Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular epidemiological study.

OBJECTIVES: Escherichia coli bloodstream infections have shown a sustained increase in England, for reasons that are unknown. Furthermore, the contribution of MDR lineages such as ST131 to overall E. coli disease burden and outcome is undetermined. METHODS: We genome-sequenced E. coli blood isolates from all patients with E. coli bacteraemia in north-west London from July 2015 to August 2016 and assigned MLST genotypes, virulence factors and AMR genes to all isolates. Isolate STs were then linked to phenotypic antimicrobial susceptibility, patient demographics and clinical outcome data to explore relationships between the E. coli STs, patient factors and outcomes. RESULTS: A total of 551 E. coli genomes were analysed. Four STs (ST131, 21.2%; ST73, 14.5%; ST69, 9.3%; and ST95, 8.2%) accounted for over half of cases. E. coli genotype ST131-C2 was associated with phenotypic non-susceptibility to quinolones, third-generation cephalosporins, amoxicillin, amoxicillin/clavulanic acid, gentamicin and trimethoprim. Among 300 patients from whom outcome was known, an association between the ST131-C2 lineage and longer length of stay was detected, although multivariable regression modelling did not demonstrate an association between E. coli ST and mortality. Several unexpected associations were identified between gentamicin non-susceptibility, ethnicity, sex and adverse outcomes, requiring further research. CONCLUSIONS: Although E. coli ST was associated with defined antimicrobial non-susceptibility patterns and prolonged length of stay, E. coli ST was not associated with increased mortality. ST131 has outcompeted other lineages in north-west London. Where ST131 is prevalent, caution is required when devising empiric regimens for suspected Gram-negative sepsis, in particular the pairing of ß-lactam agents with gentamicin.

Immunomodulatory factors and infectious agents associated with the hepatic gene expression of the IGF system in nursery pigs.

Recent findings suggest there is a complex interaction between the IGF system and the inflammatory immune response. The objective of this study was to determine whether gene expression of growth factors (IGF-1, IGF-binding protein-3 (IGFBP-3) and growth hormone receptors (GHR)) in the liver is associated with gene expression of immunomodulators in the liver, including C-reactive protein (CRP), serum amyloid A (SAA), haptoglobin (Hp), interferon-α (IFN-α), IFN-γ, tumour necrosis factor-α (TNF-α), interleukin (IL)-1ß, IL-6, IL-10 and IL-18, as well as with the presence of Salmonella spp., Lawsonia intracellularis, Brachyspira spp., enterotoxigenic Escherichia coli, methicillin-resistant Staphylococcus aureus, swine influenza virus, and porcine reproductive and respiratory syndrome virus (PRRSV) in nursery pigs (n=74) from commercial farms (n=4). Gene expression was quantified using reverse transcription quantitative-PCR (RT-qPCR) and the data were modelled using logistic regression methods. Pigs with elevated IGF-1 expression were less likely to have increased expression of TNF-α (odds ratio (OR)=0.14, P<0.01) and IL-18 (OR=0.19, P<0.05), and less likely to be colonized with PRRSV (OR=0.03, P<0.01). Pigs with increased expression of IGFBP-3 were more likely to have elevated IL-6 expression (OR=8.5, P<0.05). It was also observed that IGFBP-3 and IGF-1 were significantly associated when Hp expression was low (OR=30, P<0.05), but this association was not significant when Hp expression was high (P=0.54). Pigs with increased expression of GHR were less likely to have elevated expression of SAA (OR=0.01, P<0.05) and IL-1ß (OR=0.03, P<0.05), but more likely to have increased expression of CRP (OR=290, P<0.01). Overall, there appears to be an inverse association between the hepatic expression of the IGF system (IGF-1, IGFBP-3, GHR) and certain cytokines (IL-1ß, IL-18, TNF-α) and acute-phase proteins (SAA, Hp).

Occurrence of Salmonella, Campylobacter, Yersinia enterocolitica, Escherichia coli O157 and Listeria monocytogenes in swine.

The objective of this study was to investigate the occurrence of major bacterial foodborne pathogens in swine. In total, 359 samples from manure storage tanks (91) and fresh pooled faeces (268) obtained from finisher (110), sows (78) and weanlings (80) were collected and tested. Campylobacter, Salmonella, Yersinia enterocolitica, Escherichia coli O157 and Listeria monocytogenes were isolated from 36.5%, 31.5%, 5.8%, 3.3% and 3.3% of samples respectively. All E. coli O157 isolates found on 10 farms were tested but none was determined to be E. coli O157:H7. Salmonella and Campylobacter were more likely to be detected from stored manure rather than from fresh faecal samples. Yersinia enterocolitica tended to be detected more commonly from fresh samples than from manure pits. Listeria monocytogenes was not recovered from manure pits or from sow faecal samples and only infrequently found in the faeces of weanling pigs and finisher pigs. The proportion of positive samples showed a seasonal change. Salmonella was twice as likely not be recovered in winter, whereas the chance of culturing Campylobacter was higher in winter. The 113 Salmonella isolates recovered on 24 farms and the four most common serovars were Salmonella Typhimurium var. Copenhagen (31.0%), Salmonella Derby (12.4%), S. Typhimurium (10.6%) and Salmonella Agona (10.6%). Of 131 Campylobacter isolates recovered on 21 farms, 118 isolates were Campylobacter coli and 13 isolates could not be speciated. Fifteen of 21 Y. enterocolitica isolates found on 15 farms were detected in finisher pigs. The sero/biogroups of Y. enterocolitica were O3/biotype 4 (16 isolates), O6,30/biotype 1A (three isolates), O5/biotype 1A (one isolate) and O8/biotype 1B (one isolate). These findings provide baseline information on the distribution of important zoonotic pathogens in swine and indicate that pigs should be considered as a possible source of foodborne diseases in humans.

Evaluation of the risk factors for shedding Salmonella with or without antimicrobial resistance in swine using multinomial regression method.

A multinomial logistic regression method was used to investigate the risk factors for antimicrobial resistance (AMR) in Salmonella isolated from faecal samples collected on 80 Ontario swine farms in Canada. The samples were classified into three groups including Salmonella-negative samples (S-), Salmonella-positive samples without AMR (S+AMR-) and Salmonella-positive samples with AMR (S+AMR+). The samples collected directly from pigs had a greater chance to be positive for Salmonella with AMR compared to those samples collected from the pen floor. The odds of culturing Salmonella with or without AMR was higher if pelleted feed was used compared with mash or liquid feed (P < 0.001). The faecal samples collected on farrow-to-finish farms had a significant lower chance of testing positive for Salmonella with multidrug resistance than the samples from grow-finisher farms (P = 0.004). The chance of culturing Salmonella without AMR on farms with a continuous system was higher than on farms with an all-in/all-out system (P = 0.009). However, there was no significant association between the flow system and recovery of Salmonella with AMR. The larger farms were more likely to be in S+AMR+ group than in S- group (P < 0.001) whereas herd size did not appear as a risk factor for being in S+AMR- group compared with S- group. These findings indicate that although on-farm antimicrobial use is one component of resistance, there might be other farm management factors that also affect the development of emerging resistant bacterial foodborne pathogens on swine farms. Finding different risk factors for shedding Salmonella with or without antimicrobial resistance would help to take the appropriate approach to each group if a control programme were to be implemented or an intervention applied.

Compatibility assessment of CVD growth of carbon nanofibers on bulk CMOS devices.

We compare the level of deterioration in the basic functionality of individual transistors on ASIC chips fabricated in standard 130 nm bulk CMOS technology when subjected to three disparate CVD techniques with relatively low processing temperature to grow carbon nanostructures. We report that the growth technique with the lowest temperature has the least impact on the transistor behavior.

Evaluation of enzyme-linked immunosorbent assay (ELISA) tests and culture for determining Salmonella status of a pig herd.

The purpose of this study was to evaluate Salmonella ELISA tests and a culture technique to determine Salmonella status using samples collected from commercial herds. Faecal samples from 15 finisher pigs on each of 40 swine farms were cultured for Salmonella. Sera from the same 600 pigs were analysed for the presence of antibodies to Salmonella by means of two different ELISA kits Salmotype (Salmotype Labordiagnostik, Leipzig, Germany) and IDEXX (Herdchek* Salmonella; IDEXX Laboratories, Schiphol-Rijk, Noord-Holland, The Netherlands). The Salmotype ELISA test demonstrated a moderate ability to differentiate culture-positive pigs from culture-negative pigs while IDEXX was relatively poor in classifying those pigs correctly (The area under the curves were 0.79 and 0.65 for Salmotype and IDEXX respectively). The maximum value of sensitivity plus specificity was gained at the cut-off optical density (OD) > or =25% for Salmotype (sensitivity 0.65, specificity 0.84) and at the OD > or =9% for IDEXX (sensitivity 0.59, specificity 0.69). The maximum herd sensitivity and herd specificity was 0.64 (95% CI 0.49-0.79) and 0.72 (95% CI 0.59-0.86) for the Salmotype test and 0.73 (95% CI 0.59-0.87) and 0.62 (95% CI 0.47-0.77) for the IDEXX. Culture and the ELISA tests showed fair agreement at the herd level (kappa=0.3, P<0.05). Likewise there was significant disagreement between the two ELISA tests at the pig level, but very good agreement between the two ELISA tests (kappa=0.8, P<0.0001) at the herd level. The coating antigens in Salmotype and IDEXX represent only 48% of the antigens of Salmonella isolated in our study and need to be revised based upon the Salmonella serovar distribution in Ontario.