Bacteriological culture and direct PCR for detecting the Mycobacterium tuberculosis complex in the Italian eradication campaign: a decade of experience at the National Reference Laboratory.

AIMS: Our study evaluates the capacity of direct real-time PCR for detecting Mycobacterium tuberculosis complex (MTBC), with a focus on diagnostic performances and the feasibility of implementing this protocol in an eradication campaign. Specifically, we compare the effectiveness of the direct PCR method to various culture systems used by the Italian National Reference Laboratory over the last decade to detect MTBC. METHODS AND RESULTS: Bovine tissue samples were routinely tested and analyzed for bovine tuberculosis (bTB) confirmation using microbiological culture (solid and liquid media), histopathological analysis, and a direct PCR assay targeting IS6110, an insertion sequence specific to the MTBC that is widely used for tuberculosis diagnosis. The direct real-time PCR demonstrated a high concordance (K = 0.871) with microbiological culture, as well as good sensitivity (91.84%) and specificity (95.24%). In contrast, histopathology demonstrated lower concordance (K = 0.746) and performance levels (sensitivity 91.41%, specificity 82.88%). Liquid media promoted faster and more efficient growth of MTBC than solid media. M. bovis and M. caprae had the comparable ability to respond to the direct real-time PCR test and grow on the microbiological medium. CONCLUSIONS: This study confirms that direct real-time PCR can detect MTBC with high diagnostic accuracy within a few days. This study found no significant differences in performance between culture media and direct PCR for M. bovis and M. caprae.

Association between Clinical Characteristics and Microbiota in Bronchiectasis Patients Based on Metagenomic Next-Generation Sequencing Technology.

This study aimed to investigate the disparities between metagenomic next-generation sequencing (mNGS) and conventional culture results in patients with bronchiectasis. Additionally, we sought to investigate the correlation between the clinical characteristics of patients and their microbiome profiles. The overarching goal was to enhance the effective management and treatment of bronchiectasis patients, providing a theoretical foundation for healthcare professionals. A retrospective survey was conducted on 67 bronchiectasis patients admitted to The First Hospital of Jiaxing from October 2019 to March 2023. Clinical baseline information, inflammatory indicators, and pathogen detection reports, including mNGS, conventional blood culture, bronchoalveolar lavage fluid (BALF) culture, and sputum culture results, were collected. By comparing the results of mNGS and conventional culture, the differences in pathogen detection rate and pathogen types were explored, and the diagnostic performance of mNGS compared to conventional culture was evaluated. Based on the various pathogens detected by mNGS, the association between clinical characteristics of bronchiectasis patients and mNGS microbiota results was analyzed. The number and types of pathogens detected by mNGS were significantly larger than those detected by conventional culture. The diagnostic efficacy of mNGS was significantly superior to conventional culture for all types of pathogens, particularly in viral detection (p < 0.01). Regarding pathogen detection rate, the bacteria with the highest detection rate were Pseudomonas aeruginosa (17/58) and Haemophilus influenzae (11/58); the fungus with the highest detection rate was Aspergillus fumigatus (10/21), and the virus with the highest detection rate was human herpes virus 4 (4/11). Differences were observed between the positive and negative groups for P. aeruginosa in terms of common scoring systems for bronchiectasis and whether the main symptom of bronchiectasis manifested as thick sputum (p < 0.05). Significant distinctions were also noted between the positive and negative groups for A. fumigatus regarding Reiff score, neutrophil percentage, bronchiectasis etiology, and alterations in treatment plans following mNGS results reporting (p < 0.05). Notably, 70% of patients with positive A. fumigatus infection opted to change their treatment plans. The correlation study between clinical characteristics of bronchiectasis patients and mNGS microbiological results revealed that bacteria, such as P. aeruginosa, and fungi, such as A. fumigatus, were associated with specific clinical features of patients. This underscored the significance of mNGS in guiding personalized treatment approaches. mNGS could identify multiple pathogens in different types of bronchiectasis samples and was a rapid and effective diagnostic tool for pathogen identification. Its use was recommended for diagnosing the causes of infections in bronchiectasis patients.

Bacteria Living in Biofilms in Fluids: Could Chemical Antibiofilm Pretreatment of Culture Represent a Paradigm Shift in Diagnostics?

Biofilms are multicellular aggregates of bacteria immersed in an extracellular matrix that forms on various surfaces, including biological tissues and artificial surfaces. However, more and more reports point out the fact that even biological fluids and semifluid, such as synovial liquid, blood, urine, or mucus and feces, harbor "non-attached" biofilm aggregates of bacteria, which represent a significant phenomenon with critical clinical implications that remain to be fully investigated. In particular, biofilm aggregates in biological fluid samples have been shown to play a relevant role in bacterial count and in the overall accuracy of microbiological diagnosis. In line with these observations, the introduction in the clinical setting of fluid sample pretreatment with an antibiofilm chemical compound called dithiothreitol (DTT), which is able to dislodge microorganisms from their intercellular matrix without killing them, would effectively improve the microbiological yield and increase the sensitivity of cultural examination, compared to the current microbiological techniques. While other ongoing research continues to unveil the complexity of biofilm formation in biological fluids and its impact on infection pathogenesis and diagnosis, we here hypothesize that the routine use of a chemical antibiofilm pretreatment of fluid and semi-solid samples may lead to a paradigm shift in the microbiological approach to the diagnosis of biofilm-related infections and should be further investigated and eventually implemented in the clinical setting.

Performance of an innovative culture-based digital dipstick for detection of bacteriuria.

IMPORTANCE: In this study, we explore the transformative potential of UTI-lizer, an emerging technology not yet commercially available. Our manuscript shows that UTI-lizer is a promising alternative for detecting the five main pathogens that cause urinary tract infections (UTIs). The results also indicate that digital dipsticks have the potential to uniquely provide UTI diagnostic quality on par with that of gold-standard testing, with the added benefits of ease of testing, rapid test handling time, and simple test equipment. This technology can be helpful in quickly ruling out bacterial infections and reducing the unnecessary use of antibiotics, especially in primary care settings or at the point of care. Moreover, the UTI-lizer test can reduce the number of negative urine samples sent to central laboratories, thus easing the burden of UTI diagnostics on the healthcare system. We believe our study, as well as current and upcoming research based on this technology, is highly relevant for clinical microbiologists, microbiology scientists, general practitioners, and urologists.

Analysis of Bacterial Stent Colonization: The Role of Urine and Device Microbiological Cultures.

In this study, we explored the incidence of double J (JJ) contamination of patients who underwent an endourological procedure for urinary stones and ureteral stenosis. We developed a prospective study between January 2019 and December 2021. Ninety-seven patients, 54 male and 43 female, were enrolled. Urine culture was taken during four steps: before stent insertion, a sample from selective renal pelvis catheterization, a sample two days after the JJ insertion and finally, after the stent removal procedure. At the time of the stent removal, 1 cm of proximal and distal ends were cut off and placed in the culture for bacterial evaluation. Cohen's kappa coefficient value (k) and concordance rates of microbiological culture results were evaluated. The study group comprised 56% of male patients. Proximal and distal stent cultures were positive in 81 and 78 patients. The concordance rate of microbiological cultures between proximal and distal double J stent is 88% (k 0.6). The most common pathogens isolated from urine and stent cultures were Enterococcus spp. in 52 cases and Klebsiella spp. in 27 cases.

Microbiological culture combined with PCR for the diagnosis of onychomycosis: Descriptive analysis of 121 patients.

BACKGROUND: Onychomycosis is the most common nail pathology, involving various pathogens such as dermatophytes, moulds and yeasts. OBJECTIVE: The objective of this study was to observe the prevalence of onychomycosis, analyse the most appropriate diagnostic test, and assess the distribution of pathogens based on age, sex, quarter of the year, duration of symptoms and previous treatment. METHODS: Retrospectively, mycological culture and PCR data and results were collected from 121 patients. RESULTS: Of the 121 samples, 57% (69/121) tested positive when both microbiological study techniques were combined. The prevalence of onychomycosis was higher when PCR was performed (52.1%) compared to microbiological culture (33.1%). Among the 81 samples negative by microbiological culture, 31 were positive by PCR. Similarly, of the 58 samples negative by PCR, eight were positive by microbiological culture. Diagnostic accuracy data (with 95% confidence intervals) for PCR, using microbiological culture as the gold standard, were as follows: sensitivity of 0.8, specificity of 0.62, positive predictive value of 0.51 and negative predictive value of 0.86. The most frequently identified pathogen was Trichophyton rubrum, and the hallux nail plate was the most commonly affected location. However, no statistically significant associations were found between sex, age, quarter of the year and affected area with culture and PCR results. CONCLUSION: Combining microbiological culture and PCR can increase the detection rate of onychomycosis and help avoid false-negative results.

Histologic chorioamnionitis in extremely preterm births, microbiological findings and infant outcome.

BACKGROUND: Histologic chorioamnionitis (HCA) is most often caused by ascending bacterial infection originating from the cervicovaginal tract. OBJECTIVES: To investigate whether HCA with a fetal inflammatory response (FIR) has a worse clinical outcome than HCA alone. Further, if FIR or a positive maternal microbiologic culture obtained prior to birth were related to adverse neonatal outcomes in a cohort of extremely preterm (EP) neonates. METHODS: Prospective observational cohort study recruiting EP singleton pregnancies (gestational age at birth ≤28 weeks) with confirmed HCA. FIR was defined by fetal neutrophils in the chorionic vessels and/or umbilical vessels. Positive culture was defined as growth of potentially pathogenic bacteria in a sample from the cervicovaginal tract prior to birth, or if a cervicovaginal culture was lacking, a culture result from the placenta was used. Logistic regression was used to estimate odds ratios and 95% confidence intervals for the associations between FIR, a positive culture result and adverse outcomes, defined as bronchopulmonary dysplasia (BPD), brain pathology assessed by magnetic resonance imaging, retinopathy of prematurity, necrotizing enterocolitis, early-onset neonatal sepsis, and perinatal death. A composite outcome variable included one or more adverse outcomes. RESULTS: We included 71 cases with HCA, of which 51 (72%) had FIR. Maternal age, rate of clinical chorioamnionitis (CCA), preterm pre-labor rupture of membranes (PPROM), the number of women receiving antenatal steroids and antibiotics, and the rate of positive maternal cultures of potentially pathogenic bacteria were all significantly higher in the HCA with FIR. Neonates in the FIR group had significantly higher levels of blood leukocytes compared to those without. FIR was associated with a longer interval from PPROM to delivery (log-rank test: p = .022). Microbiological sampling had been performed in 63 (89%) cases, of which 60 (95%) were cervicovaginal samples. No associations were found between a positive culture and adverse neonatal outcomes, in contrast to FIR, that was significantly associated to BPD and brain pathology. CONCLUSIONS: In a cohort of EP pregnancies with confirmed HCA, the presence of FIR was associated with advanced maternal age, CCA, PPROM, antenatal steroids and antibiotics, and a positive maternal culture of potentially pathogenic bacteria. However, the presence of FIR, and not a positive culture, was associated with adverse neonatal outcomes.

Dithiotreitol pre-treatment of synovial fluid samples improves microbiological counts in peri-prosthetic joint infection.

PURPOSE: Synovial fluid cultures of periprosthetic joint infections (PJI) may be limited by bacteria living in the fluids as biofilm-aggregates. The antibiofilm pre-treatment of synovial fluids with dithiotreitol (DTT) could improve bacterial counts and microbiological early stage diagnosis in patients with suspected PJI. METHODS: Synovial fluids collected from 57 subjects, affected by painful total hip or knee replacement, were divided into two aliquots, one pre-treated with DTT and one with normal saline. All samples were plated for microbial counts. Sensitivity of cultural examination and bacterial counts of pre-treated and control samples were then calculated and statistically compared. RESULTS: Dithiothreitol pre-treatment led to a higher number of positive samples, compared to controls (27 vs 19), leading to a statistically significant increase in the sensitivity of the microbiological count examination from 54.3 to 77.1% and in colony-forming units count from 1884 ± 2.129 CFU/mL with saline pre-treatment to 20.442 ± 19.270 with DTT pre-treatment (P = 0.02). CONCLUSIONS: To our knowledge, this is the first report showing the ability of a chemical antibiofilm pre-treatment to increase the sensitivity of microbiological examination in the synovial fluid of patients with peri-prosthetic joint infection. If confirmed by larger studies, this finding may have a significant impact on routine microbiological procedures applied to synovial fluids and brings further support to the key role of bacteria living in biofilm-formed aggregates in joint infections.

Microbiological Profile and Clinical Features of Septic Arthritis of the Shoulder: A 10-Year Cohort Single-Centre Study.

Introduction  Septic arthritis (SA) constitutes a pressing orthopedic emergency characterized by acute, non-traumatic joint pain. Timely diagnosis and intervention are imperative to avert complications such as chondrolysis and systemic sepsis. The etiology is predominantly hematogenous, necessitating an integrated approach involving surgical and microbiological modalities. Shoulder aspiration and microbiological analysis play pivotal roles in guiding treatment, especially when positive findings prompt more aggressive therapeutic strategies. This study aims to elucidate the nuanced clinical and epidemiological characteristics of septic arthritis in both native and prosthetic joints within a singular institutional cohort over a decade. Methods  This retrospective case series analysis spanned a 10-year period, focusing on non-prosthetic shoulder joints from January 2012 to July 2021. In this timeframe, only 183 aspirations were performed and sent to the microbiology department for analysis, including cultures, microscopy, and antibiotic sensitivity tests for positive cultures. The study delved into the microbiological profile of infections, encompassing gram stain, culture positivity rates, identification of microorganisms, and antibiotic susceptibility patterns. Additionally, the incidence of primary joint infections with resistant strains, particularly methicillin-resistant Staphylococcus aureus (MRSA), was scrutinized. Statistical analysis utilized the SPSS program version 20.0 (IBM Inc., Armonk, New York), with a significance level set at 5%. The project, registered with the trust's clinical audit department (Reg #5372), adhered to the Declaration of Helsinki and good clinical practice guidelines. Data collection involved extracting non-identifiable patient modifiers from the laboratory database bank into Excel spreadsheets. Results  The study included 183 patients, with 108 (59%) females and 75 (41%) males. The average age was 76.2±16.5 years. Among them, 138 (75.4%) reported pain, and 15 (8.2%) had a body temperature over 37.8°C. Lab results showed a mean white blood cell count of 11.6±4.5 and an average C-reactive protein level of 121.7±102.1. Leucocytosis (>11,000 WBC) was seen in 82 (44.8%) cases. Elevated C-reactive protein (CRP; >10 mg/dl) was found in 136 (74.3%) patients. Synovial fluid analysis revealed no crystals in 91.3% of cases. Microbial resistance analysis showed 19 strains resistant to co-trimoxazole and 11 to erythromycin. Among co-trimoxazole-resistant strains, 73.7% were Staphylococcus aureus, a statistically significant association (p<0.001). Conclusion The evolving sensitivity patterns of microbes in septic arthritis underscore the necessity to reassess empirical antibiotic therapy. Subsequent joint damage resulting from infection can result in substantial disability.

Microbiological Profile in Patients Having Keratitis in a Tertiary Care Hospital in India.

Background Corneal ulcer or keratitis is defined as a loss of corneal epithelium with underlying stromal infiltration and suppuration associated with signs of inflammation. Corneal blindness is a significant public health problem worldwide; infectious keratitis is one of the predominant preventable causes of blindness. Several studies have evaluated microbial infectious keratitis's etiology, management, and outcome. However, there are regional variations in corneal ulcers' prevalence, risk factors, and outcome. The objective of this study was to isolate and identify the bacterial, fungal, viral, and protozoal etiological organisms causing infectious corneal ulcers along with their prevalence and antimicrobial sensitivity pattern. Methods A prospective observational study was done in the Department of Microbiology and RIO, Medical College & Hospital, Kolkata, for a period of 1 year (February 2019 to January 2020) after obtaining clearance from the Institutional Ethics Committee. Informed consent, demographic data, history of disease onset, duration of symptoms, associated co-morbidities, etc., were taken from the patients fulfilling the inclusion criteria. Corneal scraping samples were collected sterilely to detect bacterial, fungal, parasitic, and viral isolates and identified by standard laboratory procedures. Results A total of 80 patients were included in the study. The risk factors included foreign body in 24 (30%), blunt trauma in 10 (12.5%), steroid use in 8 (10%), contact lens user 4 (5%), and spontaneous in 34 (42.5%). Among these 80 patients, 18 showed growth of bacteria, including Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus pyogenes, and Pseudomonas aeruginosa; four had growth of fungi, including Aspergillus spp. and Fusarium spp, and two were positive for Herpes simplex virus by IFA. Conclusion Early diagnosis and prompt keratitis treatment are critical for preventing visual loss. The identification of the various causative agents of keratitis is essential for the proper management of the cases.

Comparison Between Gynecological Examination Methods and Sample Collection Techniques for the Diagnosis of Endometritis in Subfertile Mares.

Endometritis is a relevant cause of subfertility in mares. However, the accurate diagnosis, essential for effective treatment, can be difficult due to the variability of results and interpretations resulting from different examination methods and sample collection techniques. The present work compared gynecological evaluation methods and sample collection techniques to diagnose endometritis in subfertile mares. Forty animals with a history of subfertility were selected for gynecological evaluation using clinical methodologies, such as perineal conformation, transrectal palpation and ultrasonography, vaginoscopy, and digital examination of the cervix. In addition, we performed laboratory analyses, including uterine microbiological culture and endometrial cytology and histology, of which the latter is the gold standard for the diagnosis of endometritis. Samples were collected for microbiological culture and endometrial cytological evaluations using three different techniques: a commercial cytobrush/swab collector, low-volume uterine flush, and a new tested technique, by flush the fragment resulting from the endometrial biopsy. Transrectal palpation and ultrasound showed the best results among clinical examinations. However, they were less efficient in laboratory tests of endometrial cytology and uterine microbiological culture, in which the latter showed the highest sensitivity and specificity for endometritis compared with endometrial histology. The use of multiple results from different methods has also proved to be an effective alternative for diagnosis. Among the techniques used to collect endometrial material for cytology and microbiological culture, the most effective and practical in this study was the commercial cytobrush/swab collector.

The role of synovial fluid aspiration in shoulder joint infections.

BACKGROUND: Joint aspiration with analysis of synovial fluid white blood cell count (WBC) and microbiological culture is a widely established aspect in the diagnosis of shoulder joint infections (SJI). In case of a two stage revision for SJI, joint aspiration before re-/implantation of a total shoulder arthroplasty (TSA) was used to rule out persistent infection for years but its value is under debate. Shoulder specific data on all aspects is rare. The current study aims to answer the following research questions: Does joint aspiration have an insufficient predictive value in the diagnosis of SJI in (1) initial workup and (2) before definite arthroplasty with polymethylmethacrylate (PMMA)-Spacer in place? METHODS: This retrospective evaluation investigates 35 patients that were treated for SJI with a two staged implantation of a TSA after debridement and implantation of an PMMA-Spacer. Joint aspirations were performed preoperatively (PA) and before re-/implantation of the prosthesis while spacer was in place (interstage aspiration, IA). Samples were taken for microbiological culture and analysis of WBC. Sensitivity and specificity were calculated with reference to intraoperative microbiological samples. Receiver Operating Characteristic (ROC), Area-Under-Curve analysis (AUC) and calculation of the Youden index were performed to find optimum cut-off for WBC. RESULTS: The sensitivity of microbiological cultures from PA was 58.3% and the specificity was 88.9%. The mean WBC was 27,800 leucocytes/mm3 (range 400-96,300). The maximum Youden index (0.857) was a cut-off of 2600 leucocytes/mm3 with a sensitivity of 85.7% and a specificity of 100.0%. The sensitivity and specificity of IA were 0.0% and 88.5%, respectively. CONCLUSIONS: Preoperative aspiration is likely to miss Cutibacteria spp. and CoNS and cannot rule out infection for sure. However, we recommend it for its advantages of targeted antibiotic therapy in case of germ identification. Empiric antibiotic therapy should cover Cutibacteria and CoNS even if aspiration showed negative microbiological cultures. In contrast, the diagnostic value of interstage aspiration does not qualify for its routine use.

The subgingival cultivable bacteria of Albanian subjects with different periodontal status compared to a similar population of Spanish subjects: a case control study.

BACKGROUND: The objective was to qualitatively and quantitatively describe the subgingival cultivable bacteria in Albanian subjects and to compare it with a similar Spanish population. MATERIALS AND METHODS: Consecutive patients, diagnosed as periodontitis in stages I-II or III-IV, and as periodontally healthy or with gingivitis, were studied clinically and microbiologically by means of microbiological culture, including total anaerobic counts, proportions, and frequency of detection of target species. Outcome variables were analysed by Mann-Whitney, Kruskal-Wallis, ANOVA, ANCOVA and Chi-square tests. RESULTS: In this cross-sectional study, 83 (Albania) and 90 (Spain) subjects were included. No statistically significant differences were observed between test and control populations regarding demographic variables or smoking habit. Significantly higher total anaerobic counts in the Albanian population (p = 0.022) were observed, especially in the periodontal health/gingivitis group (p = 0.001). In the test population, the proportions of the cultivable bacteria of Fusobacterium nucleatum were significantly lower in both the healthy/gingivitis (p = 0.022) and stages I-II periodontitis (p = 0.034) groups. CONCLUSIONS: The subgingival cultivable bacteria in both periodontitis and non-periodontitis subjects from Albania showed significantly higher total anaerobic counts and lower proportions of the cultivable bacteria of F. nucleatum than a similar population of subjects from Spain.

Cirrhotic Patients with Bacterial Infection and Negative Cultures Have a More Advanced Disease and an Increased Short-Term Mortality Rate.

BACKGROUND: The negative clinical impact of bacterial infections (BI) in patients with cirrhosis is well documented. In cirrhotic patients, failure to isolate the pathogen is a frequent event, occurring in 30-40% of cases. AIM: The aim of this study was to compare the clinical characteristics, early (30-day) and short-term (90-day) mortality rates, in a cohort of cirrhotic patients with BI, between those with positive (C-pos) and those with negative (C-neg) microbiological cultures. METHODS: We retrospectively enrolled 279 consecutive hospitalized cirrhotic patients with BI. Survival and predictors of 30-day and 90-day mortality were assessed by Kaplan-Meier curves and logistic regression analysis, respectively. RESULTS: Cultures tested negative in 108/279 (38.7%) patients. C-neg patients were more frequently males (p = 0.035), had higher Child-Pugh-Turcotte (CPT; p = 0.007) and model for end-stage liver disease-sodium (MELD-Na; p = 0.043) scores, and had more frequently decompensated liver disease (p = 0.04). Mortality rate was higher in C-neg than in C-pos patients, both at 30 days (22.2% versus 11.7%, p = 0.024) and 90 days (46.3% versus 33.3%, p = 0.030). MELD-Na score and non-selective beta-blockers (NSBBs) were independent risk factors for 30-day and 90-day mortality. In particular, the use of NSBBs was independently associated with a lower 30-day and 90-day mortality risk (OR 0.41, CI95% 0.17-0.94, p = 0.040; and OR 0.43, CI95% 0.25-0.75, p = 0.003, respectively). CONCLUSIONS: Cirrhotic patients with BI and negative microbiological cultures have significantly higher mortality compared to those with positive cultures. Early mortality and short-term mortality are mainly influenced by the underlying severity of liver disease. In this contest, therapy with NSBBs has a positive impact on short-term survival.

Inflammatory Biomarkers Are Inaccurate Indicators of Bacterial Infection on Admission in Patients With Acute Exacerbation of Chronic Obstructive Pulmonary Disease-A Systematic Review and Diagnostic Accuracy Network Meta-Analysis.

Introduction: The value of inflammatory biomarkers in the diagnosis of bacterial infection induced acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is currently unclear. Our objective was to investigate the diagnostic accuracy of on-admission inflammatory biomarkers in differentiating bacterial origin in AECOPD. Methods: Systematic literature search was performed to include cross-sectional studies on AECOPD patients with microbiological culture results as gold standard, and at least one on-admission inflammatory biomarker determined from serum: C-reactive protein (CRP), procalcitonin (PCT), neutrophil/lymphocyte ratio, eosinophil percentage, CD64index; or sputum: neutrophil elastase, tumor necrosis factor alfa, interleukin-1-beta (IL-1b), interleukin-8, sputum color, as index tests. We ranked index tests by superiority indices in a network meta-analysis and also calculated pooled sensitivity and specificity. Results: Altogether, 21 eligible articles reported data on 2,608 AECOPD patients (44% bacterial). Out of the 14 index tests, sputum IL-1b showed the highest diagnostic performance with a pooled sensitivity of 74% (CI: 26-97%) and specificity of 65% (CI: 19-93%). Pooled sensitivity for CRP and PCT were: 67% (CI: 54-77%) and 54% (CI: 39-69%); specificity 62% (CI: 52-71%) and 71% (CI: 59-79%), respectively. Conclusion: Admission inflammatory biomarkers are inaccurate indicators of bacterial infection in AECOPD. Systematic Review Registration: https://www.crd.york.ac.uk/prospero/#myprospero, identifier: 42020161301.

Características microbiológicas de los pacientes con úlcera del pie diabético / Microbiologic characteristics of patients with diabetic foot ulceration

RESUMEN Introducción: Las infecciones de las úlceras del pie diabético son comunes, complejas, de alto costo y constituyen la principal causa de amputación no traumática de las extremidades inferiores. Objetivo: Identificar los microorganismos aislados para estimar tanto la sensibilidad a los antibióticos como la coincidencia entre el tratamiento empírico y los resultados microbiológicos en pacientes con úlceras del pie diabético. Métodos: Se realizó una investigación descriptiva-retrospectiva. La población de estudio estuvo constituida por 210 pacientes ingresados en el Hospital Universitario Clínico Quirúrgico "Comandante Faustino Pérez Hernández" de Matanzas entre junio de 2017 y junio de 2020. Las variables de salida fueron la frecuencia y el tipo de germen, la cantidad de gérmenes por úlcera, la sensibilidad para cada tipo de antibiótico, y el porcentaje de coincidencia entre el tratamiento empírico y el resultado microbiológico. Resultados: Se identificaron 259 gérmenes y se observaron 1,23 gérmenes por úlcera. El 62,5 por ciento de los gérmenes encontrados fueron Gram negativos, pero el germen más representado fue el Staphylococcus aureus. El 58,8 por ciento de los Staphylococcus aureus se mostraron resistentes a la meticillin. La vancomicina y el linezolid resultaron efectivos en el 100 por ciento de los Gram positivos. La amikacina fue el antibiótico más efectivo para los Gram negativos. Se observó coincidencia entre el tratamiento empírico y el resultado del antibiograma en el 27,6 por ciento de los pacientes. Conclusiones: Resulta necesario un apropiado diagnóstico microbiológico de las úlceras del pie diabético para identificar los gérmenes presentes en las lesiones y diseñar algoritmos de terapia antimicrobiana adecuados(AU)

ABSTRACT Introduction: Diabetic foot ulcer infections are common, complex, high cost and are the leading cause of non-traumatic lower extremity amputation. Objective: To identify the microorganisms isolated to estimate both the sensitivity to antibiotics and the coincidence between empirical treatment and microbiological results in patients with diabetic foot ulcers. Methods: A descriptive-retrospective investigation was performed. The study population consisted of 210 patients admitted to the University Hospital "Comandante Faustino Pérez Hernández" of Matanzas between June 2017 and June 2020. The output variables were the frequency and type of germ, the number of germs per ulcer, the sensitivity for each type of antibiotic, and the percentage of coincidence between the empirical treatment and the microbiological result. Results: A total of 259 germs were identified and 1.23 germs per ulcer were observed. The 62.5 percent of the germs found were Gram negative, but the most represented germ was Staphylococcus aureus. Of the Staphylococcus aureus, 58.8 percentwere resistant to methicillin. Vancomycin and linezolid were effective in 100 percent of Gram positives. Amikacin was the most effective antibiotic for Gram-negatives. Agreement between empirical treatment and antibiogram result was observed in 27.6 percent of patients. Conclusions: An appropriate microbiological diagnosis of diabetic foot ulcers is necessary to identify the germs present in the lesions and to design adequate antimicrobial therapy algorithms(AU)

Characterization of the Subgingival Cultivable Microbiota in Patients with Different Stages of Periodontitis in Spain and Colombia. A Cross-Sectional Study.

The objective was to characterize and compare the subgingival microbiota in patients diagnosed according to the World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions 2018. For this cross-sectional study, Spanish and Colombian subjects (characterized as health/gingivitis, periodontitis in stages I-II or stages III-IV) were clinically assessed, and subgingival samples were taken and processed by culture. The comparisons among patients with periodontal status (and between countries) was made using Mann-Whitney, Kruskal-Wallis, ANOVA and chi-square tests. The final sample consisted of 167 subjects. Eikenella corrodens and Parvimonas micra were more frequently detected in health/gingivitis and Porphyromonas gingivalis in periodontitis (p < 0.05). Higher total counts were observed in Colombia (p = 0.036). In Spain, significantly higher levels of P. gingivalis and Campylobacter rectus were observed, and of Tannerella forsythia, P. micra, Prevotella intermedia, Fusobacterium nucleatum, Actinomyces odontolyticus and Capnocytophaga spp. in Colombia (p < 0.001). P. micra was more prevalent in health/gingivitis and stage I-II periodontitis in Colombia, and P. gingivalis in all periodontitis groups in Spain (p < 0.05). As conclusions, significant differences were detected in the microbiota between health/gingivitis and periodontitis, with minor differences between stages of periodontitis. Differences were also relevant between countries, with Colombia showing larger counts and variability of bacterial species.

Assessment of Intraoperative Microbiological Culture in Patients with Empyema: Comparison with Preoperative Microbiological Culture.

PURPOSE: Assessing microbiological culture results is essential in the diagnosis of empyema and appropriate antibiotic selection; however, the guidelines for the management of empyema do not mention assessing microbiological culture intraoperatively. Therefore, we tested the hypothesis that intraoperative microbiological culture may improve the management of empyema. METHODS: We performed a retrospective analysis of 47 patients who underwent surgery for stage II/III empyema from January 2011 to May 2019. We compared the positivity of microbiological culture assessed preoperatively at empyema diagnosis versus intraoperatively. We further investigated the clinical characteristics and postoperative outcomes of patients whose intraoperative microbiological culture results were positive. RESULTS: The positive rates of preoperative and intraoperative microbiological cultures were 27.7% (13/47) and 36.2% (17/47), respectively. Among 34 patients who were culture-negative preoperatively, eight patients (23.5%) were culture-positive intraoperatively. Intraoperative positive culture was significantly associated with a shorter duration of preoperative antibiotic treatment (p = 0.002). There was no significant difference between intraoperative culture-positive and -negative results regarding postoperative complications. CONCLUSIONS: Intraoperative microbiological culture may help detect bacteria in patients whose microbiological culture results were negative at empyema diagnosis. Assessing microbiological culture should be recommended intraoperatively as well as preoperatively, for the appropriate management of empyema.

Urinary Tract Infection in Chronic Kidney Disease Population: A Clinical Observational Study.

Introduction Chronic kidney disease (CKD) is a state of chronic inflammation. Chronic inflammation weakens the body's immune response to infections. Hence, CKD patients are at an increased risk of infections. Urinary tract infection (UTI) is one of the most common types of community-acquired infection. There is a paucity of data with respect to UTI in CKD patients. Hence, our objective was to study the clinical and microbiological profile of UTI in CKD patients. Materials and methods We studied 129 CKD patients at a tertiary care hospital in south India from January 2020 to June 2020. Patients who fulfilled the inclusion criteria were included in the study. Urine samples were cultured aseptically. Only urine-culture positive samples were included in the study and antibiotic susceptibility was recorded. Results Males (76.2%) were most commonly infected. 94% were gram-negative bacteria, 3% were gram-positive bacteria and 3% were Candida species. E. coli (61.8%) was the most common isolated microorganism. Resistance to quinolones was recorded among gram-negative bacteria. Resistance to penicillin and quinolones was noted among gram-positive bacteria. Candida species were sensitive to amphotericin B and fluconazole. Conclusion The results of the study help in formulating the empiric antibiotic policy to treat UTI in CKD patients and hence prevent inadvertent use of antibiotics and the emergence of antibiotic resistance.

Next-Generation Sequencing for Pathogen Identification in Infected Foot Ulcers.

BACKGROUND: Accurate identification of primary pathogens in foot infections remains challenging due to the diverse microbiome. Conventional culture may show false-positive or false-negative growth, leading to ineffective postoperative antibiotic treatment. Next-generation sequencing (NGS) has been explored as an alternative to standard culture in orthopedic infections. NGS is highly sensitive and can detect an entire bacterial genome along with genes conferring antibiotic resistance in a given sample. We investigated the potential use of NGS for accurate identification and quantification of microbes in infected diabetic foot ulcer (DFU). We hypothesize that NGS will aid identification of dominant pathogen and provide a more complete profile of microorganisms in infected DFUs compared to the standard culture method. METHODS: Data were prospectively collected from 30 infected DFU patients who underwent operative treatment by a fellowship-trained orthopedic foot and ankle surgeon from October 2018 to September 2019. The average age of the patient was 60.4 years. Operative procedures performed were irrigation and debridement (12), toe or ray amputation (13), calcanectomies (4), and below-the-knee amputation (1). Infected bone specimens were obtained intraoperatively and processed for standard culture and NGS. Concordance between the standard culture and NGS was assessed. RESULTS: In 29 of 30 patients, pathogens were identified by both NGS and culture, with a concordance rate of 70%. In standard culture, Staphylococcus aureus (58.6%) was the most common pathogen, followed by coagulase-negative Staphylococcus (24.1%), Corynebacterium striatum (17.2%), and Enterococcus faecalis (17.2%). In NGS, Finegoldia magna (44.8%) was the most common microorganism followed by S. aureus (41.4%), and Anaerococcus vaginalis (24.1%). On average, NGS revealed 5.1 (range, 1-11) pathogens in a given sample, whereas culture revealed 2.6 (range, 1-6) pathogens. CONCLUSION: NGS is an emerging molecular diagnostic method of microbial identification in orthopedic infection. It frequently provides different profiles of microorganisms along with antibiotic-resistant gene information compared to conventional culture in polymicrobial foot infection. Clinical use of NGS for management of foot and ankle infections warrants further investigation. LEVEL OF EVIDENCE: Level II, diagnostic study.