Predictors Of Positive Culture Research Articles

Predicting the presence of infectious virus from PCR data: A meta-analysis of SARS-CoV-2 in non-human primates.

Researchers and clinicians often rely on molecular assays like PCR to identify and monitor viral infections, instead of the resource-prohibitive gold standard of viral culture. However, it remains unclear when (if ever) PCR measurements of viral load are reliable indicators of replicating or infectious virus. The recent popularity of PCR protocols targeting subgenomic RNA for SARS-CoV-2 has caused further confusion, as the relationships between subgenomic RNA and standard total RNA assays are incompletely characterized and opinions differ on which RNA type better predicts culture outcomes. Here, we explore these issues by comparing total RNA, subgenomic RNA, and viral culture results from 24 studies of SARS-CoV-2 in non-human primates (including 2167 samples from 174 individuals) using custom-developed Bayesian statistical models. On out-of-sample data, our best models predict subgenomic RNA positivity from total RNA data with 91% accuracy, and they predict culture positivity with 85% accuracy. Further analyses of individual time series indicate that many apparent prediction errors may arise from issues with assay sensitivity or sample processing, suggesting true accuracy may be higher than these estimates. Total RNA and subgenomic RNA showed equivalent performance as predictors of culture positivity. Multiple cofactors (including exposure conditions, host traits, and assay protocols) influence culture predictions, yielding insights into biological and methodological sources of variation in assay outcomes-and indicating that no single threshold value applies across study designs. We also show that our model can accurately predict when an individual is no longer infectious, illustrating the potential for future models trained on human data to guide clinical decisions on case isolation. Our work shows that meta-analysis of in vivo data can overcome longstanding challenges arising from limited sample sizes and can yield robust insights beyond those attainable from individual studies. Our analytical pipeline offers a framework to develop similar predictive tools in other virus-host systems, including models trained on human data, which could support laboratory analyses, medical decisions, and public health guidelines.

Arthrocentesis of suspected septic sternoclavicular arthritis: microbial yield and predictors of culture positivity.

Evaluate the microbial yield and factors predicting culture positivity for image-guided arthrocentesis of suspected septic sternoclavicular (SC) arthritis. An electronic health record search identified image-guided SC joint aspirations for suspected septic arthritis. Data was extracted by retrospective chart review including patient demographics, procedure characteristics, pre-procedure lab testing, joint culture results, final SC joint diagnoses and any effect of positive synovial cultures on subsequent antibiotic therapy. Factors associated with positive joint fluid cultures were assessed using a Chi-squared test for categorical predictors and logistic regression for continuous predictors. A total of 31 SC arthrocenteses met inclusion criteria with most (81%) performed using ultrasound guidance. Synovial fluid was successfully aspirated in 19/31 (61%) of cases, and in all other cases lavage fluid was successfully obtained. Synovial cultures were positive in 9/31 (29%) of cases. A final diagnosis of septic arthritis was assigned to 20/31 cases (65%) in which 9/20 (45%) had positive synovial cultures. There was no statistically significant association between synovial culture positivity and risk factors for septic arthritis, positive blood cultures, pre-aspiration antibiotics and whether synovial fluid or lavage fluid was cultured. Serum white blood cell count (WBC) and erythrocyte sedimentation rate (ESR) demonstrated statistically significant positive correlation with positive synovial cultures. Arthrocentesis is effective for microbial speciation in SC septic arthritis, and diagnostic yield may be increased with lavage when encountering a dry tap. Normal serum WBC and ESR values indicate an extremely low likelihood of positive synovial cultures.

Risk factors associated with positive bacterial culture in salvaged red blood cells during cardiac surgery and postoperative infection incidence: A prospective cohort study.

This study was designed to explore factors associated with the incidence of positive bacterial culture of salvaged red blood cells (sRBCs) recovered with a Cell Saver instrument during cardiac surgery and the impact of such positive outcomes on postoperative infection-related morbidity. The cohort study enrolled 204 patients scheduled for cardiac surgery with intraoperative blood cell salvage and retransfusion from July 2021 to July 2022. These patients were stratified into two groups based on intraoperative sRBCs bacterial culture results: culture (+) and culture (-) groups. Preoperative and intraoperative variables were compared between these groups aim to detect possible predictors of positive culture in sRBCs. In addition, differences in postoperative infection-related morbidity and other clinical outcomes were compared between these groups. Of these patients, 49% were sRBCs culture (+), with Staphylococcus epidermidis as the most commonly identified pathogen. Risk factors independently associated with the risk of positive culture in sRBCs included BMI ≥25 kg/m2, a history of smoking, an operative duration ≥277.5 min, the higher number of staff in the operating room and higher surgical case order. Patients in the sRBCs culture (+) group exhibited a longer average ICU stay [3.5 days (2.0-6.0) vs. 2 days (1.0-4.0), P < 0.01], a longer duration of ventilation [20.45 h (12.0-17.8) vs. 13 h (11.0-17.0, P = 0.02)], underwent more allogeneic blood transfusions, exhibited higher transfusion-related costs [2,962 (1,683.0-5,608.8) vs. 2,525 (1,532.3-3,595.0), P = 0.01], and had higher rates of postoperative infections (22 vs. 9.6%, P = 0.02) as compared to patients in the sRBCs culture (-) group. In addition, culture (+) in sRBCs was an independent risk factor for postoperative infection (OR 2.62, 95% CI 1.16-5.90, P = 0.02). Staphylococcus epidermidis was the most common pathogen detected in sRBCs in the culture (+) group in this study, identifying it as a potential driver of postoperative infection. Positive sRBCs culture may contribute to postoperative infection and its incidence was significantly associated with patient BMI, history of smoking, operative duration, the number of staff in the operating room and surgical case order.

Prediction of culture-positive sepsis and selection of empiric antibiotics in critically ill patients with complicated intra-abdominal infections: a retrospective study

PurposeTo compare the mortality rates between culture-positive and culture-negative sepsis in complicated intra-abdominal infections (cIAI) and investigate the predictors of culture-positivity and their causative microorganisms.Materials and methodsThe medical records of 1581 adult patients who underwent emergency gastrointestinal surgery between January 2013 and December 2018 were reviewed retrospectively. A total of 239 patients with sepsis or septic shock who were admitted to an emergency department, underwent emergency surgery for cIAI, and needed postoperative intensive care unit care were included and divided into two groups according to their initial blood and peritoneal culture results.ResultsAmong the 239 patients, 200 were culture-negative and 39 were culture-positive. The culture-positive group had higher in-hospital (35.9% vs 14.5%; P = .001) and 30-day mortality (30.8% vs 12.0%; P = .003) than the culture-negative group. Colon involvement (OR 4.211; 95% CI 1.909–9.287; P < .001) and higher Sequential Organ Failure Assessment (SOFA) score (OR 1.169; 95% CI 1.065–1.282; P = .001) were shown to be the predictors of culture-positive sepsis for cIAI. Regarding antibiotic sensitivity, 31.6% of the gram-positive bacteria were methicillin-resistant and 42.1% of the gram-negative bacteria were extended spectrum β-lactamase-producing Enterobacteriaceae.ConclusionsPatients with cIAI had higher mortality rates in culture-positive sepsis than in culture-negative sepsis. High SOFA score and colon involvement were the risk factors associated with culture-positivity. The most common single species grown in the blood or peritoneal cultures was Escherichia coli, and the most common group was Gram-positive cocci.

Incidence and predictors of positive intraoperative cultures in primary shoulder arthroplasty following prior ipsilateral shoulder surgery

BackgroundTo our knowledge, the rate of positive intraoperative cultures in patients undergoing primary shoulder arthroplasty with prior ipsilateral nonarthroplasty shoulder surgery is unknown. The aim of this study was to determine the incidence and predictors of positive cultures in these patients.MethodsWe performed a retrospective review of patients with prior ipsilateral shoulder surgery with intraoperative cultures taken at the time of primary shoulder arthroplasty. We evaluated culture results, demographics, and number of prior surgeries. Regression analysis was used to determine patient-related risk factors that predict positive cultures.ResultsA total of 682 patients underwent primary shoulder arthroplasty, 83 had at least 1 prior ipsilateral shoulder surgery: 65.1% male, mean age 64.2 ± 10.9 years. For the cohort of 83 patients, an average of 3.2 ± 1.2 tissue samples were obtained for each patient, with a mean of 0.84 ± 1.14 tissue cultures being positive (range 0-5). Thirty-seven of the 83 patients (44.5%) had at least 1 positive culture, with Cutibacterium acnes the most frequent organism (31/37; 83.4%). An average of 1.9 ± 0.96 tissue cultures resulted positive (range 1-5) for the 37 patients who had positive cultures, 40.5% (15/37) had only 1 positive tissue culture (12/15 C acnes, 2/15 Staphylococcus epidermidis, and 1/15 vancomycin-resistant enterococcus). Male sex and history of prior shoulder infection were predictive of culture positivity (odds ratios: 2.5 and 20.9, respectively). Age, race, medical comorbidities, number of prior shoulder surgeries, and time from index shoulder surgery were not predictive of culture positivity.ConclusionAbout 45% of patients with no clinical signs of infection and a history of prior ipsilateral shoulder surgery undergoing primary shoulder arthroplasty grew positive intraoperative cultures. The significance of these findings remains unclear with regard to risk of periprosthetic infection and how these patients should be managed.

Dogma without Data: A Clinical Decision-Making Tool for Postoperative Blood Cultures

Bacteremia is a worrisome postoperative complication and blood cultures (BCx) are often nondiagnostic. We previously reported a 4 per cent overall yield of positive cultures in postoperative patients. To reduce unnecessary testing, we present a predictive model to identify patients in whom growth of pathogens is unlikely and provide a clinical decision-making guide. Retrospective analysis of nonpregnant patients ≥18 years who had BCx within 10 days postoperatively was performed. Generalized linear mixed models identified clinical predictors of high- and low-yield cultures. A clinical algorithm was created using significant predictors, and positive predictive value, negative predictive value, sensitivity, and specificity calculated. Among 1759 BCx, hypotension, maximum temperature ≥101.5°F within 24 hours of culture, and culture collected after postoperative day (POD) two were statistically significant predictors of positive cultures. Forty nine per cent of BCx were sent ≤ POD 2, and <1 per cent of these were positive. When all three criteria were met, the probability of a positive culture increased to 17 per cent. When absent, the probability of a negative culture was 99 per cent. When applied to the initial data set, the model resulted in 85 per cent reduction of cultures with 9 per cent yield of positive cultures. Drawing BCx based on a single predictor is inadequate. Reducing the number of cultures reflexively ordered within the first two POD could significantly reduce the number of unnecessary BCx. Several clinical features identified patients most likely to have positive BCx within the first 10 POD and could reduce unnecessary BCx. This model should be validated in an independent, prospective cohort.

Culture confirmation of tuberculosis cases in Birmingham, UK

The proportion of culture-confirmed tuberculosis (TB) cases in Birmingham had gradually decreased to less than 65% in 2008. Reasons for this were unclear, therefore this study assessed diagnostic methods used for confirming TB and reviewed factors involved in positive culture. A cross-sectional study was carried out. A list of notified TB cases for Birmingham in those aged 16 y and over in 2009 was collated. Where no positive culture was recorded, further data were collected from hospital databases and case notes. Of 449 TB cases, 419 (93%) had samples taken for culture testing. Of all cases, 309 (69%) were confirmed by culture testing; of those receiving culture testing, 73% were confirmed. Pulmonary TB was identified as a predictor of positive culture in both the unadjusted and adjusted analyses: odds ratio (OR) 2.05, 95% confidence interval (CI) 1.32-3.19, and OR 2.32, 95% CI 1.29-4.17, respectively. Gender, age, ethnicity, UK born, and treatment delay were not significantly associated with positive culture. Of 140 cases not confirmed by culture, 129 (92%) had their diagnosis supported by at least one other test. The vast majority of TB cases had microbiological specimens taken to help confirm the disease. Furthermore, culture confirmation rates in Birmingham were meeting national targets in 2009. However culture confirmation rates were significantly lower in extrapulmonary TB, therefore further work is suggested in this group. The role of other investigations (e.g. interferon-gamma release assay (IGRA), Mantoux) is unclear. Further collaboration between clinicians, histopathologists, and microbiologists is advised to ensure samples are sent appropriately and culture confirmation is optimized.

Does Preoperative Topical Antimicrobial Scrub Reduce Positive Surgical Site Culture Rates in Men Undergoing Artificial Urinary Sphincter Placement?

We determined if the incidence of a perioperative surgical site-positive culture was reduced by a 5-day topical antimicrobial scrub before implantation of an artificial urinary sphincter. A single surgeon prospective cohort study was conducted of 100 consecutive artificial urinary sphincter implants placed between May 2003 and November 2005. We compared 50 men who performed preoperative topical antimicrobial scrub with 4% chlorhexidine to the abdominal site and perineal site with 50 men who used their normal hygiene (soap and water). All received povidone-iodine skin disinfection before incision, and bacterial cultures of the abdominal and perineal sites were collected immediately after skin disinfection and after artificial urinary sphincter implantation. Baseline comparisons between groups were done with the Wilcoxon rank sum and Fisher exact tests. Predictors of positive culture were identified using multivariate logistic regression analysis. The causes of incontinence were radical prostatectomy (90), radiation therapy (8) and transurethral resection of the prostate (2). There were no baseline differences between the groups including age, diabetes or previous urethral surgery. Overall 140 of the 400 cultures were positive with only 37% of the positive cultures (52 of 140) observed with topical antimicrobial scrub. For the perineal site the only factor affecting preoperative culture status was topical antimicrobial scrub (OR 0.23, p = 0.003). A positive postoperative culture was predicted by a positive preoperative perineal (OR 4.61, p = 0.003) and abdominal culture (OR 3.80, p = 0.013). Preoperative topical antimicrobial scrub resulted in a 4-fold reduction in preoperative perineal colonization rate and overall reduction in positive surgical site cultures. Given the low cost, safety and efficacy, topical antimicrobial scrub should be considered before artificial urinary sphincter placement.

Response to Empirical Anti-Tuberculosis Treatment in Patients with Sputum Smear-Negative Presumptive Pulmonary Tuberculosis

Background: In many cases, physicians initiate anti-tuberculosis (TB) treatment based only on symptoms or radiographic findings without confirmation of pulmonary TB by acid-fast bacilli (AFB) smear. It has not been well known which clinical characteristics could be used as predictors for positive culture or real TB in patients with sputum smear-negative presumptive pulmonary TB. Objective: We tried to elucidate treatment outcomes in patients with sputum smear-negative presumptive pulmonary TB and to find predictors of positive culture results. Methods: We reviewed data of the patients who had been treated as presumptive TB with negative AFB smear on the basis of clinical and radiographic features from December 1998 to December 2000 at a university hospital in Korea. We reviewed medical records and radiographs of patients and analyzed possible predictors for positive culture. Results: One hundred and one patients were enrolled. Among them, pulmonary TB was confirmed by culture in 32 patients (31%). Thirty-one (96.9%) out of 32 culture-positive patients showed clinical or radiographic improvement as did 50 (72.5%) out of 69 culture-negative patients. The predictor for a positive culture result is the presence of patchy consolidation in an initial radiograph (p = 0.025; OR 2.89; 95% CI 1.14–7.28). Conclusions: The empirical anti-TB treatment in patients with sputum smear-negative presumptive pulmonary TB was effective and adequate, especially presented with patchy consolidation in initial chest radiographs in Korea.

PENILE PROSTHESIS CULTURES DURING REVISION SURGERY: A MULTICENTER STUDY

Initial implantation of inflatable penile prosthesis has a 3% risk of infection. Reoperation of penile implants has a higher rate of infection, estimated between 10% and 18%. To explain the higher risk in revision surgery in this prospective study we cultured clinically uninfected prostheses requiring revision. Prosthesis pain was also investigated as a predictor of positive culture. At 3 institutions cultures were prospectively obtained from 77 clinically uninfected penile prostheses at revision surgery. Immediately upon surgical exposure of the pump cultures were obtained. If a bacterial biofilm was noted on any component it was additionally cultured. All culture isolates positive for a staphylococcus species were tested for sensitivity to rifampin and tetracycline (minocycline). An implant is now available that is coated with these antibiotics. Patient history of chronic prosthesis pain was ascertained. Culture positive bacteria were found in 54 of 77 (70%) patients with clinically uninfected penile prostheses. In some patients more than 1 organism grew and, occasionally, the pump culture was negative but the biofilm was positive. Of 54 patients 49 had positive (90%) culture for staphylococcus genus with 10 different species. All staphylococcal species were sensitive to rifampin and/or tetracycline. We did not find a significant association between prosthesis related pain and culture laboratory results. The majority of clinically uninfected penile prostheses have organisms growing in the implant spaces at reoperation. Most of these organisms are staphylococcal species that are sensitive to rifampin/minocycline.