Clinical performance evaluation of TAQPATH Enteric Bacterial Select Panel for the detection of common enteric bacterial pathogens in comparison to routine stool culture and other qPCR-based diagnostic tests.

IMPORTANCE: Enteric bacterial infections caused by Salmonella, Shigella, pathogenic Escherichia coli, and Campylobacter represent one of the most common causes of infectious enteritis worldwide. The timely and accurate diagnosis of pathogens causing gastroenteritis is crucial for patient care, public health, and disease surveillance. While stool culture has long been the standard and highly specific method for detecting enteric pathogens, it is labor-intensive and time-consuming with limited sensitivity. To improve patient outcomes, there is a need to implement new cost-effective approaches for the detection of bacterial enteric pathogens with higher sensitivity and faster time to result. This study shows that multiplex real-time polymerase chain reaction-based tests, such as the TAQPATH Enteric Bacterial Select Panel, are accurate and cost-effective diagnostic alternatives for the detection and differentiation of the most common enteric bacterial pathogens, offering quicker time to result and higher sensitivity compared to routine stool culture.

Development and validation of a bacterial gastrointestinal multiplex RT-PCR assay for use on a fully automated molecular system.

PCR-based enteric multiplex panels represent a rapid and reliable alternative to conventional "classical" phenotypic stool diagnostics. The aim of this study was to establish a laboratory-developed non-commercial multiplex Real-Time-PCR panel for the detection of the most important bacterial stool pathogens, Salmonella spp., Shigella spp., Yersinia enterocolitica/ pseudotuberculosis and Campylobacter jejuni/coli. on the "open" cobas omni Utility Channel (UC) of the cobas 6800 system (Roche). The aim was to replace the laborious phenotypical stool diagnostics with a high throughput Real-Time PCR method. The respective primers and probes were designed to cover conserved genomic regions of the pathogens and validated using Ultramer oligonucleotides, positive stool material and reference strains. To further validate the multiplex PCR-assay, the following parameters were evaluated: analytical-sensitivity and -specificity, cross-reactivity, linearity and inter- and intra-assay variance as well as limit of detection (LOD). In addition a retrospective analysis of culture positive and negative samples from daily routine was performed using 745 native stool samples. The Gastro assay was linear over a 5-log-unit and within the expected dynamic range with amplification efficiencies ranging from 94.6% to 120%. In addition, all targets showed excellent coefficients of repeatability (≤ 1.11%), intermediate precision (≤ 1.02%) and total variance (≤ 1.39%). In terms of analytical sensitivity the assay demonstrated detection limits ranging from 7.83 copies per reaction to 14.4 copies per reaction. The assay showed excellent agreement with culture methods (>95%) and a 100% sensitivity and specificity after resolution of discrepant results. The multiplex-PCR assay provides a comprehensive, rapid and sensitive alternative to conventional methods for the detection of the major bacterial stool pathogens in diagnostic laboratories.

Comparison of MICs in Escherichia coli isolates from human health surveillance with MICs obtained for the same isolates by broth microdilution.

OBJECTIVES: Human health surveillance and food safety monitoring systems use different antimicrobial susceptibility testing (AST) methods. In this study, we compared the MICs of Escherichia coli isolates provided by these methods. METHODS: E. coli isolates (n = 120) from human urine samples and their MICs were collected from six medical laboratories that used automated AST methods based on bacterial growth kinetic analyses. These isolates were retested using broth microdilution, which is used by the food safety monitoring system. The essential and categorical agreements (EA and CA), very major errors (VME), major errors (ME) and minor errors (mE) for these two methods were calculated for 11 antibiotics using broth microdilution as a reference. For statistical analysis, clinical breakpoints provided by EUCAST were used. RESULTS: Five study laboratories used VITEK®2 and one MicroScan (Walkaway Combo Panel). Out of 120 isolates, 118 isolates (98.3%) were confirmed as E. coli. The 99 E. coli isolates from five study laboratories that used VITEK®2 showed high proportions of EA and CA with full agreements for gentamicin, meropenem, imipenem and ertapenem. Additionally, 100% CA was also observed in cefepime. Few VME (0.5%), ME (1.9%) and mE (1.5%) were observed across all antibiotics. One VME for ceftazidime (7.1%) and 12 MEs for ampicillin (29.4%), cefotaxime (2.4%), ciprofloxacin (3.2%), tigecycline (1.5%) and trimethoprim (22.2%) were detected. CONCLUSIONS: MICs from E. coli isolates produced by VITEK®2 were similar to those determined by broth microdilution. These results will be valuable for comparative analyses of resistance data from human health surveillance and food safety monitoring systems.

Gallbladder Cancer Presenting as Mirizzi Syndrome Complicated by Rapidly Evolving 23 rRNA Gene-Linezolid Resistance with Vancomycin-Resistant Enterococcus Infection Resulting in Fatal Cholangial Sepsis.

We describe the case of a 71-year-old woman who presented with obstructive jaundice and subhilar bile duct stenosis. MRI showed extensive cholecystolithiasis with an impacted bile stone in the cystic duct suggesting Mirizzi syndrome. Delayed enhancement of the thickened gallbladder wall suggested inflammation instead of carcinoma. After drainage of the obstructed bile duct via ERCP, the patient developed liver abscesses with a nosocomial vancomycin-resistant enterococcus infection treated by linezolid. After 4 weeks, the VRE infection was complicated by a new-onset 23 rRNA gene-mediated linezolid resistance in the same bacterial strain, which was proven via core genome multilocus sequencing. Meropenem and tigecycline were administered according to a resistogram. Furthermore, percutaneous transhepatic biliary drainage of both sides of the liver was necessary. After demission, the patient had to be admitted again due to septic shock. An emergency operation revealed extended, inoperable gallbladder cancer. The patient died a few days later in the intensive care unit. An earlier diagnosis of bile duct infiltrating gallbladder cancer by cholangioscopy or laparoscopy and treatment of vancomycin-resistant enterococcus infection with daptomycin may have changed the clinical course of the disease.

Pushing beyond specifications: Evaluation of linearity and clinical performance of the cobas 6800/8800 SARS-CoV-2 RT-PCR assay for reliable quantification in blood and other materials outside recommendations.

BACKGROUND: The ongoing SARS-CoV-2 pandemic presents a unique challenge to diagnostic laboratories. There are preliminary studies correlating qRT-PCR results from different materials to clinical outcomes, yet, comparability is limited due to the plethora of different assays used for diagnostics. In this study we evaluate clinical performance and linear range for the SARS-CoV-2 IVD (cobas6800/8800 system, a fully automated sample-to-result platform) in different clinically relevant matrix materials outside official specifications. METHODS: Assay performance was assessed in human plasma, BAL/BL and transport medium following chemical inactivation. For analytical evaluation, respective matrix materials were spiked with SARS-CoV-2 RNA in ten-fold dilution series. The efficacy of chemical inactivation by guanidine hydrochloride solution was confirmed in cell culture infectivity experiments. For correlation, a total of 289 predetermined clinical samples including respiratory swabs, plasma and lower respiratory tract specimens were subjected to the SARS-CoV-2 IVD test and results were compared. RESULTS: The SARS-CoV-2 IVD showed excellent linearity over four to six log steps depending on matrix material. Chemical inactivation resulted in a reduction in plaque forming units of at least 3.5 log steps, while having no significant impact on assay performance. Inter-run consistency from three different testing sites demonstrated excellent comparability of RT-PCR results (maximum deviation was 1.53 CT). Clinical evaluation for respiratory swabs showed very good agreement with the comparator assay (Positive agreement 95.7 %, negative agreement 98.9 %). CONCLUSION: The SARS-CoV-2 IVD test for the cobas6800/8800 systems offers excellent linear range and inter-run consistency for quantification of SARS-CoV-2 RNA in different matrices outside official specifications.

Detection of C. difficile toxin as a model assay for performing fully automated high-throughput RT-PCR on clinical stool samples.

BACKGROUND: The cobas® omni Utility Channel enables users to integrate lab-developed tests (LDTs) on the cobas® 6800 System to perform molecular diagnostics with high-throughput capacity and full automation. At present, there are no CE- or FDA-approved tests for stool pathogens on this system. To assess the performance of stool as a matrix, we evaluated the analytical and clinical performance of an LDT for detection of Clostridioides difficile (C. difficile) toxin B using the Utility Channel (C.diff_UTC). METHODS: A 10% stool suspension prepared from liquid stool samples diluted in phosphate buffered saline was used for analysis. Limit of detection (LoD) was determined in six dilutions with 126 replicates/dilution. Clinical evaluation was performed using 514 predetermined patient stool samples from two study sites in Germany. The C.diff_UTC was compared with LC 480 amplification and an LDT or the R-BioPharm C. difficile assay. Discrepant results were further analyzed using the GeneXpert C. difficile assay. RESULTS: Limit of detection was 23.48 cfu/mL (95% Confidence Interval [CI]: 19.14-31.01) with inter-run variation of <2 cycle thresholds at 3 × and 10 × LoD. No cross-reactivity was observed with a panel of fecal organisms and pathogens. Bioinformatic analysis showed coverage of the major C. difficile toxinotypes by the primer/probe set. Clinical evaluation revealed sensitivity of 96.7% (95% CI: 88.7-99.6) and specificity of 99.3% (95% CI: 98.0-99.9) compared with the reference method; inhibition rate was 3.5% (18/514). CONCLUSION: Using a predesigned primer/probe set, the C.diff_UTC assay features analytical performance and clinical sensitivity and specificity comparable to currently available nucleic acid amplification tests (NAATs) and is suitable for high-throughput testing. This was a proof-of-concept study, indicating the cobas Utility Channel could likely be adapted for other clinically relevant stool pathogens in outbreak scenarios.

Release of Antibiotics Out of a Moldable Collagen-ß-Tricalciumphosphate-Composite Compared to Two Calcium Phosphate Granules.

Bacterial bone infections after revision surgeries and diseases, like osteomyelitis, are still a challenge with regard to surgical treatments. Local bone infections were treated with antibiotics directly or by controlled drug-releasing scaffolds, like polymethylmethacrylate (PMMA) spheres, which have to be removed at a later stage, but there is a risk of a bacterial contamination during the removement. Therefore, biomaterials loaded with antibiotics for controlled release could be the method of choice: The biomaterials degrade during the drug release, therefore, there is no need for a second surgery to remove the drug eluting agent. Even non-resorbable bone materials are available (e.g., hydroxyapatite (HA)) or resorbable bone graft materials (e.g., beta-tricalcium phosphate (ß-TCP)) that will be replaced by newly formed bone. Composite materials with organic additives (e.g., collagen) supports the handling during surgery and enhances the drug loading capacity, as well as the drug releasing time. The purpose of this study was to investigate the loading capacity and the release rate of Vancomycin and Gentamicin on TCP and HA granules in the shape of a degradable scaffold compared to composite materials from TCP mixed with porcine collagen. Its antibacterial efficacy to a more elementary drug with eluting in aqueous solution was examined. The loading capacity of the biomaterials was measured and compared according to the Minimum Inhibition Concentration (MIC) and the Minimum Biofilm Eradication Concentration (MBEC) of a bacterial biofilm after 24 h aging. Antibiotic elution and concentration of gentamycin and vancomycin, as well as inhibition zones, were measured by using the Quantitative Microparticle Systems (QMS) immunoassays. The antibiotic concentration was determined by the automated Beckman Coulter (BC) chemistry device. For examination of the antibacterial activity, inhibition zone diameters were measured. Generally, the antibiotic release is more pronounced during the first couple of days than later. Both TCP granules and HA granules experienced a significantly decline of antibiotics release during the first three days. After the fourth day and beyond, the antibiotic release was below the detection threshold. The antibiotic release of the composite material TCP and porcine collagen declined less drastically and was still in the frame of the specification during the first nine days. There was no significant evidence of interaction effect between antibiotic and material, i.e., the fitted lines for Gentamycin and Vancomycin are almost parallel. During this first in vitro study, ß-TCP-Collagen composites shows a significantly higher loading capacity and a steadily release of the antibiotics Gentamycin and Vancomycin, compared to the also used TCP and HA Granules.

Clinical evaluation of multiplex RT-PCR assays for the detection of influenza A/B and respiratory syncytial virus using a high throughput system.

BACKGROUND: Lower respiratory tract infections are a major threat to public health systems worldwide, with RSV and influenza being the main agents causing hospitalization. In outbreak situations, high-volume respiratory testing is needed. In this study, we evaluated the analytical and clinical performance of a pre-designed primer/probe set for the simultaneous multiplex detection of both viruses on a high-throughput platform, the cobas® 6800, using the "open channel" of the system for integration of lab-developed assays for the detection of influenza and RSV. RESULTS: Using the influenza/RSV qPCR Assay with swabs, LoD (95%) in TCID50/mL for influenza-A was 0.009, influenza-B 0.003, RSV-A 0.202, and RSV-B 0.009. Inter-run variability (3xLoD) was low (<1 Ct for all targets). Of 371 clinical respiratory specimens analyzed, results were concordant for 358 samples. The calculated sensitivity and specificity of the assay were 98.3% and 98.4% for Flu-A, 100% and 98.5% for Flu-B, and 98.6% and 99.7% for RSV. All quality assessment panel specimens (N = 63, including avian influenza strains) were correctly identified. None of the tested microorganisms showed cross-reactivity. CONCLUSION: Compared with CE-IVD assays, the assay evaluated here showed good analytical and clinical sensitivity and specificity with broad coverage of different virus strains. It offers high-throughput capacity with low hands-on time, facilitating the laboratory management of large respiratory outbreaks.

Validation of the FluoroType® MRSA assay for the rapid identification of methicillin-resistant Staphylococcus aureus directly from patient material.

We performed the first evaluation study of the new HyBeacon based FluoroType(®) MRSA assay for the detection of MRSA directly from 617 patient specimens. Using culture as the reference method sensitivity and specificity were higher than 95%. Results were available within 2.5h, including DNA extraction.

Evaluation of the FluoroType MTB assay for the rapid and reliable detection of Mycobacterium tuberculosis in respiratory tract specimens.

We performed the first evaluation study of the new FluoroType MTB assay, a HyBeacon based nucleic acid amplification test for the direct detection of Mycobacterium tuberculosis in respiratory tract specimens. Using mycobacterial culture as a reference, 661 specimens were tested. Sensitivity and specificity were 95.1% and 96.4% for all specimens, sensitivity was 100% for smear-positive and 84.6% for smear negative specimens, respectively. The FluoroType MTB assay showed fast and accurate results within 3 hours, including DNA extraction.

Retrospective evaluation of a PCR based assay for the direct detection of methicillin-resistant Staphylococcus aureus in clinical specimen.

We evaluated the performance of a PCR-based dipstick assay used in our routine laboratory for the direct detection of Methicillin resistant Staphylococcus aureus (MRSA). 2941 clinical swab specimens were evaluated. Sensitivity and specificity were 94.1% and 98.3%, respectively. The PCR assay combines low instrumentation costs and minor hands-on-time with reliable results for MRSA identification.

Randomized, double-blind crossover study of vaginal microflora and epithelium in women using a tampon with a "winged" apertured film cover and a commercial tampon with a nonwoven fleece cover.

This study compared the safety of a new tampon with a four-winged apertured film cover over its nonwoven cover to improve leakage performance with that of a commercial tampon with a nonwoven cover only. Healthy women (evaluable, n = 69) were randomized to crossover between test and reference tampons in two consecutive menstrual cycles. Qualitative and quantitative analyses of vaginal cultures were conducted pre-, mid-, and postmenstrually for a broad panel of microorganisms, and colposcopy was performed. Similar to previous studies, prevalence and mean colony counts of the majority of microorganisms generally increased midmenstrually and returned or began to return postmenstrually. In contrast to most previous studies, Lactobacillus species remained at similar levels throughout the cycles with both tampons. Neither tampon was associated with clinically significant microbiological changes or abnormalities or with vaginal/cervical epithelial integrity changes on colposcopy. Microbiological and colposcopic evaluations indicate that the apertured film-covered tampon is safe.

Performance of a matrix-assisted laser desorption ionization-time-of-flight mass spectrometry system for the identification of bacterial isolates in the clinical routine laboratory.

BACKGROUND: Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has emerged as a new tool for the fast and reliable identification of microorganisms. We evaluated the performance of a MALDI-TOF MS-system for the identification of various clinical isolates in the routine microbiology setting. MATERIAL AND METHODS: For the evaluation study a set of 1116 bacterial isolates were collected in the routine microbiology laboratory. Additonally 108 isolates of strain culture collections (ATTC, DSMZ) were utilized. Identification of the bacterial isolates was perfomed with a Microflex LT mass spectrometer in combination with the MALDI-Biotyper 2.0 software (Bruker Daltonik GmbH, Bremen, Germany). The results of the MALDI-TOF MS were compared to phenotypic bacterial identification systems used in our routine laboratory. Discrepancies were resolved by 16 S rDNA-sequencing. RESULTS: Of the 108 reference strains tested, 101 (93.5%) were correctly identified to species level. Overall, 1062 (95.2%) of the 1116 strains collected in the routine laboratory were correctly identified with the MALDI-Biotyper. Accuracy for the identification of Enterobacteriaceae, non-fermenting gram-negative rods, staphylococci, enterococci and streptococci with the MALDI-Biotyper was 95.5%, 79.7%, 99.5%, 100% and 93.7%, respectively. Results were available in 12 minutes for direct smear and in 20 min with an extraction method. CONCLUSIONS: The MALDI-TOF method proves to be a fast and reliable method for the identification of the most important bacterial isolates in the clinical laboratory.

A prospective, randomized, double-blind study of vaginal microflora and epithelium in women using a tampon with an apertured film cover compared with those in women using a commercial tampon with a cover of nonwoven fleece.

Healthy women with normal menstrual cycles were randomly assigned to use either a test tampon during cycle 1 and a reference tampon during cycle 2 or a reference tampon during cycle 1 and a test tampon during cycle 2. Tampons were identical except for their cover materials: apertured film for the test tampon and nonwoven fleece for the reference tampon. Product use was doubly blinded. Qualitative and quantitative analyses of vaginal cultures were done pre-, mid-, and postmenstrually for a broad panel of microorganisms, colposcopy was performed, and diary reports were collected; 101 of 105 enrolled subjects completed the study. Midmenstrual findings for a variety of organisms differed from pre- and postmenstrual observations whether subjects were using test or reference tampons. No statistically significant differences were noted in prevalence or colony counts at premenstrual versus mid- and postmenstrual visits for most microorganisms. Prevalences of Gardnerella and anaerobic gram-negative rods were significantly different between tampons at the premenstrual visit, when unusually low values were observed for the test and reference tampons, respectively. None of the changes or differences in microflora were considered to be clinically significant. It is noteworthy, however, that declines in the prevalence and abundance of Lactobacillus during the menstrual periods were less pronounced during the use of both test and reference tampons than those reported from previous studies. Colposcopy showed no abnormal findings with either tampon and no changes in vaginal or cervical epithelial integrity. Thus, all evidence from both microbiological and colposcopic evaluations indicates that the apertured film cover of the test tampon is as safe as the nonwoven cover of the reference tampon.

Two-center collaborative evaluation of performance of the BD phoenix automated microbiology system for identification and antimicrobial susceptibility testing of gram-negative bacteria.

The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, MD) was assessed for identification (ID) and antimicrobial susceptibility testing (AST) of the majority of clinically encountered bacterial isolates in a European collaborative two-center trial. A total of 494 bacterial isolates including various species of the Enterobacteriaceae and 110 nonfermentative gram-negative bacteria were investigated: of these, 385 were single patient isolates, and 109 were challenge strains tested at one center. The performance of the Phoenix extended-spectrum beta-lactamase (ESBL) test was also evaluated for 203 strains of Escherichia coli, Klebsiella pneumoniae, and Klebsiella oxytoca included in the study. Forty-two antimicrobial drugs were tested, including members of the following drug classes: aminoglycosides, beta-lactam antibiotics, beta-lactam/beta-lactamase inhibitors, carbapenems, cephems, monobactams, folate antagonists, quinolones, and others. Phoenix system ID results were compared to those of the laboratories' routine ID systems (API 20E and API CHE, ATB ID32E, ID32GN, and VITEK 2 [bioMérieux, Marcy l'Etoile, France]); Phoenix AST results were compared to those of frozen standard broth microdilution (SBM) panels according to NCCLS (now CLSI) guidelines (NCCLS document M100-S9, approved standard M7-A4). Discrepant results were repeated in duplicate. Concordant IDs of 98.4 and 99.1% were observed for the Enterobacteriaceae and the nonfermentative group, respectively. For AST results, the overall essential agreement was 94.2%; the category agreement was 97.3%; and the very major error rate, major error rate, and minor error rate were 1.6, 0.6, and 1.9%, respectively. In terms of ESBL detection, Phoenix results were 98.5% concordant with those of the reference system, with 98.0% sensitivity and 98.7% specificity. In conclusion, the Phoenix ID results showed high agreement with results of the systems to which they were being compared: the AST performance was highly equivalent to that of the SBM reference method, and the system proved to be very accurate for the detection of ESBL producers.

Two-center collaborative evaluation of the performance of the BD Phoenix automated microbiology system for identification and antimicrobial susceptibility testing of Enterococcus spp. and Staphylococcus spp.

The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, Md.) was assessed for identification (ID) and antimicrobial susceptibility testing (AST) for the majority of clinically encountered bacterial isolates in a European collaborative two-center trial. A total of 469 bacterial isolates of the genera Staphylococcus (275 isolates), Enterococcus (179 isolates), and Streptococcus (15 isolates, for ID only) were investigated; of these, 367 were single patient isolates, and 102 were challenge strains tested at one center. Sixty-four antimicrobial drugs were tested, including the following drug classes: aminoglycosides, beta-lactam antibiotics, beta-lactam-beta-lactamase inhibitors, carbapenems, cephems, folate antagonists, quinolones, glycopeptides, macrolides-lincosamides-streptogramin B (MLS), and others. Phoenix ID results were compared to those of the laboratories' routine ID systems (API 32 Staph, API 32 Strep, and VITEK 2 [bioMérieux, Marcy l'Etoile, France]); Phoenix AST results were compared to those of frozen standard broth microdilution (SBM) panels according to NCCLS guidelines (NCCLS document M 100-S 9, approved standard M 7-A 4). Discrepant results were repeated in duplicate. Concordant IDs of 97.1, 98.9, and 100% were observed for staphylococci, enterococci, and streptococci, respectively. For AST results the overall essential agreement was 93.3%; the category agreement was 97.3%; and the very major error rate, major error rate, and minor error rate were 1.2, 1.9, and 1.3%, respectively. In conclusion, the Phoenix ID results showed high agreement with results of the systems to which they were being compared; the AST performance was highly equivalent to that of the SBM reference method.