Performances, feasibility and acceptability of nasopharyngeal swab, saliva and oral-self sampling swab for the detection of severe acute respiratory syndrome coronavirus 2.

Molecular diagnosis on nasopharyngeal swabs (NPS) is the current standard for COVID-19 diagnosis, but saliva may be an alternative specimen to facilitate access to diagnosis. We compared analytic performances, feasibility and acceptability of NPS, saliva, and oral-self sampling swab for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A prospective, multicenter study was conducted in military hospitals in France among adult outpatients attending COVID-19 diagnosis centers or hospitalized patients. For each patient, all samples were obtained and analyzed simultaneously with RT-PCR or transcription-mediated amplification method. Clinical signs, feasibility, and acceptability for each type of sample were collected. A total of 1220 patients were included, corresponding to 1205 NPS and saliva and 771 OS. Compared to NPS, the sensitivity, specificity, and kappa coefficient for tests performed on saliva were 87.8% (95% CI 83.3-92.3), 97.1% (95% CI 96.1-98.1), and 0.84 (95% CI 0.80-0.88). Analytical performances were better in symptomatic patients. Ct values were significantly lower in NPS than saliva. For OS, sensitivity was estimated to be 61.1% (95% CI 52.7-69.4) and Kappa coefficient to be 0.69 (95% CI 0.62-0.76). OS was the technique preferred by the patients (44.3%) before saliva (42.4%) and NPS (13.4%). Instructions were perceived as simple by patients (> 90%) for saliva and OS. Finally, the painful nature was estimated to be 0.9 for OS, on a scale from 0 to 10, and to be 5.3 for NPS. Performances of OS are not sufficient. Saliva is an acceptable alternative to NPS for symptomatic patient but the process required additional steps to fluidize the sample.

Lessons learned from the investigation of a COVID-19 cluster in Creil, France: effectiveness of targeting symptomatic cases and conducting contact tracing around them.

BACKGROUND: This study presents the methods and results of the investigation into a SARS-CoV-2 outbreak in a professional community. Due to the limited testing capacity available in France at the time, we elaborated a testing strategy according to pre-test probability. METHODS: The investigation design combined active case finding and contact tracing around each confirmed case with testing of at-risk contact persons who had any evocative symptoms (n = 88). One month later, we performed serology testing to test and screen symptomatic and asymptomatic cases again (n = 79). RESULTS: Twenty-four patients were confirmed (14 with RT-PCR and 10 with serology). The attack rate was 29% (24/83). Median age was 40 (24 to 59), and the sex ratio was 15/12. Only three cases were asymptomatic (= no symptoms at all, 13%, 95% CI, 3-32). Nineteen symptomatic cases (79%, 95% CI, 63-95) presented a respiratory infection, two of which were severe. All the RT-PCR confirmed cases acquired protective antibodies. Median incubation was 4 days (from 1 to 13 days), and the median serial interval was 3 days (0 to 15). We identified pre-symptomatic transmission in 40% of this cluster, but no transmission from asymptomatic to symptomatic cases. CONCLUSION: We report the effective use of targeted testing according to pre-test probability, specifically prioritizing symptomatic COVID-19 diagnosis and contact tracing. The asymptomatic rate raises questions about the real role of asymptomatic infected people in transmission. Conversely, pre-symptomatic contamination occurred frequently in this cluster, highlighting the need to identify, test, and quarantine asymptomatic at-risk contact persons (= contact tracing). The local lockdown imposed helped reduce transmission during the investigation period.

COVID-19 Repeated Convalescent Plasma Collection: Analysis of 149 Donations from 88 French Military Health Workers.

BACKGROUND: Passive therapy with convalescent plasma (CP) could be an effective and safe treatment option in COVID-19 patients. Neutralizing antibodies present in CP generated in response to SARS-CoV-2 infection and directed against the receptor-binding domain of the spike protein are considered to play a major role in the viral clearance. CP infusion may also contribute to the modulation of the immune response through its immunomodulatory effect. We describe for the first time the effectiveness of a CP collection protocol from repeated donations in young patients. MATERIALS AND METHODS: We enrolled health service workers who experienced mild to moderate COVID-19 and from whom several donations have been collected. No minimal severity threshold and no biological cure criteria were required. Donors could return to a second plasma donation 14 days after the first donation. A minimal neutralizing antibody titer of 1:40 was considered for clinical use. RESULTS: Eighty-eight donors were included (median age 35 [28-48] years, 41 women), and 149 plasma products were collected. COVID-19 were mainly WHO stage 2 infections (96%). Among the 88 first donations, 76% had neutralizing antibody titers higher than or equal to 1:40. Eighty-eight percent of donors who came for a second donation had a neutralizing antibody titer of 1:40. Median durations were 15 (15-19) and 38 (33-46) days from the first to the second donation and from recovery to the second donation, respectively. Sixty-nine percent of donors who came for a third donation had a neutralizing antibody titer of 1:40. Median durations were 16 (13-37) and 54 (49-61) days from the second to the third donation and from recovery to the third donation, respectively. No significant difference was observed between the IgG ratio and the age of the donors or the time between recovery and donation. The average IgG ratio did not significantly vary between donations. When focused on repeated blood donors, no significant differences were observed either. CONCLUSION: The recruitment of young patients with a mild to moderate CO-VID-19 course is an efficient possibility to collect CP with a satisfactory level of neutralizing antibodies. Repeated donations are a well-tolerated and effective way of CP collection.

Reactivation of Epstein-Barr virus among intensive care patients: a prospective observational study.

PURPOSE: Herpesvirus reactivation has been documented among patients in the intensive care unit (ICU) and is associated with increased morbidity and mortality, particularly for cytomegalovirus (CMV). Epstein-Barr virus (EBV) has been poorly studied despite >95% of the population being seropositive. Our preliminary study suggested an association between EBV reactivation and increased morbidity and mortality. This study aimed to investigate this association among patients admitted to the ICU. METHODS: In this multicenter prospective study, polymerase chain reaction was performed to quantify EBV in patients upon ICU admission and then twice a week during their stay. Follow-up was 90 days. RESULTS: The study included 129 patients; 70 (54.3%) had EBV reactivation. On day 90, there was no difference in mortality rates between patients with and without reactivation (25.7% vs 15.3%, p = 0.22). Patients with EBV reactivation at admission had increased mortality compared with those without reactivation and those with later reactivation. EBV reactivation was associated with increased morbidity. Patients with EBV reactivation had fewer ventilator-free days at day 28 than those without reactivation (18 [1-22] vs. 21 days [5-26], p = 0.037) and a higher incidence of acute respiratory distress syndrome (34.3% vs. 17%, p = 0.04), infections (92.9% vs. 78%, p = 0.03), and septic shock (58.6% vs. 32.2%, p = 0.004). More patients with EBV reactivation required renal replacement therapy (30% vs. 11.9%, p = 0.02). EBV reactivation was also associated with a more inflammatory immune profile. CONCLUSION: While EBV reactivation was not associated with increased 90-day mortality, it was associated with significantly increased morbidity.

Abbott® ID NOW™ COVID-19 rapid molecular assay versus Hologic® Panther Aptima™ SARS-CoV-2 assay in nasopharyngeal specimens: results from 1-year retrospective study in an emergency department.

We compared ID Now™ and Hologic® Panther Aptima™ for the detection of SARS-COV-2. ID Now™ showed a positive and negative percent agreement of 86.9% and 99.7% respectively. This facilitates faster clinical decision-making, along with the rapid implementation of infection control measures, and improvement of patient flow in the emergency department toward inpatient wards.

Evaluation of the Quotient® MosaiQ™ COVID-19 antibody microarray for the detection of IgG and IgM antibodies to SARS-CoV-2 virus in humans.

The MosaiQ® COVID-19 Antibody test fulfills the minimal requirements for serological testing according to the French regulation.

Molecular epidemiological of extended-spectrum ß-lactamase producing Escherichia coli isolated in Djibouti.

INTRODUCTION: While the molecular epidemiology of extended-spectrum-b-lactamase (ESBL)-producing E. coli is well known in Europe due to effective surveillance networks and substantial literature, data for Africa are less available, especially in Djibouti. METHODOLOGY: We studied 31 isolates of ESBL-producing E. coli from Djibouti and compared these molecular results with data available in Africa. RESULTS: Susceptibility rates were 3.2% for ceftazidim, 48.4% for piperacillin-tazobactam, 90.3% for amikacine and 16.1% for ofloxacin. No isolate showed resistance to carbapenems or colistin. 30 E. coli (96.8%) were positive to blaCTX-M-15, 1 (3.2%) to blaCTX-M-14  and 10 (32.3%) to narrow-broad-spectrum blaTEM. No blaSHV were detected. Fluoroquinolone resistance analysis showed that 30 ofloxacin-resistant E. coli had the mutation Ser-83->Leu on the gyrA gene. 24 E. coli (77.4%) harboured the plasmid-borne aac(6 ')-Ib-cr gene. No E. coli carried the genes qnrA, qnrB and qepA. 10 isolates (32.3%) belonging to the ST131 clone. The plasmid incompatibility group most widely represented in our collection was IncFIA/IB/II. CONCLUSIONS: There is no major difference with African epidemiology. In particular, we notice the international diffusion of specific clonal group ST131.

Prevalence and risk factors of sexually transmitted infections among French service members.

INTRODUCTION: Sexually Transmitted Infections (STIs) have always represented a public health concern in the military, yet most studies rely on self-reports among non-random samples of military populations. In addition, most of the studies exploring STI rates among the military focus on US service members. This paper assesses the prevalence and correlates of STIs in the French military using biomarkers and compares self-reported versus diagnosed STIs. METHODS: Data are drawn from the COSEMIL study, a national sexual health survey conducted in the French military in 2014 and 2015. A random sample of 784 men and 141 women aged 18-57 years completed a self-administered questionnaire and provided biological samples for STI testing. We used logistic regression modeling to identify the correlates of STI diagnosis and self-reports. RESULTS: The prevalence of diagnosed STIs was 4.7% [3.8-5.9], mostly due to Chlamydia trachomatis. This rate was four times higher than the 12 months self-reported rate of 1.1% [0.6-2.3]. Reported STI rates were similar among men and women (1.1% versus 1.8%), but diagnosed STI rates were twice as high among females versus males (10.4% versus 4.1%, p = 0.007). There were significant differences in the determinants of reported versus diagnosed STIs. In particular, age and sexual orientation were associated with reported STIs, but not with diagnosed STIs. Conversely, STI counseling and depression were associated with STI diagnosis but not with STI reports. CONCLUSION: This study underlines the need to use biomarkers in population-based surveys, given the differential and substantial underreporting of STIs. Results also highlight the need for programmatic adaptation to address gender inequalities in STI rates, by developing women's health services in the French military. Addressing such needs not only benefits women but could also serve as a strategy to reduce overall STI rates as most military women have military partners, increasing the risk of internal transmission.

Clinical isolates of Escherichia coli solely resistant to mecillinam: prevalence and epidemiology.

In routine susceptibility testing of Gram-negative bacteria, a particular resistance phenotype was observed: an Escherichia coli isolate from a urine sample exhibited resistance solely to mecillinam (MEC) but was fully susceptible to other ß-lactam antibiotics (MEC-R-BL-S). The objectives as this study were to determine the prevalence of this phenotype and to describe the phenotype, molecular epidemiology and genetic background. Between 1 January 2014 and 31 January 2016, MEC-R-BL-S E. coli isolates from urine were collected and genes previously reported as mostly involved in MEC resistance were analysed. The genetic relatedness among isolates was investigated by repetitive element sequence-based PCR (rep-PCR) and multilocus sequence typing (MLST). Ten MEC-R-BL-S isolates were collected, accounting for 0.4% (10/2547) of all E. coli obtained from urine samples, 0.9% (10/1135) of ampicillin-susceptible E. coli isolates and 9.6% (10/104) of MEC-R E. coli isolates. The isolates appeared as small colonies with round morphology and had impaired fitness. The isolates were not clonal and belonged to various extraintestinal or commensal E. coli phylogroups. Mutations in the cysB gene were evidenced in all clinical isolates. In conclusion, microbiologists should be aware of these isolates with a particular susceptibility phenotype, which is not due to error in disk diffusion but is a real non-enzymatic antibiotic resistance pattern.

Mycoplasma genitalium: a mycoplasma still underestimated.

Three men referred to the emergency department with suspected sexually transmitted infection like urethritis. After collection of several clinical specimens, they are sent home with a probabilistic treatment. Mycoplasma genitalium research is performed in first line, as Neisseria gonorrhoeae and Chlamydia trachomatis, and comes back positive. Patients are recalled in order to evaluate probabilistic treatment efficiency. M. genitalium, still underestimated because of its recent discovery, is responsible for 10 to 35% of non gonococcal acute and chronical urethritis. Its research is performed by PCR from urogenital specimens like genital swab or first void urine. Until recently, M. genitalium treatment included azithromycin 1g, antibiotic recommended in association with ceftriaxone in the probabilistic treatment of sexually transmitted infections. However, since the discovery of therapeutic failures and the emergence of resistance to azithromycin monodose, azithromycin in extended treatment (500 mg on the first day followed by 250 mg daily during 4 days) is now recommended as first-line agent when M. genitalium is well identified. A control by PCR is expected 4 or 5 weeks after treatment.

Epstein-Barr virus reactivation in critically ill immunocompetent patients.

BACKGROUND: Herpes viruses can be reactivated among immunocompetent patients in intensive care unit (ICU). Cytomegalovirus (CMV) and herpes simplex virus (HSV) have been the most studied. We hypothesized that Epstein-Barr virus (EBV) could also be reactivated in immunocompetent patients during their stay in ICU and that this would be associated with morbidity and mortality. METHODS: This prospective observational study included 90 patients with an ICU stay of ≥ 5 days. CMV and HSV were considered when clinically suspected and DNA was researched in blood or bronchoalveolar lavage (BAL). EBV DNA viral quantification was performed in the blood samples. RESULTS: EBV DNA was detected in blood of 61 patients (median length for positivity of 7.5 days). CMV DNA was detected in blood of 16 patients (median length for positivity of 13.5 days) and BAL of 6 patients. HSV1 DNA was detected in the BAL of 28 patients (median length for positivity of 7.5 days). Nineteen patients had no viral reactivation, 1 experienced only CMV, 32 had only EBV, 5 had only HSV, 6 had EBV and CMV, 14 had EBV and HSV, and 9 patients reactivated three viruses. Mortality was higher among patients with EBV reactivation (33/61 vs. 7/25, p = 0.02). Length of stay (21 vs. 10 days, p < 0.001) and length of mechanical ventilation (15 vs. 7 days, p < 0.001) were higher among patients with EBV reactivation. CONCLUSIONS: This study shows that EBV DNA is detected in blood of diverse ICU patients with ≥ 5 days of stay and that it is associated with morbidity and mortality. Larger dynamic prospective studies are needed to correlate viral reactivation with immune system evolution during ICU stay and to determine the role of polyviral reactivations.

Sensitivity of parasitological tests in imported Plasmodium vivax malaria in adults and impact of chemoprophylaxis and attack type.

BACKGROUND: Plasmodium vivax is the second most common species among cases of imported malaria diagnosed in Europe. The objective of this study is to describe the sensitivity of the parasitological tests in imported P. vivax malaria, and the impact of chemoprophylaxis and attack type (primary infection or relapse). METHODS: A retrospective study included the imported vivax malaria cases admitted in a French military hospital between 2001 and 2013. The reference diagnosis method was microscopy corrected by polymerase chain reaction (PCR). Thin and thick blood films examination, quantitative buffy coat (QBC) test, and a rapid diagnostic test (RDT) had been systematically performed. PCR had been carried out for ambiguous profiles. RESULTS: Eighty-nine cases recorded from 78 patients were included, 65 of them having recently traveled to French Guyana. Forty-two patients had properly followed chemoprophylaxis. Forty-six cases were primary infections while 43 were relapses. The sensitivity was 91% for the thin blood smear, 96% for the concentration techniques (Giemsa thick blood smear and QBC test), and 76% for the RDT. The combination of the three conventional tools has an imperfect sensitivity, both for the positive diagnosis of malaria (96%) and for the diagnosis of vivax species (80%). In 4% of the cases, the positive diagnosis was established only by the PCR. The species identification was established in 20% by the PCR. The sensibility of thin blood smear and of RDT decreased significantly with full compliance of chemoprophylaxis or primary infection, whereas the decrease of sensibility of concentration techniques was not significant. CONCLUSIONS: This study illustrates the difficulties encountered in vivax malaria diagnosis, especially in patients who properly followed chemoprophylaxis or with primary infection due to a lower parasitemia. It underlines the lack of sensitivity of RDT for P. vivax and emphasizes the need for systematically combining various diagnosis methods.

Effectiveness of latex agglutination slide test in the diagnosis of imported invasive amoebiasis in the emergency department.

We compared a latex agglutination test (LAT) with enzyme-linked immunosorbent assay and indirect hemagglutination assay in the diagnosis of invasive amoebiasis. A retrospective biological records review has included 639 patients for whom these three serological tests were performed. The sensitivity of the LAT was 97.8% and the specificity was 97%.

The French Military influenza surveillance system (MISS): overview of epidemiological and virological results during four influenza seasons--2008-2012.

QUESTION UNDER STUDY: Influenza is a viral infection caused by a pathogen with considerable ability for genetic mutation, which is responsible for seasonal outbreaks as well as pandemics. This article presents the results of epidemiological and virological monitoring of four successive influenza outbreaks in the French armed forces, for the period 2008 to 2012. METHODS: The main events monitored were acute respiratory infection (ARI). Weekly incidence rates were calculated by relating cases to the number of servicepersons monitored. RESULTS: In continental France, the incidence rates for ARI and for medical consultation attributable to influenza were highest during the pandemic and decreased to reach their lowest values in 2010­2011 and 2011­2012. In terms of virological results, the 2008­2009 outbreak was mainly due to the A(H3N2) virus, while the 2009­2010 pandemic and the following season saw the emergence of the A(H1N1) pdm09 strain. The last season 2011­2012 was characterised by a predominant circulation of A(H3N2) viruses. CONCLUSIONS: Despite some limitations, the MISS represents a good source of information about influenza in young people. Virological results are compatible with those reported by most other influenza surveillance networks, but could be improved by a better knowledge of the other respiratory viruses in circulation in the military community.

Shigella flexneri bacteremia in two immune-competent adult travelers.

Shigella bacteremias are uncommon in immune-competent adults. We report two cases of Shigella flexneri bacteremia that occurred in healthy young travelers, who recovered. Self-medication with loperamide and ibuprofen without antibiotics (case 1) and concomitant falciparum malaria (case 2) were the only co-morbidities found in our two patients.

Circulation of genotype 4 hepatitis E virus in Europe: first autochthonous hepatitis E infection in France.

BACKGROUND: Human HEV infections reported in Europe without previous travel to endemic regions are linked to exposure to genotype 3 Hepatitis E virus (HEV).Genotype 3 is widely distributed through human cases and zoonotic reservoir. The geographical distribution of genotype 4 is limited to Asian countries. OBJECTIVES: The first human case of autochthonous genotype 4 hepatitis E infection was reported in France. STUDY DESIGN: The HEV infection was described in an immunosuppressed patient, presenting an acute myeloblastic leukemia. Investigation of the case was performed on detection of HEV markers in the patient and in the environment. RESULTS: Hepatitis E infection was diagnosed on the basis of HEV RNA viremia, and detection of anti-HEV IgM. The prognostic of leukemia was favorable and HEV was cleared without relapsing. HEV isolate was classified into genotype 4. CONCLUSIONS: The recent characterization of genotype 4 HEV through swine surveillance in Europe and the description of the first human case in France open interesting questions about the circulation of this genotype: health risks in human population, transmission patterns, and zoonotic reservoir.

Use of hepatitis E IgG avidity for diagnosis of hepatitis E infection.

The diagnosis of acute hepatitis E infection is based on the detection of HEV RNA or specific IgM in immunocompetent patients. Viraemia and excretion of HEV RNA in faeces are not observed in all patients and commercial kits vary in their performance for anti-HEV IgM detection. Additional diagnostic tests must therefore be considered. The value of anti-HEV IgG avidity index for differentiating between acute infection and previous exposure to HEV in countries of low endemicity was investigated. 132 specimens were included, with 39 serum samples from patients with known HEV infection, studied retrospectively. IgG avidity index was high (>60%) in patients with previous infection (n=16) or polyclonal activation (n=3) but was low (<40%) in patients with acute infection (n=20). Then, 93 serum samples from patients, checking for acute hepatitis (detection of anti-HEV IgM but not of HEV RNA) were investigated. IgG avidity index was <40% in 77 of these patients, consistent with acute infection. It exceeded 60% in 15 patients, providing evidence of contact with HEV up to six months previously. One patient had an uninterpretable biological profile, with an IgG avidity index between 40% and 60%. IgG mature slowly during HEV infection, over a period of six months. IgG avidity index can therefore be used to exclude primary infection. This method should improve the diagnosis of acute hepatitis E.