Rapid Isothermal Amplification for the Buccal Detection SARS-CoV-2 in the Context of Out-Patient COVID-19 Screening.

A commercially available isothermal amplification of SARS-CoV-2 RNA was applied to self-collected saliva samples using dry dental cotton rolls, which were held in the mouth for two minutes. Of 212 tests, isothermal amplification yielded three (0.14%) invalid results, 120 (56.6%) positive results and 89 (42%) negative results. Compared to reference RT-PCR assays routinely performed simultaneously on nasopharyngeal swabs, excluding the three invalid isothermal amplification assays and one RT-PCR invalid assay, these figures indicated that 119/123 (96.7%) samples were positive in both methods and 85/85 samples were negative in both methods. Four positive buccal swabs which were missed by the isothermal amplification, exhibited Ct values of 26-34 in reference RT-PCR assays. Positive isothermal amplification detection was achieved in less than 10 min. Supervision of the self-sampling procedure was key to achieve these performances. These data support the proposal to use the protocol reported in this paper, including supervised buccal self-sampling, to screen people suspected of having COVID-19 at the point of care.

Major discrepancy between factual antibiotic resistance and consumption in South of France: analysis of 539,037 bacterial strains.

The burden of antibiotic resistance is currently estimated by mathematical modeling, without real count of resistance to key antibiotics. Here we report the real rate of resistance to key antibiotics in bacteria isolated from humans during a 5 years period in a large area in southeast in France. We conducted a retrospective study on antibiotic susceptibility of 539,107 clinical strains isolated from hospital and private laboratories in south of France area from January 2014 to January 2019. The resistance rate to key antibiotics as well as the proportion of bacteria classified as Difficult-to-Treat (DTR) were determined and compared with the Mann-Whitney U test, the χ2 test or the Fisher's exact test. Among 539,037 isolates, we did not observe any significant increase or decrease in resistance to key antibiotics for 5 years, (oxacillin resistance in Staphylococcus aureus, carbapenem resistance in enterobacteria and Pseudomonas aeruginosa and 3rd generation cephalosporin resistance in Escherichia coli and Klebsiella pneumoniae). However, we observed a significant decrease in imipenem resistance for Acinetobacter baumannii from 2014 to 2018 (24.19-12.27%; p = 0.005) and a significant increase of ceftriaxone resistance in Klebsiella pneumoniae (9.9-24.03%; p = 0.001) and Enterobacter cloacae (24.05-42.05%; p = 0.004). Of these 539,037 isolates, 1604 (0.3%) had a DTR phenotype. Over a 5-year period, we did not observe a burden of AR in our region despite a high rate of antibiotic consumption in our country. These results highlight the need for implementation of real-time AR surveillance systems which use factual data.

Point-of-care multiplexed diagnosis of meningitis using the FilmArray® ME panel technology.

Infectious meningitis is a medical urgency and rapid detection of the causative pathogen into the cerebrospinal fluid (CSF) is mandatory to guide the management of patients. We compared the performances of the multiplexed PCR FilmArray® ME panel with standard microbiological analyses, for rapid diagnosis of infectious meningitis. All the CSF samples received in our routine laboratory for the diagnosis of infectious meningitis were prospectively analyzed by the FilmArray® ME panel for the detection of fourteen targets in parallel to standard routine real-time PCR assays and bacterial culture. We reviewed clinical and biological records of patients for whom a discrepant result was obtained to achieve a definite diagnosis. Among 1124 CSF samples tested over a 43-week period, 113 (10.1%) and 87 (7.74%) were positive using the FilmArray® ME panel and the standard techniques, respectively. Among 40 CSF samples which yielded discrepant results, 34 were positive only using the FilmArray® ME panel and 6 were positive only using standard techniques. A total of 16/34 (47.1%) FilmArray® ME panel-positive CSF, and 6/6 (100%) of standard technique-positive CSF were interpreted as true positive. We were able to estimate the sensitivity, the specificity, the positive predictive value, and the negative predictive value of the FilmArray® ME panel at 94.2%, 98.2%, 84.3%, and 99.4%, respectively. The FilmArray® ME panel is an efficient tool for the rapid diagnosis of infectious meningitis at the point-of-care. Its higher sensitivity compared with that of standard molecular biology and culture techniques yields an increase of true positive diagnosis.

Staphylococcus lugdunensis: a neglected pathogen of infections involving fracture-fixation devices.

PURPOSE: Cases of fracture-fixation device infection involving Staphylococcus lugdunensis are not frequent. The clinical characteristics and the choice of treatment strategies of these infections are not obviously known to date. METHODS: We performed a review of fracture-fixation device infection involving S. lugdunensis managed by our centres. RESULTS: Among the 38 cases of fracture-fixation device infection involving S. lugdunensis, 53% were located in the tibia. Most of our cases (87%) were chronic infections. Purulent discharge, which occurred in 79% of cases, was the most frequent clinical symptom, followed by pain in 63%, local inflammation in 55%, and fever in 37%. Bacteremia and severe sepsis occurred in 10% and 18% of cases, respectively. Four cases (10%) were treated exclusively with antimicrobial treatment alone. Thirty-four cases (89%) were treated with a combination of surgery with antimicrobial therapy including surgical debridement, antibiotics and osteosynthesis device retention in six cases (16%), and osteosynthesis device removal in 27 cases (71%). The mean length of antibiotic treatment was 119 days. The relapse rate was high that was not related to selection of resistant strains. Polymicrobial infection had no impact on clinical outcome. A combination of surgery with antimicrobial therapy was identified as a significant prognostic factor associated with remission (p = 0.042). CONCLUSIONS: S. lugdunensis is probably involved in more infections than has been reported. Using appropriate microbiological methods laboratories should routinely identify the species of all coagulase-negative Staphylococci isolates involved in fracture-fixation device infection to better achieve the treatment strategies of fracture-fixation device infection involving S. lugdunensis.

[Pericarditis]. / Péricardites

Pericarditis. Chest pain is the main symptom of pericarditis. The advent of echocardiography simplifies the definition of pericarditis with effusion, which is now a clinical entity. It is often diagnosed on radiological exams (ultrasound, CT scan, MRI) carried out in the exploration of other pathologies. Many etiologies are associated with pericarditis, however none accounts for more than 10% of cases and in 50-80% of cases none etiology is not found. Currently the increase in the number of percutaneous cardiac surgery, cardiac surgery and the increasing incidence of HIV modified the etiologies distribution. The biological tests depend on the medical team in charge of the patient. Long-term follow-up of idiopathic pericarditis is essential to improve the knowledge and the management of these patients.

Péricardites. La douleur thoracique est le principal symptôme de la péricardite. Elle est souvent diagnostiquée sur des examens radiologiques (échographie, tomodensitométrie, imagerie par résonance magnétique) réalisés dans l'exploration d'autres pathologies. De nombreuses causes sont associées aux péricardites, cependant aucune ne représente plus de 10 % des cas et dans 50 à 80 % des cas aucune cause n'est retrouvée. Actuellement l'augmentation du nombre d'interventions cardiaques percutanées, la chirurgie cardiaque et l'incidence croissante de l'infection par le virus de l'immunodéficience humaine ont modifié la répartition des causes. Les tests non invasifs sont généralement prescrits en fonction des données cliniques ou de l'expertise des équipes médicales. Le suivi à long terme de la péricardite idiopathique est indispensable afin d'améliorer les connaissances et la prise en charge de ces patients.

Draft Genome Sequence of Providencia heimbachae, Isolated from a Diabetic Foot Ulcer.

Providenciaspp. are ubiquitous Gram-negative bacteria of the familyEnterobacteriaceaethat are common opportunistic pathogens. In the present work, we have sequenced, annotated, and compared the draft genome ofProvidencia heimbachae, which was recovered from a diabetic foot ulcer. It is composed of 4.22 Mb and encodes 3,843 protein-coding genes and 79 RNA genes, including 11 rRNA genes.

Etiology of Pericarditis in a Prospective Cohort of 1162 Cases.

BACKGROUND: Pericarditis is a common disorder that is present in various pathologies and may be the first manifestation of an underlying systemic disease. The aims of this study were to describe the different causes of infectious and noninfectious pericarditis and compare them with those in the literature. METHODS: Between May 2007 and September 2012, we prospectively evaluated a strategy using a systematic prescription of tests for the different etiological causes of pericarditis in patients with acute pericarditis who were hospitalized in the Cardiology and Cardiac Surgery Department or admitted to the Emergency Department (University Hospital of Marseille). A total of 1162 patients with suspected pericarditis were included. A standardized diagnosis procedure was performed for 800 patients, and 362 had pericardiocentesis. RESULTS: Acute pericarditis was diagnosed in 933 patients. No diagnosis was established in 516 patients (55%), 197 patients suffered from postinjury syndromes, and 156 had previously known diseases that were associated with pericarditis. Our survey allowed us to relate the probable cause of pericarditis in 64 cases. An infectious etiological diagnosis was established in 53 cases. In our study, postinjury syndrome was the leading cause of pericarditis, a new diagnosis was made in 6.7% of cases, and 16% of the diagnoses were linked to a secondary, underlying disease. CONCLUSION: Using this strategy, we were able to reduce the number of idiopathic cases. In many cases, the etiologies were still identified. Long-term follow-up in the management of idiopathic pericarditis should remain of great interest for the future diagnosis of other disorders that remain hidden.

Point-of-care syndrome-based, rapid diagnosis of infections on commercial ships.

BACKGROUND: Suspicion of contagious disease on commercial ships tends to be poorly managed, as there is little capacity to confirm a case on board except for malaria. Here we implemented a point-of-care (POC) laboratory on one container ship and one cruise ship for the rapid syndrome-based diagnosis of infectious diseases on board. METHODS: In 2012 we implemented a POC laboratory on board a freight ship and on board a cruise ship. The POC laboratory ran a total of six different color-coded, syndrome-based kits incorporating 10 different commercially available immunochromatographic tests. The POC tests were taught within 1-hour as part of training to staff without any previous knowledge in microbiology. RESULTS: Compared with terrestrial POCs, specific constraints included the necessity to secure POC devices into the motile ship, to use robust devices, to overcome difficulties in communicating with the core laboratory, and to overcome limited intimacy of patients. However, a total of 36 POC tests were easily performed and yielded contributive negative results. CONCLUSIONS: This first experiment indicates that it is possible to run POC laboratories by nonexpert staff after providing rapid teaching course on board commercial ships. Generalization of on-board POC laboratories is expected to help in improving the medical management of staff and passengers.

Systematic PCR detection in culture-negative osteoarticular infections.

BACKGROUND: Identification of microorganisms is crucial for the successful treatment of osteoarticular infections. Molecular methods are more sensitive than culture-dependent methods but may suffer from lack of specificity. METHODS: We studied a large series of 3840 bone and joint culture-negative samples collected from 2308 patients hospitalized in Marseille University Hospitals from November 2007 to October 2009. The samples were systematically cultured for 15 days, and conventional broad-range polymerase chain reaction (PCR) (16S rDNA and 18S rDNA) as well as real-time PCR assays targeting human Bglobin, Staphylococcus aureus, and Kingella kingae were realized on one culture-negative specimen. RESULTS: Specimens from 741 patients (32.1%) tested positive by culture, including 38 in which bacteria grew only after 6 days of incubation. PCR was positive in 141 (9%) culture-negative specimens. Microorganisms identified by PCR were classified into 2 groups: fastidious bacteria (n = 35), mostly anaerobes in adult patients, and K. kingae in children; and nonfastidious bacteria (n = 106), mostly S. aureus (32.7%). A discrepancy between a positive PCR result for S. aureus and a negative culture were explained by previous antibiotherapy in 31.4% of cases. Our study highlights the usefulness of systematic 16S rDNA gene PCR for the diagnosis of bone and joint infections in culture-negative patients, thus enabling the administration of specific antibiotic treatments. CONCLUSIONS: We recommend the use of conventional broad-range PCR for culture-negative bone and joint specimens, as well as S. aureus-specific PCR for adults and K. kingae-specific PCR for children. 18S rDNA PCR should be reserved only for specific cases.

Abiotrophia defectiva knee prosthesis infection: A case report.

BACKGROUND: Abiotrophia species have rarely been implicated in osteoarticular infections. We report one case of an A. defectiva knee prosthesis infection. CASE PRESENTATION: A 71-year-old man of Italian origin presented with pain and swelling of the knee four years after the implantation of a total knee replacement prosthesis. While standard culturing of the synovial fluid resulted in no isolation of microorganisms, the direct inoculation of the synovial fluid into a rich culture medium resulted in the identification of A. defectiva by polymerase chain reaction sequencing. Repeated attempts of culturing microorganisms from blood were negative, and echocardiograms and colonoscopies were unremarkable. High-dose amoxicillin for nine months and a two-stage replacement of the knee prosthesis led to full patient recovery by the time of the 12-month follow-up examination. CONCLUSIONS: Because Abiotrophia spp. are fastidious microorganisms, it is likely that cases of Abiotrophia orthopedic infection are misdiagnosed as culture-negative infections. Direct inoculation of synovial fluids into rich broth medium and further polymerase chain reaction-based detection of culture-negative synovial fluids are key tests for accurate documentation and detection of these infections.

Finegoldia magna: a forgotten pathogen in prosthetic joint infection rediscovered by molecular biology.

In this study, we describe 13 patients with prosthetic infections due to Finegoldia magna (2% of our tested series). Patients presented with either polymicrobial infection after an open fracture or nosocomial infection after recent prosthesis implantation. Molecular techniques are critical for diagnosis, and recommended antibiotic prophylaxis has poor activity against F. magna.

Usefulness of broad-range PCR for the diagnosis of osteoarticular infections.

PURPOSE OF REVIEW: Conventional methods such as microbiological cultures may lack the sensitivity and specificity to establish definitive diagnosis of osteoarticular infections. Herein, we review the general principles and the usefulness of broad-range PCR to improve the etiological diagnosis of osteoarticular infections. RECENT FINDINGS: Broad-range PCR followed by sequencing has been successfully developed to identify microorganisms involved in infections when patients have previously received antibiotics or in the presence of slow-growing or intracellular microorganisms. For osteoarticular infections, the studies have shown that the use of this molecular tool increased mainly the identification of Kingella kingae, anaerobic bacteria, and Streptococcus spp. However, it is very important to underline that the interpretation of this molecular tool is critical because of several pitfalls, including contamination causing false-positive results. SUMMARY: Broad-range PCR followed by sequencing offers several advantages when used to complement culture results for the diagnosis of fastidious bacteria and for patients taking antibiotics. However, its use should be restricted mainly for culture-negative cases when infection is suspected on the basis of clinical signs and symptoms or inflammatory syndrome. Future developments will include the use of real-time PCR in a closed system and pathogen-specific PCR for the molecular diagnosis of osteoarticular infections.

Pericardial effusion as the only manifestation of infection with Francisella tularensis: a case report.

INTRODUCTION: Francisella tularensis, a facultative intracellular Gram-negative bacterium, has rarely been reported as an agent of pericarditis, generally described as a complication of tularemia sepsis. F. tularensis is a fastidious organism that grows poorly on standard culture media and diagnosis is usually based on serological tests. However, cross-reactions may occur. Western blotting allows the correct diagnosis. CASE PRESENTATION: A non-smoking 53-year-old woman was admitted to hospital with a large posterior pericardial effusion. Serological tests showed a seroconversion in antibody titers to F. tularensis (IgG titer = 400) and Legionella pneumophila (IgG titer = 512). F. tularensis was identified by Western immunoblotting following cross-adsorption. The patient reported close contact with rabbits 2 weeks prior to the beginning of symptoms of pericarditis. CONCLUSION: We report a rare case of pericardial effusion as the only manifestation of infection by F. tularensis. The etiological diagnosis is based on serology. Western blotting and cross-adsorption allow differential diagnosis.

Propionibacterium acnes postoperative shoulder arthritis: an emerging clinical entity.

The purpose of this study, which involved 276 patients, was to report the importance of Propionibacterium acnes in shoulder infections. The proportion of patients with shoulder infection who had infection due to P. acnes was significantly greater than the proportion of patients with lower limb infection who had infection due to P. acnes (9 of 16 patients vs. 1 of 233 patients; P < .001). This bacterium requires a prolonged incubation period and should not be considered to be a contaminant.

Molecular analysis of pericardial fluid: a 7-year experience.

AIMS: Aetiological investigations of pericardial effusion are often negative. We evaluate the interest of systematic analysis of fluid in order to diminish the number of pericarditis classified as idiopathic. METHODS AND RESULTS: We performed a systematic analysis of pericardial fluid and biopsy specimens, using cultures and molecular analyses for the identification of bacteriological, fungal, and viral agents, as well as histopathological examination of 106 pericardial fluid samples. The aetiological diagnosis was determined clinically and by non-invasive procedures in 40 and nine patients, respectively. In the remaining 57 patients, 14 neoplasias and 17 infections were diagnosed. Molecular procedures identified seven viral (Enterovirus, Herpes simplex virus, and Epstein-Barr virus in four, two, and one of the cases, respectively), one fungal (Cryptococcus neoformans), and nine bacterial infections. Four of these bacteria were not diagnosed by culture because of prior antibiotics treatment (Mycobacterium tuberculosis in two cases, Streptococcus pneumoniae in one case, and Actinomyces neuii in one case). The aetiology remained undetermined in 26 patients. CONCLUSION: The systematic use of molecular techniques permitted a significant increase in aetiological diagnoses of punctured pericardial effusions when compared with cultures (39.5 vs. 13.9%, respectively; P<0.01). It is particularly beneficial for patients with a previous antibiotic regimen or suspicion of tuberculosis.

Etiological diagnosis of pericardial effusion.

Detection and treatment of pericarditis remains a challenging problem and the etiology is unknown in 40-85% of cases. As a result, a large proportion of cases are labeled idiopathic pericarditis. The advent of echocardiography, an accurate noninvasive method for the detection of effusion, has clarified the definition from pericarditis to pericardial effusion, which is a standardized and clear entity. A systematic approach to diagnostic testing based on standardized practice guidelines has been proposed. This strategy has led to a decrease in the number of cases classified as idiopathic and to the identification of treatable conditions. Percutaneous pericardiocentesis, guided by fluoroscopy or echocardiography, can now be carried out safely and rapidly and has also allowed the intrapericardial instillation of drugs, representing a new treatment strategy. The inclusion of flexible pericardioscopy, immunohistochemistry and contemporary molecular biology tools has improved the diagnostic value of the biopsy.

Comparison of intuitive versus systematic strategies for aetiological diagnosis of pericardial effusion.

In an attempt to elucidate better the various aetiologies of pericardial effusion, we developed a diagnostic protocol that incorporated a battery of systematic tests including blood cultures, throat swab cultures and serological tests for various infectious agents and estimation of serum antinuclear antibodies and serum thyroid-stimulating hormone. Over a 2-y period ending May 2000, we evaluated prospectively and diagnostic usefulness of our strategy in a cohort (n = 136) of patients with pericardial effusion treated at Hospital Timone (HT), Marseille. We compared our findings with those observed in a retrospectively (May 1998-May 2000) drawn cohort (n = 127) of patients treated at Hospital Louis Pradel (HLP), Lyon and in which the laboratory investigation towards establishing an aetiological diagnosis was undertaken intuitively. Overall, the aetiologies were obvious clinically in 18% of cases. In other cases, specific aetiologies (27.3% vs 3.9%; p < 0.001), including treatable conditions (11.1% vs 2.4%; p < 0.001) were identified significantly more frequently in the HT cohort compared to the HLP cohort. The diagnosis strategy we propose may be helpful in elucidating the aetiological diagnosis of pericardial effusion when a cause is not obvious clinically.