Development and evaluation of an artificial intelligence for bacterial growth monitoring in clinical bacteriology.

In clinical bacteriology laboratories, reading and processing of sterile plates remain a significant part of the routine workload (30%-40% of the plates). Here, an algorithm was developed for bacterial growth detection starting with any type of specimens and using the most common media in bacteriology. The growth prediction performance of the algorithm for automatic processing of sterile plates was evaluated not only at 18-24 h and 48 h but also at earlier timepoints toward the development of an early growth monitoring system. A total of 3,844 plates inoculated with representative clinical specimens were used. The plates were imaged 15 times, and two different microbiologists read the images randomly and independently, creating 99,944 human ground truths. The algorithm was able, at 48 h, to discriminate growth from no growth with a sensitivity of 99.80% (five false-negative [FN] plates out of 3,844) and a specificity of 91.97%. At 24 h, sensitivity and specificity reached 99.08% and 93.37%, respectively. Interestingly, during human truth reading, growth was reported as early as 4 h, while at 6 h, half of the positive plates were already showing some growth. In this context, automated early growth monitoring in case of normally sterile samples is envisioned to provide added value to the microbiologists, enabling them to prioritize reading and to communicate early detection of bacterial growth to the clinicians.

Vaccination against tick-borne encephalitis elicits a detectable NS1 IgG antibody response.

Vaccine-induced protection against tick-borne encephalitis virus (TBEV) is mediated by antibodies to the viral particle/envelope protein. The detection of non-structural protein 1 (NS1) specific antibodies has been suggested as a marker indicative of natural infections. However, recent work has shown that TBEV vaccines contain traces of NS1, and immunization of mice induced low amounts of NS1-specific antibodies. In this study, we investigated if vaccination induces TBEV NS1-specific antibodies in humans. Healthy army members (n = 898) were asked to fill in a questionnaire relating to flavivirus vaccination or infection, and blood samples were collected. In addition, samples of 71 suspected acute TBE cases were included. All samples were screened for the presence of TBEV NS1-specific IgG antibodies using an in-house developed ELISA. Antibodies were quantified as percent positivity in reference to a positive control. For qualitative evaluation, cut-off for positivity was defined based on the mean OD of the lower 95% of the vaccinated individuals + 3 SD. We found significantly higher NS1-specific IgG antibody titers (i.e., quantitative evaluation) in individuals having received 2, 3, or 4 or more vaccine doses than in non-vaccinated individuals. Similarly, the percentage of individuals with a positive test result (i.e., qualitative evaluation) was higher in individuals vaccinated against tick-borne encephalitis than in unvaccinated study participants. Although NS1-specific IgG titers remained at a relatively low level when compared to TBE patients, a clear distinction was not always possible. Establishing a clear cut-off point in detection systems is critical for NS1-specific antibodies to serve as a marker for distinguishing the immune response after vaccination and infection.

Treatment and Outcomes of Clostridioides difficile Infection in Switzerland: A Two-Center Retrospective Cohort Study.

Objectives: Clostridioides difficile infection (CDI) is the leading cause of healthcare-associated diarrhea, often complicated by severe infection and recurrence with increased morbidity and mortality. Data from large cohorts in Switzerland are scarce. We aimed to describe diagnostic assays, treatment, outcomes, and risk factors for CDI in a large cohort of patients in Switzerland. Methods: We conducted a retrospective cohort study of CDI episodes diagnosed in patients from two tertiary care hospitals in Switzerland. During a 3-month follow-up, we used a composite outcome combining clinical cure at day 10, recurrence at week 8, or death, to evaluate a patient's response. Unfavorable outcomes consisted in the occurrence of any of these events. Results: From January 2014 to December 2018, we included 826 hospitalized patients with documented CDI. Overall, 299 patients (36.2%) had a severe infection. Metronidazole was used in 566 patients (83.7%), compared to 82 patients (12.1%) treated with vancomycin and 28 patients (4.1%) treated with fidaxomicin. Overall mortality at week 8 was at 15.3% (112/733). Eighty-six patients (12.7%) presented with clinical failure at day 10, and 78 (14.9%) presented with recurrence within 8 weeks; 269 (39.8%) met the composite outcome of death, clinical failure, or recurrence. The Charlson Comorbidity Index score (p < 0.001), leukocytes > 15 G/L (p = 0.008), and the use of metronidazole (p = 0.012) or vancomycin (p = 0.049) were factors associated with the composite outcome. Conclusions: Our study provides valuable insights on CDI treatment and outcomes in Switzerland, highlights the heterogeneity in practices among centers, and underlines the need for the active monitoring of clinical practices and their impact on clinical outcomes through large multicentric cohorts.

Performance Evaluation of the Quantamatrix QMAC-dRAST System for Rapid Antibiotic Susceptibility Testing Directly from Blood Cultures.

OBJECTIVES: Rapid antibiotic susceptibility testing (AST) for positive blood cultures can improve patient clinical outcomes if the time to an effective antimicrobial therapy is shortened. In this study, we tested the Quantamatrix dRAST system (QMAC-dRAST), a rapid AST system based on time-lapse microscopic imagery of bacterial colony formation in agarose. METHODS: Evaluation of the QMAC-dRAST was performed from 250 monobacterial blood cultures including 130 Enterobacterales, 20 non-fermentative Gram-negative bacteria, 69 staphylococci and 31 enterococci. Blood cultures were recovered from anonymous patients or from spiking experiments to enrich our study with bacterial species and resistant strains. Categorical agreement (CA), minor errors (me), major errors (ME) and very major errors (VME) were calculated in comparison to the results obtained from the BD Phoenix™ M50. Discrepancies between the Phoenix™ M50 and QMAC-dRAST results were investigated using the gradient strip method. The repeatability and reproducibility performance of the QMAC-dRAST was assessed for 16 strains, each strain being tested five times from a spiked blood culture. RESULTS: The overall CAs for Enterobacterales, non-fermentative Gram-negative bacteria, staphylococci and enterococci were 95.1%, 91.2%, 93.4% and 94.5%, respectively. The VME percentage was below 4% for all the groups except for staphylococci, which showed a VME rate of 7%. The median time to result was 6.7 h (range: 4.7-7.9). Repeatability and reproducibility assays showed a high reliability of AST results with best and worst ratios of 98.8% and 99.6% and 95.0% and 98.3%, respectively. CONCLUSIONS: The QMAC-dRAST is a fast and reliable system to determine AST directly from monobacterial blood cultures with a major TAT reduction compared to conventional AST testing.

Anti-SARS-CoV-2 Titers Predict the Severity of COVID-19.

Coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 is associated with a wide spectrum of disease, ranging from asymptomatic infection to acute respiratory distress syndrome. Some biomarkers may predict disease severity. Among them, the anti-SARS-CoV-2 antibody response has been related to severe disease. The aim of this study was to assess the correlation between the anti-SARS-CoV-2 serological response and COVID-19 outcome. Demographic, clinical, and biological data from nasopharyngeal-PCR confirmed COVID-19 hospitalized patients were prospectively collected between April and August 2020 at our institution. All patients had serial weekly serology testing for a maximum of three blood samples or until discharge. Two different serological assays were used: a chemiluminescent assay and an in-house developed Luminex immunoassay. Kinetics of the serological response and correlation between the antibody titers and outcome were assessed. Among the 70 patients enrolled in the study, 22 required invasive ventilation, 29 required non-invasive ventilation or oxygen supplementation, and 19 did not require any oxygen supplementation. Median duration of symptoms upon admission for the three groups were 13, 8, and 9 days, respectively. Antibody titers gradually increased for up to 3 weeks since the onset of symptoms for patients requiring oxygen supplementation with significantly higher antibody titers for patients requiring invasive ventilation. Antibody titers on admission were also significantly higher in severely ill patients and serology performed well in predicting the necessity of invasive ventilation (AUC: 0.79, 95% CI: 0.67-0.9). Serology testing at admission may be a good indicator to identify severe COVID-19 patients who will require invasive mechanical ventilation.

Acute abdominal emergency due to infectious enteritis: an observational study comparing Campylobacter spp. to other enteric pathogens in children.

BACKGROUND: Campylobacter spp. are a frequent cause of gastroenteritis, presenting in some patients as an acute abdominal emergency. Here we describe the distinctive clinical characteristics of these patients. METHODS: We designed a retrospective, single-centre, observational study. Children and adolescents under 18 years of age who had positive stool cultures for Campylobacter spp. during the period between June 1, 2008 and May 31, 2016 were identified from our database. Hospitalised patients with Campylobacter spp. were then matched for age and gender with patients hospitalised for gastroenteritis of other or unknown aetiology. Patients who had undergone abdominal radiographic investigation or had received a surgery consultation were included as "acute abdomen" (AA) cases. Demographics, clinical characteristics and management were compared between AA and non-AA cases. RESULTS: One hundred and forty-one patients with cultures positive for Campylobacter spp. were included in the analysis. Nineteen patients were identified as AA cases. Fewer of these had diarrhoea (14/19, 74% vs 117/121, 97%; p = 0.02) and more reported a lower sense of general wellbeing (8/18, 44% vs 8/108, 7%; p <0.001). Localised pain (9/18, 50% vs 20/115, 17%; p = 0.002) and abdominal tenderness (2/18, 11% vs 0/111; p = 0.02) were also more common among AA cases. Forty-four patients with Campylobacter spp. infections were hospitalised and matched with 44 patients with gastroenteritis of other or unknown aetiology. Campylobacter spp. infection (risk ratio 3.6, 95% CI 1.3-9.7; p = 0.01) was positively correlated with being seen by a surgeon and/or a prescription for radiological examination. CONCLUSIONS: We identified a subset of patients with Campylobacter spp. gastroenteritis who present as an acute abdominal emergency. The presentation of these patients was characterised mainly by the nature of the associated abdominal pain.

Multicenter Evaluation of Rapid BACpro® II for the Accurate Identification of Microorganisms Directly from Blood Cultures Using MALDI-TOF MS.

The identification of microorganisms directly from blood cultures using MALDI-TOF MS has been shown to be the most impacting application of this methodology. In this study, a novel commercial method was evaluated in four clinical microbiology laboratories. Positive blood culture samples (n = 801) were processed using a rapid BACpro® II kit and then compared with the routine gold standard. A subset of monomicrobial BCs (n = 560) were analyzed in parallel with a Sepsityper® Kit (Bruker Daltonics, Bremen, Germany) and compared with the rapid BACpro® II kit. In addition, this kit was also compared with two different in-house methods. Overall, 80.0% of the monomicrobial isolates (609/761; 95% CI 71.5-88.5) were correctly identified by the rapid BACpro® II kit at the species level (92.3% of the Gram negative and 72.4% of the Gram positive bacteria). The comparison with the Sepsityper® Kit showed that the rapid BACpro® II kit generated higher rates of correct species-level identification for all categories (p > 0.0001), except for yeasts identified with score values > 1.7. It also proved superior to the ammonium chloride method (p > 0.0001), but the differential centrifugation method allowed for higher rates of correct identification for Gram negative bacteria (p > 0.1). The percentage of accurate species-level identification of Gram positive bacteria was particularly noteworthy in comparison with other commercial and in-house methods.

Current State of Laboratory Automation in Clinical Microbiology Laboratory.

BACKGROUND: Although it has been 30 years since the first automation systems were introduced in the microbiology laboratory, total laboratory automation (TLA) has only recently been recognized as a valuable component of the laboratory. A growing number of publications illustrate the potential impact of automation. TLA can improve standardization, increase laboratory efficiency, increase workplace safety, and reduce long-term costs. CONTENT: This review provides a preview of the current state of automation in clinical microbiology and covers the main developments during the last years. We describe the available hardware systems (that range from single function devices to multifunction workstations) and the challenging alterations on workflow and organization of the laboratory that have to be implemented to optimize automation. SUMMARY: Despite the many advantages in efficiency, productivity, and timeliness that automation offers, it is not without new and unique challenges. For every advantage that laboratory automation provides, there are similar challenges that a laboratory must face. Change management strategies should be used to lead to a successful implementation. TLA represents, moreover, a substantial initial investment. Nevertheless, if properly approached, there are a number of important benefits that can be achieved through implementation of automation in the clinical microbiology laboratory. Future developments in the field of automation will likely focus on image analysis and artificial intelligence improvements. Patient care, however, should remain the epicenter of all future directions and there will always be a need for clinical microbiology expertise to interpret the complex clinical and laboratory information.

Multicenter Technical Validation of 30 Rapid Antigen Tests for the Detection of SARS-CoV-2 (VALIDATE).

During COVID19 pandemic, SARS-CoV-2 rapid antigen tests (RATs) were marketed with minimal or no performance data. We aimed at closing this gap by determining technical sensitivities and specificities of 30 RATs prior to market release. We developed a standardized technical validation protocol and assessed 30 RATs across four diagnostic laboratories. RATs were tested in parallel using the Standard Q® (SD Biosensor/Roche) assay as internal reference. We used left-over universal transport/optimum media from nasopharyngeal swabs of 200 SARS-CoV-2 PCR-negative and 100 PCR-positive tested patients. Transport media was mixed with assay buffer and applied to RATs according to manufacturer instructions. Sensitivities were determined according to viral loads. Specificity of at least 99% and sensitivity of 95%, 90%, and 80% had to be reached for 107, 106, 105 virus copies/mL, respectively. Sensitivities ranged from 43.5% to 98.6%, 62.3% to 100%, and 66.7% to 100% at 105, 106, 107 copies/mL, respectively. Automated assay readers such as ExDia or LumiraDx showed higher performances. Specificities ranged from 88.8% to 100%. Only 15 of 30 (50%) RATs passed our technical validation. Due to the high failure rate of 50%, mainly caused by lack of sensitivity, we recommend a thorough validation of RATs prior to market release.

Sensitivity of Rapid Antigen Testing and RT-PCR Performed on Nasopharyngeal Swabs versus Saliva Samples in COVID-19 Hospitalized Patients: Results of a Prospective Comparative Trial (RESTART).

Saliva sampling could serve as an alternative non-invasive sample for SARS-CoV-2 diagnosis while rapid antigen tests (RATs) might help to mitigate the shortage of reagents sporadically encountered with RT-PCR. Thus, in the RESTART study we compared antigen and RT-PCR testing methods on nasopharyngeal (NP) swabs and salivary samples. We conducted a prospective observational study among COVID-19 hospitalized patients between 10 December 2020 and 1 February 2021. Paired saliva and NP samples were investigated by RT-PCR (Cobas 6800, Roche-Switzerland, Basel, Switzerland) and by two rapid antigen tests: One Step Immunoassay Exdia® COVID-19 Ag (Precision Biosensor, Daejeon, Korea) and Standard Q® COVID-19 Rapid Antigen Test (Roche-Switzerland). A total of 58 paired NP-saliva specimens were collected. A total of 32 of 58 (55%) patients were hospitalized in the intensive care unit, and the median duration of symptoms was 11 days (IQR 5-19). NP and salivary RT-PCR exhibited sensitivity of 98% and 69% respectively, whereas the specificity of these RT-PCRs assays was 100%. The NP RATs exhibited much lower diagnostic performance, with sensitivities of 35% and 41% for the Standard Q® and Exdia® assays, respectively, when a wet-swab approach was used (i.e., when the swab was diluted in the viral transport medium (VTM) before testing). The sensitivity of the dry-swab approach was slightly better (47%). These antigen tests exhibited very low sensitivity (4% and 8%) when applied to salivary swabs. Nasopharyngeal RT-PCR is the most accurate test for COVID-19 diagnosis in hospitalized patients. RT-PCR on salivary samples may be used when nasopharyngeal swabs are contraindicated. RATs are not appropriate for hospitalized patients.

Evaluation of sixteen ELISA SARS-CoV-2 serological tests.

BACKGROUND: In response to the current COVID-19 pandemic, multiple companies marketed serological tests. Rigorous, independent and comparative performances of these assays on defined clinical specimens are needed. METHODS: In a first preliminary phase, we investigated 16 IgG, IgM, IgA and pan Ig serological ELISA using a panel of 180 sera, comprising 97 sera from patients with a positive RT-PCR, and 83 negative sera sampled before November 1, 2019. In a second phase and to complete the evaluation on the full panel (100 positive and 300 negative), tests that passed pre-defined exclusion criteria of 90% sensitivity and 97% specificity were further evaluated on 220 additional sera chosen to assess possible cross-reactivity with other human viral infections. RESULTS: Among the 16 tests evaluated in the preliminary phase, two were excluded due to insufficient sensitivity at 15 days post-symptom onset and one was excluded due to poor specificity. Of the 13 tests evaluated using the full panel comprised of a diverse pool of sera including those reactive against known respiratory viruses, no systematic cross-reactivity was observed. However, heterogeneities across tests were found. Consistent with kinetics of antibody expression, maximal sensitivity was found two weeks post-symptom onset. CONCLUSION: In this independent evaluation, we compared the performance of 16 SARS-CoV-2 serological tests using well-characterized sera and found 13 tests with more than 90% sensitivity at 15 days post-symptom onset and 97% specificity across a diverse range of negative samples.

SARS-CoV-2 seroprevalence in healthcare workers of a Swiss tertiary care centre at the end of the first wave: a cross-sectional study.

OBJECTIVE: To assess the SARS-CoV-2 transmission in healthcare workers (HCWs) using seroprevalence as a surrogate marker of infection in our tertiary care centre according to exposure. DESIGN: Seroprevalence cross-sectional study. SETTING: Single centre at the end of the first COVID-19 wave in Lausanne, Switzerland. PARTICIPANTS: 1874 of 4074 responders randomly selected (46% response rate), stratified by work category among the 13 474 (13.9%) HCWs. MAIN OUTCOME MEASURES: Evaluation of SARS-CoV-2 serostatus paired with a questionnaire of SARS-CoV-2 acquisition risk factors internal and external to the workplace. RESULTS: The overall SARS-CoV-2 seroprevalence rate among HCWs was 10.0% (95% CI 8.7% to 11.5%). HCWs with daily patient contact did not experience increased rates of seropositivity relative to those without (10.3% vs 9.6%, respectively, p=0.64). HCWs with direct contact with patients with COVID-19 or working in COVID-19 units did not experience increased seropositivity rates relative to their counterparts (10.4% vs 9.8%, p=0.69 and 10.6% vs 9.9%, p=0.69, respectively). However, specific locations of contact with patients irrespective of COVID-19 status-in patient rooms or reception areas-did correlate with increased rates of seropositivity (11.9% vs 7.5%, p=0.019 and 14.3% vs 9.2%, p=0.025, respectively). In contrast, HCWs with a suspected or proven SARS-CoV-2-infected household contact had significantly higher seropositivity rates than those without such contacts (19.0% vs 8.7%, p<0.001 and 42.1% vs 9.4%, p<0.001, respectively). Finally, consistent use of a mask on public transportation correlated with decreased seroprevalence (5.3% for mask users vs 11.2% for intermittent or no mask use, p=0.030). CONCLUSIONS: The overall seroprevalence was 10% without significant differences in seroprevalence between HCWs exposed to patients with COVID-19 and HCWs not exposed. This suggests that, once fully in place, protective measures limited SARS-CoV-2 occupational acquisition within the hospital environment. SARS-CoV-2 seroconversion among HCWs was associated primarily with community risk factors, particularly household transmission.

Implementing SARS-CoV-2 Rapid Antigen Testing in the Emergency Ward of a Swiss University Hospital: The INCREASE Study.

Following the Swiss Federal Office of Public Health (FOPH) authorization of the rapid antigen test (RAT), we implemented the use of the RAT in the emergency ward of our university hospital for patients' cohorting. RAT triaging in association with RT-PCR allowed us to promptly isolate positive patients and save resources. Among 532 patients, overall sensitivities were 48.3% for Exdia and 41.2% for Standard Q®, PanbioTM and BD Veritor™. All RATs exhibited specificity above 99%. Sensitivity increased to 74.6%, 66.2%, 66.2% and 64.8% for Exdia, Standard Q®, PanbioTM and BD Veritor™, respectively, for viral loads above 105 copies/mL, to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/mL and 100% for viral loads above 107 copies/mL. Sensitivity was significantly higher for patients with symptoms onset within four days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with the evolution of symptoms longer than four days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Among COVID-19 asymptomatic patients, sensitivity was 33%. All Immunoglobulin-A-positive patients resulted negative for RAT. The RAT might represent a useful resource in selected clinical settings as a complementary tool in RT-PCR for rapid patient triaging, but the lower sensitivity, especially in late presenters and COVID-19 asymptomatic subjects, must be taken into account.

[Fecal microbiota transplantation: from the evidence to the realty of the field]. / Transplantation de microbiote fécal : de l'évidence aux réalités du terrain.

In clinical practice, fecal microbiota transplantation (FMT) has been established as an unparalleled therapy to date for multiple recurrent Clostridioides difficile infections (CDI). The implementation of the FMT in practice requires a significant investment to meet legal, security and financial requirements. Research on the microbiota is booming and multiple investigations on FMT in indications other than CDI are ongoing.

En pratique clinique, la transplantation de microbiote fécal (TMF) s'est établie comme une thérapie sans équivalent à ce jour pour les infections à Clostridioides difficile (C. difficile) multirécidivantes. La mise en place de la TMF en pratique demande un investissement important pour répondre aux exigences légales, sécuritaires et financières. La recherche sur le microbiote est en plein essor et de multiples recherches sur la TMF dans d'autres indications que pour l'infection à C. difficile sont en cours.

[Invasive Campylobacter infections]. / Infections invasives à Campylobacter.

Campylobacter genus encompasses many species, among which C. jejuni, C. coli and C. fetus are the main human pathogens. C. jejuni/coli frequently cause self-limited enteritis in immunocompetent hosts and are seldomly associated with bacteriemia. C. fetus is less common as a human pathogen. It is rarely identified in fecal samples but can sometimes be isolated in blood samples from patients with comorbidities or immunosuppression. Campylobacter fetus bacteriemia is remarkable since it is associated with endovascular and deep-seated infections.

Le genre Campylobacter comprend plusieurs espèces pathogènes pour l'homme, en particulier C. jejuni, C. coli et C. fetus. C. jejuni et C. coli sont responsables d'entérites généralement spontanément résolutives chez l'individu sain, et peu fréquemment associées à des bactériémies. C. fetus est un pathogène méconnu, rarement identifié dans les échantillons fécaux mais parfois retrouvé dans des hémocultures, en particulier chez des patients présentant des comorbidités ou immunosupprimés. La bactériémie à C. fetus se distingue par son association avec des infections endovasculaires et des foyers infectieux profonds sans symptomatologie digestive.

Clostridioides difficile Infection, Still a Long Way to Go.

Clostridioides difficile is an increasingly common pathogen both within and outside the hospital and is responsible for a large clinical spectrum from asymptomatic carriage to complicated infection associated with a high mortality. While diagnostic methods have considerably progressed over the years, the optimal diagnostic algorithm is still debated and there is no single diagnostic test that can be used as a standalone test. More importantly, the heterogeneity in diagnostic practices between centers along with the lack of robust surveillance systems in all countries and an important degree of underdiagnosis due to lack of clinical suspicion in the community, hinder a more accurate evaluation of the burden of disease. Our improved understanding of the physiopathology of CDI has allowed some significant progress in the treatment of CDI, including a broader use of fidaxomicine, the use of fecal microbiota transplantation for multiples recurrences and newer approaches including antibodies, vaccines and new molecules, already developed or in the pipeline. However, the management of CDI recurrences and severe infections remain challenging and the main question remains: how to best target these often expensive treatments to the right population. In this review we discuss current diagnostic approaches, treatment and potential prevention strategies, with a special focus on recent advances in the field as well as areas of uncertainty and unmet needs and how to address them.

Performance evaluation of the Becton Dickinson Kiestra™ IdentifA/SusceptA.

OBJECTIVES: New automated modules are required to provide fully automated solutions in diagnostic microbiology laboratories. We evaluated the performance of a Becton Dickinson Kiestra™ IdentifA/SusceptA prototype for MALDI-TOF identification (ID) and Phoenix™ antibiotic susceptibility testing (AST). METHODS: The performance of the IdentifA/SusceptA coupled prototype was compared with manual processing for MALDI-TOF ID on 1302 clinical microbial isolates or ATCC strains and for Phoenix™ M50 AST on 484 strains, representing 61 species. RESULTS: Overall, the IdentifA exhibited similar ID performances than manual spotting. Higher performances were observed for Gram-negative bacteria with an ID at the species level (score >2) of 96.5% (369/382) and 86.9% (334/384), respectively. A significantly better performance was observed with the IdentifA (95.2%, 81/85) compared with manual spotting (75.2%, 64/85) from colonies on MacConkey agar. Contrariwise, the IdentifA exhibited lower ID performances at the species level than manual processing for streptococci (76.1%, 96/126 compared with 92%, 115/125), coagulase-negative staphylococci (73.3%, 44/60 compared with 90%, 54/60) and yeasts (41.3%, 19/46 compared with 78.2%, 36/46). Staphylococcus aureus and enterococci were similarly identified by the two approaches, with ID rates of 92% (65/70) for the IdentifA and 92.7%, (64/69) for manual processing and 94.8%, (55/58) for the IdentifA and 98.2%, (57/58) for manual processing, respectively. The SusceptA exhibited an AST overall essential agreement of 98.82% (6863/6945), a category agreement of 98.86% (6866/6945), 1.05% (6/570) very major errors, 0.16% (10/6290) major errors, and 0.91% (63/6945) minor errors compared to the reference AST. CONCLUSIONS: Overall, the automated IdentifA/SusceptA exhibited high ID and AST performances.

Comparison of SARS-CoV-2 serological tests with different antigen targets.

BACKGROUND: These last months, dozens of SARS-CoV-2 serological tests have become available with varying performances. A major effort was completed to compare 17 serological tests available in April 2020 in Switzerland. METHODS: In a preliminary phase, we compared 17 IgG, IgM, IgA and pan Ig serological tests including ELISA, LFA, CLIA and ECLIA on a panel of 182 sera, comprising 113 sera from hospitalized patients with a positive RT-PCR, and 69 sampled before 1st November 2019, expected to give a positive and negative results, respectively. In a second phase, the five best performing and most available tests were further evaluated on a total of 582 sera (178 and 404 expected positive and negative, respectively), allowing the assessment of 20 possible cross-reactions with other viruses. RESULTS: In the preliminary phase, among eight IgG/pan-Ig ELISA or CLIA/ECLIA tests, five had a sensitivity and specificity above 90 % and 98 % respectively, and on six IgM/IgA tests, only one was acceptable. Only one LFA test on three showed good performances for both IgG and IgM. For all the tests IgM and IgG aroused concomitantly. In the second phase, no test showed particular cross-reaction. We observed an important heterogeneity in the development of the antibody response. CONCLUSIONS: The majority of the evaluated tests exhibited high performances of IgG/pan-Ig sensitivity and specificity to detect the serological response of moderately to critically ill hospitalized patients. The IgM and IgA tests showed mostly insufficient performances with no added value for the early diagnostic on the cohort tested in this study.

Changes in SARS-CoV-2 Spike versus Nucleoprotein Antibody Responses Impact the Estimates of Infections in Population-Based Seroprevalence Studies.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibody responses to the spike (S) protein monomer, S protein native trimeric form, or the nucleocapsid (N) proteins were evaluated in cohorts of individuals with acute infection (n = 93) and in individuals enrolled in a postinfection seroprevalence population study (n = 578) in Switzerland. Commercial assays specific for the S1 monomer, for the N protein, or within a newly developed Luminex assay using the S protein trimer were found to be equally sensitive in antibody detection in the acute-infection-phase samples. Interestingly, compared to anti-S antibody responses, those against the N protein appear to wane in the postinfection cohort. Seroprevalence in a "positive patient contacts" group (n = 177) was underestimated by N protein assays by 10.9 to 32.2%, while the "randomly selected" general population group (n = 311) was reduced by up to 45% relative to the S protein assays. The overall reduction in seroprevalence targeting only anti-N antibodies for the total cohort ranged from 9.4 to 31%. Of note, the use of the S protein in its native trimer form was significantly more sensitive compared to monomeric S proteins. These results indicate that the assessment of anti-S IgG antibody responses against the native trimeric S protein should be implemented to estimate SARS-CoV-2 infections in population-based seroprevalence studies.IMPORTANCE In the present study, we have determined SARS-CoV-2-specific antibody responses in sera of acute and postinfection phase subjects. Our results indicate that antibody responses against viral S and N proteins were equally sensitive in the acute phase of infection, but that responses against N appear to wane in the postinfection phase where those against the S protein persist over time. The most sensitive serological assay in both acute and postinfection phases used the native S protein trimer as the binding antigen, which has significantly greater conformational epitopes for antibody binding compared to the S1 monomer protein used in other assays. We believe these results are extremely important in order to generate correct estimates of SARS-CoV-2 infections in the general population. Furthermore, the assessment of antibody responses against the trimeric S protein will be critical to evaluate the durability of the antibody response and for the characterization of a vaccine-induced antibody response.