Evaluation of two RT-PCR screening assays for identifying SARS-CoV-2 variants.

BACKGROUND: The recent emergence of new SARS CoV-2 variants (variants of concern, VOC) that spread rapidly and may lead to immune escape has emphasized the urgent need to monitor and control their spread. METHODS: We analyzed 2018 SARS-CoV-2 positive specimens collected between February 9 and March 22, 2021 using the Thermofisher® TaqPath™ COVID-19 CE-IVD RT-PCR kit (TaqPath) and the ID solutions® ID™ SARS-CoV-2/UK/SA Variant Triplex RT-PCR (ID triplex) assay to screen for VOCs. RESULTS: The ID triplex assay identified 62.8% of them as VOCs: 61.8% B.1.1.7 and 0.9% B.1.351/P.1. The agreement between the ID triplex results for B.1.1.7 and the TaqPath S gene target failure (SGTF)/ S gene target late detection (SGTL) profile for this variant agreed very well (k = 0.86). A low virus load was the main cause of discrepancies. Sequencing discordant results with both assays indicated that the TaqPath assay detected the B.1.1.7 lineage slightly better. Both assays suggested that the virus loads of B.1.1.7 variants were significantly higher than those of non-B.1.1.7 strains. Only 10/20 B1.351/P.1 strains detected with the ID triplex assay were confirmed by sequencing. CONCLUSIONS: We conclude that the SGTF/SGTL profiles identified using the TaqPath assay and ID triplex results are suitable for detecting the B.1.1.7 lineage. The ID triplex assay, which rapidly determines all three current VOCs simultaneously, could be a valuable tool for limiting virus spread by supporting contact-tracing and isolation.

[Coccidioidomycosis presenting as a pulmonary nodule after pneumonia]. / Opacité tumorale apparue au decours d'une pneumonie fébrile révélant une coccidioïdomycose thoracique.

Coccidioidomycosis is a fungal infection endemic in the south west of the United States. Sixty percent of infected individuals remain asymptomatic. Symptomatic disease manifests itself with variable signs such as pneumonia, pleural effusion, empyema or acute respiratory distress syndrome. Residual disease includes pulmonary nodules and fibrosis. We report a case of a woman, returning from a trip to Arizona, presenting with an acute respiratory infection associated with erythema nodosum and arthralgia. She was successfully treated with routine antibiotics. The acute pneumonia resolved and the radiological infiltrate contract into a solitary pulmonary nodule. We suspected a malignant nodule in a previous smoker. The diagnosis of pulmonary Coccidioidomycosis was made after surgical resection. One year later, the patient is asymptomatic and well. This review focuses on the most common clinical manifestations, the diagnostic strategy and the treatment and management of pulmonary Coccidioidomycosis.

Characteristics of patients with respiratory allergy in France and factors influencing immunotherapy prescription: a prospective observational study (REALIS).

To describe the sensitization profile of respiratory allergies in France, identifying factors influencing the prescription of allergen immunotherapy (AIT) [Transversal phase (T)], and assess treatment efficacy, tolerability, compliance and satisfaction [Longitudinal phase (L)]. French allergists (600) and pneumo-allergists (600) were offered participation and asked to recruit the first 20 new patients with allergic rhinitis (AR) and/or asthma, consulting for a first time allergy check-up with skin prick-test (T), and 5 patients sensitized to pollens (skin test and/or specific IgE) for whom SLIT with pollens was prescribed (L). In the T phase, 2,714 patients were recruited by 169 specialists, mostly allergists (76.5%). The majority (98%) suffered from AR, alone (57.7%) or with asthma (40.3%) and 80.3% suffered from moderate-to-severe rhinitis, mostly persistent (65.8%). Asthma, when present, was mostly intermittent (63.7%) or mild persistent (20.1%). Sensitization to house dust mites was the most common (64.5%), followed by grass pollens (61.5%), tree pollens (41.6%) and cat danders (30.5%). Poly-sensitization was seen in 73.6% of patients. AIT, mostly sublingual, was recommended in 55.6% of the patients, mostly (78.1%) because of insufficient control with symptomatic treatments. The overall impact of symptoms on QOL, positive skin test to grass pollens, ocular pruritus and/or nasal obstruction and moderate-to-severe rhinitis were significant predictors of SLIT prescription. Poly-sensitization or concomitant asthma were not seen as deterrents. Most patients consulting a specialist for allergy testing suffer from moderate-to-severe rhinitis. Treatment in current practice includes immunotherapy in half of the patients, and follows ARIA recommendations.

[Skin sensitisation profiles of outpatients with symptoms of respiratory allergies]. / Profils de sensibilisation cutanée aux pneumallergènes des patients consultant pour allergie respiratoire.

AIM: The main objective of the survey was to determine the frequency of the mono and polysensitizations in patients consulting for respiratory allergy, rhinitis or/and asthma. The secondary objectives were to evaluate the severity, the number and the type of the sensitizations, the frequency of the asthma or rhinitis as a function of the sensitizations, the evolution of the sensitizations with age, and identify the principal responsible pneumallergens. PATIENTS AND METHODS: The multicentric survey included a patient questionnaire allowing the collection and anonymous treatment of data on socio-demographic characteristics, clinical symptoms, cutaneous tests and sensitizations. RESULTS: A sample of 505 patients, mean age 24 years, consulting for rhinitis or asthma, monosensitized (36%) or polysensitized (64%), was evaluated. The percentage of polysensitized patients was similar in asthmatics, patients with rhinitis, and patients with both asthma and rhinitis (60%, 65%, and 63%, respectively). The mean number of the sensitizations was 2.4 for patients with asthma, 2.6 for those with rhinitis, and 2.6 for patients with both asthma and rhinitis. The greater the severity of the rhinitis or asthma, the higher the number of the sensitizations. Sensitizations to acarids, gramineae and cat were the most frequent. When practioners were asked about their intention to undertake desensitization in polysensitized patients, 52% of them replied positively. CONCLUSION: Data collected during this survey showed that a large proportion of the patients who consulted for rhinitis or asthma were monosensitized (36%). Sensitization to acarids was the most frequent. Even in polysensitized patients, more than half the practioners said they would use desensitization.

[Mandibular advancement surgery in patients with severe obstructive sleep apnea uncontrolled by continuous positive airway pressure. A retrospective review of 25 patients between 1998 and 2004]. / Prise en charge par chirurgie d'avancée des maxillaires des patients porteurs d'un syndrome d'apnées du sommeil sévère en échec d'un traitement par pression positive continue: étude rétrospective de 25 patients entre 1998 et 2004.

INTRODUCTION: Continuous positive airway pressure (CPAP) is ineffective in some patients with obstructive sleep apnoea syndrome (OSAS) and some patients do not tolerate it. This study evaluated the outcomes of maxillo-mandibular advancement in OSAS patients without morbid obesity or severe maxillo-mandibular deformity who had first been treated with CPAP for at least 6 months. METHODS: A retrospective study reporting on the experience of the CHU Toulouse Rangueil sleep disorder centre between 1998 and 2004. We performed polysomnography and cephalometry before and 3 months after surgery. RESULTS: 25 male patients with mean apnoea hypopnoea index at 45/hour (+/-15) were treated by maxillo-mandibular advancement. The mean age of participants was 48 years (+/-7), and the mean body mass index was 28 kg/m2 (+/-3.4). Cephalometry demonstrated a retroposition of the mandible (SNB < 80 degrees +/-5) and narrow linguopharyngeal space (ELP = 8 mm+/-3). 3 months after surgery the apnoea hypopnoea index (AHI) had decreased from 45+/-15 to 7+/-7 (p < 0.0001), the Epworth sleepiness scale decreased from 11+/-5 to 6+/-4 (p < 0.01). The linguopharyngeal space was larger (ELP = 14 mm). Success rate defined as an AHI < 15/hour was 89%, and 74% for an AHI < 10/hour. 16 patients underwent polysomnography one year after surgery. The results were the same. There were no post surgical complications, except for one patient who developed permanent labial hypoesthesia. CONCLUSIONS: Maxillo-mandibular advancement seems to be an effective 2nd line therapy for the treatment of severe OSAS.

[Actinomycosis presenting as a chronic excavated pneumonia in a young woman]. / Pneumopathie abcédée chronique chez une jeune femme, révélant une actinomycose thoracique.

INTRODUCTION: Pulmonary actinomycosis is an anaerobic bacterial infection occurring primarily in debilated patients with poor oral hygiene. Before the penicillin era, thoracic actinomycosis looked like tuberculosis or neoplasia with chest wall invasion and fistula formation. OBSERVATION: We report the case of a 39 years old woman presenting with a chronic lung abscess of the left upper lobe hospitalised after several unsuccessful courses of antibiotics. The diagnosis was made after thoracic surgery. Three years after lobectomy, which had been followed by three months of amoxycillin and multiple dental extractions, there was no sign of relapse of the infection. CONCLUSIONS: We review the role of thoracic surgery, antibiotic treatment and diagnosis in pulmonary actinomycosis.

Urine collection for nicotine and cotinine measurement in studies on nicotine addicts.

One of the reasons for the paucity of tabagism exposure data on the consequences of smoking is the difficulty in obtaining urine samples and the fact that the optimal storage conditions remains undetermined. The authors therefore assessed the influence of storage on urinary nicotine and cotinine levels both at room temperature and after freezing. The variations observed were not statistically significant for up to 30 hours at room temperature or for up to 8 days at -25 degrees C. They then studied the excretion of cotinine and nicotine in overnight and 24-h urine specimens collected from 90 non-smokers exposed to tobacco smoke and 40 smokers. The correlation between overnight and 24-h excretion was excellent in the case of cotinine (r = 0.89) and poor for nicotine (r = 0.18), probably because of their respective half-lives. Lastly, the usefulness of referring the urinary cotinine to the urinary creatinine was questioned. The authors conclude that valuable studies should be based on overnight urines samples stored at room temperature for up to 30 hours and then frozen at -25 degrees C until quantification of cotinine expressed in microgram/fraction.

Concentrations of high-density lipoprotein subfraction HDL2 and lipoprotein A-I in a random population of healthy subjects.

High-density lipoproteins (HDL) are now currently subdivided according either to density and size-HDL2 and HDL3--or to surface apoprotein composition--lipoprotein A-I (LpA-I) without A-II, and LpA-I:A-II. In samples from blood bank donors (60 women, 47 men), we evaluated HDL subclasses, LpA-I particles, and other classic risk factors for atherosclerosis and compared them with each other. We found a good correlation between HDL2 and LpA-I (r = 0.74, P less than 0.001), the correlation being more marked in women (r = 0.74) than in men (r = 0.67). LpA-I was also strongly correlated with total apolipoprotein A-I (apoA-I) (r = 0.61), which suggests that LpA-I represents a significant portion of the variable pool of apoA-I. By contrast, LpA-I:A-II but not LpA-I was correlated with HDL3, confirming the preferential association of LpA-I with HDL2. The difference between the sexes was more marked for HDL2 (+66% in women) than for LpA-I (+25%). We conclude that in normolipemic subjects the size of the HDL2 pool depends on that of LpA-I. Considering the speed and low cost of the assay, determination of HDL2 cholesterol might be a useful tool for assessing cardiovascular risk.

[Detection of extended broad-spectrum beta-lactamases with the ATB MIC system]. / Détection des bêtalactamases à spectre élargi avec le système ATB CMI.

The Enterobacteriaceae producing extended broad-spectrum beta-lactamases (ESB) must be detected even when their MIC to oxyiminocephalosporins are low. We tested 164 isolates (133 ESB, 31 non ESB) on two experimental ATB MIC plates containing cefotaxime or ceftazidime (0.06-128 mg/l) alone or associated with sulbactam (4 mg/l). Fifty four per cent of the ESB isolates are sensitive to cefotaxime, and 30% to ceftazidime. Respectively 95% and 94% of these bacteria have a synergism index (MIC CIII alone/MIC CIIII + sulbactam) greater than or equal to 4 with cefotaxime and ceftazidime. The isolates that do not produce ESB have all a rate less than 4. The ATB system can detect the extended broad spectrum beta-lactamases when low concentrations of cephalosporins are used, alone and in association with an inhibitor of beta-lactamases.

[Interpretation of the values of urinary cotinine in smokers and non-smokers]. / Interprétation des valeurs de la cotininurie chez les fumeurs et les non-fumeurs.

The values of urinary cotinine measured using high performance liquid chromatography in 125 adults (44 men and 81 women) were compared with the degree of intoxication and/or exposure to tobacco experienced over six consecutive days by auto-questionnaire. The subjects were classified in 6 groups: non exposed non smokers and non smokers exposed for less than one hour (1, n = 16); non smokers exposed for between 1 and 10 hours (2, n = 26); non smokers exposed for more than 10 hours and less than 30 hours (3, n = 33); non smokers exposed for more than 30 hours (4, n = 13); smokers smoking less than 20 cigarettes per day (5, n = 16); smokers smoking 20 cigarettes or more per day (6, n = 21). The measurements were made on urine specimens from the first morning (fraction F1), from the day and night (F2) and those of the second morning (F3). The results were expressed in micrograms/fraction and were as follows: Group 1: 37.3 (F1); 149.5 (F2); 26.8 (F3)--Group 2: 81.2; 234.1; 75.4--Group 3: 121.1; 383.1; 80.7--Group 4: 98.8; 253.7; 117.2--Group 5: 206.9; 773.8; 188--Group 6: 483.1; 1908.2; 431.3. Cotinine was found in all individuals whether they declared that they were exposed or non exposed (with the exception of a single person amongs the latter). In spite of a certain amount of overlapping between the results of the individuals in groups 4 and 5, the values obtained enabled a differentiation between the degrees of tobacco absorption.(ABSTRACT TRUNCATED AT 250 WORDS)

Pulsed Doppler echocardiography in the diagnosis of pulmonary hypertension in COPD.

We used pulsed Doppler echocardiography to examine the systolic ejection flow from the right ventricle in 66 patients with chronic obstructive pulmonary disease. Adequate recordings were obtained in 60 patients, in conjunction with right heart catheterization. Patients without pulmonary artery hypertension at rest (mean pulmonary artery pressure less than 20 mm Hg) underwent an exercise test which identified a group with PAH during exercise (MPAP greater than 30 mm Hg). The patients were divided into four groups: group 1, or control group: 17 healthy nonsmokers without normal respiratory function data; group 2: COPD without PAH (n = 12); group 3: PAH during exercise (n = 26); group 4: PAH at rest (n = 22). Analysis of Doppler data included time to peak velocity, right ventricular pre-ejection period, and ejection period. Pulsed Doppler echocardiography was a simple and reliable method of detecting PAH. Latent PAH, revealed by the exercise test, was accompanied by significant changes in Doppler findings, confirming the sensitivity of the method.

[In vitro activity of 4 fluoroquinolones against Klebsiella pneumoniae. Distribution according to phenotype resistance to aminoglycosides or beta-lactams]. / Activité in vitro de quatre fluoroquinolones sur Klebsiella pneumoniae. Répartition selon les phénotypes de résistance aux aminosides et aux bêta-lactamines.

Minimal inhibitory concentrations (MIC) of pefloxacin (PEF), norfloxacin (NOR), ofloxacin (OFL) and ciprofloxacin (CIP) are evaluated by agar dilution against 100 Klebsiella pneumoniae strains isolated in hospital. MIC 50 and 90%, micrograms/ml, are respectively: CIP (0.25/8), OFL (1/16), NOR (1/32), PEF (2/64). We determined the phenotypes PEF/NOR/OFL/CIP by taking into account the critic concentrations of the French Committee for Antibiogram. The results are: SSSS = 45%, RI/RI/RI/RI = 20%, RI/SSS = 19%, RI/RI/RI/S = 8%, RI/RI/SS = 7%. When a strain is resistant to pefloxacin alone, the MICs of the other fluoroquinolones are higher than those of the sensitive strains. The resistance to fluoroquinolones is most frequent in strains that have acquired resistance to aminoglycosides or betalactams, but exists also in strains that have no acquired resistance to these antibiotics.

Elimination of caffeine interference in HPLC determination of urinary nicotine and cotinine.

We report an analytical reversed-phase liquid-chromatographic procedure for quantifying nicotine and cotinine in urine, taking into account the presence of interfering caffeine frequently encountered in such specimens. These analytes are extracted from the alkalinized urine with chloroform. After evaporation of the chloroform, the residue is dissolved in methanol and injected into a chromatographic C18 column. Extraction recoveries averaged 80% to 97%. Chromatographic conditions were investigated to obviate caffeine interference. The proposed eluent mobile phase is a polar mixture of water, acetonitrile, methanol, and a pH 4 acetoacetate buffer (65/2/29/4 by vol) adjusted to pH 4.30 +/- 0.02 with triethylamine. High resolution and linearity were obtained for each analyte up to a concentration of 200 mg/L. The minimum detectable amount of each compound was 20 ng per injection, corresponding to 10 micrograms per liter of urine. Correlation with results of gas-liquid chromatography was excellent (r = 0.99). This simple, rapid procedure allows routine screening of tobacco exposure with acceptable precision: within- and between-run coefficients of variation were less than 2% and less than 5%, respectively.

[Broad spectrum beta-lactamases and the API ATB 244 system: the need for detection]. / Bêtalactamases à spectre élargi et système API ATB 24H: nécessité d'une détection.

API ATB 24H is an automated system designed to test the sensitivity of bacteria to antibiotics. Using this system we found that it was not fully able to detect acquired resistance to oxy-iminocephalosporins in enterobacteriaceae producing extended broad spectrum betalactamase (CTX-1, SHV-3, SHV-4). However, the frequency of detection varied with the type of API SYSTEM (ATB G-, ATB PSE), the nature of beta lactam antibiotic (cefotaxime, ceftazidime) and the type of beta lactamase produced. Considering the fact that this new mechanism of resistance must be taken into account, we suggest that the most simple method for the detection of oxy-imini beta lactamases is a double disk test of synergy between Augmentin (acid clavulanic + amoxycillin) and 1 disk of oxy-iminocephalosporin.

[In vitro and in vivo activity of a combination of clavulanic acid and amoxicillin against Klebsiella pneumoniae producing extended broad-spectrum betalactamase (CTX-1, SHV-3, SHV-4)]. / Activité in vitro et in vivo de l'association acide clavulanique - amoxicilline chez Klebsiella pneumoniae productrice de bêtalactamase à spectre élargi (CTX-1, SHV-3, SHV-4).

In vitro activity of an aminopenicillin (amoxicillin or ampicillin) combined with a betalactamase inhibitor (clavulanic acid or sulbactam, 2 mg/l) was examined against 39 strains of K. pneumoniae producing 3 types of extended broad spectrum betalactamases (CTX-1, SHV-3, SHV-4). Clavulanic acid produces the best synergistic effect. The in vivo activity of Augmentin (amoxicillin + clavulanic acid), 1 g once or twice a day, during 10 +/- 3 days was evaluated on 10 cases urinary tract infections in paraplegic patients. After 3 days, no leucocyturia was observed and bacteria were no more detected. The inhibitory effect of clavulanic acid for the extended broad-spectrum betalactamases shows that such an association could be probably chosen as well for treatment urinary infection.

[Current status of aminoglycoside resistance in hospital Enterobacteriaceae]. / Etat actuel de la résistance aux aminosides d'entérobactéries hospitalières.

We studied the susceptibility of Enterobacteriaceae to four aminoglycosides (gentamicin, tobramycin, netilmicin et amikacin). We determined their phenotypes of resistance by taking into account both the critic concentrations of the CFA (french committee for antibiogram) and the MIC of the main susceptible population of each species. The most frequent phenotypes were GTNt, TNtA and GTNtA. Amikacin resistance including phenotypes were essentially found in Klebsiella and Serratia (35% and 53% of the strains, respectively); with respect to amikacin, the phenotype expression may be insufficient to exceed the sensitive critic concentration of the CFA. Amikacin resistant strains were isolated from chronically infected patients with devices, such as urinary catheters or tracheal cannula. These results suggest a strains or plasmids outbreak.