Diagnostic yield of bacteriological tests and predictors of severe outcome in adult patients with COVID-19 presenting to the emergency department.

BACKGROUND: Guidelines recommend maximal efforts to obtain blood and sputum cultures in patients with COVID-19, as bacterial coinfection is associated with worse outcomes. The aim of this study was to evaluate the yield of bacteriological tests, including blood and sputum cultures, and the association of multiple biomarkers and the Pneumonia Severity Index (PSI) with clinical and microbiological outcomes in patients with COVID-19 presenting to the emergency department (ED). METHODS: This is a substudy of a large observational cohort study (PredictED study). The PredictED included adult patients from whom a blood culture was drawn at the ED of Haga Teaching Hospital, The Netherlands. For this substudy, all patients who tested positive for SARS-CoV-2 by PCR in March and April 2020 were included. The primary outcome was the incidence of bacterial coinfection. We used logistic regression analysis for associations of procalcitonin, C reactive protein (CRP), ferritin, lymphocyte count and PSI score with a severe disease course, defined as intensive care unit admission and/or 30-day mortality. The area under the receiver operating characteristics curve (AUC) quantified the discriminatory performance. RESULTS: We included 142 SARS-CoV-2 positive patients. On presentation, the median duration of symptoms was 8 days. 41 (29%) patients had a severe disease course and 24 (17%) died within 30 days. The incidence of bacterial coinfection was 2/142 (1.4%). None of the blood cultures showed pathogen growth while 6.3% was contaminated. The AUCs for predicting severe disease were 0.76 (95% CI 0.68 to 0.84), 0.70 (0.61 to 0.79), 0.62 (0.51 to 0.74), 0.62 (0.51 to 0.72) and 0.72 (0.63 to 0.81) for procalcitonin, CRP, ferritin, lymphocyte count and PSI score, respectively. CONCLUSION: Blood cultures appear to have limited value while procalcitonin and the PSI appear to be promising tools in helping physicians identify patients at risk for severe disease course in COVID-19 at presentation to the ED.

Positive Culture and Prognosis in Patients With Sepsis: A Prospective Cohort Study.

PURPOSE: To analyze the prognostic role of positive cultures in patients with sepsis. METHODS: A prospective cohort study in a tertiary referral hospital in Medellín, Colombia. Adults older than 18 years of age with a bacterial infection diagnosis according to Centers for Disease Control criteria and sepsis (evidence of organ dysfunction) were included. A logistic regression model was used to determine the association between positive cultures and hospital mortality, and a Cox regression with a competing risk modeling approach was used to determine the association between positive cultures and hospital stay as well as secondary infections. RESULTS: Overall, 408 patients had positive cultures, of which 257 were blood culture, and 153 had negative cultures. Patients with positive cultures had a lower risk of mortality (odds ratio [OR], 0.43; 95% confidence interval [CI], 0.27-0.68), but this association was not maintained after adjusting for confounding factors (OR, 0.56; 95% CI, 0.31-1.01). No association was found with the hospital stay (adjusted subhazard ratio [SHR], 1.06; 95% CI, 0.83-1.35). There was no association between positive cultures and the presence of secondary infections (adjusted SHR, 0.99; 95% CI, 0.58-1.71). CONCLUSION: Positive cultures are not associated with prognosis in patients with sepsis.

Current Status of Helicobacter pylori Diagnosis and Eradication Therapy in Japan Using a Nationwide Database.

BACKGROUND: Helicobacter pylori infection increases the risk of stomach cancer; therefore, eradication therapy is recommended for infected individuals. Although several methods are recommended for the diagnosis and therapy of H. pylori infection, their frequency and effectiveness have not been fully investigated in Japan. METHODS: A nationwide claims database including >1.6 million patients (April 2008 - -October 2016) in Japan was utilized. We analyzed the distribution of methods for H. pylori diagnosis and therapy, waiting period between eradication and diagnostic test, and success rate of primary therapy. RESULTS: Data for 481,041 patients were extracted. After primary eradication therapy, urea breath test was used for >80% of diagnoses, and antibody measurement for 0.7%. The success rate of primary eradication was >80% for most diagnostic methods and 69.0% for antibody measurement; inappropriately-timed antibody measurement may have contributed to this disparity. The overall success rate of eradication therapy decreased from 2011 to 2014, but increased from 2015, coinciding with launch of the potassium-competitive acid blocker vonoprazan, which showed a higher success rate of eradication than proton-pump inhibitors. CONCLUSIONS: Diagnostic tests of H. pylori infection mostly followed Japanese Society for Helicobacter Research guidance, although some antibody measurements were timed inappropriately. Vonoprazan appears to increase the success rate of primary therapy.

Strategy for Intercorrelation Identification between Metabolome and Microbiome.

Accumulating evidence points to the strong and complicated associations between the metabolome and the microbiome, which play diverse roles in physiology and pathology. Various correlation analysis approaches were applied to identify microbe-metabolite associations. Given the strengths and weaknesses of the existing methods and considering the characteristics of different types of omics data, we designed a special strategy, called Generalized coRrelation analysis for Metabolome and Microbiome (GRaMM), for the intercorrelation discovery between the metabolome and microbiome. GRaMM can properly deal with two types of omics data, the effect of confounders, and both linear and nonlinear correlations by integrating several complementary methods such as the classical linear regression, the emerging maximum information coefficient (MIC), the metabolic confounding effect elimination (MCEE), and the centered log-ratio transformation (CLR). GRaMM contains four sequential computational steps: (1) metabolic and microbial data preprocessing, (2) linear/nonlinear type identification, (3) data correction and correlation detection, and (4) p value correction. The performances of GRaMM, including the accuracy, sensitivity, specificity, false positive rate, applicability, and effects of preprocessing and confounder adjustment steps, were evaluated and compared with three other methods in multiple simulated and real-world datasets. To our knowledge, GRaMM is the first strategy designed for the intercorrelation analysis between metabolites and microbes. The Matlab function and an R package were developed and are freely available for academic use (comply with GNU GPL.V3 license).

Nationwide observational study of mortality from complicated intra-abdominal infections and the role of bacterial cultures.

BACKGROUND: The benefit of taking intra-abdominal cultures during source control procedures in patients with complicated intra-abdominal infection (CIAI) is unknown. The aim of this study was to evaluate whether intra-abdominal cultures reduce the mortality rate of CIAI. METHODS: The Japanese Diagnosis Procedure Combination database was used to identify adult patients with CIAI who had undergone source control procedures on the first day of admission to hospital between April 2014 and March 2016. In-hospital mortality was compared between patients who did and those who did not have intra-abdominal cultures taken. A generalized linear mixed-effect logistic regression model and a random intercept per hospital were used to adjust for baseline confounders and institutional differences. Subgroup analyses were also performed according to disease cause, site of onset and severity of CIAI. RESULTS: Intra-abdominal cultures were taken from 16 303 of 41 495 included patients. Multivariable logistic regression analysis showed that patients with intra-abdominal cultures had a significantly lower mortality than those without (odds ratio 0·85, 95 per cent c.i. 0·77 to 0·95). Subgroup analyses revealed statistically significant differences in mortality between patients with and without cultures among those with lower intestinal perforation, biliary tract infection/perforation, healthcare-associated CIAI and high-risk community-acquired CIAI. CONCLUSIONS: Intra-abdominal cultures obtained during source control procedures may reduce in-hospital mortality, especially in patients with lower intestinal perforation, biliary tract infection/perforation, or healthcare-associated or high-risk community-acquired CIAI.

Perianal Tuberculosis: Lessons Learned in 57 Patients From 743 Samples of Histopathology and Polymerase Chain Reaction and a Systematic Review of Literature.

BACKGROUND: Few data are published on perianal tuberculosis. OBJECTIVE: This study aimed to determine the best method to diagnose tuberculosis in patients with fistula-in-ano and to conduct a systematic review to determine the incidence and characteristics of tuberculosis fistula-in-ano. DATA SOURCES: The prospective study data and existing literature were derived from PubMed, Google scholar, and Scopus STUDY SELECTION:: Prospective analysis of patients with tuberculous fistula-in-ano treated between 2014 and 2018 was conducted, and a systematic review of studies describing ≥3 patients with tuberculosis fistula-in-ano was completed. INTERVENTION: Testing of tuberculosis was performed by histopathology or polymerase chain reaction of tissue or pus from the fistula tract. MAIN OUTCOME MEASURES: The primary outcomes measured were the detection rate of various tests to detect tuberculosis in fistula-in-ano and the prevalence rate of tuberculosis in simple versus complex fistulas. RESULTS: In 637 samples (410 patients) tested, tuberculosis was detected in 49 samples (43 patients). Additional samples (n = 106) sent in patients with a high index of suspicion tested positive in 14 more patients. Thus, overall, 63 samples tested positive in 57 patients (total: 743 samples in 410 patients were tested). Tuberculosis was detected in 2 of 181 patients (1.1%) in tissue (histopathology), in 28 of 341 patients (8.2%) in tissue (polymerase chain reaction), and in 19 of 115 patients (16.5%) in pus (polymerase chain reaction) samples. To detect tuberculosis, tissue (polymerase chain reaction) was significantly better than tissue (histopathology) (28/341 vs 2/181, p < 0.00001) and pus (polymerase chain reaction) was significantly better than tissue (polymerase chain reaction) (19/115 vs 28/341, p < 0.0009). Tuberculosis was significantly more common in complex fistulas than in simple fistulas (20.3% vs 7.2%, p = 0.0002). The systematic review (n = 199) highlighted that tubercular fistulas are more common in recurrent and complex fistulas and in tuberculosis endemic regions. LIMITATIONS: The true sensitivity and specificity of each testing modality could not be determined because not all patients with tuberculosis fistula-in-ano were tested by every diagnostic modality studied. CONCLUSIONS: The tuberculosis detection rate of polymerase chain reaction was significantly higher than histopathology. Among polymerase chain reaction, pus had higher detection rate than tissue. Tuberculosis was associated with more complex and recurrent fistulas.

Testing Pneumonia Vaccines in the Elderly: Determining a Case Definition for Pneumococcal Pneumonia in the Absence of a Gold Standard.

Clinical assessments of vaccines to prevent pneumococcal community-acquired pneumonia (CAP) require sensitive and specific case definitions, but there is no gold standard diagnostic test. To develop a new case definition suitable for vaccine efficacy studies, we applied latent class analysis (LCA) to the results from 7 diagnostic tests for pneumococcal etiology on clinical specimens from 323 elderly persons with radiologically confirmed pneumonia enrolled in the Finnish Community-Acquired Pneumonia Epidemiology study during 2005-2007. Compared with the conventional use of LCA, which is mainly to determine sensitivities and specificities of different tests, we instead used LCA as an appropriate instrument to predict the probability of pneumococcal etiology for each CAP case based on individual test profiles, and we used the predictions to minimize the sample size that would be needed for a vaccine efficacy trial. When compared with the conventional laboratory criteria of encapsulated pneumococci in culture, in blood culture or high-quality sputum culture, or urine antigen positivity, our optimized case definition for pneumococcal CAP resulted in a trial sample size that was almost 20,000 subjects smaller. We believe that the novel application of LCA detailed here to determine a case definition for pneumococcal CAP could also be similarly applied to other diseases without a gold standard.

Statistical optimization of culture medium to produce recombinant viral protein by Escherichia coli host for diagnostic kit to detect human immunodeficiency virus (HIV) infection.

The maximal production of recombinant HIV1 gp41 by E. coli was examined in optimal culture condition and medium compositions. The culture condition such as growth, initial medium pHs, IPTG concentrations, induction times, temperature (0.5 OD, 7.6, 0.75 mM, 4.6 h, 32 °C respectively), and yeast extract (7.51 g/l), tryptone (7.26 g/l), glucose (2.45 g/l), NaCl (20.40 g/l), betaine (10.41 mM) and ampicillin (71.23 µg/ml) was optimized using statistical experimental design and response surface method (RSM). One of the main popular methods to attain high cell density in fed-batch culture is by controlling the nutrient feeding, which is often necessary for high yield in protein (0.63-0.72 mg/l) and cell (1.7-2 g/l) of the desired product in four litter fermentations.

Evaluation of the use of sonication of retrieved implants for the diagnosis of prosthetic joint infection in a routine setting.

In order to evaluate the usefulness of sonication of retrieved implants for the diagnosis of prosthetic joint infection (PJI) in a large group of patients in a routine setting, we designed a 3-year retrospective study. Patients were classified into two groups: those meeting the clinical criteria of PJI and those that did not (control group). Two hundred patients and 276 samples were included. The types of infection were early (n = 44), delayed (n = 53), positive intraoperative cultures (n = 13) and late-acute (n = 8). The culture sensitivities of sonicate fluid, periprosthetic tissue, synovial fluid and combination of periprosthetic tissue and/or synovial fluid were 69.5, 52.8, 54.8 and 60.2%, respectively. The specificities were 97.6, 90.3, 93.0 and 89.9%, respectively. Sonicate fluid culture of implants was more sensitive than peri-implant tissue, synovial fluid and combination of periprosthetic tissue and/or synovial fluid for all infection types, though it was especially useful in delayed infection: 91.3% vs. 60.0% (p = 0.0015), 63.2% (p = 0.0005) and 66.7% (p = 0.0001), respectively. When sonicate fluid culture of implants was performed in addition to conventional cultures, the sensitivity increased significantly in total (from 60.2 to 77.1%) and delayed PJI (from 45.1 to 71.7%). On the other hand, for early PJI, sonicate fluid culture of prosthesis was not superior to conventional diagnostic methods.

Distribution of Mycobacterium tuberculosis in Korea in the preceding decade.

BACKGROUND: Tuberculosis (TB) is an infectious disease caused by the bacillus Mycobacterium tuberculosis (MTB); it is transmitted among people through air. The aim of this study was to assess the prevalence of TB and its clinical trends by collecting and analyzing data on specimens in Korea. METHODS: All clinical specimens referred to the Dankook University Hospital Laboratory in Cheonan, Korea, from September 2005 to June 2016 were tested to isolate MTB using solid and liquid cultures, acid-fast bacilli (AFB) smears, and polymerase chain reactions (PCR). RESULTS: In total, 146 150 specimens were collected; the mean TB positivity rate was 7.8%. The highest positivity rate was observed among patients 30-39 years of age (12.6%), followed by those 20-29 years of age (12.2%). The mean positivity rate was highest in 2010 and lowest in 2016 (10.7% and 6.7%, respectively). When comparing 2015-2011, we saw a decrease in the number of TB-positive patients of 3.4%; this represented an annual decrease in 0.9%. CONCLUSION: Our data revealed a trend for a decrease in TB prevalence over time. Moreover, TB positivity rates were highest among the younger age groups in our study. Therefore, rapid diagnosis and treatment of TB in younger individuals are crucial.

Candidaemia: Risk factors and validity of tools to predict risk of Candidaemia in Intensive care unit patients in Teaching Hospital Karapitiya

Introduction: The ability to predict candidaemia gives a significant advantage to the clinician by enabling pre-emptive treatment to reduce mortality. Objectives: To identify the prevalence, risk factors, and to validate candida colonization index (CI), candida score (CS) to reliably predict the development of candidaemia in the identified study sample. Methods: Cross sectional analytical study of consecutive admissions fulfilling inclusion criteria to intensive care units (ICUs) of Teaching Hospital Karapitiya from 1st December 2015 to 30th March 2016. Candida colonization of non-blood body sites was measured by culture on admission and repeated every 3rd day until discharge from ICU, death or development of candidaemia. CI, corrected CI (CCI), and CS were calculated for the study patients. Results: Candida colonization was found in 100 (65.7%) patients out of 152 patients screened. The presence of sepsis, gastro-intestinal infection or surgery, central venous line colonization, higher density of rectal, oral and urine colonization was significantly different among the infected and non-infected groups. Change of species of colonizing candida was also a significant new risk factor found in the study. All the indices and scores had excellent sensitivity and negative predictive values. However none of the scores had good specificity except for CCI, which was 94%. Conclusions: A combination of CI, CCI and CS formulated for the study sample could reliably predict candidaemia.

Modeling conditional dependence among multiple diagnostic tests.

When multiple imperfect dichotomous diagnostic tests are applied to an individual, it is possible that some or all of their results remain dependent even after conditioning on the true disease status. The estimates could be biased if this conditional dependence is ignored when using the test results to infer about the prevalence of a disease or the accuracies of the diagnostic tests. However, statistical methods correcting for this bias by modelling higher-order conditional dependence terms between multiple diagnostic tests are not well addressed in the literature. This paper extends a Bayesian fixed effects model for 2 diagnostic tests with pairwise correlation to cases with 3 or more diagnostic tests with higher order correlations. Simulation results show that the proposed fixed effects model works well both in the case when the tests are highly correlated and in the case when the tests are truly conditionally independent, provided adequate external information is available in the form of fixed constraints or prior distributions. A data set on the diagnosis of childhood pulmonary tuberculosis is used to illustrate the proposed model.

Cost-effectiveness analysis of universal screening for carbapenemase-producing Enterobacteriaceae in hospital inpatients.

The purpose of this study was to assess the cost-effectiveness of screening all hospital inpatients for carbapenemase-producing Enterobacteriaceae (CPE) at the time of hospital admission, compared to not screening, from a US hospital perspective. We used a linked transmission/Markov model to compare outcomes for a typical hospitalized medical patient, from a community with a colonization prevalence of 0.05%. Outcomes were number of colonized patients, CPE-related clinical infections and deaths, expected quality-adjusted life years (QALYs), cost, and the incremental cost-effectiveness ratio (ICER). Sensitivity analyses were performed to assess the effect of parameter uncertainty, using a willingness-to-pay threshold of $100,000 per QALY gained. Screening prevented six CPE colonization cases per 1000 patients (1/1000 colonized with screening, 7/1000 without screening), over half of all symptomatic CPE infections (2/10,000 symptomatic with screening, 5/10,000 symptomatic without screening), and nearly half of all CPE-related deaths (8/100,000 deaths with screening, 15/100,000 deaths without screening). Screening accrued 0.0009 additional QALYs and cost an additional $24.68, compared to not screening, and was cost-effective (ICER $26,283 per QALY gained). Our results were sensitive to uncertainty in prevalence and the number of secondary colonizations per colonized patient. Screening was not cost-effective at a prevalence below 0.015% or if transmission to fewer than 0.9 new patients occurred for each colonized patient. At prevalence levels above 0.3%, screening was cost-saving compared to not screening. Screening inpatients for CPE carriage is likely cost-effective, and may be cost-saving, depending on the local prevalence of carriage.

Clinical value of antistreptolysin O levels in adult patients with tonsillitis: report I.

To assess the clinical value of antistreptolysin O (ASO) level in adult patients with acute tonsillitis of group A beta-hemolytic streptococcus (GABHS) etiology and its interaction with the Centor score and throat cultures data. ASO antibody titers and throat cultures were obtained from 260 adult patients with acute tonsillitis of GABHS etiology initially proven by the Centor score. The results were compared with the group of 100 adult patients with recurrent tonsillitis who underwent tonsillectomy and with the group of 100 healthy adults. Throat cultures revealed GABHS-positive results in 69 acute cases (26.5%) and in 24 recurrent cases (24%), i.e., with no significant differences between the groups (p = 0.845). There was no significant difference between cases with GABHS-positive and with GABHS-negative throat culture in ASO titers results (mean 250 and 280, respectively, p = 0.44) but these titers were significantly higher than established normative data (p < 0.01). For the group of recurrent tonsillitis cases, the mean ASO titer was 363 being significantly higher in comparison with acute cases (p = 0.015). The ASO antibody titers are significantly higher than normative ranges in cases of acute tonsillitis in adults. The detection of the elevated titers may lead to early antibiotherapy to tonsillitis. The Centor score is supported by the ASO data and less supported by throat cultures data. Further research should reveal if these titers might have predictive value for possible further recurrence or serve as an indicator for tonsillectomy in cases of recurrent tonsillitis.

[Diagnostic value of different detection methods for Mycobacterium tuberculosis in bronchoalveolar lavage fluid from pulmonary tuberculosis patients].

OBJECTIVE: To investigate the diagnostic value of different detection methods for Mycobacterium tuberculosis in bronchoalveolar lavage fluid (BALF) from patients with pulmonary tuberculosis.
 Methods: BALF from100 patients in Changsha Central Hospital from January 2013 to December 2015 was collected. Among 100 patients, 65 cases were clinically diagnosed as tuberculosis, and 35 cases served as control. BALF smear method, polymerase chain reaction (PCR) and membrane reverse dot blot (RDB) were used for synchronous detection of Mycobacterium tuberculosis.
 Results: The positive rates by BALF smear method, PCR and RDB were 43.08%, 73.84% and 92.31%, respectively (P<0.05). Sensitivity, specificity, accuracy, and negative predictive value for BALF smear were 43.08%, 88.57%, 59.00%, and 45.59%, respectively; for PCR were 73.85%, 100%, 83.00%, and 67.31%, respectively; for RDB were 92.31%, 100.00%, 95.00%, and 87.50%, respectively.
 Conclusion: The technique of membrane RDB can not only accurately diagnose Mycobacterium tuberculosis, but also can rapidly and easily identify the resistance of Mycobacterium tuberculosis to streptomycin (SM), rifampicin (RFP) and isoniazid (INH) genotypes. It possesses high clinical value.

Asymptomatic and yet C. difficile-toxin positive? Prevalence and risk factors of carriers of toxigenic Clostridium difficile among geriatric in-patients.

BACKGROUND: Clostridium difficile infections (CDI) are the most frequent cause of diarrhoea in hospitals. Geriatric patients are more often affected by the condition, by a relapse and complications. Therefore, a crucial question is how often colonization with toxigenic Clostridium difficile strains occurs in elderly patients without diarrhoea and whether there is a "risk pattern" of colonized patients that can be defined by geriatric assessment. Furthermore, the probability for those asymptomatic carriers to develop a symptomatic infection over time has not been sufficiently explored. METHODS: We performed a cohort study design to assess the association of clinical variables with Clostridium difficile colonization. The first stool sample of 262 consecutive asymptomatic patients admitted to a geriatric unit was tested for toxigenic Clostridium difficile using PCR (GeneXpert, Cepheid). A comprehensive geriatric assessment (CGA) including Barthel Index, Mini Mental State Examination (MMSE) and hand grip-strength was performed. In addition, Charlson Comorbidity Index, body mass index, number and length of previous hospital stays, previous treatment with antibiotics, institutionalization, primary diagnoses and medication were recorded and evaluated as possible risk factors of colonization by means of binary logistic regression. Secondly, we explored the association of C. difficile colonization with subsequent development of CDI during hospital stay. RESULTS: At admission, 43 (16.4%) patients tested positive for toxin B by PCR. Seven (16.3%) of these colonized patients developed clinical CDI during hospital stay, compared to one out of 219 patients with negative or invalid PCR testing (Odds ratio 12,3; Fisher's exact test: p = 0.000). Overall, 7 out of 8 (87.5%) CDI patients had been colonized at admission. Risk factors of colonization with C. difficile were a history of CDI, previous antibiotic treatment and hospital stays. The parameters of the CGA were not significantly associated with colonization. CONCLUSION: Colonization with toxigenic Clostridium difficile strains occurs frequently in asymptomatic patients admitted to a geriatric unit. Previous CDI, antibiotic exposure and hospital stay, but not clinical variables such as CGA, are the main factors associated with asymptomatic Clostridium difficile carriage. Colonization is a crucial risk factor for subsequent development of symptomatic CDI.

An appropriately performed conventional blood culture can facilitate choice of therapy in resource-constrained settings-comparison with BACTEC 9050.

AIMS: Comparison of conventional blood culture with BACTEC 9050 for rate and time to detection of microorganisms. SETTINGS AND DESIGN: A prospective study was carried out in a multispecialty tertiary care teaching hospital. SUBJECTS AND METHODS: A total of 835 paired specimens (797 blood and 38 nonblood specimens) were collected and processed according to standard microbiological procedures by both conventional method as well as by BACTEC 9050 automated culture system. Clinical details of patients were recorded. Data were analyzed for time to detection and isolation rate by the two systems and compared. RESULTS: Overall culture positivity for BACTEC 9050 and the conventional system was 32% and 19.88%, respectively. Eighty-five demonstrated concordant growth, 136 specimens were culture positive by BACTEC only, and 38 specimens were culture positive by conventional only. Twelve contaminants in BACTEC and nine contaminants in conventional system were detected. Using BACTEC 9050, higher isolation was observed for Acinetobacter spp., coagulase negative Staphylococcus spp., Streptococcus spp., and Candida spp. A total of 410 patients were on antimicrobial treatment and culture positivity was significantly higher with BACTEC 9050 (P < 0.0001). There was a significant difference in the mean time to detection with BACTEC 9050 recovering 86.8% of isolates within 48 h (P < 0.0001). CONCLUSIONS: Although BACTEC 9050 demonstrated a significantly higher recovery of microorganisms from blood, an appropriately performed conventional blood culture can facilitate the choice of therapy.

Diagnostic testing for Clostridium difficile in Italian microbiological laboratories.

A laboratory diagnosis survey of Clostridium difficile infection (CDI) was performed in Italy in 2012-2013. Questionnaires from 278 healthcare settings from 15 regions of Italy were collected and analysed. Eighty seven percent of the laboratories declared to routinely perform CDI diagnosis, 99% of them only after the clinician's request. Among the 216 laboratories providing information on the size of the hospitals in which they were located, 65 had more than 500 beds (large hospitals), while 151 had less than 500 beds (small hospitals). The average percentage of positive tests for C. difficile toxins was 12.2%. Almost half of the laboratories (42%) used immunoenzymatic assay (EIA) for Tox A/B as a stand-alone method, while only 34% used an algorithm for CDI as indicated by the European guidelines. A low percentage of laboratories performed molecular assays or C. difficile culture, 25% and 29%, respectively. Most laboratories (161/278) declared to type C. difficile strains, the majority in collaboration with a reference laboratory. Among the 103 C. difficile clinical isolates collected during the study, 31 different PCR-ribotypes were identified. PCR-ribotype 356/607 (27%) was predominant, followed by 018 (12%). These two PCR-ribotypes show 87.5% of similarity in ribotyping profile. PCR-ribotypes 027 and 078 represented 8% and 4% of the strains, respectively. Four PCR-ribotypes (027, 033, 078 and 126) were positive for the binary toxin CDT. In particular, PCR-ribotype 033 produces only CDT, and it has recently been associated with symptomatic cases. The majority of strains were multidrug resistant. In particular, all strains PCR-ribotypes 356/607 and 018 were resistant to moxifloxacin, rifampicin, erythromycin and clindamycin. The results obtained highlight the need to raise awareness to the microbiological diagnosis of CDI among clinicians and to implement and harmonize diagnostic methods for CDI in Italian laboratories in the perspective of a future national surveillance.

Physician practices in requesting stool samples for patients with acute gastroenteritis, France, August 2013-July 2014.

A better understanding of physician practices in requesting stool samples for patients with acute gastroenteritis (AG) is needed to more accurately interpret laboratory-based surveillance data. A survey was conducted in General Practitioners (GPs) between August 2013 and July 2014 to estimate the proportion of stool samples requested for patients with AG and to identify factors associated with GP requests for a stool sample. National health insurance (NHI) data together with surveillance data from a French Sentinel GP network were also used to estimate the proportion of stool samples requested. This proportion was estimated at 4·3% in the GP survey and 9·1% (95% confidence interval 8·7-9·6) using NHI data. Multivariate analysis indicated that the ratio of stool samples requested was almost five times higher in patients with bloody diarrhoea and 10-20 times higher in patients with a long duration of illness before consultation. Laboratory-based surveillance data underestimates the actual burden of disease as fewer than one in 10 AG cases consulting their GP will be requested to submit a stool sample for laboratory testing. This underestimation varies by pathogen as stool samples are more frequently requested for severe illness.

Recovery and time to growth of isolates in blood culture bottles: comparison of BD Bactec Plus Aerobic/F and BD Bactec Plus Anaerobic/F bottles.

BACKGROUND: This study was done to compare the growth of pathogens in paired aerobic/anaerobic blood culture bottles versus the use of only aerobic bottles, and to analyze the time to growth in both atmospheres. METHODS: We retrospectively evaluated the results of all blood cultures collected over a 2-y period for the diagnosis of central venous catheter-related bloodstream infections or other severe infections in oncology patients. RESULTS: Among the 487 isolates, 174 (35.7%), all aerobic, grew only in the aerobic bottle; 250 (51.3%), all aerobic, grew in both bottles; and 63 (12.9%) grew only in the anaerobic bottle, of which 24 were anaerobic and 39 were aerobic microorganisms (8% of positive blood cultures). Of these 39 aerobic microorganisms, 12 were Gram-negative, 17 staphylococci (4 were Staphylococcus aureus), 5 streptococci, 2 Gram-positive bacilli, and 3 mixed growth. Though the mean time to positivity of pathogens grown in both atmospheres was significantly lower in the aerobic bottle than in the anaerobic bottle, in 71 cases (28.4%) the pathogens developed earlier in the anaerobic bottle than in the aerobic bottle - in 36 of these cases at least 1 h earlier, which is significant for starting targeted therapy. CONCLUSIONS: The use of paired aerobic/anaerobic blood culture bottles allowed the diagnosis of a percentage of bacteraemia due to either anaerobic or aerobic pathogens that would have been missed, as they grew only in the anaerobic atmosphere. Moreover in 8% of bacteraemia we identified a significant decrease in the time to detection, resulting in the opportunity to better manage the infections without an increase in costs.