Comparison of Salmonella enterica serovar Heidelberg isolates from human patients with those from animal and food sources.

Seventy-eight Salmonella enterica serovar Heidelberg isolates from humans were tested for antimicrobial susceptibility, resistance genes, and plasmids and genotyped by pulsed-field gel electrophoresis (PFGE). Most (88%) contained plasmids, and 47% were resistant to antimicrobials. The overall results were compared to those of previous S. Heidelberg studies of food- and animal-related sources, and multiple similarities were observed.

Evaluation of virulence factor profiling in the characterization of veterinary Escherichia coli isolates.

Escherichia coli has been used as an indicator organism for fecal contamination of water and other environments and is often a commensal organism in healthy animals, yet a number of strains can cause disease in young or immunocompromised animals. In this study, 281 E. coli isolates from bovine, porcine, chicken, canine, equine, feline, and other veterinary sources were analyzed by BOXA1R PCR and by virulence factor profiling of 35 factors to determine whether they had utility in identifying the animal source of the isolates. The results of BOXA1R PCR analysis demonstrated a high degree of diversity; less than half of the isolates fell into one of 27 clusters with at least three isolates (based on 90% similarity). Nearly 60% of these clusters contained isolates from more than one animal source. Conversely, the results of virulence factor profiling demonstrated clustering by animal source. Three clusters, named Bovine, Chicken, and Porcine, based on discriminant components analysis, were represented by 90% or more of the respective isolates. A fourth group, termed Companion, was the most diverse, containing at least 84% of isolates from canine, feline, equine, and other animal sources. Based on these results, it appears that virulence factor profiling may have utility, helping identify the likely animal host species sources of certain E. coli isolates.

Characterization of antimicrobial resistance in Salmonella enterica serotype Heidelberg isolated from food animals.

Fifty-eight Salmonella enterica serovar Heidelberg isolates isolated from food animals were tested for antimicrobial susceptibilities and further characterized for select antimicrobial resistance genes, plasmid carriage, class 1 integrons, and genetic relatedness using pulsed-field gel electrophoresis (PFGE). Seventy-two percent of isolates displayed resistance to at least one of the antimicrobial agents tested, while 24% exhibited resistance to eight or more antimicrobial agents. Resistance was most commonly observed to tetracycline (71%), streptomycin (62%), and kanamycin (52%). Isolates obtained from cattle and swine displayed the highest rates of resistance while isolates from chickens more often displayed susceptibility to the tested antimicrobials. When resistance was detected, a corresponding resistance gene was detected in 97.3% of the isolates. Thirteen percent of the isolates contained class 1 integrons containing at least one resistance gene, most often either the aadA or dhfrA genes, which are often associated with resistance to streptomycin and trimethoprim, respectively. Twenty isolates contained plasmids estimated to be at least 75 kb in size, 17 of which exhibited resistance to five or more antimicrobial agents. Thirty PFGE patterns were generated among the 58 isolates tested using XbaI, indicating extensive heterogeneity among this serotype across different animal origins. Results confirm the presence of multidrug-resistance (MDR) phenotypes among food animal isolates of serovar Heidelberg, especially those obtained from mammalian species. The observed MDR was typically associated with the presence of large plasmids.

Characterization of Salmonella enterica serovar Heidelberg from turkey-associated sources.

Salmonella enterica serovar Heidelberg strains are frequently associated with food-borne illness, with recent isolates showing higher rates of resistance to multiple antimicrobial agents. One hundred eighty S. enterica serovar Heidelberg isolates, collected from turkey-associated production and processing sources, were tested for antimicrobial susceptibility and compared by pulsed-field gel electrophoresis (PFGE) and plasmid profile analysis. The potential for the transfer of resistance between strains was studied by conjugation experiments. PFGE analysis using XbaI digestion identified eight clusters (based on 90% similarity), with the largest containing 71% of the isolates. Forty-two percent of the isolates were resistant to at least 1 of the 15 antimicrobial agents tested, and 4% of the isolates were resistant to 8 or more antimicrobial agents. Resistances to streptomycin (32%), tetracycline (30%), and kanamycin (24%) were most commonly detected. Interestingly, the XbaI PFGE profiles of selective multidrug-resistant strains (n = 22) of S. enterica serovar Heidelberg from turkey-associated sources were indistinguishable from the predominant profile (JF6X01.0022) detected in isolates associated with human infections. These isolates were further differentiated into seven distinct profiles following digestion with the BlnI enzyme, with the largest cluster comprising 15 isolates from veterinary diagnostic and turkey processing environments. Conjugation experiments indicated that resistance to multiple antimicrobial agents was transferable among strains with diverse PFGE profiles.

Validation of a metabolite panel for early diagnosis of type 2 diabetes.

BACKGROUND: Accurate, early diagnosis of type 2 diabetes (T2D) would enable more effective clinical management and a reduction in T2D complications. Therefore, we sought to identify plasma metabolite and protein biomarkers that, in combination with glucose, can better predict future T2D compared with glucose alone. METHODS: In this case-control study, we used plasma samples from the Bavarian Red Cross Blood Transfusion Center study (61 T2D cases and 78 non-diabetic controls) for discovering T2D-associated metabolites, and plasma samples from the Personalized Medicine Research Project in Wisconsin (56 T2D cases and 445 non-diabetic controls) for validation. All samples were obtained before or at T2D diagnosis. We tested whether the T2D-associated metabolites could distinguish incident T2D cases from controls, as measured by the area under the receiver operating characteristic curve (AUC). Additionally, we tested six metabolic/pro-inflammatory proteins for their potential to augment the ability of the metabolites to distinguish cases from controls. RESULTS: A panel of 10 metabolites discriminated better between T2D cases and controls than glucose alone (AUCs: 0.90 vs 0.87; p=2.08×10(-5)) in Bavarian samples, and associations between these metabolites and T2D were confirmed in Wisconsin samples. With use of either a Bayesian network classifier or ridge logistic regression, the metabolites, with or without the proteins, discriminated incident T2D cases from controls marginally better than glucose in the Wisconsin samples, although the difference in AUCs was not statistically significant. However, when the metabolites and proteins were added to two previously reported T2D prediction models, the AUCs were higher than those of each prediction model alone (AUCs: 0.92 vs 0.87; p=3.96×10(-2) and AUCs: 0.91 vs 0.71; p=1.03×10(-5), for each model, respectively). CONCLUSIONS: Compared with glucose alone or with previously described T2D prediction models, a panel of plasma biomarkers showed promise for improved discrimination of incident T2D, but more investigation is needed to develop an early diagnostic marker.

Results of a pilot study using self-collected mid-turbinate nasal swabs for detection of influenza virus infection among pregnant women.

BACKGROUND: We evaluated the feasibility of asking pregnant women to self-collect and ship respiratory specimens. METHODS: In a preliminary laboratory study, we compared the RT-PCR cycle threshold (CT) values of influenza A and B viruses incubated at 4 storage temperatures (from 4 to 35°C) for 6 time periods (8, 24, 48, 72, and 168 hours and 30 days), resulting in 24 conditions that were compared to an aliquot tested after standard freezing (-20°C) (baseline condition). In a subsequent pilot study, during January-February, 2014, we delivered respiratory specimen collection kits to 53 pregnant women with a medically attended acute respiratory illness using three delivery methods. RESULTS: CT values were stable after storage at temperatures <27°C for up to 72 hours for influenza A viruses and 48 hours for influenza B viruses. Of 53 women who received kits during the pilot, 89% collected and shipped nasal swabs as requested. However, 30% (14/47) of the women took over 2 days to collect and ship their specimen. The human control gene, ribonuclease P (RNase P), was detected in 100% of nasal swab specimens. However, the mean CT values for RNase P (26.5, 95% confidence interval [CI] = 26.0-27.1) and for the 8 influenza A virus positives in our pilot (32.2, 95% CI = 28.9-35.5) were significantly higher than the CTs observed in our 2010-2012 study using staff-collected nasal pharyngeal swabs (P-values < 0.01). DISCUSSION: Self-collection of respiratory specimens is a promising research method, but further research is needed to quantify the sensitivity and specificity of the approach.

DNA sequence analysis of plasmids from multidrug resistant Salmonella enterica serotype Heidelberg isolates.

Salmonella enterica serovar Heidelberg is among the most detected serovars in swine and poultry, ranks among the top five serotypes associated with human salmonellosis and is disproportionately associated with invasive infections and mortality in humans. Salmonella are known to carry plasmids associated with antimicrobial resistance and virulence. To identify plasmid-associated genes in multidrug resistant S. enterica serovar Heidelberg, antimicrobial resistance plasmids from five isolates were sequenced using the 454 LifeSciences pyrosequencing technology. Four of the isolates contained incompatibility group (Inc) A/C multidrug resistance plasmids harboring at least eight antimicrobial resistance genes. Each of these strains also carried a second resistance plasmid including two IncFIB, an IncHI2 and a plasmid lacking an identified Inc group. The fifth isolate contained an IncI1 plasmid, encoding resistance to gentamicin, streptomycin and sulfonamides. Some of the IncA/C plasmids lacked the full concert of transfer genes and yet were able to be conjugally transferred, likely due to the transfer genes carried on the companion plasmids in the strains. Several non-IncA/C resistance plasmids also carried putative virulence genes. When the sequences were compared to previously sequenced plasmids, it was found that while all plasmids demonstrated some similarity to other plasmids, they were unique, often due to differences in mobile genetic elements in the plasmids. Our study suggests that Salmonella Heidelberg isolates harbor plasmids that co-select for antimicrobial resistance and virulence, along with genes that can mediate the transfer of plasmids within and among other bacterial isolates. Prevalence of such plasmids can complicate efforts to control the spread of S. enterica serovar Heidelberg in food animal and human populations.

Characterisation of antibiotic resistance in host-adapted Salmonella enterica.

Salmonella enterica serovars Dublin, Choleraesuis and Pullorum are host-adapted serovars that cause disease primarily in cattle, swine and poultry, respectively. In addition, serovars Dublin and Choleraesuis are important human pathogens that are disproportionately associated with severe invasive infections that require antimicrobial therapy. Because of the potential increased emergence and spread of antimicrobial resistance, isolates of 42 S. enterica serovars Dublin, Choleraesuis and Pullorum were characterised to evaluate resistance. Antimicrobial susceptibility testing, detection of resistance genes and integrons, pulsed-field gel electrophoresis and plasmid analysis were carried out to characterise the isolates. Seventy-nine percent of the isolates were resistant to at least one of the antimicrobial agents tested, whilst 38% of the isolates were resistant to six or more antimicrobial agents. Resistance was most commonly detected to tetracycline (64%), streptomycin (57%) and kanamycin (52%). Overall, when resistance was seen, a corresponding resistance gene was detected 86.7% of the time. The results of this study indicate that antimicrobial resistance is a major concern in serovars Dublin and Choleraesuis isolates owing to the presence of multidrug resistance.

Human diallelic insertion/deletion polymorphisms.

We report the identification and characterization of 2,000 human diallelic insertion/deletion polymorphisms (indels) distributed throughout the human genome. Candidate indels were identified by comparison of overlapping genomic or cDNA sequences. Average confirmation rate for indels with a > or =2-nt allele-length difference was 58%, but the confirmation rate for indels with a 1-nt length difference was only 14%. The vast majority of the human diallelic indels were monomorphic in chimpanzees and gorillas. The ratio of deletionrcolon;insertion mutations was 4.1. Allele frequencies for the indels were measured in Europeans, Africans, Japanese, and Native Americans. New alleles were generally lower in frequency than old alleles. This tendency was most pronounced for the Africans, who are likely to be closest among the four groups to the original modern human population. Diallelic indels comprise approximately 8% of all human polymorphisms. Their abundance and ease of analysis make them useful for many applications.