Combined oropharyngeal/nasal swab is equivalent to nasopharyngeal sampling for SARS-CoV-2 diagnostic PCR.

BACKGROUND: Early 2020, a COVID-19 epidemic became a public health emergency of international concern. To address this pandemic broad testing with an easy, comfortable and reliable testing method is of utmost concern. Nasopharyngeal (NP) swab sampling is the reference method though hampered by international supply shortages. A new oropharyngeal/nasal (OP/N) sampling method was investigated using the more readily available throat swab. RESULTS: 35 patients were diagnosed with SARS-CoV-2 by means of either NP or OP/N sampling. The paired swabs were both positive in 31 patients. The one patient who tested negative on both NP and OP/N swab on admission, was ultimately diagnosed on bronchoalveolar lavage fluid. A strong correlation was found between the viral RNA loads of the paired swabs (r = 0.76; P < 0.05). The sensitivity of NP and OP/N analysis in hospitalized patients (n = 28) was 89.3% and 92.7% respectively. CONCLUSIONS: This study demonstrates equivalence of NP and OP/N sampling for detection of SARS-CoV-2 by means of rRT-PCR. Sensitivity of both NP and OP/N sampling is very high in hospitalized patients.

To pool or not to pool? Screening of Chlamydia trachomatis and Neisseria gonorrhoeae in female sex workers: pooled versus single-site testing.

OBJECTIVES: As Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are the most commonly reported STIs in Belgium and the majority of women infected are asymptomatic, targeted screening of patients in specified risk groups is indicated. To prevent long-term complications and interrupt transmission, extragenital samples should be included. As this comes with a substantial extra cost, analysis of a pooled sample from vaginal and extragenital sites could be a solution. In this study, we evaluated the feasibility of molecular testing for CT and NG in pooled versus single-site samples in a large cohort of female sex workers. METHODS: Women were sampled from three anatomical sites: a pharyngeal, a vaginal and a rectal swab. Each sample was vortexed, and 400 µL of transport medium from each sample site was pooled into an empty tube. NAAT was performed using the Abbott RealTime CT/NG assay on the m2000sp/rt system. RESULTS: We included 489 patients: 5.1% were positive for CT; 2.0% were positive for NG and 1.4% were coinfected, resulting in an overall prevalence of 6.5% (95% CI 4.5% to 9.1%) for CT and 3.5% (95% CI 2.0% to 5.5%) for NG. From the 42 patients positive on at least one non-pooled sample, only 5 gave a negative result on the pooled sample, resulting in a sensitivity of 94% (95% CI 79% to 99%) for CT and 82% (95% CI 57% to 96%) for NG. The missed pooled samples were all derived from single-site infections with low bacterial loads. The possibility of inadequate self-sampling as a cause of false negativity was excluded, as 4/5 were collected by the physician. Testing only vaginal samples would have led to missing 40% of CT infections and 60% of NG infections. CONCLUSIONS: Pooling of samples is a cost-saving strategy for the detection of CT and NG in women, with minimal decrease in sensitivity. By reducing costs, more patients and more extragenital samples can be tested, resulting in higher detection rates.

Interpretation of EBV serology for human body material donors: Is there a need for early antigen IgG and heterophile antibodies testing?

In this report we evaluated a diagnostic algorithm, proposed by the Belgian Superior Health Council, to detect acute and past Epstein-Barr virus (EBV) infections by means of serology in donors of human body material for transplantation. The available EBV serology parameters were tested on eighty serum samples on three random access analysers: Architect i2000 SR, Liasion XL and BioPlex 2200. The EBV sero-status was determined according to the proposed algorithm and results were compared between the different analysers. Seventy one % of the samples gave concordant interpretations on the three analysers. Most of the discordant results were attributable to early antigen (EA) IgG. The knowledge of the EA IgG and heterophile antibodies (HA) IgM status provided only limited added value and was only useful to distinguish between a very early acute infection and false positivity of viral capsid antigen IgM. The diagnostic algorithm proposed by the Belgian Superior Health Council is merely directive and each individual lab remains responsible for the interpretation and implementation of test combinations for the detection of EBV infections. Our study shows the limited added value of testing for EA IgG and HA IgM, based both on clinical and technical performance.

Improving timelines in reporting results from positive blood cultures: simulation of impact of rapid identification on therapy on a real-life cohort.

For patients with bloodstream infections, rapid initiation of the appropriate antimicrobial therapy is essential in reducing mortality and morbidity. New developments and automation in clinical microbiology labs speed up the identification and susceptibility results but are expensive. To gain insight in the added value of the new workflows, we simulated the possible impact of rapid identification and susceptibility tests on a real-life cohort of 158 positive blood culture episodes. Our routine workflow was theoretically challenged against two new workflows, one based on rapid identification with MALDI-TOF MS and one based on molecular testing. First, we observed an important role of the rapid communication of the gram stain results, as about one third of patients needed an adaptation of the antimicrobial therapy based on these results. Antibiotic adaptation based on the microorganism identification was necessary in 10% and in another 25% of cases after the availability of the susceptibility results. The added value of the newer workflow methods lies mainly in the field of the rapid identification and was rather limited in our cohort. In conclusion, for optimizing the blood culture workflow, each microbiology lab should critically scan its own workflow and know its own blood culture epidemiology, before investing in expensive or time-consuming processes.

Faecal calprotectin: comparative study of the Quantum Blue rapid test and an established ELISA method.

BACKGROUND: Faecal calprotectin is a non-invasive marker for neutrophilic intestinal inflammation. It can be used in the differential diagnosis between functional and organic bowel disease. Moreover, it correlates with endoscopic organic bowel disease activity. The objective of this study is to evaluate a recently launched quantitative immunochromatographic point-of-care test: Quantum Blue Calprotectin (Bühlmann Laboratories AG, Schönenbuch, Switzerland) in comparison to an established ELISA method (Bühlmann Laboratories AG). METHODS: We included 142 samples, either archived (­80°C) faecal extracts or fresh routine samples. Both the normal range cartridges as well as the high range cartridge from the point-of-care test were used. The ELISA was compared with the point-of-care test and the optimal the point-of-care test cut-off values were searched for using Microsoft® Excel 2002 and MedCalc Software version 10.0.0.0 (Mariakerke, Belgium). RESULTS: In the method comparison a determination coefficient (R2) of 0.89 was found. The Passing Bablok regression analysis showed a significant deviation from linearity (y=­40.8+1.0x). The use of a cut-off value of 30 µg/g faeces and a grey zone of 30­110 µg/g faeces resulted in the best agreement between the ELISA interpretation and the point-of-care test interpretation, with 89.4% (127/142) agreement and 10.6% (15/142) mismatches. CONCLUSIONS: We may conclude that the point-of-care test can serve as a reliable alternative to the time consuming ELISA in the differential diagnosis between functional and organic bowel disease. Furthermore, it seems to be reliable in the follow-up of inflammatory bowel disease patients.

VIDAS3® TB-IGRA assay: evaluation of performance characteristics in a predominantly low risk, low incidence population.

OBJECTIVES: To evaluate the analytical performance of the TB-IGRA® assay on the VIDAS3 platform (bioMérieux) when testing a predominantly low risk population in a low incidence area. RESULTS: Eighty-eight percent of the results were concordant between QuantiFERON®-TB Gold-Plus (QFT®-Plus, QIAGEN) and TB-IGRA®. All 12 of 99 (12.1%) discordant results were determined positive only with the TB-IGRA® assay. In 11 of 12 of these discordant cases, no explanation could be found in the medical record. Five of these discrepant results were probably caused by the use of contaminated stimulation reagents. The remaining 6 discrepant samples were also part of the reproducibility experiment and only 2 results were reproducible positive. Overall, in the reproducibility experiment 5 of 25 (20.0 %) results were not repeatable. CONCLUSIONS: the TB-IGRA® assay seems prone to contamination. Besides, we documented a reproducibility of only 80.0% with the TB-IGRA® assay.

Guideline for management of septic arthritis in native joints (SANJO).

This clinical guideline is intended for use by orthopedic surgeons and physicians who care for patients with possible or documented septic arthritis of a native joint (SANJO). It includes evidence and opinion-based recommendations for the diagnosis and management of patients with SANJO.

Different long-term avidity maturation for IgG anti-spike and anti-nucleocapsid SARS-CoV-2 in hospitalized COVID-19 patients.

INTRODUCTION: The high variability of SARS-CoV-2 serological response after COVID-19 infection hampers its use as indicator of the timing of infection. A potential alternative method is the determination of affinity maturation of SARS-CoV-2 IgG, expressed as the SARS-CoV-2 IgG avidity. METHODS: SARS-CoV-2 IgG concentration and avidity were measured in sera of hospitalized COVID-19 patients sampled at two weeks and ≥12 weeks post symptom onset using an in-house developed protocol based on EUROIMMUN (anti-spike) and EDI™ (anti-nucleocapsid) SARS-CoV-2 IgG ELISA protocols. RESULTS: We included 68 confirmed COVID-19 patients that tested positive for SARS-CoV-2 IgG in both the initial and follow-up specimen sampled at a median of 14 (range 10-18) days and 120 (range 84-189) days, respectively, post symptom onset. The median anti-spike and anti-nucleocapsid SARS-CoV-2 IgG avidity response was 40% (range 9-93%) and 72% (range 27-104%), respectively, for the first sample, and 66% (range 28-90%) and 57% (range 25-94%), respectively, for the second sample. The proportion of SARS-CoV-2 IgG avidity results ≥60% was significantly lower for anti-spike compared to anti-nucleocapsid IgG for initial samples (p< 0.01) and vice versa for follow-up samples (p< 0.01). CONCLUSION: Anti-nucleocapsid SARS-CoV-2 IgG maturation occurs faster and avidity decreases faster than anti-spike IgG, indicating different kinetics of anti-spike and anti-nucleocapsid IgG. Further, affinity maturation after SARS-CoV-2 infection is frequently incomplete.

Effects of cascade reporting of susceptibility profiles for Enterobacterales on broad-spectrum antibiotics use and resistance.

OBJECTIVE: To reduce the inappropriate use of broad-spectrum antibiotics in a 1000+ bed acute tertiary care hospital by the introduction of cascade antimicrobial susceptibility reporting for Enterobacterales. METHODS: Over a 1-year period, we selectively suppressed reporting of susceptibility to the broad-spectrum antibiotics piperacillin-tazobactam (TZP) and meropenem (MEM) for Enterobacterales strains susceptible to amoxicillin-clavulanic acid (AMC) and negative for extended-spectrum ß-lactamase (ESBL). We measured the effects on hospital-wide antibiotic consumption (defined daily doses/1000 admissions) and resistance of Escherichia coli and Klebsiella pneumoniae on two levels. First, we compared resistance and antibiotic use for the antibiotics impacted by the intervention (AMC, TZP and MEM) with control antibiotics that were consistently reported (fluoroquinolones, trimethoprim-sulfamethoxazole and third-generation cephalosporins). Second, we compared the resistance for TZP and MEM with a control pathogen (Pseudomonas aeruginosa) and studied the impact on rate of Clostridioides difficile-associated diarrhoea in our hospital. RESULTS: We observed an overall increased use of AMC relative to overall antibiotic consumption (20.0%, p<0.0001) together with a decreased use of TZP (-11.9%, p=0.049) and unchanged use of MEM (p=0.68) relative to overall antibiotic consumption. As for resistance, the number of ESBL-positive K. pneumoniae strains diminished by 5.9% (p<0.0001). When focusing on intensive care units, the carbapenemase-producing Enterobacterales (CPE) rate also decreased by 4.5% (p=0.0091). For E. coli, no significant difference in ESBL (p=0.33) and CPE (p=0.48) rates were observed. No significant difference in the rate of C. difficile infections was observed (p=0.40). CONCLUSIONS: Restricted susceptibility reporting of TZP and MEM was associated with a significant increased use of AMC and decreased use of TZP relative to overall antibiotic consumption and significant reduction in ESBL- and CPE-positive K. pneumoniae strains.

Sensitivity and specificity of 14 SARS-CoV-2 serological assays and their diagnostic potential in RT-PCR negative COVID-19 infections.

BACKGROUND: Molecular detection of SARS-CoV-2 in respiratory samples is the gold standard for COVID-19 diagnosis but it has a long turnaround time and struggles to detect low viral loads. Serology could help to diagnose suspected cases which lack molecular confirmation. Two case reports are presented as illustration. OBJECTIVES: The aim of this study was to evaluate the performance of several commercial assays for COVID-19 serology. We illustrated the added value of COVID-19 serology testing in suspect COVID-19 cases with negative molecular test. STUDY DESIGN: Twenty-three sera from 7 patients with a confirmed molecular diagnosis of SARS-CoV-2 were tested using 14 commercial assays. Additionally, 10 pre-pandemic sera and 9 potentially cross-reactive sera were selected. We calculated sensitivity and specificity. Furthermore, we discuss the diagnostic relevance of COVID-19 serology in a retrospective cohort of 145 COVID-19 cases in which repetitive molecular and serological SARS-CoV-2 tests were applied. RESULTS: The interpretation of the pooled sensitivity of IgM/A and IgG resulted in the highest values (range 14-71% on day 2-7; 88-94% on day 8-18). Overall, the specificity of the assays was high (range 79-100%). Among 145 retrospective cases, 3 cases (2%) remained negative after sequential molecular testing but positive on final SARS-CoV-2 serology. CONCLUSION: Sensitivity of COVID-19 serological diagnosis was variable but consistently increased at >7 days after symptom onset. Specificity was high. Our data suggest that serology can complement molecular testing for diagnosis of COVID-19, especially for patients presenting the 2nd week after symptom onset or later.

Tintelnotia destructans as an emerging opportunistic pathogen: First case of T. destructans superinfection in herpetic keratitis.

PURPOSE: Only recently Tintelnotia was described as a new genus in the Phaeosphaeriaceae family of fungi containing two species, T. opuntiae and T. destructans. Until now, T. destructans keratitis was associated with contact lens wear and ocular trauma. We present the first case of T. destructans keratomycosis presenting as a superinfection in herpetic keratitis. OBSERVATIONS: We present a case of a 53-year-old woman who presented with a unilateral keratitis since 3 weeks without history of trauma or contact lens wear, not responding to topical ofloxacin. Polymerase Chain Reaction (PCR) of the corneal ulcer was positive for Herpes Simplex Virus type 1 (HSV-1). Signs and symptoms progressively improved after starting topical and systemic antiviral therapy. Six weeks later however, our patient presented with a new white infiltrate in the previous herpetic epithelial defect. In vivo confocal microscopy showed fungal hyphae and culture from corneal scrapings identified a hyphomycete. Intensive antimycotic therapy could not prevent a corneal perforation 1 week later. Penetrating keratoplasty was performed with intracameral injection of amphotericin B. Culture of the corneal button and PCR and sequence analysis on the fungal isolate confirmed the diagnosis of T. destructans keratomycosis. Six months after penetrating keratoplasty, biomicroscopy showed a clear graft without recurrence of fungal activity. CONCLUSIONS AND IMPORTANCE: T. destructans is an emerging opportunistic pathogen causing severe keratomycosis. Despite intensive antimycotic therapy, rapid progression to corneal perforation can be seen. Early diagnosis using confocal microscopy, fungal culture and PCR can allow prompt initiation of treatment, which should be guided by in vitro susceptibility testing.

Evaluation of the Seegene Allplex™ Respiratory Panel for diagnosis of acute respiratory tract infections.

Objectives: The Seegene AllplexTM Respiratory panel was retrospectively challenged using a collection of quality control samples (QCMD) and clinical samples previously analysed with validated routine methods. Methods: A collection of 111 samples [43 QCMD samples, 13 bronchoalveolar lavage fluids and 55 nasopharyngeal aspirates/swabs] was tested with Seegene AllplexTM. The clinical samples were tested previously using either FTD® Respiratory Pathogens 21 qPCR assay (Fast Track Diagnostics), an in-house multiplex PCR for Bordetella, or BioGX Sample-ReadyTM Atypical pneumo panel (Becton Dickinson). Samples were stored at -80°C prior to analysis with Seegene Allplex™, nucleic acids were automatically extracted with NucliSENS Easymag (bioMérieux). Samples returning discordant results were subjected to repeat testing and/or additional testing by reference laboratories. Results: Seegene correctly identified 41/43 QCMD samples (95.4%); two samples positive for respiratory syncytial virus (RSV) and human metapneumovirus, respectively, were only correctly identified following repeat testing. In the 56 clinical samples, overall, 97 pathogens were identified: 65 pathogens (67.0%) were detected both by routine methods and Seegene, 24 pathogens (24.7%) only by routine methods, and 8 pathogens (8.2%) only by Seegene. The majority of discordant results was detected in samples with low pathogen load (22/32, 68.8%) and in samples containing multiple pathogens (25/32, 78.1%). Full agreement between methods was observed for influenza, RSV, adenovirus, Bordetella (para)pertussis and Chlamydia pneumoniae. Discordance was observed for human metapneumovirus, coronavirus OC43, bocavirus and parainfluenza virus, mainly type 4. Conclusion: Overall, the Seegene AllplexTM assay performed well for routine detection of important respiratory targets. Acceptable agreement was observed between Seegene and other routine assays.

A recurrent and transesophageal echocardiography-associated outbreak of extended-spectrum ß-lactamase-producing Enterobacter cloacae complex in cardiac surgery patients.

Background: We report a recurrent outbreak of postoperative infections with extended-spectrum ß-lactamase (ESBL)-producing E. cloacae complex in cardiac surgery patients, describe the outbreak investigation and highlight the infection control measures. Methods: Cases were defined as cardiac surgery patients in Ghent University Hospital who were not known preoperatively to carry ESBL-producing E. cloacae complex and who postoperatively had a positive culture for this multiresistant organism between May 2017 and January 2018. An epidemiological investigation, including a case-control study, and environmental investigation were conducted to identify the source of the outbreak. Clonal relatedness of ESBL-producing E. cloacae complex isolates collected from case patients was assessed using whole-genome sequencing-based studies. Results: Three separate outbreak episodes occurred over the course of 9 months. A total of 8, 4 and 6 patients met the case definition, respectively. All but one patients developed a clinical infection with ESBL-producing E. cloacae complex, most typically postoperative pneumonia. Overall mortality was 22% (4/18). Environmental cultures were negative, but epidemiological investigation pointed to transesophageal echocardiography (TEE) as the outbreak source. Of note, four TEE probes showed a similar pattern of damage, which very likely impeded adequate disinfection. The first and second outbreak episode were caused by the same clone, whereas a different strain was responsible for the third episode. Conclusions: Health professionals caring for cardiac surgery patients and infection control specialists should be aware of TEE as possible infection source. Caution must be exercised to prevent and detect damage of TEE probes.

Are vaginal swabs comparable to cervical smears for human papillomavirus DNA testing?

OBJECTIVE: Human papillomavirus (HPV) testing is widely incorporated into cervical cancer screening strategies. Current screening requires pelvic examination for cervical sampling, which may compromise participation. The acceptance could be raised by introducing testing on vaginal swabs. We explored the interchangeability of vaginal swabs and cervical smears for HPV testing, by means of a prospective study conducted in female sex workers (FSWs). Besides, we report on the occurrence of 32 different HPV genotypes in FSW with low-grade squamous intraepithelial lesion (LSIL) or high-grade squamous intraepithelial lesion (HSIL). METHODS: Paired physician-collected vaginal swabs and cervical smears from 303 FSW were tested for HPV using the Abbott RealTime High-Risk HPV assay. Cervical cytology was examined on cervical smears. In case of HSIL/LSIL cytological classification (n=52), both samples were genotyped using INNO-LiPa HPV Genotyping Extra II. RESULTS: The overall prevalence of high-risk (HR)-HPV was 51%. In FSW with HSIL/LSIL cervical cytology, the sensitivity and specificity of vaginal samples for the detection of HR-HPV was 100% and 70% and for probable HR-HPV 100% and 91%. The mean number of genotypes identified in vaginal samples (mean=3.5; 95% confidence interval [CI]=2.8-4.2) was significantly higher than in cervical smear samples (mean=2.6; 95% CI=2.1-3.0) (p=0.001). The most frequently encountered HR-HPV genotypes were HPV16, 31, 51, and 52. CONCLUSION: As our study shows that vaginal swabs are equivalent to cervical smears for the detection of (probable) HR-HPV, vaginal swabs can be used for HPV testing in cervical cancer screening strategies. Given the acceptance of vaginal sampling, this finding offers an opportunity to boost screening coverage.

Macrolide resistance in Mycoplasma genitalium from female sex workers in Belgium.

OBJECTIVES: Mycoplasma genitalium is emerging as an aetiological agent of sexually transmitted infections (STIs). Although M. genitalium is commonly treated with azithromycin, macrolide resistance associated with point mutations in the 23S rRNA gene is emerging. METHODS: In this study, the prevalence of M. genitalium and macrolide resistance in female sex workers (FSW) in Belgium was evaluated by a prospective study conducted between 2015 and 2016. Vaginal swabs were sampled from 303 FSW who underwent testing for M. genitalium along with standard STI screening. All samples positive for M. genitalium were subsequently tested for mutations associated with macrolide resistance. RESULTS: M. genitalium was detected in 10.8% of participants and macrolide resistance-associated mutations (A2058G and A2059G) were found in 6.5% of isolates. CONCLUSIONS: M. genitalium is clearly present in FSW in Belgium. In contrast to other reports, for now the occurrence of macrolide resistance appears limited in this specific target population.

Three cases of OXA-48-like carbapenemase producing Enterobacteriaceae (not) detected using Xpert® Carba-R.

The increasing prevalence of carbapenemase-producing Enterobacteriaceae necessitates laboratories to invest in the detection of these bacteria, both with phenotypic and to a lesser extent molecular methods. OXA-48-like strains are rapidly emerging, especially in Europe. Since the expression level of OXA-48 is low and some strains present with several alleles, some types might be missed by some molecular assays. Three cases of OXA-48-like strains are described here, where the detection was not straightforward.

Enterococcus cecorum sepsis in a patient with liver cirrhosis, successfully treated with ceftriaxone.

Enterococcus cecorum septicemia is rare in humans. This case describes a man with underlying liver cirrhosis, a comorbidity that contributes to half of the E. cecorum infections described in the current literature. The patient was successfully treated with ceftriaxone. Identification of this species was accurately made with Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry and confirmed by 16S rDNA sequencing.