Bayesian approach to urinary ESBL-producing Escherichia coli

This is a retrospective study about the prevalence of ESBL-producing Escherichia coli (EEC) in urinary specimens from patients from the Comunitat Valenciana from January 2007 to December 2008. Data were retrieved from RedMIVA, and Bayesian generalized linear mixed models were considered to study the prevalence of EEC with regard to demographical and microbiological factors. The total number of infections considered was 164,502, the amount of urinary isolates was 70,827 belonging to 49,304 different patients, and 5,161 (7.3%) of the urinary isolates were EEC. Three out of four E. coli were isolated in women (76.8%), men showed higher rates of EEC (9.7% in men vs. 6.5% in women). EEC patients were, in average, 10.8 years older, and hospitalization was more frequent (9.9% vs. 6.9%). Resistance to non-β-lactams antimicrobials was higher in EEC. The rates of ciprofloxacin and co-trimoxazol resistance in EEC were 75.5% and 52.0%, respectively, whereas it ranged between 1.4-12.4% for the rest of antimicrobials.Prior EEC infection and hospitalization were the most relevant risk factors and increased the expected EEC probability approximately 400% and 50% respectively. Other infections played an important and positive role too, Enterobacteriaceae, P. aeruginosa and other bacteria being the most relevant elements. Female gender was a protective factor and reduced the risk by approximately 25% while age was an additive risk factor. Finally, an open-access web-based software was constructed to compute the probability that an E. coli in a urinary infection be an EEC from a specific combination of risk factors. This pharmacovigilance tool should prove useful to monitor and control antimicrobial resistance spread

Starkeya nomas sp. nov., a prosthecate and budding bacterium isolated from an immunocompromized patient

Strain HF14-78462T is an environmental bacterium found in clinical samples from an immunocompromized patient in 2014 at Hospital Universitari i Politècnic La Fe (Valencia, Spain). Phenotypically, strain HF14-78462T cells were Gram-stain-negative, aerobic, non-spore forming and non-motile small rods which formed mucous and whitish-translucent colonies when incubated at 20-36 °C. Phylogenetic analyses based on the 16S rRNA genes and the whole genomes of closest sequenced relatives confirmed that strain HF14-78462T is affiliated with the genus Starkeya. The strain was oxidase, catalase and urease positive; but indole, lysine decarboxylase, ornithine decarboxylase and DNase negative, did not produce H2S and was able to utilize a wide variety of carbon sources including acetamide, adonitol, amygdalin, l-arabinose, citric acid, glucose, mannitol and melibiose. Unlike Starkeya novella and Starkeya koreensis, strain HF14-78462T failed to grow in thiosulphate-oxidizing media and had a narrower temperature growth range. Its genome was characterized by a size of 4.83 Mbp and a C+G content of 67.75 mol%. Major fatty acids were C18:1 ω7c, cyclo C19 : 0 and C16 : 0, its polar acids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an aminophospholipid; while the ubiquinones were Q9 (1.8 %) and Q10 (98.2 %). Digital DNA-DNA hybridization values were 41 and 41.4 against S. novella and S. koreensis, respectively, while average nucleotide identity values were around 84 %. Phenotypic, average nucleotide identity and phylogenomic comparative studies suggest that strain HF14-78462T is a new representative of the genus Starkeya and the name Starkeya nomas sp. nov. is proposed. The type strain is HF14-78462T (=CECT 30124T=LMG 31874T).Financial support was obtained by the IIS project 2013/0437.S

A surface plasmon resonance based approach for measuring response to pneumococcal vaccine

Incidence of pneumococcal disease has increased worldwide in recent years. Response to pneumococcal vaccine is usually measured using the multiserotype enzyme-linked immunosorbent assay (ELISA) pneumococcal test. However, this approach presents several limitations. Therefore, the introduction of new and more robust analytical approaches able to provide information on the efficacy of the pneumococcal vaccine would be very beneficial for the clinical management of patients. Surface plasmon resonance (SPR) has been shown to offer a valuable understanding of vaccines' properties over the last years. The aim of this study is to evaluate the reliability of SPR for the anti-pneumococcal capsular polysaccharides (anti-PnPs) IgGs quantification in vaccinated. Fast protein liquid chromatography (FPLC) was used for the isolation of total IgGs from serum samples of vaccinated patients. Binding-SPR assays were performed to study the interaction between anti-PnPs IgGs and PCV13. A robust correlation was found between serum levels of anti-PnPs IgGs, measured by ELISA, and the SPR signal. Moreover, it was possible to correctly classify patients into "non-responder", "responder" and "high-responder" groups according to their specific SPR PCV13 response profiles. SPR technology provides a valuable tool for reliably characterize the interaction between anti-PnPs IgGs and PCV13 in a very short experimental time

Antimicrobial Resistance in More than 100,000 Escherichia coli Isolates According to Culture Site and Patient Age, Gender, and Location ▿ †

Escherichia coli and the antimicrobial pressure exerted on this microorganism can be modulated by factors dependent on the host. In this paper, we describe the distribution of antimicrobial resistance to amikacin, tobramycin, ampicillin, amoxicillin clavulanate, cefuroxime, cefoxitin, cefotaxime, imipenem, ciprofloxacin, fosfomycin, nitrofurantoin, and trimetoprim-sulfametoxazole in more than 100,000 E. coli isolates according to culture site and patient age, gender, and location. Bayesian inference was planned in all statistical analysis, and Markov chain Monte Carlo simulation was employed to estimate the model parameters. Our findings show the existence of a marked difference in the susceptibility to several antimicrobial agents depending on from where E. coli was isolated, with higher levels of resistance in isolates from medical devices, the respiratory system, and the skin and soft tissues; a higher resistance percentage in men than in women; and the existence of a clear difference in antimicrobial resistance with an age influence that cannot be explained merely by means of an increase of resistance after exposure to antimicrobials. Both men and women show increases in resistance with age, but while women show constant levels of resistance or slight increases during childbearing age and greater increases in the premenopausal age, men show a marked increase in resistance in the pubertal age. In conclusion, an overwhelming amount of data reveals the great adaptation capacity of E. coli and its close interaction with the host. Sex, age, and the origin of infection are determining factors with the ability to modulate antimicrobial resistances

Use of sera cell free DNA (cfDNA) and exovesicle-DNA for the molecular diagnosis of chronic Chagas disease.

Chagas disease, a neglected tropical disease, is now considered a worldwide health concern as a result of migratory movements from Central and South America to other regions that were considered free of the disease, and where the epidemiological risk is limited to transplacental transmission or blood or organ donations from infected persons. Parasite detection in chronically ill patients is restricted to serological tests that only determine infection by previous infection and not the presence of the parasite, especially in patients undergoing treatment evaluation or in newborns. We have evaluated the use of nucleic acids from both circulating exovesicles and cell-free DNA (cfDNA) from 50 samples twice randomly selected from a total of 448 serum samples from immunologically diagnosed patients in whom the presence of the parasite was confirmed by nested PCR on amplicons resulting from amplification with kinetoplastid DNA-specific primers 121F-122R. Six samples were randomly selected to quantify the limit of detection by qPCR in serum exovesicles. When the nucleic acids thus purified were assayed as a template and amplified with kinetoplastid DNA and nuclear satellite DNA primers, a 100% positivity rate was obtained for all positive samples assayed with kDNA-specific primers and 96% when SAT primers were used. However, isolation of cfDNA for Trypanosoma cruzi and amplification with SAT also showed 100% positivity. The results demonstrate that serum exovesicles contain DNA of mitochondrial and nuclear origin, which can be considered a mixed population of exovesicles of parasitic origin. The results obtained with serum samples prove that both cfDNA and Exovesicle DNA can be used to confirm parasitaemia in chronically ill patients or in samples where it is necessary to demonstrate the active presence of the parasite. The results confirm for the first time the existence of exovesicles of mitochondrial origin of the parasite in the serum of those affected by Chagas disease

Risk factors for multidrug-resistant pathogens in bronchiectasis exacerbations

Background: Non-cystic fibrosis bronchiectasis is a chronic structural lung condition that courses with recurrent infectious exacerbations that lead to frequent antibiotic treatment making this population more susceptible to acquire pathogens with antibiotic resistance. We aimed to investigate risk factors associated with isolation of multidrug-resistant pathogens in bronchiectasis exacerbations. Methods: A prospective observational study was conducted in two tertiary-care hospitals, enrolling patients when first exacerbation appeared. Multidrug-resistance was determined according to European Centre of Diseases Prevention and Control classification. Results: Two hundred thirty three exacerbations were included and microorganisms were isolated in 159 episodes. Multidrug-resistant pathogens were found in 20.1% episodes: Pseudomonas aeruginosa (48.5%), methicillin-resistant Staphylococcus aureus (18.2%) and Extended spectrum betalactamase + Enterobacteriaceae (6.1%), and they were more frequent in exacerbations requiring hospitalization (24.5% vs. 10.2%, p: 0.016). Three independent multidrugresistant risk factors were found: chronic renal disease (Odds ratio (OR), 7.60, 95% CI 1.92-30.09), hospitalization in the previous year (OR, 3.88 95% CI 1.37-11.02) and prior multidrug-resistant isolation (OR, 5.58, 95% CI 2.02-15.46). The proportion of multidrug-resistant in the 233 exacerbations was as follows: 3.9% in patients without risk factors, 12.6% in those with 1 factor and 53.6% if ≥2 risk factors. Conclusions: Hospitalization in the previous year, chronic renal disease, and prior multidrug-resistant isolation are risk factors for identification multidrug-resistant pathogens in exacerbations. This information may assist clinicians in choosing empirical antibiotics in daily clinical practice

Prospective cohort study on hospitalised patients with suspected urinary tract infection and risk factors por multidrug resistance

Abstract Urinary tract infections (UTIs) are among the most common bacterial infections and a frequent cause for hospitalization in the elderly. The aim of our study was to analyse epidemiological, microbiological, therapeutic, and prognostic of elderly hospitalised patients with and to determine independent risk factors for multidrug resistance and its outcome implications. A single-centre observational prospective cohort analysis of 163 adult patients hospitalized for suspected symptomatic UTI in the Departments of Internal Medicine, Infectious Diseases and Short-Stay Medical Unit of a tertiary hospital was conducted. Most patients currently admitted to hospital for UTI are elderly and usually present high comorbidity and severe dependence. More than 55% met sepsis criteria but presented with atypical symptoms. Usual risk factors for multidrug resistant pathogens were frequent. Almost one out of five patients had been hospitalized in the 90 days prior to the current admission and over 40% of patients had been treated with antibiotic in the previous 90 days. Infection by MDR bacteria was independently associated with the previous stay in nursing homes or long-term care facilities (LTCF) (OR 5.8, 95% CI 1.17–29.00), permanent bladder catheter (OR 3.55, 95% CI 1.00–12.50) and urinary incontinence (OR 2.63, 95% CI 1.04–6.68). The degree of dependence and comorbidity, female sex, obesity, and bacteraemia were independent predictors of longer hospital stay. The epidemiology and presentation of UTIs requiring hospitalisation is changing over time. Attention should be paid to improve management of urinary incontinence, judicious catheterisation, and antibiotic therapy