Clinical and Microbiological Impact of Implementing a Decision Support Algorithm through Microbiologic Rapid Diagnosis in Critically Ill Patients: An Epidemiological Retrospective Pre-/Post-Intervention Study.

BACKGROUND: Data on the benefits of rapid microbiological testing on antimicrobial consumption (AC) and antimicrobial resistance patterns (ARPs) are scarce. We evaluated the impact of a protocol based on rapid techniques on AC and ARP in intensive care (ICU) patients. METHODS: A retrospective pre- (2018) and post-intervention (2019-2021) study was conducted in ICU patients. A rapid diagnostic algorithm was applied starting in 2019 in patients with a lower respiratory tract infection. The incidence of nosocomial infections, ARPs, and AC as DDDs (defined daily doses) were monitored. RESULTS: A total of 3635 patients were included: 987 in the pre-intervention group and 2648 in the post-intervention group. The median age was 60 years, the sample was 64% male, and the average APACHE II and SOFA scores were 19 points and 3 points. The overall ICU mortality was 17.2% without any differences between the groups. An increase in the number of infections was observed in the post-intervention group (44.5% vs. 17.9%, p < 0.01), especially due to an increase in the incidence of ventilator-associated pneumonia (44.6% vs. 25%, p < 0.001). AC decreased from 128.7 DDD in 2018 to 66.0 DDD in 2021 (rate ratio = 0.51). An increase in Pseudomonas aeruginosa susceptibility of 23% for Piperacillin/tazobactam and 31% for Meropenem was observed. CONCLUSION: The implementation of an algorithm based on rapid microbiological diagnostic techniques allowed for a significant reduction in AC and ARPs without affecting the prognosis of critically ill patients.

Evaluation of five immunoassays and one lateral flow immunochromatography for anti-SARS-CoV-2 antibodies detection.

INTRODUCTION: In order to deal with the current pandemic caused by the novel SARS-CoV-2 coronavirus several serological immunoassays have been recently developed with the objective of being used as a complementary diagnostic tool and to support the RT-PCR technique currently considered the "gold-standard" method. However, these new assays need to be evaluated and validated. The purpose of this study was to assess the performance of five immunoassays (two ELISA and three CLIA assays) and one rapid immunochromatographic test for the detection of anti-SARS-CoV-2 antibodies. METHODS: Five semiquantitative immunoassays (MENARINI®, PALEX®, VIRCLIA®, ROCHE® and SIEMENS®) and one lateral flow rapid test (WONDFO®) were performed. A total of 124 samples were studied. Case serum samples (n=78) were obtained from COVID-19 patients confirmed by real-time RT-PCR/epidemiological-clinical-radiological criteria, and control non-SARS-CoV-2 samples (n=46) belonged to healthy healthcare workers involved in a seroprevalence study. RESULTS: Overall, the tests showed sensitivities around 70-90% and specificities greater than 95%, including the immunochromatographic test. In addition, we observed very good agreements among them, being better for the detection of IgG than for IgM antibodies (Cohen's kappa index of 0.95 for VIRCLIA® IgG with ROCHE®), as well as good diagnostic power of the tests as determined by the ROC curves. CONCLUSIONS: This study demonstrates the proper performance of the different immunoassays in order to be applied in the clinical practice as support in the diagnostic approach and in the development of vaccines and seroepidemiological studies of COVID-19.

Evaluation of five immunoassays and one lateral flow immunochromatography for anti-SARS-CoV-2 antibodies detection / Evaluación de cinco inmunoensayos y una inmunocromatografía de flujo lateral para la detección de anticuerpos anti-SARS-CoV-2

Introduction: In order to deal with the current pandemic caused by the novel SARS-CoV-2 coronavirus several serological immunoassays have been recently developed with the objective of being used as a complementary diagnostic tool and to support the RT-PCR technique currently considered the “gold-standard” method. However, these new assays need to be evaluated and validated. The purpose of this study was to assess the performance of five immunoassays (two ELISA and three CLIA assays) and one rapid immunochromatographic test for the detection of anti-SARS-CoV-2 antibodies. Methods: Five semiquantitative immunoassays (MENARINI®, PALEX®, VIRCLIA®, ROCHE® and SIEMENS®) and one lateral flow rapid test (WONDFO®) were performed. A total of 124 samples were studied. Case serum samples (n=78) were obtained from COVID-19 patients confirmed by real-time RT-PCR/epidemiological-clinical-radiological criteria, and control non-SARS-CoV-2 samples (n=46) belonged to healthy healthcare workers involved in a seroprevalence study. Results: Overall, the tests showed sensitivities around 70–90% and specificities greater than 95%, including the immunochromatographic test. In addition, we observed very good agreements among them, being better for the detection of IgG than for IgM antibodies (Cohen's kappa index of 0.95 for VIRCLIA® IgG with ROCHE®), as well as good diagnostic power of the tests as determined by the ROC curves. Conclusions: This study demonstrates the proper performance of the different immunoassays in order to be applied in the clinical practice as support in the diagnostic approach and in the development of vaccines and seroepidemiological studies of COVID-19.(AU)

Introducción: Para hacer frente a la pandemia actual causada por el nuevo coronavirus SARS-CoV-2 se han desarrollado recientemente varios inmunoensayos serológicos con el objetivo de ser utilizados como herramienta diagnóstica complementaria y apoyar la técnica de RT-PCR actualmente considerada como el “estándar de oro”. Sin embargo, estos nuevos ensayos deben evaluarse y validarse. El objetivo de este estudio fue evaluar cinco inmunoensayos (dos ELISA y tres ensayos CLIA) y una prueba inmunocromatográfica rápida para la detección de anticuerpos anti-SARS-CoV-2. Métodos: Se utilizaron cinco inmunoensayos semicuantitativos (MENARINI®, PALEX®, VIRCLIA®, ROCHE® y SIEMENS®) y un test de inmunocromatografía rápida (WONDFO®). Se estudiaron un total de 124 muestras. Las muestras de suero (n=78) se obtuvieron de pacientes COVID-19 confirmados por RT-PCR en tiempo real/criterios epidemiológicos-clínico-radiológicos. Las muestras control negativas (n=46) pertenecieron a personal sanitario involucrado en un estudio de seroprevalencia. Resultados: En general, las pruebas mostraron sensibilidades en torno al 70-90% y especificidades superiores al 95%, incluso la prueba inmunocromatográfica. Además, observamos muy buenas concordancias entre ellas, presentando mayores sensibilidades para la detección de anticuerpos IgG que para IgM (índice kappa de Cohen de 0,95 para VIRCLIA® IgG con ROCHE®), así como un buen poder diagnóstico de las técnicas determinado por las curvas ROC. Conclusiones: Este estudio demuestra el buen rendimiento de los diferentes inmunoensayos para ser empleados en la práctica clínica como apoyo en el proceso de diagnóstico, en el desarrollo de vacunas y estudios seroepidemiológicos de COVID-19.(AU)

Improvement of pneumococcal pneumonia diagnosis using quantitative real-time PCR targeting lytA in adult patients: a prospective cohort study.

OBJECTIVES: The aim of the study was to assess the performance of real-time PCR targeting the lytA gene (rtPCR-lytA) in plasma, urine and nasopharyngeal (NP) samples for the diagnosis of pneumococcal community-acquired pneumonia (P-CAP). METHODS: Prospective observational study including all consecutive adults with CAP from November 2015 to May 2017. P-CAP was defined if pneumococcus was identified using conventional methods (CM) and/or a positive rtPCR-lytA was detected in blood, urine or NP samples (NP cut-off ≥8000 copies/mL). Diagnostic performance of each test was calculated. RESULTS: A total of 133 individuals with CAP were included. Of these, P-CAP was diagnosed in 62 (46.6%). The proportion of P-CAP diagnosed by rtPCR-lytA methods was significantly higher than that diagnosed by CM (87.1% versus 59.7%, p 0.005). The rtPCR-lytA identified Streptococcus pneumoniae in 25 patients (40.3% of all individuals with P-CAP) whose diagnosis would have been missed by CM. NP-rtPCR-lytA allowed diagnosis of 62.3% of P-CAP. A nasopharyngeal colonization density ≥2351 copies/mL predicted P-CAP diagnosis (area under the curve = 0.82, sensitivity 83.3%, specificity 80.9%). There was a positive correlation between increasing bacterial load in blood and CURB-65 score (Spearman correlation coefficient r = 0.4, p 0.001), pneumonia severity index (r = 0.3, p 0.02) and time to clinical stability (r = 0.33, p 0.01). Median bacterial load in blood was higher in P-CAP patients with bacteraemia (0.65 × 103 versus 0 × 103 copies/mL, p 0.002), intensive care unit admission (0.68 × 103 versus 0 × 103 copies/mL, p 0.04) or mechanical ventilation (7.45 × 103 versus 0 × 103 copies/mL, p 0.04). CONCLUSIONS: The use of rtPCR-lytA methods significantly increased the diagnosis of P-CAP compared with CM. Nasopharyngeal swabs rtPCR-lytA detection, with an accurate cut-off value, was the most promising among molecular methods for the diagnosis of P-CAP.

Evaluation of five immunoassays and one lateral flow immunochromatography for anti-SARS-CoV-2 antibodies detection.

INTRODUCTION: In order to deal with the current pandemic caused by the novel SARS-CoV-2 coronavirus several serological immunoassays have been recently developed with the objective of being used as a complementary diagnostic tool and to support the RT-PCR technique currently considered the "gold-standard" method. However, these new assays need to be evaluated and validated. The purpose of this study was to assess the performance of five immunoassays (two ELISA and three CLIA assays) and one rapid immunochromatographic test for the detection of anti-SARS-CoV-2 antibodies. METHODS: Five semiquantitative immunoassays (MENARINI®, PALEX®, VIRCLIA®, ROCHE® and SIEMENS®) and one lateral flow rapid test (WONDFO®) were performed. A total of 124 samples were studied. Case serum samples (n=78) were obtained from COVID-19 patients confirmed by real-time RT-PCR/epidemiological-clinical-radiological criteria, and control non-SARS-CoV-2 samples (n=46) belonged to healthy healthcare workers involved in a seroprevalence study. RESULTS: Overall, the tests showed sensitivities around 70-90% and specificities greater than 95%, including the immunochromatographic test. In addition, we observed very good agreements among them, being better for the detection of IgG than for IgM antibodies (Cohen's kappa index of 0.95 for VIRCLIA® IgG with ROCHE®), as well as good diagnostic power of the tests as determined by the ROC curves. CONCLUSIONS: This study demonstrates the proper performance of the different immunoassays in order to be applied in the clinical practice as support in the diagnostic approach and in the development of vaccines and seroepidemiological studies of COVID-19.

Biomarkers and short-term prognosis in COVID-19.

PURPOSE: The aim of our study was to analyse the short-term prognostic value of different biomarkers in patients with COVID-19. METHODS: We included patients admitted to emergency department with COVID-19 and available concentrations of cardiac troponin I (cTnI), D-dimer, C-reactive protein (CRP) and lactate dehydrogenase (LDH). Patients were classified for each biomarker into two groups (low vs. high concentrations) according to their best cut-off point, and 30-day all-cause death was evaluated. RESULTS: After multivariate adjustment, cTnI ≥21 ng/L, D-dimer ≥1112 ng/mL, CRP ≥10 mg/dL and LDH ≥334 U/L at admission were associated with an increased risk of 30-day all-cause death (hazard ratio (HR) 4.30; 95% CI 1.74-10.58; p = 0.002; HR 3.35; 95% CI 1.58-7.13; p = 0.002; HR 2.25; 95% CI 1.13-4.50; p = 0.021; HR 2.00; 95% CI 1.04-3.84; p = 0.039, respectively). The area under the curve for cTnI was 0.825 (95% CI 0.759-0.892) and, in comparison, was significantly better than CRP (0.685; 95% CI 0.600-0.770; p = 0.009) and LDH (0.643; 95% CI 0.534-0.753; p = 0.006) but non-significantly better than D-dimer (0.756; 95% CI 0.674-0.837; p = 0.115). CONCLUSIONS: In patients with COVID-19, increased concentrations of cTnI, D-dimer, CRP and LDH are associated with short-term mortality. Of these, cTnI provides better mortality risk prediction. However, differences with D-dimer were non-significant.

False-seronegative HCV infection motivated by interference with cryoglobulins.

Objectives: Cryoglobulins (CGs) are serum proteins that undergo a reverse cold-induced precipitation in vitro. The CGs are a well-known cause of analytical interferences in several laboratory tests, leading to spurious results. With this in view, we present a case of a patient initially misdiagnosed due to CGs interference in Hepatitis C Virus (HCV) serology. Case presentation: We report a case of a woman of advanced age affected by acute renal failure that required urgent haemodialysis. In the absence of infections and other causes of CGs production, a diagnosis of acute renal failure secondary to essential cryoglobulinemia was established. However, an unexpected positive HCV viral load was encountered. At this point, a false-seronegative HCV infection conditioned to CGs interference in vitro was suspected, confirmed by repeating serology in pre-warmed serum. Finally, the patient was correctly diagnosed with HCV-secondary cryoglobulinemia. Conclusions: As shown in the case, the presence of CGs in blood may represent a challenge for the correct interpretation of several laboratory tests. The identification of CGs and the pre-treatment of serum are decisive to avoid spurious results and reach a genuine diagnosis.

Use of predictive tools in the management of COVID-19 patients: a key role of clinical laboratories.

Objectives: Coronavirus disease 2019 (COVID-19) is widely spreading and represents a critical threat to global health. In the fight against this pandemic, provincial hospitals urgently need rapid diagnostic of COVID-19 infected patients to avoid collapsing of emergency units. However, the high demand of patients with severe acute respiratory symptoms limits the fast delivery of results by the gold standard method reverse transcription-polymerase chain reaction real time (rRT-PCR) for the identification of COVID-19 positive pneumonia. The principal aim is to find other useful laboratory indicators to assist rRT-PCR tests and to help controlling of this outbreak. Methods: Blood, coagulation and inflammatory parameters were collected from a total of 309 patients classified as negative (128) and positive (181) rRT-PCR test groups. Patients were classified as positive by molecular diagnostic test. Results: Leukocyte count (WBC), neutrophils count, lymphocytes count and lactate dehydrogenase (LDH) were statistically different between both groups of patients. The use of LDH/WBC ratio increases the diagnostic performance with the best area under the curve (0.783), sensibility (82%) and the best percentage (80.5%) of correctly identified COVID-19 positive patients. Conclusions: The combination of predictive LDH/WBC ratio with clinical illness features could help in medical management of patients and improve the technical resources of hospitals, especially in a critical scenario with a large shortage of medical equipment and lack of reagents for performing rRT-PCR.

Infección grave por Coronavirus SARS-CoV-2: Experiencia en un hospital de tercer nivel con pacientes afectados por COVID-19 durante la pandemia 2020 / Severe infection due to the SARS-CoV-2 CORONAVIRUS: Experience of a tertiary hospital with COVID-19 patients during the 2020 pandemic

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Automated urinalysis combining physicochemical analysis, on-board centrifugation, and digital imaging in one system: A multicenter performance evaluation of the cobas 6500 urine work area.

BACKGROUND: We evaluated the analytical performance of the fully automated cobas® 6500 urine work area and its automated components-cobas u 601 and cobas u 701. DESIGN AND METHODS: The study was conducted at three European centers using un-centrifuged surplus routine urine samples; all measurements were performed within 2 h of sample collection. Precision, sample carry-over, and method comparisons were evaluated per Clinical and Laboratory Standards Institute guidelines. Method comparisons: cobas u 601 versus Urisys 2400 and cobas u 411 urine test strips; and cobas u 701 versus KOVA® visual microscopy and iQ200 analyzer. Operability and functionality were assessed using questionnaires. RESULTS: Precision of the entire cobas 6500 system was within predefined acceptance limits and no significant carry-over was observed. Erythrocytes, leukocytes, nitrites, and protein were in good agreement (≥93%) with cobas u 411 reflectometry. High correlation was shown between the cobas u 701 analyzer and KOVA visual microscopy for red blood cells (RBC; slope, 0.89; Pearson's r, 0.95) and white blood cells (WBC; slope, 0.96; Pearson's r, 0.96), demonstrating equivalence of test results. The 97.5% percentile reference values on the cobas u 701 analyzer were 5.3 cells/µL (RBC) and 6.2 cells/µL (WBC). The cobas 6500 system showed good sensitivity for small bacteria (>1 µm) and pathological casts, and the user interface, maintenance wizards, and system design were highly rated by operators. CONCLUSIONS: The fully automated workflow, high precision, and high throughput of the cobas 6500 system have the potential to facilitate standardization of urine screening.

Group B streptococcal bacteriuria during pregnancy as a risk factor for maternal intrapartum colonization: a prospective cohort study.

PURPOSE: Current evidence is inconclusive regarding the intrapartum administration of chemoprophylaxis, merely based on the presence of group B streptococcal (GBS) bacteriuria of any colony count, in the prevention of early-onset neonatal GBS infection. The aim of this study was to assess whether GBS bacteriuria is a risk factor for intrapartum colonization (IPC) regardless of urinary concentration or the results of late third-trimester rectovaginal screening cultures (RVSCs). METHODOLOGY: Six hundred and eight pregnant women, with urine specimens cultured between May 2011 and May 2013, were enrolled in this prospective cohort study. RVSCs were available for 582 women and intrapartum rectovaginal cultures for 246. RESULTS: The prevalence of GBS bacteriuria and positive RVSCs was 10.8 and 16.5 %, respectively. The frequency of IPC was 15.9 % (39/246). Sensitivity, specificity, positive and negative predictive values of urine culture and of RVSC in predicting GBS IPC were 41, 94.7, 59.3 and 89.5 %, and 76.9, 95.4, 76.9 and 95.4 %, respectively. GBS bacteriuria was significantly associated with IPC, overall [relative risk (RR) 5.6] and in women with negative RVSC (RR 8.5), with bacteriuria <104 c.f.u. ml-1 (RR 5.9) or when both circumstances coexisted (RR 8.9). The urinary colony count was <104 c.f.u. ml-1 in 13 of the 16 women with GBS bacteriuria and IPC. CONCLUSION: GBS bacteriuria is a risk factor for IPC, irrespective of urinary GBS concentration or of colonization status at late gestation. Therefore, microbiology laboratories should search, and report, GBS of any colony count in urine from pregnant women, and not only in the presence of ≥104 c.f.u. ml-1 as the 2010 CDC guidelines recommend.

ß-Lactamases, transferable quinolone resistance determinants, and class 1 integron-mediated antimicrobial resistance in human clinical Salmonella enterica isolates of non-Typhimurium serotypes.

This work investigates the occurrence and features of class 1 integrons and the presence of transferable quinolone resistance determinants (TQRD) among 382 clinical Salmonella enterica isolates of non-Typhimurium serotypes as well as the ß-lactamases produced by amoxicillin-resistant isolates. These isolates were recovered in 2001 and from 2004 to 2009 from patients from the health region of Terres de l'Ebre (Catalonia, Spain) and comprised 41 different serotypes, mostly of serovar Enteritidis (n=272), being 16.5% multidrug-resistant (MDR). Among the 93 amoxicillin-resistant isolates, 84 produced TEM-1,4 produced an extended-spectrum ß-lactamase (CTX-M-9 in one S. Grumpensis and in one S. Virchow, CTX-M-15 in S. Kapemba, and SHV-12 in S. Enteritidis), one produced DHA-1 (S. Newport), and 4 did not present any of the investigated ß-lactamases. TQRD were found in 2 isolates (qnrA1 in CTX-M-9-producing S. Grumpensis and qnrB4 in DHA-1-producing S. Newport). Overall, 35 isolates (9.2% of all isolates and 54% of MDR isolates) belonging to 15 different serotypes carried class 1 integrons that were transferred by conjugation in 17 isolates. Eleven distinct cassette arrangements were identified, with dfrA1-aadA1, dfrA17-aadA5, and dfrA12-orfF-aadA2 being the most prevalent and widely distributed ones. Atypical sul3-associated integrons were detected in 5 isolates of serotypes Rissen and Enteritidis. Moreover, the presence of integrons in the serotypes Kapemba, Mikawasima, and [9,12:Iv:i:-], of the estX-psp (linked to sul3) and aadA13-sat cassette arrangements in S. enterica, of extended-spectrum ß-lactamases in S. Kapemba and S. Grumpensis, and of TQRD in S. Grumpensis is reported here for the first time.

Molecular epidemiology and resistance mechanisms involved in reduced susceptibility to amoxicillin/clavulanic acid in Klebsiella pneumoniae isolates from a chronic care centre.

The aim of this work was to investigate the molecular epidemiology and mechanisms responsible for reduced susceptibility to amoxicillin/clavulanic acid (AMC) amongst cefazolin-susceptible Klebsiella pneumoniae isolates from patients admitted to a chronic care institution. In total, 51 (29.8%) of 171 K. pneumoniae isolates recovered between 2006 and 2008 were non-susceptible to AMC, of which 45 were susceptible to cefazolin. Nucleotide sequencing analysis revealed that 19 produced IRT-11 and the remaining 26 were OXA-1-producers. All of the OXA-1-producing isolates harboured the aac(6')-Ib-cr-bla(OXA-1) cassette array, which in 23 isolates was located together with catB3 and arr3 within a class 1 integron and associated with qnrS2 (in 3 cases the integron lacked the qacEΔ1 and sul1 or sul3 genes). Genotyping analysis performed by enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) identified three different patterns amongst IRT-11-producing isolates (E1 to E3), with E1 being the most prevalent (63.2%), whilst the OXA-1-producing isolates were assigned to patterns E3 and E3a (isolates carrying typical class 1 integrons), E4 (isolates carrying defective integrons) and E5 (isolates without integrons). Genes encoding IRT-11 and OXA-1 were transferred by conjugation, and aac(6')-Ib-cr and qnrS2 were systematically co-transferred with bla(OXA-1). These results demonstrate that the high prevalence of decreased susceptibility to AMC amongst K. pneumoniae isolates from a chronic care hospital was mainly due to the simultaneous spread of two different clones, one of which comprised isolates producing IRT-11 and the other one comprised isolates that had acquired either the bla(OXA-1) gene located in a class 1 integron and linked to qnrS2 or the bla(IRT-11) gene.