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.

Diagnostic Accuracy of Dermatoscopy Versus Microbiological Culture and Polymerase Chain Reaction in the Diagnosis of Onychomycosis: A Cross-Sectional Study.

BACKGROUND: Several clinical signs in dermatoscopy are very characteristic of onychomycosis and can be a quick complement for the diagnosis of onychomycosis. OBJECTIVES: The aim of this study was to evaluate the diagnostic accuracy of dermatoscopy compared to microbiological culture and polymerase chain reaction (PCR), as well as the clinical signs associated with onychomycosis. METHODS: The clinical signs of 125 patients were assessed cross-sectionally using dermatoscopy, and a positive or negative result was assigned. A sample was then taken for PCR and microbiological culture. RESULTS: Of the 125 patients, 69.6% (87/125) had positive results when both laboratory tests were combined. When they were not combined, the prevalence was lower at 48% (60/125) with PCR and at 43.2% (54/125) with culture. Furthermore, 76.8% (96/125) were classified as positive with dermatoscopy with a sensitivity of 1, a specificity of 0.76, positive predictive value of 0.91 and negative predictive value of 1 (with 95% confidence intervals). Of the 96 dermatoscopy-positive samples, 36 were negative with PCR (p < 0.001), 42 were negative with culture (p < 0.001) and nine were negative when both tests were combined (p < 0.001). Clinical signs that were significantly associated with the presence of onychomycosis were subungual hyperkeratosis (dermatoscopy: p = 0.004, odds ratio (OR) = 2.438; PCR + microbiological culture: p = 0.004, OR = 3.221), subungual detritus (p = 0.033, OR = 3.01, only with dermatoscopy) and dermatophytoma (dermatoscopy: p = 0.049, OR = 3.02; PCR + microbiological culture: p = 0.022, OR = 2.40). CONCLUSIONS: The results suggest that dermatoscopy is a good tool for the diagnosis of onychomycosis but should be used as a complementary test or for screening patients to be sampled for laboratory testing. The combination of the three tests can lead to a reduction of false-positive and false-negative clinical and laboratory results. This allows for early diagnosis and specific treatment based on test results.

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.

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.

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.

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.

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.

Biofilm on the tracheoesophageal voice prosthesis: considerations for oral decontamination.

The tracheoesophageal puncture (TEP) restores verbal communication after total laryngectomy using a one-way valved voice prosthesis (VP). Microbial colonization can shorten VP device life. Our aims were to investigate patterns of prosthetic and oral colonization, and record changes in VP device life after targeted decontamination. We conducted a retrospective review of TEP clinic patients who underwent microbial analysis of the VP between 01/2003 and 07/2013. Two subgroups were analyzed: (1) patients with microbial analysis of the VP and the mouth were analyzed to identify patterns of common contamination, and (2) patients who were prescribed targeted oral decontamination on the basis of the microbial analysis of the VP were analyzed to evaluate effects on device life. Among 42 patients, 3 patients had only fungal, 5 only bacterial, and 33 had polyspecies fungal and bacterial colonization. In the TEP-oral microflora subgroup (n = 15), 7 had common microorganisms in the mouth and on the VP. Among the decontamination subgroup (n = 23), 6 patients received broad spectrum rinse, 16 antifungal agents and 13 antibiotics, or a combination thereof. After targeted decontamination, the median device life of prostheses improved from 7.89 to 10.82 weeks (p = 0.260). The majority of patients with a suboptimal VP device life in this pilot had polyspecies bacterial and fungal colonization. VPs rarely had fungal contamination alone (3 %), and non-albicans fungal species were more common than expected. For these reasons, we are exploring the use of targeted decontamination regimens that were associated with 1.4-fold improvement in VP duration.

Case Series Study of Invasive Pulmonary Aspergillosis.

Diagnosis of invasive pulmonary aspergillosis (IPA) is challenging. The objective of the study was to assess the value of microbiological tests to the diagnosis of IPA in the absence of non-specific radiological data. A retrospective study of 23 patients with suspicion of IPA and positivity of some microbiological diagnostic tests was performed. These tests included conventional microbiological culture, detection of Aspergillus galactomannan (GM) antigen and in some patients (1 â†’ 3)-ß-D-glucan (BDG) and Aspergillus fumigatus DNA using the LightCycler® SeptiFast test. In 10 patients with hematological malignancy, 6 cases were considered 'probable' and 4 'non-classifiable.' In 8 patients with chronic lung disease, 7 cases were classified as 'probable' and 1 as 'proven,' and in 5 patients with prolonged ICU stay (>7 days), there were 2 'proven' cases, 2 'non-classifiable' and 1 putative case. Microbiological culture was positive in 17 cases and 18 Aspergillus spp. were isolated (one mixed culture). A. fumigatus was the most frequent (44.4%) followed by A. tubingensis. The Aspergillus galactomannan (GM) antigen assay was positive in 21 cases (91.3%). The GM antigen and the (1 â†’ 3)-ß-D-glucan (BDG) assays were both performed in 12 cases (52.2%), being positive in 9. The SeptiFast test was performed in 7 patients, being positive in 4. In patients with non-classifiable pulmonary aspergillosis and one or more positive microbiological tests, radiological criteria may not be considered a limiting factor for the diagnosis of IPA.

Haematological malignancy in the intensive care unit: microbiology results and mortality.

BACKGROUND: Mortality prediction models of patients with a haematological malignancy admitted to an intensive care unit (ICU) do not include the presence of neutropenia and microbiology results. We performed a registry-based retrospective study of haematology patients admitted to the ICU to investigate the relation between neutropenia, microbiology results and outcome of these patients. METHODS: Neutropenia and microbiology culture results within 24 h before or after ICU admission of patients with a haematological malignancy admitted between 2004 and 2010 were described and analysed for association with 28-day mortality. RESULTS: We identified 234 individual patients with a current malignant haematological condition, of which 27% were neutropenic and 21% had a positive blood culture at admission. Most prevalent from blood cultured species were Escherichia coli and coagulase-negative staphylococci. The overall 28-day mortality was 38%. In patients with a positive blood culture but no neutropenia, 28-day mortality was 28% and in patients with neutropenia but without positive blood culture, it was 36%. The 28-day mortality of patients with both neutropenia and a positive blood culture was 55% with an adjusted (for APACHE-II score) hazard ratio (HR) of 1.8 (95%CI 1.0-3.4) compared to other hematologic patients admitted to the ICU. CONCLUSION: In patients with haematological malignancy admitted to the ICU, culture results are diverse. The combination of neutropenia and positive blood culture is associated with increased 28-day mortality. We suggest this could be of additional value when assessing mortality risk in this patient group.

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.

Report on the diagnosis and treatment of 3 cases of emphysematous pyelonephritis with two different outcomes.

Background: Emphysematous pyelonephritis (EPN) is a rare acute severe necrotising infection of the kidneys in clinical practice. It is characterized by the presence of gas in the renal parenchyma, collecting system, or perirenal tissue. The prognosis is poor, with a high nephrectomy rate and a mortality rate of up to 20-40%. Methods: Retrospective analysis of 3 cases of emphysematous pyelonephritis with two different outcomes. Results: Three patients who we described were all female with diabetes mellitus, and their blood sugar was poorly controlled. One patient with the advanced age and poor general health died due to the patient's family choosing to terminate therapy. Two patients underwent surgical procedures achieved an excellent clinical recovery. Both of them underwent percutaneous nephrostomy and perinephric abscess puncture drainage before nephrectomy. Escherichia coli were the microorganisms implicated. Conclusion: EPN is a rare and severe urinary system infection. Computed tomography (CT) and microbiological culture confirmed the diagnosis. Control of diabetes, sensitive antibiotic therapy, fluid resuscitation and prompt surgical intervention are crucial.

Detection value of third-generation sequencing to identify the pathogenic organisms in prosthetic joint infection.

To compare the detection value of third-generation sequencing (TGS) with pathogenic microbial culture in prosthetic joint infection (PJI). Arthrocentesis was performed on 29 patients who underwent hip and knee revision surgeries. In the PJI group, TGS detected 85.71 % of positive cases, while pathogenic microbial culture detected only 42.85 %. TGS identified 17 different pathogenic microorganisms, including Staphylococcus epidermidis, Staphylococcus aureus, Streptococcus lactis, and Mycobacterium tuberculosis complex. In the loosening group, TGS was positive in one patient, while microbial culture was negative in all cases. TGS showed higher sensitivity (85.71 % vs. 42.85 %), comparable specificity (93.33 % vs. 100 %), and similar positive predictive value (92.31 % vs. 100 %) compared to culture.However, TGS had a higher negative predictive value (87.5 % vs. 65.22 %).Additionally, TGS provided faster results (mean time 23.8±3.6 h) compared to microbial culture (mean time 108.0±9.4 h).These findings suggest that TGS holds promise for detecting pathogenic microorganisms in PJI and has potential for clinical application.

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.

Usability application of multiplex polymerase chain reaction in the diagnosis of microorganisms isolated from urine of patients treated in cancer hospital.

BACKGROUND: THE OBJECTIVE OF THIS STUDY WAS: i) to compare the results of urine culture with polymerase chain reaction (PCR) -based detection of microorganisms using two commercially available kits, ii) to assess antimicrobial susceptibility of urine isolates from cancer patients to chosen antimicrobial drugs and, if necessary, to update the recommendation of empirical therapy. MATERIALS AND METHODS: A one-year hospital-based prospective study has been conducted in Greater Poland Cancer Centre and Genetic Medicine Laboratory CBDNA Research Centre in 2011. Urine cultures and urine PCR assay from 72 patients were examined. RESULTS: Urine cultures and urine PCR assay from 72 patients were examined. Urine samples were positive for 128 strains from which 95 (74%) were identical in both tests. The most frequently isolated bacteria in both culture and PCR assay were coliform organisms and Enterococcus spp. The Gram negative bacilli were most resistant to cotrimoxazol. 77.2% of these bacilli and 100% of E. faecalis and S. agalactiae were sensitive to amoxicillin-clavulanic acid. 4.7% of Gram positive cocci were resistant to nitrofurantoin. CONCLUSIONS: The PCR method quickly finds the causative agent of urinary tract infection (UTI) and, therefore, it can help with making the choice of the proper antimicrobial therapy at an early stage. It appears to be a viable alternative to the recommendations made in general treatment guidelines, in cases where diversified sensitivity patterns of microorganisms have been found.

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.

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.

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.