Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens. - Related Documents




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147601.0000Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens. OBJECTIVES: The performance of the investigational-use-only version of the BioFire FilmArray Pneumonia Panel (FA-Pneumo), a high-order nested multiplex PCR, was evaluated for the detection of typical respiratory bacterial pathogens and antibiotic resistance genes in sputa and endotracheal aspirate (ETA) specimens. METHODS: Thirty-one sputa and 69 ETA specimens were analyzed. The diagnostic performance of FA-Pneumo was assessed using routine microbiological methods as the reference standard. RESULTS: Overall sensitivity and specificity for organism detection using FA-Pneumo were 98.5% and 76.5%, respectively. The sensitivity for each pathogen was 100%, except for Klebsiella aerogenes, and the range of specificity was 83.3-99.0%. FA-Pneumo detected antimicrobial resistance genes in 17 out of 18 specimens (94.4%) that were resistant by antimicrobial susceptibility testing. FA-Pneumo additionally detected 25 resistance genes in 22 specimens, and sequencing for the presence of resistance genes confirmed the majority of these results (20/25, 80%). Semi-quantitative analysis of bacterial nucleic acid amounts by FA-Pneumo revealed that 88.2% of the identified bacteria (67/76) with ≥10(6) copies/ml also gave culture-positive results with significant amounts of bacteria. CONCLUSIONS: FA-Pneumo is a rapid test with high sensitivity for the detection of bacteria and antimicrobial resistance genes in sputum and ETA specimens and could aid in determining antibiotic therapy.202032179139
147910.9997BioFire FilmArray BCID2 versus VITEK-2 System in Determining Microbial Etiology and Antibiotic-Resistant Genes of Pathogens Recovered from Central Line-Associated Bloodstream Infections. Central line-associated bloodstream infection (CLABSI) is among the most serious hospital acquired infections. Therefore, the rapid detection of the causative microorganism is of crucial importance to allow for the appropriate antimicrobial therapy. In the present study, we analyzed the clinical performance of the BioFire FilmArray Blood Culture Identification 2 (BCID2) panel in the identification of 33 microbial species and 10 antibiotic resistance genes in comparison to the VITEK-2 system. A total of 104 blood specimens were included. The FilmArray BCID2 results were concordant with the VITEK-2 system in 69/97 specimens (71.1%). Non-concordance was either due to the detection of more pathogens by the FilmArray BCID2 23/28 (82%) or microbial species were misidentified 5/28 (18%). Hence, in comparison to the VITEK-2 system, the FilmArray BCID2 panel showed an overall sensitivity of 75.8% (95% CI, 66-83%) and an overall specificity of 98% (95% CI, 97-98.8%) in detecting microbial species. For the resistance genes, the FilmArray BCID was able to detect the presence of blaCTX-M gene in 23 Gram-negative isolates, blaNDM and blaOXA-48- like genes in 14 and 13 isolates, respectively. The mecA and mecC genes were found in 23 Staphylococcus species, while mecA, mecC and MREJ genes were found in 4 Staphylococcus aureus isolates. The sensitivity and specificity for detecting resistance genes by the FilmArray BCID2 was 90% (95% CI, 81.4-95%) and 99.6% (95% CI, 99-100%), respectively. As concluded, the present study emphasizes the high sensitivity and specificity of the FilmArray BCID2 in the rapid and reliable detection of different bacteria and fungi from positive blood culture bottles, as well as the accurate detection of various antibiotic resistance markers.202236358274
149020.9996Rapid detection of Gram-negative bacteria and their drug resistance genes from positive blood cultures using an automated microarray assay. We evaluated the performance of the Verigene Gram-negative blood culture (BC-GN) assay (CE-IVD version) for identification of Gram-negative (GN) bacteria and detection of resistance genes. A total of 163 GN organisms (72 characterized strains and 91 clinical isolates from 86 patients) were tested; among the clinical isolates, 86 (94.5%) isolates were included in the BC-GN panel. For identification, the agreement was 98.6% (146/148, 95% confidence interval [CI], 92.1-100) and 70% (7/10, 95% CI, 53.5-100) for monomicrobial and polymicrobial cultures, respectively. Of the 48 resistance genes harbored by 43 characterized strains, all were correctly detected. Of the 19 clinical isolates harboring resistance genes, 1 CTX-M-producing Escherichia coli isolated in polymicrobial culture was not detected. Overall, BC-GN assay provides acceptable accuracy for rapid identification of Gram-negative bacteria and detection of resistance genes, compared with routine laboratory methods despite that it has limitations in the number of genus/species and resistance gene included in the panel and it shows lower sensitivity in polymicrobial cultures.201525591999
147830.9996Multicenter Evaluation of the FilmArray Blood Culture Identification 2 Panel for Pathogen Detection in Bloodstream Infections. The FilmArray Blood Culture Identification 2 panel (BCID2; bioMérieux) is a fully automated PCR-based assay for identifying bacteria, fungi, and bacterial resistance markers in positive blood cultures (BC) in about 1 h. In this multicenter study, we evaluated the performance of the BCID2 panel for pathogen detection in positive BC. Conventional culture and BCID2 were performed in parallel at four tertiary-care hospitals. We included 152 positive BC-130 monomicrobial and 22 polymicrobial cultures-in this analysis. The BCID2 assay correctly identified 90% (88/98) of Gram-negative and 89% (70/79) of Gram-positive bacteria. Five bacterial isolates targeted by the BCID2 panel and recovered from five positive BC, including three polymicrobial cultures, were missed by the BCID2 assay. Fifteen isolates were off-panel organisms, accounting for 8% (15/182) of the isolates obtained from BC. The mean positive percent agreement between the BCID2 assay and standard culture was 97% (95% confidence interval, 95 to 99%), with agreement ranging from 67% for Candida albicans to 100% for 17 targets included in the BCID2 panel. BCID2 also identified the bla(CTX-M) gene in seven BC, including one for which no extended-spectrum β-lactamase (ESBL)-producing isolate was obtained in culture. However, it failed to detect ESBL-encoding genes in three BC. Two of the 18 mecA/C genes detected by the BCID2 were not confirmed. No carbapenemase, mecA/C, or MREJ targets were detected. The median turnaround time was significantly shorter for BCID2 than for culture. The BCID2 panel may facilitate faster pathogen identification in bloodstream infections. IMPORTANCE Rapid molecular diagnosis combining the identification of pathogens and the detection of antibiotic resistance genes from positive blood cultures (BC) can improve the outcome for patients with bloodstream infections. The FilmArray BCID2 panel, an updated version of the original BCID, can detect 11 Gram-positive bacteria, 15 Gram-negative bacteria, 7 fungal pathogens, and 10 antimicrobial resistance genes directly from a positive BC. Here, we evaluated the real-life microbiological performance of the BCID2 assay in comparison to the results of standard methods used in routine practice at four tertiary care hospitals.202336519852
222040.9996Rapid detection and molecular survey of blaVIM, blaIMP and blaNDM genes among clinical isolates of Acinetobacter baumannii using new multiplex real-time PCR and melting curve analysis. BACKGROUND: Acinetobacter baumannii is a cosmopolitan bacterium that is frequently reported from hospitalized patients, especially those patients who admitted in the intensive care unit. Recently, multiplex real-time PCR has been introduced for rapid detection of the resistance genes in clinical isolates of bacteria. The current study aimed to develop and evaluate multiplex real-time PCR to detect common resistance genes among clinical isolates of A. baumannii. RESULTS: Multiplex real-time PCR based on melting curve analysis showed different T(m) corresponding to the amplified fragment consisted of 83.5 °C, 93.3 °C and 89.3 °C for blaIMP, blaVIM and blaNDM, respectively. Results of multiplex real-time PCR showed that the prevalence of blaIMP, blaVIM and blaNDM among the clinical isolates of A. baumannii were 5/128(3.9%), 9/128(7.03%) and 0/128(0%), respectively. Multiplex real-time PCR was able to simultaneously identify the resistance genes, while showed 100% concordance with the results of conventional PCR. CONCLUSIONS: The current study showed that blaVIM, was the most prevalent MBL gene among the clinical isolates of A. baumannii while no amplification of blaNDM was seen. Multiplex real-time PCR can be sensitive and reliable technique for rapid detection of resistance genes in clinical isolates.201931182026
148750.9995Potential impact of a microarray-based nucleic acid assay for rapid detection of Gram-negative bacteria and resistance markers in positive blood cultures. We evaluated the Verigene Gram-negative blood culture (BC-GN) test, a microarray that detects Gram-negative bacteria and several resistance genes. A total of 102 positive blood cultures were tested, and the BC-GN test correctly identified 97.9% of the isolates within its panel. Resistance genes (CTX-M, KPC, VIM, and OXA genes) were detected in 29.8% of the isolates, with positive predictive values of 95.8% (95% confidence interval [CI], 87.7% to 98.9%) in Enterobacteriaceae and 100% (95% CI, 75.9% to 100%) in Pseudomonas aeruginosa and negative predictive values of 100% (95% CI, 93.9% to 100%) and 78.6% (95% CI, 51.0% to 93.6%), respectively.201424478405
148860.9995Evaluation of an automated rapid diagnostic assay for detection of Gram-negative bacteria and their drug-resistance genes in positive blood cultures. We evaluated the performance of the Verigene Gram-Negative Blood Culture Nucleic Acid Test (BC-GN; Nanosphere, Northbrook, IL, USA), an automated multiplex assay for rapid identification of positive blood cultures caused by 9 Gram-negative bacteria (GNB) and for detection of 9 genes associated with β-lactam resistance. The BC-GN assay can be performed directly from positive blood cultures with 5 minutes of hands-on and 2 hours of run time per sample. A total of 397 GNB positive blood cultures were analyzed using the BC-GN assay. Of the 397 samples, 295 were simulated samples prepared by inoculating GNB into blood culture bottles, and the remaining were clinical samples from 102 patients with positive blood cultures. Aliquots of the positive blood cultures were tested by the BC-GN assay. The results of bacterial identification between the BC-GN assay and standard laboratory methods were as follows: Acinetobacter spp. (39 isolates for the BC-GN assay/39 for the standard methods), Citrobacter spp. (7/7), Escherichia coli (87/87), Klebsiella oxytoca (13/13), and Proteus spp. (11/11); Enterobacter spp. (29/30); Klebsiella pneumoniae (62/72); Pseudomonas aeruginosa (124/125); and Serratia marcescens (18/21); respectively. From the 102 clinical samples, 104 bacterial species were identified with the BC-GN assay, whereas 110 were identified with the standard methods. The BC-GN assay also detected all β-lactam resistance genes tested (233 genes), including 54 bla(CTX-M), 119 bla(IMP), 8 bla(KPC), 16 bla(NDM), 24 bla(OXA-23), 1 bla(OXA-24/40), 1 bla(OXA-48), 4 bla(OXA-58), and 6 blaVIM. The data shows that the BC-GN assay provides rapid detection of GNB and β-lactam resistance genes in positive blood cultures and has the potential to contributing to optimal patient management by earlier detection of major antimicrobial resistance genes.201424705449
148670.9995Multicenter evaluation of the Verigene Gram-negative blood culture nucleic acid test for rapid detection of bacteria and resistance determinants in positive blood cultures. The Verigene Gram-Negative Blood Culture Nucleic Acid Test (BC-GN) is a microarray-based assay that enables rapid detection of 9 common Gram-negative bacteria and 6 resistance determinants directly from positive blood cultures. We compared the performance of BC-GN with currently used automated systems, testing 141 clinical blood cultures and 205 spiked blood cultures. For identification of BC-GN target organisms in clinical and spiked blood cultures, the BC-GN assay showed 98.5% (130/132) and 98.9% (182/184) concordance, respectively. Of 140 resistance genes positively detected in clinical and spiked blood cultures with the BC-GN test, 139 (99.3%) were confirmed by PCR, and the detection results were consistent with the resistance phenotypes observed. The BC-GN assay, thus, can potentially improve care for sepsis patients by enabling timely detection and targeted antimicrobial therapy.201526361710
223480.9995Clinical relevance of molecular identification of microorganisms and detection of antimicrobial resistance genes in bloodstream infections of paediatric cancer patients. BACKGROUND: Bloodstream infections (BSIs) are the major cause of mortality in cancer patients. Molecular techniques are used for rapid diagnosis of BSI, allowing early therapy and improving survival. We aimed to establish whether real-time quantitative polymerase chain reaction (qPCR) could improve early diagnosis and therapy in paediatric cancer patients, and describe the predominant pathogens of BSI and their antimicrobial susceptibility. METHODS: Blood samples were processed by the BACTEC system and microbial identification and susceptibility tests were performed by the Phoenix system. All samples were screened by multiplex 16 s rDNA qPCR. Seventeen species were evaluated using sex-specific TaqMan probes and resistance genes blaSHV, blaTEM, blaCTX, blaKPC, blaIMP, blaSPM, blaVIM, vanA, vanB and mecA were screened by SYBR Green reactions. Therapeutic efficacy was evaluated at the time of positive blood culture and at final phenotypic identification and antimicrobial susceptibility results. RESULTS: We analyzed 69 episodes of BSI from 64 patients. Gram-positive bacteria were identified in 61 % of the samples, Gram-negative bacteria in 32 % and fungi in 7 %. There was 78.2 % of agreement between the phenotypic and molecular methods in final species identification. The mecA gene was detected in 81.4 % of Staphylococcus spp., and 91.6 % were concordant with the phenotypic method. Detection of vanA gene was 100 % concordant. The concordance for Gram-negative susceptibilities was 71.4 % for Enterobacteriaceae and 50 % for Pseudomonas aeruginosa. Therapy was more frequently inadequate in patients who died, and the molecular test was concordant with the phenotypic susceptibility test in 50 %. CONCLUSIONS: qPCR has potential indication for early identification of pathogens and antimicrobial resistance genes from BSI in paediatric cancer patients and may improve antimicrobial therapy.201627585633
147790.9994Multicenter Evaluation of the BIOFIRE Blood Culture Identification 2 Panel for Detection of Bacteria, Yeasts, and Antimicrobial Resistance Genes in Positive Blood Culture Samples. Diagnostic tools that can rapidly identify and characterize microbes growing in blood cultures are important components of clinical microbiology practice because they help to provide timely information that can be used to optimize patient management. This publication describes the bioMérieux BIOFIRE Blood Culture Identification 2 (BCID2) Panel clinical study that was submitted to the U.S. Food & Drug Administration. Results obtained with the BIOFIRE BCID2 Panel were compared to standard-of-care (SoC) results, sequencing results, PCR results, and reference laboratory antimicrobial susceptibility testing results to evaluate the accuracy of its performance. Results for 1,093 retrospectively and prospectively collected positive blood culture samples were initially enrolled, and 1,074 samples met the study criteria and were included in the final analyses. The BIOFIRE BCID2 Panel demonstrated an overall sensitivity of 98.9% (1,712/1,731) and an overall specificity of 99.6% (33,592/33,711) for Gram-positive bacteria, Gram-negative bacteria and yeast targets which the panel is designed to detect. One hundred eighteen off-panel organisms, which the BIOFIRE BCID2 Panel is not designed to detect, were identified by SoC in 10.6% (114/1,074) of samples. The BIOFIRE BCID2 Panel also demonstrated an overall positive percent agreement (PPA) of 97.9% (325/332) and an overall negative percent agreement (NPA) of 99.9% (2,465/2,767) for antimicrobial resistance determinants which the panel is designed to detect. The presence or absence of resistance markers in Enterobacterales correlated closely with phenotypic susceptibility and resistance. We conclude that the BIOFIRE BCID2 Panel produced accurate results in this clinical trial.202337227281
2210100.9994Beyond Culture: Real-Time PCR Performance in Detecting Causative Pathogens and Key Antibiotic Resistance Genes in Hospital-Acquired Pneumonia. Introduction: The rise in hospital-acquired pneumonia (HAP) due to antibiotic-resistant bacteria is increasing morbidity, mortality, and inappropriate empirical antibiotic use. This prospective research aimed to evaluate the performance of a real-time polymerase chain reaction (PCR) assay for detecting causative microorganisms and antibiotic-resistance genes from respiratory specimens compared to traditional methods. Additionally, we aimed to determine the molecular epidemiology of antibiotic resistance genes among HAP patients at The University of Jordan hospital. Methods: Lower respiratory tract samples were collected from HAP patients, including those with ventilator-associated pneumonia (VAP), between May 2024 and October 2024. Clinical data from the medical files were used to collect and analyze demographic and clinical information, including clinical outcomes. Real-time PCR was run to detect causative microbes and antibiotic resistance genes. Results: Among 83 HAP patients (median age 63, 61.45% male), 48.15% died. Culture identified Klebsiella (25.53%), Acinetobacter (22.34%), and Candida (24.47%) as the most common pathogens, while qPCR showed higher detection rates, including for A. baumannii (62.20%, p = 0.02) and K. pneumoniae (45.12%, p < 0.001). Carbapenem resistance was high; A. baumannii showed 100% resistance to most antibiotics except colistin (92.31%). The resistance genes ndm (60%) and oxa-48 (58.46%) were frequently detected and significantly associated with phenotypic resistance (p < 0.001). The qPCR identified resistance genes in all carbapenem-resistant cases. No gene significantly predicted mortality. Conclusions: Real-time PCR diagnostic technique combined with epidemiology of antibiotic resistance genes data may be a rapid and effective tool to improve HAP management. Large, multicenter studies are needed in the future to validate the performance of real-time PCR in HAP diagnosis, and appropriate management is also required.202541009915
1484110.9994Use of a commercial PCR-based line blot method for identification of bacterial pathogens and the mecA and van genes from BacTAlert blood culture bottles. In this study, the PCR-based DNA strip assay GenoType BC for the identification of bacteria and the resistance genes mecA, vanA, vanB, vanC1, and vanC2/3 directly from positive BacTAlert blood culture bottles was evaluated in a multicenter study. Of a total of 511 positive blood cultures, correct identification percentages for Gram-negative bacteria, Gram-positive bacteria, and the mecA gene were 96.1%, 89.9%, and 92.9%, respectively. Results were available 4 h after growth detection.201222075585
2477120.9994Evaluation of targeted next-generation sequencing for microbiological diagnosis of acute lower respiratory infection. PURPOSE: To evaluate the performance of targeted next-generation sequencing (tNGS) in pathogen detection in acute lower respiratory infection. METHODS: The retrospective study was conducted between July 2023 and May 2024 at the Yantai Yuhuangding Hospital. Patients with acute lower respiratory infections were included. Qualified sputum or bronchoalveolar lavage fluid samples were collected for tNGS and conventional microbiological tests(CMTs), including culture, staining, polymerase chain reaction (PCR), and reverse transcription-PCR (RT-PCR). The time required and cost were counted. RESULTS: A total of 968 patients were enrolled. Study analysis discovered 1,019 strains of bacteria, 259 strains of fungi, 302 strains of viruses, 76 strains of Mycoplasma pneumoniae, and two strains of Chlamydia psittaci using tNGS. In addition, tNGS also identified 39 mecA, four KPC, 19 NDM, and two OXA-48 genes. The positive rates for bacteria, fungi, viruses, mycoplasma, and chlamydia obtained using tNGS were significantly higher than those determined using traditional methods. Among them, tNGS showed high consistence with mycobacterium DNA test, influenza A (H1N1) virus nucleic acid test and COVID-19 nucleic acid test. Poor consistency between drug resistance genes and bacterial resistance phenotypes was found. In addition, tNGS also had advantages over traditional methods in terms of detection time and cost. CONCLUSION: Compared to traditional methods, tNGS had higher sensitivity in detecting bacteria, fungi, viruses, and other pathogens in acute lower respiratory infection, and also had the advantages of timeliness and cost-effectiveness, making it a promising method for guiding clinical diagnosis.202540901079
2172130.9994Detection of blaPER-1 & blaOxa10 among imipenem resistant isolates of Pseudomonas aeruginosa isolated from burn patients hospitalized in Shiraz Burn Hospital. BACKGROUND AND OBJECTIVES: Pseudomonas aeruginosa is one of the most important Gram negative opportunistic bacteria which causes infection among burn patients. Resistance to the antibiotics in this group of bacteria is increased due to the activity of extended spectrum β-lactamase (ESBLs) genes. In the current study, we investigated the prevalence of two genes (blaPER-1 & blaOxa10 ) related β-lactamase genes among imipenem resistance clinical isolates of P. aeruginosa in hospitalized patients. MATERIALS AND METHODS: From May 2010 to March 2011, 270 P. aeruginosa isolated from hospitalized burned patients' wounds in Shiraz Burn Hospital, were tested for Imipenem resistance by disk diffusion method. Presence of ESBLs exo-enzyme, blaPER-1 and blaOxa10 genes were also evaluated in the resistant isolate. RESULTS: 210 (77.7%) of 270 P. aeruginosa isolates were resistant to imipenem. blaPER-1 and blaOxa10 were detected among 168 (80.0%) of imipenem resistant isolates. Furthermore, 160 (76.2%) of them had blaOxa10 gene and 84 (40.0%) of them had blaPER-1 while 63 (30.0%) resistant isolates contained both genes simultaneously. CONCLUSION: This study showed a high prevalence of blaPER-1 and blaOxa10 genes in hospitalized burn patients in south west of Iran. Therefore, it's highly recommended to perform such tests routinely to evaluate the resistance pattern in order to better antibiotic selection in the burned patients.201526644867
2200140.9994Bloodstream infections and antibiotic resistance at a regional hospital, Colombia, 2019-2021. OBJECTIVES: To assess antibiotic susceptibility of World Health Organization (WHO) priority bacteria (Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Salmonella spp., Staphylococcus aureus, and Streptococcus pneumoniae) in blood cultures at the Orinoquía regional hospital in Colombia. METHODS: This was cross-sectional study using routine laboratory data for the period 2019-2021. Data on blood samples from patients suspected of a bloodstream infection were examined. We determined: the total number of blood cultures done and the proportion with culture yield; the characteristics of patients with priority bacteria; and the type of bacteria isolated and antibiotic resistance patterns. RESULTS: Of 25 469 blood cultures done, 1628 (6%) yielded bacteria; 774 (48%) of these bacteria were WHO priority pathogens. Most of the priority bacteria isolated (558; 72%) were gram-negative and 216 (28%) were gram-positive organisms. Most patients with priority bacteria (666; 86%) were hospitalized in wards other than the intensive care unit, 427 (55%) were male, and 321 (42%) were ≥ 60 years of age. Of the 216 gram-positive bacteria isolated, 205 (95%) were Staphylococcus aureus. Of the 558 gram-negative priority bacteria isolated, the three most common were Escherichia coli (34%), Klebsiella pneumoniae (28%), and Acinetobacter baumannii (20%). The highest resistance of Staphylococcus aureus was to oxacillin (41%). For gram-negative bacteria, resistance to antibiotics ranged from 4% (amikacin) to 72% (ampicillin). CONCLUSIONS: Bacterial yield from blood cultures was low and could be improved. WHO priority bacteria were found in all hospital wards. This calls for rigorous infection prevention and control standards and continued surveillance of antibiotic resistance.202337082533
2347150.9994Multiple drug resistance of Listeria monocytogenes isolated from aborted women by using serological and molecular techniques in Diwaniyah city/Iraq. BACKGROUND AND OBJECTIVES: The study was sought to detect the effect of Listeria monocytogenes on pregnant Iraqi women at Al-Diwaniya hospitals and determination of virulence genes and antimicrobial susceptibility of isolates. MATERIALS AND METHODS: 360 specimens including blood, urine, vaginal and endocervical were collected from 90 patients with spontaneous abortions. Blood samples were displayed to immunological study and remaining specimens were subjected to bacteriological diagnosis. PCR was used to determine the virulence factors and antimicrobial resistance genes. RESULTS: Fifteen positive samples (16.6%) of patients and thirteen isolates (14.5%) from patients were recognized based on ELISA and PCR assay respectively. The general isolation of L. monocytogenes strains in cases of abortive women was 13/270 (4.8%). L. monocytogenes strains were highly virulent because of presence of virulence factors associated genes, namely actA, hlyA, plcA and prfA in all strains. Multiple drug resistance (MAR) index values of 15.4% of isolates were >0.2. CONCLUSION: It is necessary for conducting susceptibility testing and to select the suitable antibiotics and avoid the effects of these bacteria in pregnant women.202032994901
1491160.9994Evaluation of an expanded antibiotic resistance gene panel on prediction of antimicrobial susceptibility results for Gram-negative bacteria in blood cultures. The QIAstat-Dx BCID Panels (RUO) ("QIAstat," QIAGEN, Hilden, Germany) for identification of 13 Gram-negative bacteria and 18 antimicrobial resistance (AMR) gene groups was evaluated. The study was conducted in two phases; in phase 1, analytical performance was evaluated against 154 challenge isolates against whole genome sequencing data. In this phase, sensitivity and specificity of organism identification calls were 153/154 (99.3%) and 1,748/1,749 (99.8%), respectively. For AMR genes, sensitivity was 434/435 (99.8%) and specificity was 2,334/2,337 (99.9%). One false-negative bla(IMP), one false-positive bla(CTX-M), and two false-positive aac-6'-lb detections were noted in this challenge set of organisms. In phase 2, 101 clinical blood culture isolates of Gram-negative rods were evaluated by the multiplexed PCR versus reference broth microdilution, for the ability of identification combined with AMR genes to predict final susceptibility results. Negative predictive values were 92.8% for ampicillin resistance (100% for Escherichia coli), 93.4% for ceftriaxone, 97.4% for ceftazidime, and 98.7% for cefepime. In constrast, negative predictive values for current standard of care (identification plus detection of bla(CTX-M)) ranged from 56.5% to 88.8%. This study demonstrated additive value of additional beta-lactamase genes for bacteria isolated from blood cultures. IMPORTANCE: Prediction of Gram-negative bacteria resistance through detection of resistance genes is complex. This study evaluated a novel, direct-from-blood or bacterial isolate multiplexed PCR for the detection of 17 resistance genes, and evaluated the prediction of antimicrobial susceptibility.202439297627
2191170.9994Microbial profile, antimicrobial resistance, and molecular characterization of diabetic foot infections in a university hospital. INTRODUCTION: Diabetic foot infections (DFIs) are among the most severe complications of diabetes. The aim of this study was to determine the etiological pathogens of DFIs in different Wagner's and IDSA/IWGDF grades, and to assess their antimicrobial susceptibility pattern together with molecular characterization of antibiotic resistance genes. METHODS: A prospective study was conducted on 120 DFI patients at Main Alexandria University Hospital, Egypt. The aerobic and anaerobic etiological pathogens were determined using semi-quantitative culture and PCR respectively. The antimicrobial susceptibility pattern was done according to Clinical Laboratory Standards Institute guidelines. Detection of carbapenemases and class-1 integron genes was carried out by polymerase chain reaction (PCR). RESULTS: A total of 178 (124 aerobic, 54 anaerobic) pathogens were identified from patients with DFI, with an average of 1.82 isolates/subject. Among aerobic pathogens, Gram-negative predominated (98/124; 79%), of which Pseudomonas spp. and Proteus spp. were the most common. MRSA constituted more than 50% of Gram-positive isolates. Polymicrobial infection was found in 42 (42.9%) subjects. The proportion of Gram-negative bacteria and anaerobes increased with increased DFI grades and severity. Multidrug and extensively drug resistant isolates were observed in 86 patients (87.7%). PCR identified carbapenemases genes in 14 (11.7%) and class 1 integron in 28 (23.3%) DFI cases. Vancomycin, teicoplanin, linezolid were the most effective antimicrobial agents against Gram-positive pathogens, while colistin, imipenem, meropenem, and piperacillin-tazobactam were effective against Gram-negative pathogens. CONCLUSIONS: Multidrug and extensively drug resistant Gram-negative bacteria were the dominant pathogens among all DFI severity grades. However, the proportion of Gram-positive bacteria decreased with the severity of infection. The clinical role of our relatively high rate of anaerobes should be investigated. The results found in this study could be beneficial for designing future empiric antimicrobial protocols in relation to the severity of DFIs.202133898340
2204180.9994Multidrug resistance pattern of bacterial agents isolated from patient with chronic sinusitis. BACKGROUND: Treatment of chronic sinusitis is complicated due to increase of antibiotic-resistant bacteria. The aim of this study was to determine the multidrug resistance (MDR) pattern of the bacteria causing chronic sinusitis in north of Iran. METHODS: This cross-sectional study was carried out on patients with chronic sinusitis. Bacterial susceptibility to antimicrobial agents was determined according to the CLSI 2013 standards. Double-disk synergy (DDS) test was performed for the detection of extended-spectrum beta-lactamase (ESBL) producing bacteria; also methicillin-resistant Staphylococcus (MRSA) strains were identified by MRSA screen agar. The MDR isolates were defined as resistant to 3 or more antibiotics. Data were analyzed using SPSS 17 software. Descriptive statistics was used to describe the features of the data in this study. RESULTS: The rate of ESBL-producing bacteria was 28.75-37.03% among enterobacteriaceae and the rate of MRSA was 42.75%-60% among Staphylococcus strains. The most detectable rate of the MDR bacterial isolates was Gram-negative bacteria 39 (76.47%) and Enterobacter spp. 19(70.37%) was the most multidrug resistant isolate among Gram negative bacteria. Also 36 (73.46%) of the gram positive bacterial isolated were multidrug resistance and Staphylococcus aureus 9(90%) was the most MDR among Gram positive bacteria. CONCLUSION: Antimicrobial resistance is increasing in chronic bacterial sinusitis. The emergence of MRSA and ESBL bacteria causing chronic sinusitis is increasing.201627386063
2175190.9993Drug-resistant genes carried by Acinetobacter baumanii isolated from patients with lower respiratory tract infection. BACKGROUND: Acinetobacter baumanii (A. baumanii ) remains an important microbial pathogen resulting in nosocomial acquired infections with significant morbidity and mortality. The mechanism by which nosocomial bacteria, like A. baumanii, attain multidrug resistance to antibiotics is of considerable interest. The aim in this study was to investigate the spread status of antibiotic resistance genes, such as multiple β-lactamase genes and aminoglycoside-modifying enzyme genes, from A. baumanii strains isolated from patients with lower respiratory tract infections (LRTIs). METHODS: Two thousand six hundred and ninety-eight sputum or the bronchoalveolar lavage samples from inpatients with LRTIs were collected in 21 hospitals in the mainland of China from November 2007 to February 2009. All samples were routinely inoculated. The isolated bacterial strains and their susceptibility were analyzed via VITEK-2 expert system. Several kinds of antibiotic resistant genes were further differentiated via polymerase chain reaction and sequencing methods. RESULTS: Totally, 39 A. baumanii strains were isolated from 2698 sputum or bronchoalveolar lavage samples. There was not only a high resistant rate of the isolated A. baumanii strains to ampicillin and first- and second-generation cephalosporins (94.87%, 100% and 97.44%, respectively), but also to the third-generation cephalosporins (ceftriaxone at 92.31%, ceftazidine at 51.28%) and imipenem (43.59%) as well. The lowest antibiotic resistance rate of 20.51% was found to amikacin. The OXA-23 gene was identified in 17 strains of A. baumanii, and the AmpC gene in 23 strains. The TEM-1 gene was carried in 15 strains. PER-1 and SHV-2 genes were detected in two different strains. Aminoglycoside-modifying enzyme gene aac-3-Ia was found in 23 strains, and the aac-6'-Ib gene in 19 strains. aac-3-Ia and aac-6'-Ib genes hibernated in three A. baumanii strains that showed no drug-resistant phenotype. CONCLUSIONS: A. baumanii can carry multiple drug-resistant genes at the same time and result in multi-drug resistance. Aminoglycoside-modifying enzyme genes could be hibernating in aminoglycoside sensitive strains without expressing their phenotype.201021034630