Predictors and Dynamics of the Humoral and Cellular Immune Response to SARS-CoV-2 mRNA Vaccines in Hemodialysis Patients: A Multicenter Observational Study.

BACKGROUND: Preliminary evidence suggests patients on hemodialysis have a blunted early serological response to SARS-CoV-2 vaccination. Optimizing the vaccination strategy in this population requires a thorough understanding of predictors and dynamics of humoral and cellular immune responses to different SARS-CoV-2 vaccines. METHODS: This prospective multicenter study of 543 patients on hemodialysis and 75 healthy volunteers evaluated the immune responses at 4 or 5 weeks and 8 or 9 weeks after administration of the BNT162b2 or mRNA-1273 vaccine, respectively. We assessed anti-SARS-CoV-2 spike antibodies and T cell responses by IFN-γ secretion of peripheral blood lymphocytes upon SARS-CoV-2 glycoprotein stimulation (QuantiFERON assay) and evaluated potential predictors of the responses. RESULTS: Compared with healthy volunteers, patients on hemodialysis had an incomplete, delayed humoral immune response and a blunted cellular immune response. Geometric mean antibody titers at both time points were significantly greater in patients vaccinated with mRNA-1273 versus BNT162b2, and a larger proportion of them achieved the threshold of 4160 AU/ml, corresponding with high neutralizing antibody titers in vitro (53.6% versus 31.8% at 8 or 9 weeks, P <0.0001). Patients vaccinated with mRNA-1273 versus BNT162b2 exhibited significantly greater median QuantiFERON responses at both time points, and a larger proportion achieved the threshold of 0.15 IU/ml (64.4% versus 46.9% at 8 or 9 weeks, P <0.0001). Multivariate analysis identified COVID-19 experience, vaccine type, use of immunosuppressive drugs, serum albumin, lymphocyte count, hepatitis B vaccine nonresponder status, and dialysis vintage as independent predictors of the humoral and cellular responses. CONCLUSIONS: The mRNA-1273 vaccine's greater immunogenicity may be related to its higher mRNA dose. This suggests a high-dose vaccine might improve the impaired immune response to SARS-CoV-2 vaccination in patients on hemodialysis.

Epidemiology and clinical impact of viral, atypical, and fungal respiratory pathogens in symptomatic immunocompromised patients: a two-center study using a multi-parameter customized respiratory Taqman® array card.

The prevalence of respiratory viruses in immunocompromised adult patients and the association with clinical outcomes is still underexplored. Our goal was to assess the epidemiology and the potential clinical impact of respiratory viral infections in a high-risk patient population. Two large hospitals performed a respiratory Taqman array card (TAC), targeting 24 viruses, 8 bacteria, and 2 fungi simultaneously, on 435 samples from 397 symptomatic immunocompromised patients. Clinical details were collected retrospectively using a structured case report form. An overall positivity rate of 68% was found (51% mono- and 17% co-infections). Pathogen distribution was as follows: influenza A (20.7%), rhinoviruses (15.2%), coronaviruses (7.8%), Pneumocystis jirovecii (7.4%), RSV (7.1%), and CMV (6.0%) were the most frequently encountered, followed by HSV (5.5%), hMPV (4.4%), parainfluenza viruses (3.9%), influenza B (3.7%), and Aspergillus species (3.7%). Other pathogens were not detected or detected only in ≤ 1% of samples. Hospital and ICU admission rates were 84% and 11%, respectively. The presence of a pathogen was strongly associated with higher need for supplemental oxygen (p = 0.001), but it had no impact on ICU admission, mechanical ventilation requirement, antibacterial therapy, or mortality. In conclusion, our study described the epidemiology of respiratory pathogens in a large group of symptomatic immunocompromised patients and provides evidence of a relationship between pathogen detection and the need for supplemental oxygen. This association was still found after the exclusion of the results positive for influenza viruses, suggesting that non-influenza viruses contribute to severe respiratory illness in patients with compromised immunity.

Screening for Chlamydia trachomatis and Neisseria gonorrhoeae Infections in Men Who Have Sex With Men: Diagnostic Accuracy of Nucleic Acid Amplification Test on Pooled Urine, Anorectal, and Pharyngeal Specimens.

Neisseria gonorrhoeae and Chlamydia trachomatis screening was performed in a cohort of 100 men who have sex with men. A nucleic acid amplification test on a pooled sample of first-pass urine, pharyngeal, and anorectal specimens was compared with results on nonpooled samples. Despite an excellent agreement (Cohen κ, 0.932), pooling specimens reduced test sensitivity to 89.5%.

Fluoroquinolone resistant rectal colonization predicts risk of infectious complications after transrectal prostate biopsy.

PURPOSE: Infection after transrectal prostate biopsy has become an increasing concern due to fluoroquinolone resistant bacteria. We determined whether colonization identified by rectal culture can identify men at high risk for post-transrectal prostate biopsy infection. MATERIALS AND METHODS: Six institutions provided retrospective data through a standardized, web based data entry form on patients undergoing transrectal prostate biopsy who had rectal culture performed. The primary outcome was any post-transrectal prostate biopsy infection and the secondary outcome was hospital admission 30 days after transrectal prostate biopsy. We used chi-square and logistic regression statistical analysis. RESULTS: A total of 2,673 men underwent rectal culture before transrectal prostate biopsy from January 1, 2007 to September 12, 2013. The prevalence of fluoroquinolone resistance was 20.5% (549 of 2,673). Fluoroquinolone resistant positive rectal cultures were associated with post-biopsy infection (6.6% vs 1.6%, p <0.001) and hospitalization (4.4% vs 0.9%, p <0.001). Fluoroquinolone resistant positive rectal culture increased the risk of infection (OR 3.98, 95% CI 2.37-6.71, p <0.001) and subsequent hospital admission (OR 4.77, 95% CI 2.50-9.10, p <0.001). If men only received fluoroquinolone prophylaxis, the infection and hospitalization proportion increased to 8.2% (28 of 343) and 6.1% (21 of 343), with OR 4.77 (95% CI 2.50-9.10, p <0.001) and 5.67 (95% CI 3.00-10.90, p <0.001), respectively. The most common fluoroquinolone resistant bacteria isolates were Escherichia coli (83.7%). Limitations include the retrospective study design, nonstandardized culture and interpretation of resistance methods. CONCLUSIONS: Colonization of fluoroquinolone resistant organisms in the rectum identifies men at high risk for infection and subsequent hospitalization from prostate biopsy, especially in those with fluoroquinolone prophylaxis only.

Failure of PCR-Based IS6110 analysis to detect vertebral spondylodiscitis caused by Mycobacterium bovis.

Mycobacterium bovis is responsible for a zoonosis originating in cattle. We report a case of a man with vertebral spondylodiscitis caused by Mycobacterium bovis. Diagnosis was complicated because of the lack of IS6110. These strains are rare, but microbiologists should be aware of their existence.

Clinical and microbiological evaluation of temocillin for bloodstream infections with Enterobacterales: a Belgian single-centre retrospective study.

Background: Expanding the use of temocillin could be an important weapon in the fight against antimicrobial resistance. However, EUCAST defined clinical breakpoints for a limited number of species and only for urinary tract infections (UTI), including urosepsis but excluding severe sepsis and septic shock. Moreover, a dosage of 2 g q8h is advised in most cases. Objectives: Evaluation of temocillin use for the treatment of bacteraemia, correlating clinical and microbiological outcomes with infection site, infection severity, temocillin dosage, Enterobacterales species and MIC. Patients and methods: All adult patients with blood cultures positive for temocillin-susceptible Enterobacterales and treated with temocillin for ≥72 h from June 2018 until June 2021 were considered for inclusion. The primary outcome was clinical success, defined as resolution of infection signs, no relapse of the same infection and no antibiotic switch due to insufficient clinical improvement. The secondary outcome was microbiological success. Results: In total, 182 episodes were included [140 UTI versus 42 non-UTI, 171 Escherichia coli, Klebsiella species (except Klebsiella aerogenes) and Proteus mirabilis (EKPs) versus 11 non-EKPs]. Clinical and microbiological failure were low (8% and 3%, respectively). No difference in outcome was observed for dosages of 2 g q12h versus 2 g q8h, either for EKP versus non-EKP isolates or MIC values ≤8 versus 16 mg/L. Considering only bacteraemia episodes of UTI origin, using the 16 mg/L breakpoint, there was no difference in success rate between regimens of 2 g q12h and 2 g q8h. Conclusions: Temocillin 2 g q12h can be successfully used for the treatment of systemic UTI. Prospective studies are needed to assess outcomes and evaluate non-inferiority compared with other broad-spectrum antibiotics in non-UTI infections, including bacteraemia.

Population-wide persistent hemostatic changes after vaccination with ChAdOx1-S.

Various vaccines were developed to reduce the spread of the Severe Acute Respiratory Syndrome Cov-2 (SARS-CoV-2) virus. Quickly after the start of vaccination, reports emerged that anti-SARS-CoV-2 vaccines, including ChAdOx1-S, could be associated with an increased risk of thrombosis. We investigated the hemostatic changes after ChAdOx1-S vaccination in 631 health care workers. Blood samples were collected 32 days on average after the second ChAdOx1-S vaccination, to evaluate hemostatic markers such as D-dimer, fibrinogen, α2-macroglobulin, FVIII and thrombin generation. Endothelial function was assessed by measuring Von Willebrand Factor (VWF) and active VWF. IL-6 and IL-10 were measured to study the activation of the immune system. Additionally, SARS-CoV-2 anti-nucleoside and anti-spike protein antibody titers were determined. Prothrombin and fibrinogen levels were significantly reduced after vaccination (-7.5% and -16.9%, p < 0.0001). Significantly more vaccinated subjects were outside the normal range compared to controls for prothrombin (42.1% vs. 26.4%, p = 0.026) and antithrombin (23.9% vs. 3.6%, p = 0.0010). Thrombin generation indicated a more procoagulant profile, characterized by a significantly shortened lag time (-11.3%, p < 0.0001) and time-to-peak (-13.0% and p < 0.0001) and an increased peak height (32.6%, p = 0.0015) in vaccinated subjects compared to unvaccinated controls. Increased VWF (+39.5%, p < 0.0001) and active VWF levels (+24.1 %, p < 0.0001) pointed toward endothelial activation, and IL-10 levels were significantly increased (9.29 pg/mL vs. 2.43 pg/mL, p = 0.032). The persistent increase of IL-10 indicates that the immune system remains active after ChAdOx1-S vaccination. This could trigger a pathophysiological mechanism causing an increased thrombin generation profile and vascular endothelial activation, which could subsequently result in and increased risk of thrombotic events.

Combination of line immunoassays Mikrogen recomLine CMV IgG and recomLine CMV IgG Avidity helps to date the onset of CMV primary infection.

CMV IgG avidity assays are widely used and can be helpful in pregnant women to date the onset of CMV primary infection; however, these tests are not standardized and sometimes give inconclusive results. We evaluated the performances of Mikrogen recomLine CMV IgG and IgG Avidity compared to the VIDAS CMV IgG Avidity. On a first sample set of 89 sequential sera collected from 40 women with precisely determined onset of CMV primary infection, the combination of Mikrogen recomLine CMV IgG and IgG Avidity showed an accurate interpretation in 83.1% (74/89), an incorrect result in 4.5% (4/89), and an inconclusive result in 12.4% (11/89) and showed a better sensitivity to diagnose infections <14 weeks compared to VIDAS (85.9% vs. 76.9%). On a second sample set of 89 sera with an intermediate VIDAS CMV IgG Avidity, the combination of line immunoassays provided additional information on the time of infection in 79% (70/89) of the samples. This combination of line assays is useful as additional confirmatory testing and can help to date more precisely the onset of CMV primary infection.

Nocardia polymerase chain reaction (PCR)-based assay performed on bronchoalveolar lavage fluid after lung transplantation: A prospective pilot study.

BACKGROUND: Transplant recipients are at risk of pulmonary nocardiosis, a life-threatening opportunistic infection caused by Nocardia species. Given the limitations of conventional diagnostic techniques (i.e., microscopy and culture), a polymerase chain reaction (PCR)-based assay was developed to detect Nocardia spp. on clinical samples. While this test is increasingly being used by transplant physicians, its performance characteristics are not well documented. We evaluated the performance characteristics of this test on bronchoalveolar lavage (BAL) fluid samples from lung transplant recipients (LTRs). METHODS: We prospectively included all BAL samples from LTRs undergoing bronchoscopy at our institution between December 2016 and June 2017 (either surveillance or clinically-indicated bronchoscopies). Presence of microbial pathogens was assessed using techniques available locally (including microscopy and 10-day culture for Nocardia). BAL samples were also sent to the French Nocardiosis Observatory (Lyon, France) for the Nocardia PCR-based assay. Transplant physicians and patients were blinded to the Nocardia PCR results. RESULTS: We included 29 BAL samples from 21 patients (18 surveillance and 11 clinically-indicated bronchoscopies). Nocardiosis was not diagnosed in any of these patients by conventional techniques. However, Nocardia PCR was positive in five BAL samples from five of the patients (24%, 95% confidence interval: 11-45%); four were asymptomatic and undergoing surveillance bronchoscopy, and one was symptomatic and was later diagnosed with influenza virus infection. None of the five PCR-positive patients died or were diagnosed with nocardiosis during the median follow-up of 21 months after the index bronchoscopy (range: 20-23 months). CONCLUSIONS: In this prospective study, Nocardia PCR was positive on BAL fluid from one fourth of the LTRs. Nocardia PCR-based assays should be used with caution on respiratory samples from LTRs because of the possible detection of airway colonization using this technique. Larger studies are required to determine the usefulness of the Nocardia PCR-based assay in transplant recipients.

MALDI-TOF MS typing of a nosocomial methicillin-resistant Staphylococcus aureus outbreak in a neonatal intensive care unit.

BACKGROUND: The early detection of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak is decisive to control its spread and rapidly initiate adequate infection control measures. Therefore, prompt determination of epidemiologic relatedness of clinical MRSA isolates is essential. Genetic typing methods have a high discriminatory power but their availability remains restricted. In this study, we aimed to challenge matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a typing tool of a nosocomial MRSA outbreak in a neonatal intensive care unit. METHODS: Over a 2-year period, 15 MRSA isolates were recovered from patients (n = 14) and health care workers (n = 1) at the neonatal intensive care unit. Five reference strains were included for comparison. Identification was performed by MALDI-TOF MS and susceptibility profiles determined by automated broth microdilution. Typing analysis by MALDI-TOF MS included mean spectrum profiles and subsequent dendrogram creation using BioNumerics software. Results were compared with spa typing and pulsed-field gel electrophoresis (PFGE). RESULTS: Our study showed good concordance (93%) between PFGE, spa typing, and MALDI-TOF MS for the outbreak-related MRSA strains. MALDI-TOF MS typing showed excellent typeability and discriminatory power but showed poor reproducibility. CONCLUSIONS: This study is one of the first to document the potential usefulness of MALDI-TOF MS with standardized data analysis as a typing tool for investigating a nosocomial MRSA outbreak. A concordance of 93% compared to reference typing techniques was observed. However, because of poor reproducibility, long-term follow-up of prospective isolated strains is not practical for routine use. Further studies are needed to confirm our observations.

Performance evaluation of direct fluorescent antibody, Focus Diagnostics Simplexa™ Flu A/B & RSV and multi-parameter customized respiratory Taqman® array card in immunocompromised patients.

BACKGROUND: Molecular assays for diagnosis of Flu A, Flu B, and RSV with short turn-around-time (TAT) are of considerable clinical importance. In addition, rapid and accurate diagnosis of a large panel of viral and atypical pathogens can be crucial in immunocompromised patients. OBJECTIVES: First, to evaluate the performance of the Simplexa™ Direct assay system in comparison with direct fluorescent antibody (DFA) and customized Taqman® Array Card (TAC) testing for RSV, Flu A, and Flu B in immunocompromised patients. Second, to evaluate different algorithms for the detection of respiratory pathogens in terms of cost, turn-around-time (TAT) and diagnostic yield. STUDY DESIGN: We collected 125 nasopharyngeal swabs (NTS) and 25 BAL samples from symptomatic immunocompromised patients. Samples for which Simplexa™ and TAC results were discordant underwent verification testing. The TAC assay is based on singleplex RT-PCR, targeting 24 viruses, 8 bacteria and 2 fungi simultaneously. RESULTS: The overall sensitivity was significantly lower for DFA testing than for the two molecular methods (p<0.05). Performance characteristics of Simplexa™ testing were not significantly different compared to TAC testing (p>0.1). For BAL samples only, the sensitivity and specificity of the Simplexa™ assay was 100%. In total, 6.7, 16 and 18% of samples were positive for Flu A, Flu B or RSV by DFA, Simplexa™ and TAC testing, respectively. When considering not only these pathogens but also all results for TAC, the method identified 93 samples with one or more respiratory pathogens (62%). A co-infection rate of 15.3% was found by TAC. The estimated costs and TAT were 8.2€ and 2h for DFA, 31.8€ and 1.5h for Simplexa™ and 55€ and 3h for TAC testing. CONCLUSIONS: Performing the Simplexa™ test 24h a day/7 days a week instead of DFA would considerably improve the overall sensitivity and time-to-result, albeit at a higher cost generated in the laboratory. Performing the TAC would increase the diagnostic yield and detection of co-infections significantly.

HCV false positive immunoassays in patients with LVAD: A potential trap!

BACKGROUND: Left ventricular assist devices (LVAD) are a therapeutic choice for patients with advanced heart failure prior cardiac transplantation. Patients with a LVAD implant are frequently monitored for hepatitis C virus (HCV) as a positive result may be an exclusion criterion for transplantation. OBJECTIVES: To determine the rate of false positive results with immunoassays for HCV antibodies in a LVAD population. STUDY DESIGN: Between June 2011 and January 2015, HCV antibody testing using a chemiluminescent immunoassay (CLIA) (Liaison, Diasorin) was performed for 32 patients prior and post LVAD implantation. A HCV reactive result by CLIA was repeated and further tested by an enzyme linked fluorescent assay (ELFA) (VIDAS, bioMérieux). For patients with a positive HCV CLIA and ELFA test, immunoblot and HCV RNA detection were performed. RESULTS: Prior to LVAD implantation, all patients showed a negative HCV serology. After LVAD implantation, 19 patients (59%) had positive results for HCV antibody using CLIA and ELFA technologies. The HCV immunoblot was negative for 17 patients and indeterminate for two patients. For 15 patients, HCV RNA detection was performed and was undetectable. Actually, no HCV infections were observed among those who were tested for HCV RNA. CONCLUSIONS: HCV serological tests routinely used in our laboratories are not reliable in patients with cardiac devices. A positive CLIA and/or ELFA reaction in patients with a LVAD should be confirmed by HCV immunoblot and by HCV RNA PCR detection in order to rule out a HCV infection.

Clinical evaluation of a multi-parameter customized respiratory TaqMan(®) array card compared to conventional methods in immunocompromised patients.

BACKGROUND: Respiratory viral infections can cause significant morbidity and mortality in immunocompromised patients. Conventional tests routinely available at most institutions are limited by the number of detectable pathogens, by a poor sensitivity and/or a long turnaround time. OBJECTIVES: To compare the performance of routine conventional testing with direct fluorescent antibody assays and viral culture to a customized TaqMan® array card (TAC) real-time PCR method, targeting 24 viruses, 8 bacteria and 2 fungi simultaneously. STUDY DESIGN: We collected 143 respiratory samples from 120 symptomatic immunocompromised patients. Samples for which conventional and TAC results were discordant underwent further verification testing. RESULTS: The TAC assay identified viral pathogens in more samples than did conventional testing (77/143 versus 27/143; McNemar P<0.0001), even when TAC results for viruses that could not be detected by conventional testing were excluded from analysis (59/143 versus 26/143; P<0.0001). In addition, the TAC assay identified 18 samples with non-viral pathogens. Verification testing confirmed positive TAC results for 50 out of 55 samples for which conventional testing was negative. Two out of three samples with a positive conventional test but negative TAC result were confirmed positive. A viral and a total pathogen co-infection rate of 5.6% and 11.8% were found, respectively. CONCLUSIONS: The customized TAC assay resulted in a significantly increased identification of respiratory viruses. This study provides a practical real-life assessment of the performance of the TAC assay in a population for whom rapid and accurate diagnosis of viral and atypical pathogens is crucial for appropriate clinical management.

Towards multitarget testing in molecular microbiology.

Advantages of PCR assays over more conventional culture-based diagnostics include significantly higher sensitivities and shorter turnaround times. They are particularly useful when patient treatment has already been initiated or for specimens that may contain microorganisms that are slow-growing, difficult to culture, or for which culture methods do not exist. However, due to genome variability, single target testing might lead to false-negative results. This paper focuses on examples from our own experiences and the literature to provide insight into the limitations of single target testing in molecular biology. Lessons learned from these experiences include the careful design of diagnostic assays, preferably multitargeted, the importance of investigating the incidence and epidemiology of infection in detail, the frequent participation in appropriate quality assurance schemes, and the importance of continuous attentiveness by investigators when confronted with inconsistent results. In conclusion, multitargeted testing in microbiological molecular assays should be a rule.