Intraoperative bile duct cultures in patients undergoing pancreatic head resection: Prospective comparison of bile duct swab versus bile duct aspiration.

BACKGROUND: Postoperative surgical site infection is a major source of morbidity after pancreatic head resections, and data suggest bacterobilia as a leading cause. Some centers use intraoperative bile duct cultures to guide postoperative antimicrobial prophylaxis. This prospective study evaluates culture differences between traditional bile duct swab versus bile duct aspiration intraoperative samples. METHODS: Prospective patients undergoing pancreatic head resection with both bile duct swab and bile duct aspiration were included. Cultures were reviewed for organism characteristics. Any growth of organisms was considered a positive culture. Bile duct swab yield and characteristics were compared with bile duct aspiration. Postoperative surgical site infection complications were compared to bile duct culture results. RESULTS: Fifty patients were included. Bile duct aspiration resulted in a significantly higher median number of organisms compared to bile duct swab (6 vs 3; P < .001). There were no differences in the number of patients (37 vs 33) having positive bile duct aspiration and bile duct swab cultures (P = .385). Anaerobic cultures (not possible with bile duct swab) were positive in 21 patients with bile duct aspiration. A total of 37 (74%) patients had preoperative biliary stenting, which highly associated (P < .001) with positive cultures. Bile duct culture organisms correlated with postoperative surgical site infection in 12/17 (71%) patients. CONCLUSION: Use of bile duct aspiration improves intraoperative bile duct culture organism yield over bile duct swab and may improve tailoring of antibiotics in patients undergoing pancreatic head resection.

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.

Patient pathway analysis of tuberculosis diagnostic delay: a multicentre retrospective cohort study in China.

OBJECTIVES: Delay in diagnosis of tuberculosis (TB) is an important but under-appreciated problem. Our study aimed to analyse the patient pathway and possible risk factors of long diagnostic delay (LDD). METHODS: We enrolled 400 new bacteriologically diagnosed patients with pulmonary TB from 20 hospitals across China. LDD was defined as an interval between the initial care visit and the confirmation of diagnosis exceeding 14 days. Its potential risk factors were investigated by multivariate logistic regression and multilevel logistic regression. Hospitals in China were classified by increasing size, from level 0 to level 3. TB laboratory equipment in hospitals was also evaluated. RESULTS: The median diagnostic delay was 20 days (IQR: 7-72 days), and 229 of 400 patients (57.3%, 95%CI 52.4-62.1) had LDD; 15% of participants were diagnosed at the initial care visit. Compared to level 0 facilities, choosing level 2 (OR 0.27, 95%CI 0.12-0.62, p 0.002) and level 3 facilities (OR 0.34, 95%CI 0.14-0.84, p 0.019) for the initial care visit was independently associated with shorter LDD. Equipping with smear, culture, and Xpert at initial care visit simultaneously also helped to avoid LDD (OR 0.28, 95%CI 0.09-0.82, p 0.020). The multilevel logistic regression yielded similar results. Availability of smear, culture, and Xpert was lower in level 0-1 facilities than in level 2-3 facilities (p < 0.001, respectively). CONCLUSIONS: Most patients failed to be diagnosed at the initial care visit. Patients who went to low-level facilities initially had a higher risk of LDD. Improvement of TB laboratory equipment, especially at low-level facilities, is urgently needed.

Number, type and cost of microbiological tests during HIV Pre-Exposure Prophylaxis: The experience of a French hospital.

BACKGROUND: Microbiological tests are required for individuals on HIV Pre-Exposure Prophylaxis (PrEP), but their real-life numbers, types and cost are poorly described. METHODS: Number, type, and results of microbiological tests performed in a Besançon Hospital-associated laboratory, France, from 2016 to 2019, in the setting of PrEP consultations were retrospectively collected. Costs were estimated by the current reimbursement rate set by the French national protection system. RESULTS: 756 consultations for PrEP initiation or follow-up of 135 persons were performed over 4 years. Among 3434 tests performed in the institution-associated laboratory, 1083 and 2351 were virological and bacteriological tests, respectively. Serology was predominant in virology (98% of virological tests), with HIV, HCV, and HBV screening as the 3 more frequent assays, whereas molecular biology was predominant in bacteriology (63.1% of bacteriological tests) with N. gonorrhoeae and C. trachomatis screening as leader assays. Agar-based culture accounted for 1% of bacterial tests. The global cost of microbiological tests was 45,983.20 euros, corresponding to a mean cost of 60.80 euros per consultation. Virological and bacteriological tests accounted for 37.7% and 62.3% of this budget, respectively. No seroconversion was observed for HIV or HCV. N. gonorrhoeae and C. trachomatis were detected at least once in 39.3% and 22.4% of individuals, respectively, with 15% of symptomatic episodes in both cases. Active syphilis infection was detected in 15.4% of individuals. CONCLUSIONS: Since numerous microbiological tests are required during PrEP, the availability of specific technical platforms should not be neglected by centers wishing to set up PrEP consultations.

Day-of-Free Tissue Transfer Qualitative Cultures Do Not Predict Limb Salvage Outcomes.

BACKGROUND: Successful free tissue transfer is critical for lower extremity salvage in the chronic wound population. The rates of lower extremity free tissue transfer success lag behind those for other anatomical sites. The aim of this study was to evaluate whether positive qualitative day-of-free tissue transfer cultures or pathogen virulence negatively impacts short- and long-term outcomes of lower extremity free tissue transfer. METHODS: Between April of 2011 and January of 2018, 105 lower extremity free tissue transfer procedures were performed. Growth level and speciation were identified from qualitative cultures taken during free tissue transfer. The relationship between demographics, comorbidities, culture data, postoperative infection, free tissue transfer survival, and long-term limb salvage was examined using logistic regression. RESULTS: The median Charlson Comorbidity Index was 3. Intraoperative free tissue transfer cultures were positive in 39.1 percent. Flap survival was 93.3 percent. Postoperative infection developed in 12.4 percent. The limb salvage rate was 81.0 percent. Positive culture was not significant for flap survival, postoperative infection, or amputation. Cultures positive for Enterococcus species had a significant relationship with flap success (OR, 0.08; p = 0.01) and amputation (OR, 7.32; p = 0.04). Insufficient antimicrobial coverage had a significant relationship with postoperative infection (OR, 6.56; p = 0.01) despite the lack of pathogen concordance. On multivariate analysis, postoperative infection (OR, 12.85; p < 0.01) and Charlson Comorbidity Index were predictive of eventual amputation (OR, 1.44; p = 0.01). CONCLUSIONS: Positive day-of-free tissue transfer cultures, regardless of pathogen, had limited predictive value for short- and long-term outcomes of free tissue transfer in the authors' cohort. These findings call for a broader multicenter prospective analysis and consideration of health care-associated infections and their impact on limb salvage outcomes. CLINICAL QUESTION/LEVEL OF EVIDENCE: Risk, III.

Factors associated with recovery and the abandonment of tuberculosis treatment in the incarcerated population. / Fatores associados à cura e ao abandono do tratamento da tuberculose na população privada de liberdade.

OBJECTIVE: This study aimed to investigate the factors associated with the outcomes of recovery and abandonment in the incarcerated population with tuberculosis. METHODS: A quantitative and observational analytical study was performed with data from the Notification Disease Information System (Sinan), tuberculosis data from the incarcerated population in the state of Paraiba from 2007 to 2016; Notifications of individuals over the age of 18, reported as "new cases" and the outcome, "recovery" or "abandonment" status were included. Those people who until December 2016 had no outcome information were excluded. Analyses were performed using bivariate and multivariate statistics from the Poisson regression. RESULTS: Of the 614 notifications, most were male (93.8%). In the bivariate analysis, there was a statistically relevant association of outcomes with Acquired Immunodeficiency Syndrome (p = 0.044), Human Immunodeficiency Virus (HIV) serology (p = 0.048) and lack of completion of follow-up bacilloscopy (p = 0.001). In the adjusted multivariate analysis, Acquired Immunodeficiency Syndrome (RR = 1.998; 95%CI 1.078 - 3.704; p = 0.028) and lack of completion of follow-up bacilloscopy (RR = 5.251; 95%CI 2.158 - 12.583; p <0.001*) remained significantly associated with the dropout outcome. CONCLUSION: Recovery and abandonment outcomes were mainly associated with whether the follow-up bacilloscopy was performed or not and Acquired Immunodeficiency Syndrome.

Bacteriology of Sputum Samples: A Descriptive Cross-sectional Study in a Tertiary Care Hospital.

INTRODUCTION: Lower respiratory tract infection is a common infection and accounts for a greater burden of disease worldwide. It is a great challenge to the clinician and still more, with increasing antimicrobial resistance. Its empirical treatment may vary according to the type of causative organisms. The objective of this study is to identify the pathogenic microorganisms and their antimicrobial susceptibility pattern from sputum sample. METHODS: This descriptive cross-sectional study was conducted in KIST Medical College and Teaching Hospital from February 2015 to January 2016. Ethical approval was taken from institutional review committee prior to the study with reference no. 0051/2014/15. Data on culture and sensitivity of isolates from sputum samples were collected from the records of the hospital. Sample collection, processing, identification of microorganisms and antimicrobial susceptibility tests were performed according to the Clinical and Laboratory Standards Institute guidelines. All the data were tabulated in an Excel sheet and analyzed using SPSS version 20. RESULTS: Out of 2318 samples, 694 (29.93%) sputum samples at 95% confidence interval (737.21- 650.79) were reported as culture positive. Klebsiella was the most common isolate followed by Pseudomonas, Escherichia coli, Acinetobacter, Staphylococcus aureus, Candida albicans, Streptococcus pneumoniae, Streptococcus pyogenes, and others. Imipenem and vancomycin showed the most sensitivity towards gram-negative and gram-positive bacteria respectively. CONCLUSIONS: Proper diagnosis, identification of causative agents and their antimicrobial susceptibility pattern are important steps to limit the irrational use of antimicrobials. Prescribing antimicrobials empirically in the case of suspected lower respiratory tract infection is difficult.

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.

Will more sensitive diagnostics identify tuberculosis missed by clinicians? Evaluating Xpert MTB/RIF testing in Guatemala.

OBJECTIVE: To assess the impact of introducing Xpert as a follow-on test after smear microscopy on the total number pulmonary TB notifications. METHOD: Genexpert systems were installed in six departments across Guatemala, and Xpert was indicated as a follow-on test for people with smear-negative results. We analyzed notifications to national tuberculosis (TB) programmes (NTP) and the project's laboratory data to assess coverage of the intervention and case detection yield. Changes in quarterly TB notifications were analyzed using a simple pre/post comparison and a regression model controlling for secular notification trends. Using a mix of project and NTP data we estimated the theoretical yield of the intervention if testing coverage achieved 100%. RESULTS: Over 18,000 smear-negative individuals were eligible for Xpert testing during the intervention period. Seven thousand, one hundred and ninety-three people (39.6% of those eligible) were tested on Xpert resulting in the detection of 199 people with smear-negative, Xpert positive results (2.8% positivity rate). In the year before testing began 1098 people with smear positive and 195 people with smear negative results were notified in the six intervention departments. During the intervention, smear-positive notification remained roughly stable (1090 individuals, 0.7%), but smear-negative notifications increased by 167 individuals (85.6%) to an all-time high of 362. After controlling for secular notifications trends over an eight-quarter pre-intervention period, combined pulmonary TB notifications (both smear positive and negative) were 19% higher than trend predictions. If Xpert testing coverage approached 100% of those eligible, we estimate there would have been a+41% increase in TB notifications. CONCLUSIONS: We measured a large gain in pulmonary notifications through the introduction of Xpert testing alone. This indicates a large number of people with TB in Guatemala are seeking health care and being tested, yet are not diagnosed or treated because they lack bacteriological confirmation. Wider use of more sensitive TB diagnostics and/or improvements in the number of people clinically diagnosed with TB have the potential to significantly increase TB notifications in this setting, and potentially in other settings where a low proportion of pulmonary notifications are clinically diagnosed.

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.

Fatores associados à cura e ao abandono do tratamento da tuberculose na população privada de liberdade / Factors associated with recovery and the abandonment of tuberculosis treatment in the incarcerated population

RESUMO: Objetivo: Este estudo objetivou investigar os fatores associados aos desfechos de cura e abandono na população privada de liberdade com tuberculose. Métodos: Estudo quantitativo, observacional e analítico. Realizado com dados oriundos do Sistema de Informação de Agravos de Notificação (Sinan), de tuberculose da população privada de liberdade nos anos de 2007 a 2016 no estado da Paraíba. Foram incluídas as notificações de indivíduos maiores de 18 anos notificados como "casos novos" e como encerramento por "cura" ou "abandono". Excluíram-se aqueles que até dezembro de 2016 não tinham a situação de encerramento. Realizaram-se estatísticas bivariada e multivariada, por meio de regressão de Poisson. Resultados: Com 614 notificações, a maioria foi do sexo masculino (93,8%). Na análise bivariada, houve associação estaticamente relevante dos desfechos com síndrome da imunodeficiência adquirida (p = 0,044), sorologia para vírus da imunodeficiência humana (p = 0,048) e não realização de baciloscopia de acompanhamento (p = 0,001). Na análise multivariada ajustada, a síndrome da imunodeficiência adquirida (risco relativo - RR = 1,998; intervalo de confiança de 95% - IC95% 1,078 - 3,704; p = 0,028) e a não realização de baciloscopia de acompanhamento (RR = 5,211; IC95% 2,158 - 12,583; p < 0,001*) permaneceram significativamente associadas ao desfecho de abandono. Conclusão: Os desfechos de cura e abandono estão associados principalmente com a realização ou não da baciloscopia de acompanhamento e com a síndrome da imunodeficiência adquirida.

ABSTRACT: Objective: This study aimed to investigate the factors associated with the outcomes of recovery and abandonment in the incarcerated population with tuberculosis. Methods: A quantitative and observational analytical study was performed with data from the Notification Disease Information System (Sinan), tuberculosis data from the incarcerated population in the state of Paraiba from 2007 to 2016; Notifications of individuals over the age of 18, reported as "new cases" and the outcome, "recovery" or "abandonment" status were included. Those people who until December 2016 had no outcome information were excluded. Analyses were performed using bivariate and multivariate statistics from the Poisson regression. Results: Of the 614 notifications, most were male (93.8%). In the bivariate analysis, there was a statistically relevant association of outcomes with Acquired Immunodeficiency Syndrome (p = 0.044), Human Immunodeficiency Virus (HIV) serology (p = 0.048) and lack of completion of follow-up bacilloscopy (p = 0.001). In the adjusted multivariate analysis, Acquired Immunodeficiency Syndrome (RR = 1.998; 95%CI 1.078 - 3.704; p = 0.028) and lack of completion of follow-up bacilloscopy (RR = 5.251; 95%CI 2.158 - 12.583; p <0.001*) remained significantly associated with the dropout outcome. Conclusion: Recovery and abandonment outcomes were mainly associated with whether the follow-up bacilloscopy was performed or not and Acquired Immunodeficiency Syndrome.

Long-term Experience with Rapid Screening for Platelet Bacterial Contamination in a High-volume Transfusion Service.

Bacterial sepsis after platelet transfusion is a major cause of transfusion-transmitted infections in the US. The Food and Drug Administration (FDA) recommends performing quality control for platelet bacterial detection on days 4 and 5 before platelet transfusion. We assessed the feasibility of implementing the Pan Genera Detection (PGD) test, an FDA-approved immunoassay for platelet bacterial detection, for the primary and secondary bacterial screening of platelet units in a high-volume setting. Records were reviewed from January 2010 through December 2015. All apheresis platelets underwent primary screening by using culture methods. Additional screening with the PGD test was performed daily until February 2013, when PGD testing of apheresis platelets was performed at the start of storage day 5. In April 2015, PGD testing of apheresis platelet products was performed at the start of storage day 4. Post-storage pooled whole blood-derived platelets were screened by using the PGD test on the day of use. During the 6-year study period, 16,839 PGD tests were performed. If the PGD test was reactive, repeat PGD testing was performed. In cases of repeat reactivity, units were quarantined and cultured. Initially, 42 (0.25%) tests were reactive; 26/42 (61.91%) were repeatedly reactive and resulted in an overall PGD repeat reactivity rate of 0.15%. Only one sample grew coagulase-negative Staphylococcus No transfusion-transmitted infections were reported. The PGD bacterial detection assay was feasible and efficient in our high-volume transfusion service.

Effect of Different Doses of Inhaled Corticosteroids on the Isolation of Nasopharyngeal Flora in Children with Asthma.

OBJECTIVE: To find the effects of inhaled corticosteroids and the impact of different doses of inhaled corticosteroids on the isolation of nasopharyngeal flora in asthmatic children aged 1-15 years. METHODS: The study included 75 children with asthma and 25 age-matched controls. Nasopharyngeal swabs were obtained. Bacteria were identified by standard techniques. RESULTS: Pathogenic organisms were isolated from 36% of asthmatic children and 20% of controls, the difference was not significant statistically (OR=2.25, 95% CI=0.75-6.67, P=0.13). There was no statistically significant association of using a high dose of inhaled corticosteroids with the isolation of pathogenic organisms. Usage of biomass fuel for cooking in the household of asthmatic children increases the risk of colonization (OR=3.4, 95% CI= 1.26-9.10, P=0.03). CONCLUSIONS: Inhaled corticosteroids are safe in the treatment of asthma and there is no association between different doses of Inhaled corticosteroids and isolation of the pathogenic organism.

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.

Lack of Additional Diagnostic Yield of 16s rRNA Gene PCR for Prosthetic Joint Infections.

INTRODUCTION: Medical management of prosthetic joint infections (PJIs) relies on the identification of causative organisms through traditional culture-based approaches to guide therapy. However, diagnosis of many PJIs remains challenging, with many clinically apparent infections remaining culture-negative. Molecular diagnostics have the potential to increase diagnostic yield, particularly among culture-negative PJIs. METHODS: Bone, tissue, or synovial fluid from patients with clinically identified PJIs were collected for inclusion in this study. Samples were assessed with traditional cultures and classified as culture-positive or -negative after 48 h. Samples subsequently underwent a Staphylococcus aureus-/Kingella kingae-specific PCR followed by a 16s rRNA gene PCR. RESULTS: A total of 77 unique patients with clinically identified PJIs contributed a total of 89 samples for inclusion in the study. There were 54 culture-negative and 35 culture-positive samples evaluated. The sensitivity and specificity of S. aureus PCR in culture-positive samples was 57.1% (95% CI, 34.1%-78.1%) and 92.9% (95% CI, 66.1%-98.9%), respectively. Among culture-positive samples, 16s rRNA gene PCR correctly identified 3 of 21 (14.3%) samples with S. aureus and 2 of 5 (40%) samples with Streptococcus spp. All molecular tests were negative in those with clinically identified, culture-negative PJI. CONCLUSIONS: Our study suggests that these diagnostic tools have a limited role in PJI diagnosis.

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).

[A flowchart is always useful: application to the interpretation of the cytobacteriological examination of urine]. / Un logigramme est toujours utile : application à l'interprétation de l'examen cytobactériologique des urines.

The cytobacteriological examination of urine (CBEU) is the most prescribed test in a microbiology laboratory. The objectives of this work were to present our experience in carrying out the CBEU and to share one of the means that we consider very useful in the daily practice of this crucial analysis. This is a 28-month prospective study (March 2016 to June 2018). The CBEU was carried out in accordance with the recommendations of the medical microbiology referential (REMIC). Antibiotic susceptibility was studied in accordance with the recommendations of the l'European committee on antimicrobial susceptibility testing (EUCAST). Cultures were positive for urinary tract infection in 5.09% (n=769) of cases and for colonization in 4.88% (n=737) of cases. E. coli alone accounted for 57.8% (n=850) of all isolates. In our experience, the display of the interpretation flowchart at the bench level, as well as the availability of clinical information and cytology results when examining urocultures, allows our technicians to decide, independently, what action to take for each CBEU according to the particular context of the patient for whom it has been prescribed. Similarly, this flowchart allows the unique microbiologist in the laboratory to contextually interpret each CBEU.

Epidemiological characteristics of pulmonary tuberculosis in Shandong, China, 2005-2017: A retrospective study.

This study aimed to analyze the epidemiology of pulmonary tuberculosis (PTB) and gained insight into the future TB control plan in China.We extracted epidemiological, clinical, and geographic data from TB prevention and control institutions in 6 cities of Shandong province, China, during 2005 to 2017.Among 224,480 diagnosed PTB, rural residents accounted for 93%, smear-positive PTB 52%, and new cases 92%. The incidence rate of overall PTB declined from 40.8 to 26.25 per 100,000 during 2005 to 2017. Except smear-negative PTB (7.57-19.87 per 100,000), the incidence of smear-positive PTB and all that stratified by age, sex, and treatment history decreased. With 80% reduction, the incidence of smear-positive PTB (6.38 per 100,000) and relapse cases (1.01 per 100,000) were already very low in 2017.With persistent efforts to combat TB, the disease burden had shifted from smear-positive PTB to smear-negative PTB. While new cases need continuous attention, further reducing the incidence of smear-negative PTB and elderly patients may have a greater impact on future TB control.

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.

Detection and prevalence of carbapenem-resistant Gram-negative bacteria among European laboratories in the COMBACTE network: a COMBACTE LAB-Net survey.

Antimicrobial resistance (AMR) represents a global public health threat that jeopardises the progress medicine has made over the last century. To confront AMR, the Innovative Medicines Initiative (IMI) has supported the development of a large network of hospitals and laboratories in Europe as part of the New Drugs for Bad Bugs (ND4BB) programme and the COMBACTE projects. COMBACTE LAB-Net conducted a pilot survey on distribution and usage of carbapenem resistance detection methods among laboratories in the COMBACTE network in two clinical trials as part of the COMBACTE-CARE project. The survey was sent out to 211 laboratories in 20 European countries between May 2015 and June 2017. Answers were collected from 165 laboratories (78%). Sixty laboratories (36%) reported an outbreak of carbapenem-resistant (CR) Enterobacteriaceae during one of the two years preceding the completion of the survey. High rates of CR Acinetobacter spp. above 50% were reported by 74 laboratories (47%), particularly in the Western Balkan countries where the rates were sometimes higher than 90%. Apart from determining the antimicrobial susceptibility of isolates, laboratories also used various methods, such as Matrix Assisted Laser Desorption Ionization - Time of Flight (MALDI-TOF), Carbapenemase Nordmann-Poirel (Carba NP) test or molecular methods, to detect CR Gram-negative bacteria. The survey resulted in the selection of sites with high resistance rates that successfully recruited many patients in the EURECA observational clinical trial.