Comparison of five SARS-CoV-2 rapid antigen detection tests in a hospital setting and performance of one antigen assay in routine practice: a useful tool to guide isolation precautions?

BACKGROUND: In a hospital setting, there is a need for rapid detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to guide isolation measures and targeted admission. AIM: To evaluate the diagnostic performance of five SARS-CoV-2 rapid nucleocapsid protein antigen detection (RAD) assays (Biosynex, Biotical, Orient Gene, Panbio and SD Biosensor), and describe the performance and impact of implementation of the SD Biosensor assay in an emergency department. METHODS: Sensitivity and specificity of the five RAD assays were analysed on 100 respiratory samples: 60 real-time reverse transcriptase polymerase chain reaction (rRT-PCR)-confirmed SARS-CoV-2-positive samples, 24 SARS-CoV-2 RNA-negative samples and 16 samples positive for other respiratory pathogens. The manufacturer's protocol was adapted to validate the antigen tests on transport media used for rRT-PCR in the authors' routine practice. The SD Biosensor RAD assay was implemented as a screening method for rapid diagnosis and targeted admission. FINDINGS: Sensitivity of the five RAD assays ranged from 88.9% to 100% for samples with cycle threshold values <26, and specificity ranged from 46.2% to 100%. During the implementation period, 4195 RAD tests were performed. Due to the rapid RAD result, 157 patients were transferred directly to the coronavirus disease 2019 (COVID-19) cohort ward instead of the regular ward (N=47) or the temporary COVID-19 ward (N=110). CONCLUSION: The SD Biosensor, Biotical and Panbio SARS-CoV-2 antigen tests showed acceptable overall performance, and identified the majority of contagious patients. In the context of high prevalence of SARS-CoV-2, RAD tests can be used as a rapid screening tool to guide infection prevention measures and aid targeted admission.

Travel history can make the difference.

Entamoeba histolytica infections are rare in developed countries such as Belgium. A 53-year-old female patient presented with 10 days of fever and mild persisting pain in the right hypochondriac despite 6 days of antibiotic therapy. The anamnesis further revealed that the patient was born in Colombia and visits her native country on a regular basis. An abdominal CT-scan demonstrated a large hepatic abscess of 10×8 cm. The diagnosis of Entamoeba histolytica- infection was confirmed with real-time PCR (RT-PCR) from the aspirated material of the abscess. Remarkably, a half year ago, this patient also presented to the gastro-enterology consultation with intermittent rectal bleeding, loose stools and abdominal discomfort. Rectosigmoidoscopy at that time showed sigmoiddiverticulosis and biopsies were taken. RT-PCR on this material was performed during this second episode and was positive for E. histolytica, confirming an episode of amoebic colitis a half year prior to the discovery of the liver abscess.

Novel Tropheryma species in a lung biopsy sample from a kidney transplant recipient.

OBJECTIVES: A kidney transplant recipient with recurrent pleuritis underwent an open lung biopsy, the results of which revealed multiple nodular infiltrates. Grocott and periodic acid-Schiff staining were positive. Fungal and Tropheryma whipplei PCR were, however, negative. Further identification was needed. METHODS: Formalin-fixed, paraffin-embedded (FFPE) extraction was performed using an FFPE extraction kit. T. whipplei was searched for using a real-time PCR targeting the noncoding repeat specific for T. whipplei. Identification of the bacteria in the extract was done using 16S rDNA and 23S rDNA sequencing and BLAST analysis. Internal transcribed spacer PCR was used for fungal DNA identification. RESULTS: The FFPE extract was negative for fungi and T. whipplei. 16S rDNA sequence analysis of a 1375 bp fragment gave T. whipplei as the best match with 26 mismatches, resulting in only 98% agreement. Sequence analysis of the 23S rDNA gene again gave T. whipplei as the best match, but with only 91% agreement. A pan-Tropheryma 16S rDNA real-time PCR was developed, and both the biopsy sample and a respiratory sample of the patient were strongly positive. The patient received antimicrobial treatment targeting T. whipplei with good clinical outcome. CONCLUSIONS: 16S and 23S rDNA sequencing gave T. whipplei as the best hit, although with limited agreement. These findings suggest that a novel Tropheryma species that lacks the noncoding repeat, most frequently used for molecular detection of Whipple disease, might be the cause of the pulmonary disease. Adaptation of current PCR protocols is warranted in order to detect all Tropheryma species.

A hospital-level cost-effectiveness analysis model for toxigenic Clostridium difficile detection algorithms.

BACKGROUND: Despite thorough analyses of the analytical performance of Clostridium difficile tests and test algorithms, the financial impact at hospital level has not been well described. Such a model should take institution-specific variables into account, such as incidence, request behaviour and infection control policies. AIM: To calculate the total hospital costs of different test algorithms, accounting for days on which infected patients with toxigenic strains were not isolated and therefore posed an infectious risk for new/secondary nosocomial infections. METHODS: A mathematical algorithm was developed to gather the above parameters using data from seven Flemish hospital laboratories (Bilulu Microbiology Study Group) (number of tests, local prevalence and hospital hygiene measures). Measures of sensitivity and specificity for the evaluated tests were taken from the literature. List prices and costs of assays were provided by the manufacturer or the institutions. The calculated cost included reagent costs, personnel costs and the financial burden following due and undue isolations and antibiotic therapies. Five different test algorithms were compared. FINDINGS AND CONCLUSION: A dynamic calculation model was constructed to evaluate the cost:benefit ratio of each algorithm for a set of institution- and time-dependent inputted variables (prevalence, cost fluctuations and test performances), making it possible to choose the most advantageous algorithm for its setting. A two-step test algorithm with concomitant glutamate dehydrogenase and toxin testing, followed by a rapid molecular assay was found to be the most cost-effective algorithm. This enabled resolution of almost all cases on the day of arrival, minimizing the number of unnecessary or missing isolations.

Staphylococcus saprophyticus bacteremia after ESWL in an immunocompetent woman.

Staphylococcus saprophyticus is a well-known cause of uncomplicated urinary tract infections, especially in young and sexually active women. Presence in blood cultures is rare and often attributed to contamination. When bacteremia is significant, it occurs mostly in patients with hematologic malignancies and is predominantly catheter-related. However, we describe a case of significant bacteremia with S. saprophyticus associated with urinary tract infection after extracorporeal shock wave lithotripsy of an ureterolithiasis in an otherwise healthy patient.

Establishing quality control ranges for temocillin following CLSI-M23-A3 guideline.

OBJECTIVES: This study aimed to establish acceptable quality control ranges for temocillin disk diffusion tests and Etest(®) minimal inhibitory concentrations. METHODS: According to Clinical and Laboratory Standards Institute (CLSI) guideline, a Tier 2 quality control study was performed and involves seven laboratories. Each of them tested 10 replicates of two quality control strains (Escherichia coli ATCC 25922 and E. coli ATCC 35218) on three different media lots and, for disk diffusion, two disk lots. RESULTS: Proposed zone diameter quality control ranges were 12-25 mm for E. coli ATCC 25922 and 19-28 mm for E. coli ATCC 35218. Proposed Etest quality control ranges were 3-24 mg/l for E. coli ATCC 25922 and 2-6 mg/l E. coli ATCC 35218. CONCLUSION: Based on our results, we would advise the use of E. coli ATCC 35218 as QC strain for temocillin susceptibility testing and Etest because ranges obtained are narrower than with E. coli ATCC 25922 and do not overlap temocillin breakpoint.

Let's not forget herpes simplex virus in case of fulminant hepatic failure.

Fulminant herpes simplex virus (HSV) hepatitis is a rare condition, which is usually identified only after orthotopic liver transplantation (OLT) or at autopsy. The most commonly affected individuals are immunosuppressed patients, although HSV hepatitis can occur in immunocompetent patients as well. A high degree of suspicion combined with early diagnostic modalities may improve survival. We present a case report of fulminant herpetic hepatitis, requiring OLT. In addition, a review of the literature was performed.

Brain abscesses with Peptostreptococcus: not unusual after oesophageal dilatation.

A case of a brain abscess following oesophageal dilatation for caustic stenosis in a 67-year old woman is reported. Previously reported cases of brain abscess development after oesophageal dilatation are reviewed. Following oesophageal dilatation, bacteraemia and fever are common but the occurrence of metastatic brain abscesses is rare. The clinical presentation is non-specific, with high fever and neurological findings as most reported signs. The isolated organisms belong to the normal oropharyngeal bacterial flora. Prognosis is satisfactory after early diagnosis and correct management. As a result, clinicians dealing with oesophageal strictures should keep in mind that brain abscess formation is a potential complication of oesophageal dilatation.

Atypical pneumonia due to Chlamydophila psittaci: 3 case reports and review of literature.

Chlamydophila psittaci is the causative agent of psittacosis or ornithosis. The disease is transmitted to men predominantly from birds. Most commonly noted symptoms are fever, headache and cough, but a number of other symptoms or complications may arise such as renal impairment, hepatitis or neurological symptoms. In this article 3 cases of psittacosis are presented, with a review of the literature with emphasis on laboratory diagnosis.

Simultaneous detection of human bocavirus and adenovirus by multiplex real-time PCR in a Belgian paediatric population.

Since the discovery of human bocavirus (hBoV), the virus has been detected worldwide in respiratory tract samples from young children by various polymerase chain reaction (PCR) assays and real-time PCRs (Q-PCR). Until now, no data have been reported on the presence of hBoV in Belgium and the detection of hBoV in a multiplex Q-PCR setting has not been described. The aim of this study was to develop a fast and reliable multiplex Q-PCR for the simultaneous detection of hBoV DNA and adenovirus (AdV) DNA. During the winter of 2004-2005, 445 nasopharyngeal aspirates (NPAs) were analysed from 404 Belgian children up to 5 years old with acute respiratory tract infections (ARTIs). (Co)infections with hBoV, AdV, respiratory syncytial virus (RSV), human metapneumovirus (hMPV) and influenza A virus were investigated. A viral agent was detected in 61% (n = 272/445) of the NPAs. Multiplex Q-PCR found a prevalence of 11% (n = 51/445) hBoV and 13% (n = 58/445) AdV. Coinfections were more frequently found with AdV (62%; n = 36/58) than with hBoV (49%; n = 25/51). Follow-up samples were available from 22 patients with ARTIs. In three patients, hBoV DNA persisted for one month. Multiplex Q-PCR may help in closing the diagnostic gap by addressing a broader range of potential respiratory pathogens.

Monitoring of herpes simplex virus in the lower respiratory tract of critically ill patients using real-time PCR: a prospective study.

Herpes simplex virus (HSV) has increasingly been associated with pulmonary disease in critically ill patients. However, the clinical relevance of HSV is still a topic of debate. Monitoring of HSV in a quantitative way could potentially give relevant information on its role in the pathogenesis of lower respiratory tract infection. A fast and reliable quantitative real-time PCR (Q-PCR) for the quantitative detection of HSV-1 and HSV-2 DNA was developed. A prospective observational study was performed in an intensive-care unit (ICU) to monitor the HSV viral load in lower respiratory tract aspirates of long-term mechanically ventilated patients. HSV was common in the lower respiratory tract (LRT) of critically ill patients with mechanical ventilation for at least 48 h (62%, n = 65/105). Detection of HSV was significantly associated with prolonged mechanical ventilation (p <0.01), prolonged ICU stay (p <0.01), and development of ventilator-associated pneumonia (p = 0.02). Corticosteroid administration (p <0.01) in the ICU and anti-HSV IgG seropositivity (p <0.01) were risk factors for the occurrence of HSV in the LRT. The fact that no HSV-seronegative patient became positive suggests that all HSV DNA-positive patients had HSV reactivations. Monitoring the HSV viral load in the LRT of critically ill patients showed a typical homogeneous pattern of HSV kinetics. HSV emerged in tracheal and bronchial aspirates after a median of 7 days of intubation (5-11 days), and this was followed by an exponential increase (c. 1 log copies/mL/day) to reach very high HSV peaks (10(6)-10(10) copies/mL) in 78% of the HSV DNA-positive patients.

Pathogens in early-onset and late-onset intensive care unit-acquired pneumonia.

OBJECTIVES: To compare the type of pathogens isolated from patients with early-onset intensive care unit (ICU)-acquired pneumonia with those isolated from patients with late-onset ICU-acquired pneumonia and to study risk factors for the isolation of pathogens that are potentially resistant to multiple drugs. DESIGN: Prospective cohort study. SETTING: Patients admitted to the ICU of a 677-bed, university-affiliated teaching hospital in Belgium during 1997-2002. METHODS: ICU-acquired pneumonia was defined as a case of pneumonia that occurred 2 days or more after admission to the ICU in combination with a positive results of radiologic analysis, clinical signs and symptoms, and a positive culture result. All cases of pneumonia were categorized as either early onset (within 7 days after admission) and late onset (7 days or more after admission), with or without previous antibiotic treatment, and the corresponding pathogens were analyzed. Risk factors for the isolation of pathogens potentially resistant to multiple drugs (ie, Pseudomonas aeruginosa, Serratia marcescens, Enterobacter species, Morganella morganii, methicillin-resistant Staphylococcus aureus, Citrobacter species, Acinetobacter species, Burkholderia species, extended-spectrum beta -lactamase-producing pathogens, and Stenotrophomonas maltophilia) were analyzed using logistic regression analysis. RESULTS: A total of 4,200 patients stayed at the ICU for 2 or more days, 298 of whom developed ICU-acquired pneumonia, for an overall incidence of 13 cases (95% confidence interval [CI], 11-14 cases) per 1,000 ICU-days. Pathogens potentially resistant to multiple drugs were isolated from 52% of patients with early-onset pneumonia. Risk factors for the isolation of these pathogens were greater age and previous receipt of antibiotic prophylaxis (adjusted odds ratio [aOR], 4.6 [95% CI, 1.6-13.0]) or antibiotic therapy (aOR, 8.2 [95% CI, 2.8-23.8]). The length of ICU admission and hospital stay were weaker risk factors for the isolation of these pathogens. CONCLUSIONS: Pathogens potentially resistant to multiple drugs were isolated in 52% of cases of early-onset ICU-acquired pneumonia. Previous antibiotic use (both prophylactic and therapeutic) is the main risk factor for the isolation of these pathogens.

Use of a multiplex real-time PCR to study the incidence of human metapneumovirus and human respiratory syncytial virus infections during two winter seasons in a Belgian paediatric hospital.

Viruses are an important cause of acute respiratory tract infection (ARTI) in children. This study aimed to develop and evaluate a rapid molecular diagnostic test (duplex real-time PCR) for human respiratory syncytial virus (hRSV) and human metapneumovirus (hMPV), and to determine the frequency of these two viruses as causative agents of ARTI in Belgium. Nasopharyngeal aspirates were collected over two winter and spring seasons (November 2003 to May 2004 and November 2004 to May 2005) from children aged <5 years with ARTI (n = 778). The duplex real-time PCR showed a linear range of 10(4)-10(10) copies/mL for both hMPV and hRSV. Analysis of the stability of the hRSV and hMPV genomes revealed that nasopharyngeal aspirates could be stored at room temperature for up to 1 month without significant loss of detection. hRSV was detected by antigen testing and by real-time PCR; hMPV was detected by real-time PCR only. The hRSV antigen test was less sensitive than PCR, and failed to detect one-third of the hRSV infections. Overall, 54 (6.9%) and 306 (39.3%) of the 778 samples were positive for hMPV and hRSV, respectively. Both viruses infected young infants, but the mean age of infants infected by hRSV was lower than that of infants infected by hMPV (12 months vs. 17 months, respectively).

Polyclonal emergence and importation of community-acquired methicillin-resistant Staphylococcus aureus strains harbouring Panton-Valentine leucocidin genes in Belgium.

OBJECTIVES: Worldwide spread of a limited number of Panton-Valentine leucocidin (PVL) -producing methicillin-resistant Staphylococcus aureus (MRSA) clones has been reported in various communities. The objective of this study was to describe the molecular characteristics of the first PVL-positive MRSA strains isolated in Belgium. METHODS: Clinical MRSA isolates (n = 41) collected from 2002 to 2004 from Belgian patients were investigated for the PVL gene by PCR. PVL-positive isolates were genotyped by PFGE, staphylococcal cassette chromosome mec (SCCmec) typing, spa sequence typing, accessory gene regulator (agr) polymorphism and multi-locus sequence typing (MLST). Susceptibility to 14 antimicrobials was determined by the disc diffusion method. Genes encoding resistance to tetracyclines, aminoglycosides and macrolide-lincosamide-streptogramin were determined by PCR. RESULTS: Sixteen isolates carried lukS-lukF genes that encode the PVL toxin. All but one isolate were community-acquired. Three patients reported recent travel to North Africa and South America. They were associated with skin or soft tissue infections, bacteraemia and peritonitis. By molecular typing, they belonged to five genotypes: ST80-SCCmec IV, ST8-SCCmec IV, ST30-SCCmec IV, ST153-SCCmec IV and ST88-SCCmec IV. They belonged to the agr type 3 except for ST8 strains, which showed agr type 1. All isolates were susceptible to fluoroquinolones. Approximately, half of them were resistant to tetracycline, fusidic acid and kanamycin. Tetracycline-resistant strains harboured the tet(K) gene and resistance to kanamycin was associated with the aph3'-IIIa gene. The single erythromycin-resistant isolate harboured msr(A/B) genes conferring the M resistance phenotype. CONCLUSIONS: These results indicate the recent emergence and sporadic importation into Belgium of PVL-positive community-associated MRSA strains belonging to five distinct clones.

A change in Belgian epidemic methicillin-resistant Staphylococcus aureus phage types in 2000: phenotypic and genotypic characterization of isolates from a general hospital.

During 2000, new methicillin-resistant Staphylococcus aureus (MRSA) epidemic phage types became preponderant in Belgium. In the present study, phenotypic and genotypic characteristics of 130 MRSA isolates from a general Belgian hospital were investigated. The MRSA nature of the isolates was confirmed by coagulase test, oxacillin screen plate test and detection of the mecA gene by polymerase chain reaction. Phage typing categorized the MRSA strains into two main groups: the [O]* types and the [J]* types. SmaI macrorestriction analysis by pulsed-field gel electrophoresis gave the same pulsotype in the majority of strains. All strains of the [O]* and [J]* groups, except one, belonged to this pulsotype. Aminoglycoside-modifying-enzyme genes could only be detected in a minority of strains. Although the epidemic phage types of the mid-1990s appear to have been supplanted by the [O]* and [J]* groups, the MRSA population examined showed a remarkably uniform profile corresponding to the previous major clone B.

Ten years phage-typing of Belgian clinical methicillin-resistant Staphylococcus aureus isolates (1992-2001).

Gradual changes have been observed in the phage-types of methicillin-resistant Staphylococcus aureus (MRSA) isolates from Belgian hospitals. A total of 6551 isolates, collected in 93 Belgian hospitals over 10 years (1992-2001), was examined. A decreasing incidence of the main early Belgian epidemic phage-types ([A], [B], [H]*, Jo*) was observed. Since 1997 and 2000, a new series of phage-types ([Hv]*, [J]*, [O]*), which were likely related to the previous group [H]*, have been noted. The general trends were confirmed in two particular hospitals. Local epidemic and/or endemic phage-types were also encountered.

Mycobacterium paratuberculosis and Mycobacterium avium subsp. silvaticum DNA cannot be detected by PCR in Crohn's disease tissue.

BACKGROUND: The etiology of Crohn's disease remains unknown. A putative mycobacterial cause of the disease is still controversial. AIMS: To assess the mycobacterial hypothesis in Crohn's disease using a polymerase chain reaction technique. PATIENTS AND METHODS: Nested polymerase chain reaction with primers on the 16S-rRNA coding region (16S-rDNA) and with primers specific both to the insertion sequences (IS) 900, and IS 901/902 were used to amplify Mycobacterium paratuberculosis or Mycobacterium avium subsp. silvaticum DNA in frozen endoscopic intestinal biopsies or surgical resection specimens from patients with Crohn's disease (n = 47: 25 endoscopic biopsies and 22 surgical resection samples, +/- lymph nodes), ulcerative colitis (n = 27), and non inflammatory bowel diseases (n = 20: colonic tumors and diverticulitis). Positive as well as negative controls were used throughout the study. RESULTS: All strains of Mycobacterium paratuberculosis and Mycobacterium avium subsp. silvaticum tested were positive for both primer systems. Of the 94 biopsies tested, 5 (2 Crohn's disease, 1 ulcerative colitis and 2 controls) were positive with the 16S-rDNA primers but did not correspond to Mycobacterium paratuberculosis or Mycobacterium avium subsp. silvaticum. None of the specimens was positive with the IS primers. CONCLUSION: These results do not support the hypothesis that Mycobacterium paratuberculosis, or Mycobacterium avium subsp. silvaticum play a role in Crohn's disease.

Evaluation of the INNO-LiPA Rif. TB assay, a reverse hybridization assay for the simultaneous detection of Mycobacterium tuberculosis complex and its resistance to rifampin.

Mycobacterium tuberculosis resistance to rifampin results from nucleotide changes in the gene encoding the beta-subunit of the RNA polymerase (rpoB). We developed a reverse hybridization-based line probe assay (LiPA; the INNO-LiPA Rif. TB) carrying one oligonucleotide probe for the detection of M. tuberculosis complex strains and nine probes designed to detect nucleotide changes in the relevant part of rpoB. This assay was evaluated with 107 M. tuberculosis isolates with known rpoB sequences, 52 non-M. tuberculosis complex strains, and 61 and 203 clinical isolates found to be sensitive and resistant, respectively, by in vitro testing. The results indicated that (i) the M. tuberculosis complex probe was 100% specific, (ii) when compared to the results of nucleotide sequencing, no discrepancies with the results of INNO-LiPA Rif. TB were observed, (iii) all strains sensitive by in vitro susceptibility testing were correctly identified, and (iv) among the strains resistant by in vitro susceptibility testing, only 4 (2%) yielded conflicting results. The INNO-LiPA Rif. TB is therefore a reliable and widely applicable assay and a valuable tool for routine diagnostic use, given its simplicity and rapid performance.

Detection of fastidious mycobacteria in human intestines by the polymerase chain reaction.

The aim of this study was to determine whether difficult-to-grow mycobacteria are present in human intestines. Intestinal tissue samples were subjected to both mycobacterial culture and a polymerase chain reaction (PCR) assay. After detection by PCR, species identity was determined by hybridizing the amplified 16S rRNA gene fragments with species-specific oligonucleotides. Intestinal biopsies from 63 patients with noninflammatory bowel diseases (n = 22), Crohn's disease (n = 31), or ulcerative colitis (n = 10) were analyzed. Culture and PCR revealed mycobacteria in four (6%) and 25 (40%) samples, respectively. Samples positive by PCR were negative with all probes specific to nine common cultivable species but were positive with Mycobacterium genavense-specific probe in 68% of cases. Mycobacterial isolates were identified as Mycobacterium gordonae and Mycobacterium chelonae. Findings were similar in Crohn's disease samples compared to non-Chron's disease samples. This study shows that difficult-to-grow mycobacteria can be detected by PCR in large and similar proportions of inflamed intestinal tissue from patients with inflammatory bowel disease and intestinal tissue that appears normal from patients with noninflammatory bowel disease.