charge-discharge process hinders its practical application. A novel phosphorus composite framed by reduced graphene oxide-C3N4 (rGO-C3N4) and cost-effective red phosphorus is proposed in the study. P–N and P–C chemical bonds between the red phosphorus and rGO-C3N4 framework facilitate to construct a robust architecture with admirable interface interconnection for stable mechanical structure and continuous Li ion/electron diffusion tunnels. Excellent electrochemical performance is demonstrated. The red phosphorus/rGO-C3N4 composite maintains a reversible capacity of 1032.6 mAh g−1 with a high coulombic efficiency of approximately 99.0% after 600 cycles.

Shiga toxin-producing E. coli (STEC) belonging to serogroups O26, O45, O111, O103, O121, O145, and O157, called ‘top-7’, are major foodborne pathogens. Cattle are a major reservoir, in which STEC colonize the hindgut and are shed in the feces, which is a major source of contamination of food. Our objective was to evaluate the impact of a proprietary yeast-based synbiotic product (prebiotic and probiotic; Alltech, Inc., Nicholasville, KY) on fecal shedding of top-7 STEC in feedlot cattle. Twenty existing pens, housing 40–112 steers per pen, with an estimated 60 to 90 days to slaughter, were randomly assigned to a control group or a treatment group that received 22 g of the synbiotic product per steer per day, as a top dress, in a finishing diet. Twenty pen-floor fecal samples were collected from each pen on days 0, 21, 42, and 54. Fecal samples were enriched and subjected to a multiplex PCR assay targeting serogroup-specific genes for the top-7 STEC and three major virulence genes, stx1 (Shiga toxin 1), stx2 (Shiga toxin 2), and eae (intimin). Bivariate descriptive statistics for the major serogroups and virulence genes were assessed prior to multivariable analysis using mixed effects logistic regression. The overall prevalence of the top-7 serogroups were 44.5% of O26, 41.3% of O157, 15.1% of O103, 13.7% of O45, 7.8% of O121, and 0.6% of O111. The overall prevalence of stx1, stx2, and eae were 43.9%, 70.8%, and 49%, respectively. E. coli O26, O157, and O45 had a significant treatment and sampling day interaction (P < 0.0001). On d 42, fecal samples from treated group had lower prevalence (P < 0.01) of O26, O103, and O45 compared to the control group. In conclusion, the in-feed administration of the synbiotic product appears to reduce fecal shedding of certain top-7 STEC serogroups in the feedlot cattle.

The interplay between the structural configuration and the intrinsic semi-conductive property constrains the further enhancement of the electrochemical performance of TiO2 as an anode material for lithium ion batteries. In this study, hierarchical TiO2@C microrods featured with a macrostructure of microrods composed of a substructure of ultrathin TiO2@C nanosheets with efficient conducting network of carbon surface are constructed strategically on the base of the admirable confluence of the structural configuration and the surface modification. The admirable hierarchical structure facilitates the synergic effect between the surface psedocapacitance for high power density and the electrochemical redox capacity for high energy density, which plays an important role in the enhancement of rate performance. The hierarchical TiO2@C microrods exhibit remarkable rate performance and ultra-long cycling ability with a high reversible capacity of 344.2 mA h g−1 close to its theoretic specific capacity in the first cycle at 0.5C. A reversible capacity of 125.6 mA h g−1 at 60 C has been gained in the second cycle with an average capacity-fading loss of only 0.00375% per cycle over 10,000 cycles. The results clearly reveal that the rational confluence of favourable structure and sound surface modification is effective to improve the electrochemical performance of TiO2.

Probiotics, an antibiotic alternative, are widely used as feed additives for performance benefits in cattle and swine production systems. Among bacterial species contained in probiotics, Enterococcus faecium is common. Antimicrobial resistance (AMR), particularly multidrug resistance, is a common trait among enterococci because of their propensity to acquire resistance and horizontally transfer AMR genes. Also, E. faecium is an opportunistic pathogen, and in the United States, it is the second most common nosocomial pathogen. There has been no published study on AMR and virulence potential in E. faecium contained in probiotic products used in cattle and swine in the United States. Therefore, our objectives were to determine phenotypic susceptibilities or resistance to antimicrobials, virulence genes (asa1, gelE, cylA, esp, and hyl) and assess genetic diversity of E. faecium isolated from commercial products. Twenty-two commercially available E. faecium-based probiotic products used in cattle (n = 13) and swine (n = 9) were procured and E. faecium was isolated and species confirmed. Antimicrobial susceptibility testing to determine minimum inhibitory concentrations was done by micro-broth dilution method using National Antimicrobial Resistance Monitoring Systems Gram-positive Sensititre panel plate (CMV3AGPF), and categorization of strains as susceptible or resistant was as per Clinical Laboratory and Standards Institute's guidelines. E. faecium strains from 7 products (3 for swine and 4 for cattle) were pan-susceptible to the 16 antimicrobials tested. Strains from 15 products (6 for swine and 9 for cattle) exhibited resistance to at least one antimicrobial and a high proportion of strains was resistant to lincomycin (10/22), followed by tetracycline (4/22), daptomycin (4/22), ciprofloxacin (4/22), kanamycin (3/22), and penicillin (2/22). Four strains were multidrug resistant, with resistant phenotypes ranging from 3 to 6 antimicrobials or class. None of the E. faecium strains were positive for any of the virulence genes tested. The clonal relationships among the 22 E. faecium strains were determined by pulsed-field gel electrophoresis (PFGE) typing. A total of 10 PFGE patterns were observed with 22 strains and a few of the strains from different probiotic products had identical (100% Dice similarity) PFGE patterns. In conclusion, the E. faecium strains in a few commercial probiotics exhibited AMR to medically-important antimicrobials, but none contained virulence genes.

Escherichia coli O103, harbored in the hindgut and shed in the feces of cattle, can be enterohemorrhagic (EHEC), enteropathogenic (EPEC), or putative non-pathotype. The genetic diversity particularly that of virulence gene profiles within O103 serogroup is likely to be broad, considering the wide range in severity of illness. However, virulence descriptions of the E. coli O103 strains isolated from cattle feces have been primarily limited to major genes, such as Shiga toxin and intimin genes. Less is known about the frequency at which other virulence genes exist or about genes associated with the mobile genetic elements of E. coli O103 pathotypes. Our objective was to utilize whole genome sequencing (WGS) to identify and compare major and putative virulence genes of EHEC O103 (positive for Shiga toxin gene, stx1, and intimin gene, eae; n = 43), EPEC O103 (negative for stx1 and positive for eae; n = 13) and putative non-pathotype O103 strains (negative for stx and eae; n = 13) isolated from cattle feces. Six strains of EHEC O103 from human clinical cases were also included. All bovine EHEC strains (43/43) and a majority of EPEC (12/13) and putative non-pathotype strains (12/13) were O103:H2 serotype. Both bovine and human EHEC strains had significantly larger average genome sizes (P < 0.0001) and were positive for a higher number of adherence and toxin-based virulence genes and genes on mobile elements (prophages, transposable elements, and plasmids) than EPEC or putative non-pathotype strains. The genome size of the three pathotypes positively correlated (R2 = 0.7) with the number of genes carried on mobile genetic elements. Bovine strains clustered phylogenetically by pathotypes, which differed in several key virulence genes. The diversity of E. coli O103 pathotypes shed in cattle feces is likely reflective of the acquisition or loss of virulence genes carried on mobile genetic elements.

To develop a high-yield pyruvate strain, we first engineered a pyruvate-producing Escherichia coli KLPP from wild-type E. coli MG1655 by blocking the pathways for byproduct formation via gene knockout. Then, we built a library of mutant containing 7 197 monoclones by using the pUT Mini-Tn5 transposon vector for random mutagenesis with E. coli KLPP. We developed a high-throughput method for pyruvate detection based on dinitrophenylhydrazine reaction using 96-well microplate reader. After two-round screening we successfully obtained six mutants with increased pyruvate titer using this method, the titer of pyruvate was increased by 38%, 31%, 19%, 28%, 44% and 14%, respectively. The position of transposon insertion was determined by whole genome re-sequencing, and the gene locus possibly influencing pyruvate production was analyzed, which laid the foundation for subsequent strain improvement by metabolic engineering.为了开发丙酮酸高产菌株，以大肠杆菌MG1655 为出发菌株，通过基因敲除阻断副产物途径构建了产丙酮酸大肠杆菌工程菌KLPP。进一步利用pUT Mini-Tn5 载体进行转座子随机突变，构建了含有7 197 个单克隆的突变体文库。使用基于丙酮酸的二硝基苯肼显色法，建立了96 孔板-酶标仪快速筛选方法，经过两轮的筛选，成功筛选到了6 个突变体菌株，比KLPP 丙酮酸产量提高了38%、31%、19%、28%、44%和14%。利用全基因组重测序确定了其转座子插入的位置，进而确定了可能影响丙酮酸产量的基因位点，为后续菌株改造工作奠定了基础。.

Application of functional imaging to radiotherapy (RT) is a rapidly expanding field with the development of new modalities and techniques. Functional imaging of PET in conjunction with RT provides new avenues towards the clinical application of dose painting - a new RT strategy delivering optimized dose redistribution according to the functional imaging information to further improve tumour control. Two prototypical strategies of dose painting are reviewed: dose painting by contours (DPBC) and dose painting by numbers (DPBN). DPBN set a linear correlation of the boost dose and image intensity of this same voxel while homogeneous dose is given to the subvolume contoured by a threshold created in PET images in DPBC. Both comply with strict organs at risk (OAR) constraints and are alternatives for boosting subvolumes in clinical practice. This review focuses on the rationale, target validation, dose prescription verification and evaluation and recent clinical achievements in the field of integrating PET imaging into RT treatment planning. Further research is necessary in order to investigate unresolved problems in its routine clinical application thoroughly.

Cattle harbor and shed in their feces several Escherichia coli O104 serotypes. All O104 strains examined were intimin negative and belonged to the B1 phylogroup, and some were Shiga toxigenic. We report here the genome sequences of bovine O104:H7 ( n = 5), O104:H23 ( n = 2), O104:H8 ( n = 1), and O104:H12 ( n = 1) isolates and human clinical isolates of O104:H7 ( n = 5).

The study objective was to determine effects of fluoroquinolone metaphylaxis on fecal prevalence of Salmonella and Campylobacter and fecal prevalence of quinolone-resistant Salmonella and Campylobacter in feedlot cattle. On Day 0, cattle (n = 288) at risk for bovine respiratory disease (BRD) were randomly assigned to either a nontreated control pen (12 pens) or a fluoroquinolone-treated (enrofloxacin; Baytril® 100) pen (12 pens). Rectal fecal samples were collected from cattle on days 0, 7, 14, 21, and 28. Feces were cultured for Salmonella enterica and Campylobacter spp. using enrichment and selective isolation methods, and confirmed by serology and PCR. Susceptibilities to nalidixic acid and ciprofloxacin were determined using microbroth dilution methods. Data analyses were performed using linear mixed models. Overall, Salmonella sp. and Campylobacter spp. were recovered from 10.2% (139/1,364) and 12.4% (170/1,364) of the fecal samples, respectively. Campylobacter species included hyointestinal...

Cattle are a major reservoir of the six major Shiga toxin-producing non-O157 Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) responsible for foodborne illnesses in humans. Besides prevalence in feces, the concentrations of STEC in cattle feces play a major role in their transmission dynamics. A subset of cattle, referred to as super shedders, shed E. coli O157 at high concentrations (≥4 log CFU/g of feces). It is not known whether a similar pattern of fecal shedding exists for non-O157. Our objectives were to initially validate the spiral plating method to quantify the six non-O157 E. coli serogroups with pure cultures and culture-spiked fecal samples and then determine the applicability of the method and compare it with multiplex quantitative PCR (mqPCR) assays for the quantification of the six non-O157 E. coli serogroups in cattle fecal samples collected from commercial feedlots. Quantification limits of the spiral plating method were 3 log, 3 to 4 log, and 3 to 5 log CFU/mL or CFU/g for individual cultures, pooled pure cultures, and cattle fecal samples spiked with pooled pure cultures, respectively. Of the 1,152 cattle fecal samples tested from eight commercial feedlots, 122 (10.6%) and 320 (27.8%) harbored concentrations ≥4 log CFU/g of one or more of the six serogroups of non-O157 by spiral plating and mqPCR methods, respectively. A majority of quantifiable samples, detected by either spiral plating (135 of 137, 98.5%) or mqPCR (239 of 320, 74.7%), were shedding only one serogroup. Only one of the quantifiable samples was positive for a serogroup carrying Shiga toxin (stx

To delineate the clinical features and potential mutation of the ATP7A gene in a family affected with Menkes disease.Clinical data of a patient and his family members were analyzed. Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) assays were performed to detect the mutation of the ATP7A gene.The patient was admitted at the age of 5 months due to severe epilepsy and marked delayed psychomotor development. Significantly light complexion, pudgy cheeks and sparse fuzzy wooly hair were noted. Cranial magnetic resonance imaging and angiography revealed cortical atrophy, leukoencephalopathy and circuitous of intracranial vessels. The plasma ceruloplasmin was decreased. MLPA has identified a deletion spanning exons 8 to 12 of the ATP7A gene. His mother was found to be a heterozygous carrier of the same mutation.The clinical features and a novel mutation of the ATP7A gene of the family have been delineated.

Shiga toxin producing Escherichia coli (STEC) are important foodborne pathogens responsible for human illnesses. Cattle are a major reservoir that harbor the organism in the hindgut and shed in the feces. Shiga toxins (Stx) are the primary virulence factors associated with STEC illnesses. The two antigenically distinct Stx types, Stx1 and Stx2, encoded by stx1 and stx2 genes, share approximately 56% amino acid sequence identity. Genetic variants exist within Stx1 and Stx2 based on differences in amino acid composition and in cytotoxicity. The objective of our study was to identify the stx subtypes in strains of STEC serogroups, other than O157, isolated from cattle feces. Shiga toxin gene carrying E. coli strains (n = 192), spanning 27 serogroups originating from cattle (n = 170) and human (n = 22) sources, were utilized in the study. Shiga toxin genes were amplified by PCR, sequenced, and nucleotide sequences were translated into amino acid sequences using CLC main workbench software. Shiga toxin subtypes were identified based on the amino acid motifs that define each subtype. Shiga toxin genotypes were also identified at the nucleotide level by in silico restriction fragment length polymorphism (RFLP). Of the total 192 STEC strains, 93 (48.4%) were positive for stx1 only, 43 (22.4%) for stx2 only, and 56 (29.2%) for both stx1 and stx2. Among the 149 strains positive for stx1, 132 (88.6%) were stx1a and 17 (11.4%) were stx1c. Shiga toxin 1a was the most common subtype of stx1 among cattle (87.9%; 123/140) and human strains (100%; 9/9) of non-O157 serogroups. Of the total 99 strains positive for stx2, 79 were stx2a (79.8%), 11 (11.1%) were stx2c, 12 (12.1%) were stx2d. Of the 170 strains originating from cattle feces, 58 (34.1%) were stx2a subtype, 11 (6.5%) were stx2c subtype, and 11 were of subtype stx2d (6.5%). All but one of the human strains were positive for stx2a. Three strains of cattle origin were positive for both stx2a and stx2d. In conclusion, a number of non-O157 STEC serogroups harbored by cattle possess a wide variety of Shiga toxin subtypes, with stx1a and stx2a being the most predominant stx subtypes occurring individually or in combination. Cattle are a reservoir of a number of non-O157 STEC serogroups and information on the Shiga toxin subtypes is useful in assessing the potential risk as human pathogens.

Escherichia coli O26 is second only to O157 in causing foodborne, Shiga toxin-producing E. coli (STEC) infections. Our objectives were to determine fecal prevalence and characteristics of E. coli O26 in commercial feedlot cattle (17,148) that were enrolled in a study to evaluate an E. coli O157:H7 siderophore receptor and porin (SRP(®)) vaccine (VAC) and a direct-fed microbial (DFM; 10(6) colony-forming units [CFU]/animal/day of Lactobacillus acidophilus and 10(9) CFU/animal/day of Propionibacterium freudenreichii). Cattle were randomly allocated to 40 pens within 10 complete blocks; pens were randomly assigned to control, VAC, DFM, or VAC+DFM treatments. Vaccine was administered on days 0 and 21, and DFM was fed throughout the study. Pen-floor fecal samples (30/pen) were collected weekly for the last 4 study weeks. Samples were enriched in E. coli broth and subjected to a multiplex polymerase chain reaction (PCR) designed to detect O26-specific wzx gene and four major virulence genes (stx1, stx2, eae, and ehxA) and to a culture-based procedure that involved immunomagnetic separation and plating on MacConkey agar. Ten presumptive E. coli colonies were randomly picked, pooled, and tested by the multiplex PCR. Pooled colonies positive for O26 serogroup were streaked on sorbose MacConkey agar, and 10 randomly picked colonies per sample were tested individually by the multiplex PCR. The overall prevalence of E. coli O26 was higher (p0.001) by the culture-based method compared to the PCR assay (22.7 versus 10.5%). The interventions (VAC and or DFM) had no impact on fecal shedding of O26. Serogroup O26 was recovered in pure culture from 23.9% (260 of 1089) of O26 PCR-positive pooled colonies. Only 7 of the 260 isolates were positive for the stx gene and 90.1% of the isolates possessed an eaeβ gene that codes for intimin subtype β, but not the bfpA gene, which codes for bundle-forming pilus. Therefore, the majority of the O26 recovered from feedlot cattle feces was atypical enteropathogenic E. coli, and not STEC.

Shiga toxin-producing Escherichia coli (STEC) are important human pathogens, and attention to non-O157 serogroups has increased in recent years. Although cattle are normally considered the primary reservoir for STEC, recent illnesses associated with goat contact have indicated that these animals are important potential reservoirs for the organisms. The prevalence of STEC, particularly non-O157 serogroups, in U.S. goats has not been well described. Our objective was to determine the prevalence of six major non-O157 STEC serogroups in the feces of meat goats. Rectal contents from 296 goats were collected postevisceration at a slaughter plant in the southeastern United States over 9 days during a 12-week period from August through October 2012. Samples were enriched in E. coli broth, and DNA was extracted and used as template in an 11-gene multiplex PCR that detected six non-O157 serogroups (O26, O45, O103, O121, O111, and O145) and virulence genes. Samples were considered positive when at least one non-O157 STEC serotype was present with either stx 1 or stx 2. All six non-O157 serogroups were detected by PCR in our samples, and 14.5% of samples were positive for at least one serogroup. Prevalence of O26 was highest, with 6.4% of goat fecal samples positive. The prevalence of O45 was 3.4%, O103 was 4.4%, O111 was 4.1%, O121 was 1.4%, and O145 was 3.0%. Twenty-two (7.4%) of 296 fecal samples had more than one non-O157 serogroup detected in the feces. Two samples had evidence of three non-O157 STEC serogroups. Goats appear to be an important reservoir for non-O157 STEC, and further work to understand the characteristics, epidemiology, and ecology of STEC in these animals is warranted.

A multiplex PCR was designed to detect Escherichia coli O104:H4, a hybrid pathotype of Shiga toxigenic and enteroaggregative E. coli , in cattle feces. A total of 248 fecal samples were tested, and 20.6% were positive for serogroup O104. The O104 isolates did not carry genes characteristic of the virulent hybrid strain.

Distillers grains (DG), a co-product of ethanol production used as protein and energy supplements in cattle diets, have been shown to increase fecal shedding of Escherichia coli O157:H7, a major foodborne pathogen. The reason for the positive association is not known. Because DG often replaces grain in the diet, decreased starch content and flow to the hindgut may create a favorable environment for E. coli O157:H7. Our objective was to determine whether the addition of starch to a corn DG-supplemented diet negates the effects of DG on fecal shedding of E. coli O157:H7. We conducted a study with 21 steers fed 1 of 3 diets: a corn grain-based basal diet (CON), basal diet supplemented with 25% corn dried DG (DDG), and basal diet supplemented with 25% DDG with corn starch (DDG+S) added at a level intended to increase starch concentration to that of the CON diet. Steers, housed individually in a biosafety level 2 animal facility, were randomly allocated to treatment diets and orally inoculated with a 5-strain mixture (10(9) cfu per steer) of nalidixic acid-resistant (Nal(R)) E. coli O157:H7. Fecal samples were collected for 5 wk, and on d 35, steers were euthanized and necropsied to collect gut content samples. Fecal or gut samples were cultured to determine prevalence and concentrations of Nal(R) E. coli O157:H7. Dietary starch concentrations, based on feed analysis, were 46.3% in the CON compared with 43.3 and 41.3% in the DDG and DDG+S diets, respectively. Steers fed DDG or DDG+S diets shed Nal(R) E. coli O157:H7 more often (P = 0.0027 and 0.0003, respectively) and at greater concentrations (1.9 or 2.0 cfu/g; P = 0.0025 and 0.0006) than those fed CON diet (1.4 cfu/g), but no difference was observed between DDG and DDG+S diets. Cumulative prevalence and concentrations of Nal(R) E. coli O157:H7 were greater in gut samples collected at necropsy in steers fed DDG and DDG+S diets compared with those fed CON diet, but no difference was observed between DDG and DDG+S diets. The lack of effect of starch addition to the DDG diet on fecal shedding of E. coli O157:H7 may be because either the decreased starch content in the DG-supplemented diet is not a factor in the increased shedding of E. coli O157:H7 or inclusion of pure starch in the diet may not have achieved our intended goal to have starch flow into the hindgut similar to that of corn grain. The study confirms our previous finding of the positive association between feeding DG and fecal shedding of E. coli O157:H7.

Salmonella is an important foodborne pathogen and antimicrobial resistance can be a human health concern. The objectives of this cross-sectional study were to (1) determine the prevalence and quinolone susceptibility of Salmonella in feces of preharvest commercial feedlot cattle and (2) determine if the prevalence and susceptibility of Salmonella isolates were associated with previous fluoroquinolone use within pens. Five feedlots in western Kansas and Texas were selected based on their use of a commercially licensed fluoroquinolone for initial treatment of bovine respiratory disease (BRD). Twenty pen floor fecal samples were collected from each of 10 pens from each feedlot during early summer of 2012. Salmonella isolation was performed and microbroth dilution was used to determine susceptibility of isolates to nalidixic acid and ciprofloxacin. Prior antimicrobial treatment data were retrieved from feedlots' operational data. Generalized linear mixed models were used to assess associations between Salmonella prevalence and the number of fluoroquinolone treatments within pens while taking into consideration cattle demographic and management factors, as well as the hierarchical structure of the data. Overall, cumulative fecal prevalence of Salmonella was 38.0% (380/1000), but prevalence varied significantly (p

Shiga toxin-producing Escherichia coli (STEC), particularly O157, are major food borne pathogens. Non-O157 STEC, particularly O26, O45, O103, O111, O121, and O145, have also been recognized as a major public health concern. Unlike O157, detection procedures for non-O157 have not been fully developed. Our objective was to develop a multiplex PCR to distinguish O157 and the ‘top six’ non-O157 serogroups (O26, O45, O103, O111, O121, and O145) and evaluate the applicability of the multiplex PCR to detect the seven serogroups of E. coli in cattle feces. Published sequences of O-specific antigen coding genes, rfbE (O157) and wzx and wbqE-F (non-O157), were analyzed to design serogroup-specific primers. The specificity of amplifications was confirmed with 138 known STEC strains and the reaction yielded the expected amplicons for each serogroup. In feces spiked with pooled 7 STEC strains, the sensitivity of the detection was 4.1 × 10 5 CFU/g before enrichment and 2.3 × 10 2 after 6 h enrichment in E. coli broth. Additionally, 216 fecal samples from cattle were collected and tested by multiplex PCR and cultural methods. The multiplex PCR revealed a high prevalence of all seven serogroups (178 [O26], 108 [O45], 149 [O103], 30 [O111], 103 [O121], 5 [O145], and 160 [O157]) of 216 samples in fecal samples. Cultural procedures identified 33.1% (53/160) and 35.5% (11/31) of PCR-positive samples for E. coli O157 and non-O157 serogroups, respectively. Samples that were culture-positive were all positive by the multiplex PCR. The multiplex PCR can be used to identify serogroups of putative STEC isolates.

Cattle are asymptomatic reservoirs for Escherichia coli O157, a major foodborne pathogen. The organism generally colonizes the hindgut of cattle and is shed in the feces at low concentrations. The objective of this research was to evaluate a multiplex, real-time polymerase chain reaction (mqPCR) assay for quantification of E. coli O157 in cattle feces using stx1, stx2, and rfbE gene targets. Primer efficiency and analytical sensitivity of the assay were evaluated with a single or pooled (five strain) culture of E. coli O157. In pure culture, the minimum detection limit of the assay was 1.4×10(3) CFU/mL and 3.6×10(3) CFU/mL for the single and five-strain mixture of E. coli O157, respectively. Diagnostic sensitivity was analyzed using DNA extracted from cattle feces spiked with E. coli O157. In feces spiked with the pooled mixture of five E. coli O157 strains, the minimum detection limit was 3.6×10(4) CFU/g. We also evaluated the assay with feces from cattle experimentally inoculated with E. coli O157 by comparing the results to a culture-based method. For the majority of samples tested, the concentration of E. coli O157 detected by the real-time and culture methods was within one log difference. However, the assay could only be evaluated for cattle shedding high concentrations of E. coli O157. In conclusion, the mqPCR quantifying E. coli O157 in cattle feces using stx1, stx2, and rfbE gene targets may have use in detecting and quantifying super shedders, but is not applicable for quantification in animals shedding low concentrations (10(2) to 10(3) CFU/g feces).

Copper, as copper sulfate, is increasingly used as an alternative to in-feed antibiotics for growth promotion in weaned piglets. Acquired copper resistance, conferred by a plasmid-borne, transferable copper resistance ( tcrB ) gene, has been reported in Enterococcus faecium and E. faecalis . A longitudinal field study was undertaken to determine the relationship between copper supplementation and the prevalence of tcrB- positive enterococci in piglets. The study was done with weaned piglets, housed in 10 pens with 6 piglets per pen, fed diets supplemented with a normal (16.5 ppm; control) or an elevated (125 ppm) level of copper. Fecal samples were randomly collected from three piglets per pen on days 0, 14, 28, and 42 and plated on M- Enterococcus agar, and three enterococcal isolates were obtained from each sample. The overall prevalence of tcrB- positive enterococci was 21.1% (38/180) in piglets fed elevated copper and 2.8% (5/180) in the control. Among the 43 tcrB- positive isolates, 35 were E. faecium and 8 were E. faecalis . The mean MICs of copper for tcrB- negative and tcrB- positive enterococci were 6.2 and 22.2 mM, respectively. The restriction digestion of the genomic DNA of E. faecium or E. faecalis with S1 nuclease yielded a band of ∼194-kbp size to which both tcrB and the erm (B) gene probes hybridized. A conjugation assay demonstrated cotransfer of tcrB and erm (B) genes between E. faecium and E. faecalis strains. The higher prevalence of tcrB- positive enterococci in piglets fed elevated copper compared to that in piglets fed normal copper suggests that supplementation of copper in swine diets selected for resistance.

Our objectives were to determine factors associated with fecal prevalence of Salmonella at feedlot entry and within 24 h of harvest (preharvest), and to assess potential persistence of Salmonella strains within cattle populations. This repeated cross-sectional study followed 5559 beef cattle within 30 feedlot cohorts. Samples (n = 30) of fresh feces were collected from the pen floor of each cohort at feedlot entry and preharvest. Samples were subjected to a selective Salmonella isolation protocol and serotypes were determined for Salmonella isolates. Genetic similarity of a subset of isolates was determined using pulsed-field gel electrophoresis (PFGE). Cattle health and performance data were recorded electronically by feedlot personnel. Cohort-level generalized linear mixed models were used to assess bivariable associations. Fecal prevalence of Salmonella within a cohort at feedlot entry (mean = 64.7%) was not associated with preharvest prevalence (mean = 72.6%). Prevalence at feedlot entry was negatively associated with mean entry weight (p = 0.02). Preharvest prevalence was positively associated with the number of days in the feedlot (p = 0.02), cumulative morbidity (p = 0.01), and cumulative mortality (p = 0.03). We recovered Salmonella isolates with identical PFGE profiles both at feedlot entry and preharvest from 14 cohorts of cattle. Fecal prevalence of Salmonella immediately before harvest may be higher in subsets of the feedlot population, but does not appear to be affected by prevalence at feedlot entry. However, PFGE subtypes of Salmonella appear to persist within and among feedlot cohorts throughout the feeding period.

Escherichia coli serotype O157:H7 continues to pose a serious health threat to human beings. Cattle, a major reservoir of the pathogen, harbor E. coli O157:H7 in their gastrointestinal tract and shed variable concentrations of E. coli O157:H7 into the environment. Genetic characterization of cattle-shed E. coli O157 strains is of interest to the livestock industry, food business, and public health community. The present study applied whole genome shotgun sequencing (WGS) and single nucleotide variant (SNV) calling to characterize 279 cattle-shed E. coli O157:H7 strains isolated from a single feedlot located in southwestern region of the US. More than 4,000 SNVs were identified among the strains and the resultant phylogenomic tree revealed three major groups. Using the Sakai strain genome as reference, more than 2,000 SNVs were annotated and a detailed SNV map generated. Results clearly revealed highly polymorphic loci along the E. coli O157:H7 genome that aligned with the prophage regions and highly variant genes involved in processing bacterial genetic information. The WGS data were further profiled against a comprehensive virulence factor database (VFDB) for virulence gene identification. Among the total 285 virulence genes identified, only 132 were present in all the strains. There were six virulence genes unique to single isolates. Our findings suggested that the genome variations of the E. coli O157:H7 were mainly attributable to dynamics of certain phages, and the bacterial strains have variable virulence gene profiles, even though they came from a single cattle population, which may explain the differences in pathogenicity, host prevalence, and transmissibility by E. coli O157:H7.

Summary Cattle are a primary reservoir of Escherichia coli O157:H7, a major foodborne pathogen. The organism causes haemorrhagic colitis which can lead to serious complications, including haemolytic–uraemic syndrome. Although E. coli O157:H7 is widely prevalent in cattle and cattle environments, the number of human cases remain relatively low, suggesting possible strain diversity and differences in virulence between human and bovine strains. Shiga toxins, Stx1 and Stx2, are the major virulence factors. Differences in Stx2 production between human and bovine strains have been demonstrated previously, and isolates possessing the stx2 gene, but not producing Stx2 [toxin non-producing (TNP) strains] have been identified. In this study, 150 isolates (56 human, 94 bovine) were tested by PCR for stx2 upstream regions associated with TNP and the Q933 gene, which has been previously associated with toxin production. A reverse passive latex agglutination test was used to evaluate 107 isolates (50 human, 57 bovine) for Stx1 and Stx2 production. The percentages of human and bovine isolates positive for presence of the TNP regions were similar (57.1% and 53.1% respectively), while a higher percentage of human isolates was positive for Q933 gene (89.3% versus 54.3%). Stx2 production of ≥1 : 8 was found in 86.0% of human isolates compared with 26.3% of bovine isolates. Bovine isolates with the presence of the TNP regions were associated with significantly lower Stx2 production (P 0.05) with low Stx2 production in human isolates. Therefore, Q933 was a better indicator of high Stx2 production by human and bovine isolates and may be a useful screening method to assess their potential to cause human disease.

A multiplex PCR procedure that detects six major virulence genes, fliC, stx1, stx2, eae, rfbE, and hlyA, in Escherichia coli O157:H7 was developed. Analyses of the available sequences of the six major virulence genes and the published primers allowed us to develop the six-gene, multiplex PCR protocol that maintained the specificity of each primer pair. The resulting six bands for fliC, stx1, stx2, eae, rfbE, and hlyA were even and distinct with product sizes of 949, 655, 477, 375, 296, and 199 bp, respectively. The procedure was validated with a total of 221 E. coli strains that included 4 ATCC, 84 cattle, and 57 human E. coli O157:H7 strains as well as 76 non-O157 cattle and human E. coli strains. The results of all 221 strains were similar to the results generated by established multiplex PCR methods that involved two separate reactions to detect five virulence genes (stx1, stx2, eae, fliC, and hlyA). Specificity of the O antigen was indicated by amplification of only O157, and not O25, O26, O55, O78, O103, O111, O127, and O145 E. coli serotypes. Sensitivity tests showed that the procedure amplified genes from a fecal sample spiked with a minimum of 104 CFU/g (10 cells/reaction) of E. coli O157. After a 6-h enrichment of E. coli O157-spiked samples, a sensitivity level of 10 CFU/g was achieved.

Escherichia coli O104:H4, a hybrid pathotype reported in a large 2011 foodborne outbreak in Germany, has not been detected in cattle feces. However, cattle harbor and shed in the feces other O104 serotypes, particularly O104:H7, which has been associated with sporadic cases of diarrhea in humans. The objective of our study was to assess the virulence potential of Shiga toxin-producing E. coli (STEC) O104:H7 isolated from feces of feedlot cattle using DNA microarray. Six strains of STEC O104:H7 isolated from cattle feces were analyzed using FDA-E. coli Identification (ECID) DNA microarray to determine their virulence profiles and compare them to the human strains (clinical) of O104:H7, STEC O104:H4 (German outbreak strain), and O104:H21 (milk-associated Montana outbreak strain). Scatter plots were generated from the array data to visualize the gene-level differences between bovine and human O104 strains, and Pearson correlation coefficients (r) were determined. Splits tree was generated to analyze relatedness between the strains. All O104:H7 strains, both bovine and human, similar to O104:H4 and O104:H21 outbreak strains were negative for intimin (eae). The bovine strains were positive for Shiga toxin 1 subtype c (stx1c), enterohemolysin (ehxA), tellurite resistance gene (terD), IrgA homolog protein (iha), type 1 fimbriae (fimH), and negative for genes that code for effector proteins of type III secretory system. The six cattle O104 strains were closely related (r = 0.86-0.98) to each other, except for a few differences in phage related and non-annotated genes. One of the human clinical O104:H7 strains (2011C-3665) was more closely related to the bovine O104:H7 strains (r = 0.81-0.85) than the other four human clinical O104:H7 strains (r = 0.75-0.79). Montana outbreak strain (O104:H21) was more closely related to four of the human clinical O104:H7 strains than the bovine O104:H7 strains. None of the bovine E. coli O104 strains carried genes characteristic of E. coli O104:H4 German outbreak strain and unlike other human strains were also negative for Shiga toxin 2. Because cattle E. coli O104:H7 strains possess stx1c and genes that code for enterohemolysin and a variety of adhesins, the serotype has the potential to be a diarrheagenic foodborne pathogen in humans.

Our objective was to define and compare pulsed-field gel electrophoresis (PFGE) profiles of Escherichia coli O157 isolated from cattle feces and carcass samples to evaluate relationships between beef carcass contamination and fecal shedding of E. coli O157 at harvest. We used PFGE separation of Xba1-digested DNA to characterize E. coli O157 isolates (n = 174) from preevisceration carcasses (n = 39) and feces (n = 135) that were recovered from 37 E. coli O157-positive truckloads sampled at a commercial abattoir. Semiquantitative fecal culture techniques differentiated high-shedding, low-shedding, and negative cattle. Among all isolates, there were 17 PFGE types (95% homology) and 37 subtypes (100% homology). Specific subtypes were detected on multiple occasions and from different sample types within loads, among loads, and among days. Seventeen subtypes were recovered from carcasses; most were also recovered from feces of high-shedding cattle (13) and low-shedding cattle (14). Within truckload, the percentages of carcass isolates that were identical to high-shedder or low-shedder fecal isolates, as determined by PFGE, were 69.2% and 46.0%, respectively, whereas among different truckloads within the same study day, the percentages of carcass isolates that were the same subtype as high-shedder or low-shedder fecal isolates were 35.3% and 58.8%, respectively. Our results suggest that cattle feces from both low- and high-shedders pose a potential risk for E. coli O157 contamination of carcasses. Truckload may be an important factor in the potential transmission of E. coli O157, but isolates from carcasses also may be similar to those from feces of cattle on different truckloads and harvest days.

Fecal shedding of Escherichia coli O157:H7 in cattle, except those that shed transiently, is due to the organism's ability to persist in the gut. Site of prevalence in the gut is important for understanding the mechanisms and factors affecting gut persistence and fecal shedding and is a potential target for intervention. The prevalence of E. coli O157:H7 in the rumen, cecum, colon, and rectum was determined with contents collected from slaughtered cattle (n = 815) at an abattoir. Isolation and identification of E. coli O157:H7 were by selective enrichment, immunomagnetic separation, plating on selective medium, agglutination for O157 antigen, and presence of virulence genes. Prevalence in the rumen, cecum, colon, and rectum was 4.9%, 9.9%, 7.6%, and 11.1%, respectively. The overall prevalence of E. coli O157:H7 in the cattle sampled, based on being positive in any one gut location, was 20.3%. E. coli O157:H7 in rectal contents was positively associated (p < 0.01) with presence in the rumen or colon but not in the cecum. Pulsed-field gel electrophoresis (PFGE) was performed to compare the clonal similarity of isolates (n = 144) obtained from the rectum with that of rumen, cecum, or colon within cattle (n = 77). The majority (79-90%) of isolates obtained within the same animal shared a common PFGE type. There were no significant differences in PFGE type between positive samples from the rectum and samples from other locations within the same animal. Acid tolerance for cattle with positive rumen (pregastric) isolates and with at least one other positive hindgut (postgastric) isolate within the same animal was determined. There was no significant difference between gut locations in log reduction following acid challenge. The hindgut was the major site of prevalence of E. coli O157:H7 in cattle, a majority of the isolates within the same animal were clonally similar, and acid tolerance of hindgut isolates were not different from that of ruminal isolates.

In cattle, Escherichia coli O157 generally persists in the large intestine more often than in the rumen. In contrast to the rumen, the large intestine is lined by an epithelial membrane that secretes mucus. We hypothesize that substrates contained in intestinal mucus may constitute a source of energy that is preferentially used by E. coli O157. Therefore, our objective was to test the effects of mucin and its carbohydrate constituents on in vitro growth of E. coli O157 in ruminal or fecal microbial fermentations. Ruminal contents and feces were collected from a ruminally cannulated donor steer fed a corn grain-based finishing diet. Ruminal contents were strained through 2 layers of cheesecloth and incubated at 39 degrees C for 1 h; the floating hay mat was removed with a vacuum suction; and the remaining material was utilized as rumen microbial inoculum. Feces were suspended in physiologic saline to increase fluidity, blended, and strained through 2 layers of cheesecloth. The resulting fluid was utilized as fecal microbial inoculum. Fermentations (50 mL) were performed in serum bottles with a 2:1 mineral buffer to microbial inoculum ratio. Substrates (mucin, fucose, galactose, mannose, gluconic acid, galacturonic acid, glucuronic acid, galactosamine, and glucosamine) were added at 10 mg/mL. A mixture of 5 strains of nalidixic acid-resistant (Nal(R)) E. coli O157 strains was added to each fermentation and concentrations were determined after 0, 6, 12, and 24 h of incubation. In ruminal fermentations, fucose, mannose, glucuronic acid, galacturonic acid, glucosamine, galactosamine, and mucin had no effect on Nal(R) E. coli O157 concentration compared with the control (no substrate added) fermentation. At 24 h of fermentation, the mean concentration of Nal(R) E. coli O157 in fermentations with galactose was less than the control. However, including gluconic acid as substrate increased Nal(R) E. coli O157 concentration at 24 h. In fecal fermentations, mannose, galactose, gluconic acid, glucuronic acid, galacturonic acid, glucosamine, and mucin increased Nal(R) E. coli O157 growth compared with control at 24 h, whereas galactosamine and fucose did not. Gluconic acid was the most stimulatory substrate, increasing Nal(R) E. coli O157 by more than 1.0 log in ruminal fermentations and 2.0 log in fecal fermentations. In summary, availability of mucous constituents, particularly gluconic acid, may explain the greater prevalence of E. coli O157 in the large intestine compared with the rumen of the digestive tract.

A total of 180 weanling pigs (PIC TR4 ×1050, initially 11.1 lb and 21 d of age) were used in a 42-d growth trial to compare the effects of supplemental zinc, copper, and in-feed antimicrobial on weanling pig growth and antibiotic resistance of fecal Escherichia coli. There were 5 dietary treatments with 6 pens per treatment and 5 pigs per pen. Pens were assigned to dietary treatments in a randomized complete block design. Treatments were arranged in a 2 × 2 factorial design with main effects of copper sulfate (0 or 125 ppm) and zinc oxide (0 or 3,000 ppm for 14 d and 0 or 2,000 for 28 d). The fifth treatment was in-feed antimicrobial (50 g/ton neomycin sulfate and 50 g/ton oxytetracycline HCl). All diets were supplemented with165 ppm zinc and 16.5 ppm copper from the trace mineral premix. Fecal samples were collected from 3 pigs per pen on d 14 and 42 to determine total coliform and E. coli counts as well as E. coli antibiotic resistance rates.

Bison is becoming a popular meat source for consumers, but very little is known about the bison's status with respect to Escherichia coli O157:H7. We conducted a study to determine the prevalence and identify virulence genes and pulsed-field genetic types of E. coli O157:H7 in bison. Rectal contents and rectoanal mucosal swab (RAMS) samples were collected from a total of 342 bison at slaughter on seven different dates. Isolation of E. coli O157:H7 was by enrichment, immunomagnetic separation, and plating on selective medium, and identification was based on sorbitol fermentation reaction, indole production, and O157 agglutination test. An overall E. coli O157:H7 prevalence of 47.4% was observed. Fecal prevalence across sampling days ranged from 17 to 83%, with an average of 42.1%. The prevalence in the rectoanal mucosal region ranged from 2.2 to 50%, with an average of 19.9%. All E. coli O157:H7 isolates (n = 212) possessed eae, hlyA, fliC, and stx2 genes. The antiterminator Q gene, Q933, was present in 50.7% of fecal and 38% of RAMS isolates, and Q21 was present in 52.1% of fecal and 61.5% of RAMS isolates. The pulsed-field gel electrophoresis analysis of isolates revealed 11 types (95% Dice similarity) and 19 subtypes (100% Dice similarity). Two pulsed-field genetic types accounted for 76.4% of total isolates. Our study suggests that the prevalence of E. coli O157:H7 in rectal contents or on rectal mucosa of bison is variable, but relatively high overall and bison could serve as an important reservoir for human infection.