We report Mycobacterium chimaera pulmonary disease in 4 patients given a diagnosis of cystic fibrosis in a university hospital in Montpellier, France. All patients had M. chimaera-positive ...expectorated sputum specimens, clinical symptoms of pulmonary exacerbation, or a decrease in spirometry test results that improved after specific treatment.
Zoonotic species of
Capnocytophaga
genus belong to the oral microbiota of dogs and cats. They may be responsible for serious human infections, mainly after animal bites, with a high mortality rate. ...In France, only few cases have been reported and no multicenter study has been conducted. Our aim was to describe the French epidemiology of
Capnocytophaga
zoonosis. We conducted a multicenter (21 centers) retrospective non-interventional, observational study in France describing the epidemiology of
Capnocytophaga
zoonosis (
C. canimorsus
,
C. cynodegmi
,
C. canis
) over 10 years with regard to clinical and bacteriological data. From 2009 to 2018, 44 cases of
Capnocytophaga
zoonotic infections were described (
C. canimorsus
,
n
= 41;
C. cynodegmi
,
n
= 3). We observed an increase (2.5 times) in the number of cases over the study period (from the first to the last 5 years of the study). The most frequent clinical presentations were sepsis (
n
= 37), skin and soft tissue infections (
n
= 12), meningitis (
n
= 8), osteoarticular infections (
n
= 6), and endocarditis (
n
= 2). About one-third of patients with sepsis went into septic shock. Mortality rate was 11%. Mortality and meningitis rates were significantly higher for alcoholic patients (
p
= 0.044 and
p
= 0.006, respectively). Other comorbidities included smoking, splenectomy, diabetes mellitus, and immunosuppressive therapy are associated to zoonotic
Capnocytophaga
infection. Eighty-two percent of cases involved contact with dogs, mostly included bites (63%). Despite all isolates were susceptible to the amoxicillin-clavulanic acid combination, three of them were resistant to amoxicillin.
The FilmArray Blood Culture Identification 2 panel (BCID2; bioMérieux) is a fully automated PCR-based assay for identifying bacteria, fungi, and bacterial resistance markers in positive blood ...cultures (BC) in about 1 h. In this multicenter study, we evaluated the performance of the BCID2 panel for pathogen detection in positive BC. Conventional culture and BCID2 were performed in parallel at four tertiary-care hospitals. We included 152 positive BC-130 monomicrobial and 22 polymicrobial cultures-in this analysis. The BCID2 assay correctly identified 90% (88/98) of Gram-negative and 89% (70/79) of Gram-positive bacteria. Five bacterial isolates targeted by the BCID2 panel and recovered from five positive BC, including three polymicrobial cultures, were missed by the BCID2 assay. Fifteen isolates were off-panel organisms, accounting for 8% (15/182) of the isolates obtained from BC. The mean positive percent agreement between the BCID2 assay and standard culture was 97% (95% confidence interval, 95 to 99%), with agreement ranging from 67% for Candida albicans to 100% for 17 targets included in the BCID2 panel. BCID2 also identified the
gene in seven BC, including one for which no extended-spectrum β-lactamase (ESBL)-producing isolate was obtained in culture. However, it failed to detect ESBL-encoding genes in three BC. Two of the 18
genes detected by the BCID2 were not confirmed. No carbapenemase,
, or MREJ targets were detected. The median turnaround time was significantly shorter for BCID2 than for culture. The BCID2 panel may facilitate faster pathogen identification in bloodstream infections.
Rapid molecular diagnosis combining the identification of pathogens and the detection of antibiotic resistance genes from positive blood cultures (BC) can improve the outcome for patients with bloodstream infections. The FilmArray BCID2 panel, an updated version of the original BCID, can detect 11 Gram-positive bacteria, 15 Gram-negative bacteria, 7 fungal pathogens, and 10 antimicrobial resistance genes directly from a positive BC. Here, we evaluated the real-life microbiological performance of the BCID2 assay in comparison to the results of standard methods used in routine practice at four tertiary care hospitals.
The clinical laboratory methods used to diagnose yeast infections should be rapid, reliable, and capable of detecting mixed infections with species exhibiting a distinct antifungal susceptibility ...profile. In this study, we report the performance of a procedure combining the detection of mixed yeast cultures with a chromogenic medium and MALDI-TOF identification of the colonies. We then evaluated the impact that (i) the isolation medium and (ii) lowering the identification log score (LS) threshold value have on yeast identification performance in the routine laboratory.
Among 15,661 clinical samples analyzed, 5,671 tested positive and 6,192 yeasts of 42 distinct species were identified. Overall, 6,117 isolates (98.79%) were identified on the first or second MALDI-TOF Mass Spectrometry (MS) attempt, yielding an average yeast species identification turnaround time of 0.346 days (95% CI 0.326 to 0.364). The 75 remaining isolates were identified via nucleotide sequencing. Mixed infections accounted for 498 (8.78%) of the positive samples. The MALDI-TOF MS identification procedure performed well, regardless of the culture media tested. Lowering the recommended 2.0 LS threshold value to 1.8 would reduce the number of required (i) second MALDI-TOF MS identification attempts (178 vs. 490) and (ii) ITS2 and D1-D2 sequence-based identifications (17 vs. 75), while achieving an adequate identification rate (6,183/6,192, 99.85%).
In conclusion, we propose applying a 1.8 LS threshold combined with chromogenic medium subculture to optimize the yeast identification workflow and detect mixed infection in the clinical laboratory.
ObjectiveLimited macrolide and fluoroquinolone resistance data are available in France for Mycoplasma genitalium. We performed a multicentre cross-sectional study to investigate the prevalence of ...macrolide and fluoroquinolone resistance-associated mutations in M. genitalium-positive patients in metropolitan France between 2018 and 2020 and in overseas France in 2018 and 2019.MethodsEach year, a 1-month prospective collection of M. genitalium-positive specimens was proposed to metropolitan French microbiology diagnostic laboratories, and a similar 3-month collection was proposed to overseas French laboratories. Resistance-associated mutations were detected using commercial kits and sequencing.ResultsA total of 1630 M. genitalium-positive specimens were analysed. In metropolitan France, the prevalence of macrolide resistance-associated mutations ranged between 34.7% (95% CI 29.4% to 40.4%) and 42.9% (95% CI 37.1% to 49.0%) between 2018 and 2020 and was significantly higher in men (95% CI 52.4% to 60.2%) than in women (95% CI 15.9% to 22.2%) (p<0.001). These prevalences were significantly higher than those of 6.1% (95% CI 3.7% to 10.3%) and 14.7% (95% CI 10.9% to 19.6%) observed in overseas France in 2018 and 2019 (p<0.001), where no difference between genders was noted. The prevalence of fluoroquinolone resistance-associated mutations was also significantly higher in metropolitan France (14.9% (95% CI 11.2% to 19.5%) to 16.1% (95% CI 12.1% to 21.2%)) than in overseas France (1.3% (95% CI 0.4% to 3.7%) and 2.6% (95% CI 1.3% to 5.3%) in 2018 and 2019, respectively) (p<0.001), with no difference between men and women regardless of the location.ConclusionThis study reports the high prevalence of macrolide and fluoroquinolone resistance-associated mutations in M. genitalium in metropolitan France and highlights the contrast with low prevalence in overseas France. In metropolitan France, macrolide resistance-associated mutation prevalence was three times higher in men than in women, which was likely to be driven by the proportion of men who have sex with men. This suggests that gender and sexual practice should also be taken into account for the management of M. genitalium infections.
Rôle des bactéries anaérobies en clinique humaine Dumont, Yann; Michon, Anne-Laure; Laurens, Chrislène ...
Revue francophone des laboratoires,
September-October 2018, 2018-09-00, Letnik:
2018, Številka:
505
Journal Article
Recenzirano
L’avènement du séquençage à haut débit et le développement des analyses bio-informatiques ont mis en évidence le rôle majeur et complexe des anaérobies au sein du microbiote humain. La connaissance ...croissante du rôle de ces bactéries dans des infections graves chez l’homme nécessite d’avoir des laboratoires de microbiologie médicale de plus en plus performants pour le diagnostic clinico-microbiologique de ces pathogènes. De nombreux travaux mettent en exergue le rôle majeur des bactéries anaérobies dans la protection ou dans la promotion de maladies chroniques comme le cancer, les maladies inflammatoire ou encore métabolique. À ce jour, nous ne sommes qu’au début de la compréhension des interactions au sein de ces écosystèmes, où les bactéries anaérobies ont un rôle clef dans ces processus.
The advent of high throughput sequencing and development of bioinformatic ana-lyzes has highlighted the major and complex rôle of anaerobes within the human microbiota. The growing knowledge of the rôle of these bacteria in serious infections in humans requires more and more efficient microbiology laboratories for clinico-microbiological diagnosis of these pathogens. Many studies highlight the major rôle of anaerobic bacteria in the protection or promotion of chronic diseases such as cancer, inflammatory or metabolic diseases. To date, we are only at the beginning of understanding the interactions within these ecosystems, where anaerobic bacteria play a key rôle in these processes.
Bactéries anaérobies et résistances aux antibiotiques Dumont, Yann; Froissart, Remy; Bañuls, Anne-Laure ...
Revue francophone des laboratoires,
September-October 2018, 2018-09-00, Letnik:
2018, Številka:
505
Journal Article
Recenzirano
Le terme « bactéries anaérobies » recouvre de nombreuses espèces phylogénétiquement très différentes. Ainsi, si on retrouve quelques résistances naturelles communes, chaque espèce présente des ...résistances naturelles et une épidémiologie de la résistance différente qu'il faut connaître pour orienter les médecins vers des antibiothérapies efficaces. Les résistances acquises peuvent toucher la majorité des molécules utilisées dans les infections à anaérobies, même si dans la majorité des cas les souches restent fréquemment sensibles aux associations pénicilline inhibiteur de béta-lactamase (et notamment à la pipéracilline tazobactam), aux carbapénèmes et au métronidazole. Cependant, la mise en évidence de souches multirésistantes parmi les Bacteroides du groupe fragilis, très fréquemment impliqué dans les infections, les échecs cliniques associés à ces souches, et l'évolution des résistances pour certains antibiotiques, montre que, comme pour les entérobactéries au cours des dernières décennies, la situation est en train de changer. Il est donc essentiel de tester la sensibilité des souches isolées dans les situations cliniques critiques et pour les espèces les plus pourvoyeuses de résistance. Pour les souches les plus résistantes, l'utilisation d'autres classes antibiotiques (oxazolidinones, nouvelles cyclines) devra alors être envisagée.
The term “anaerobic bacteria” covers many phylogenetically very different species. Thus, if we find some common natural resistance, each species has natural resistance and epidemiology of the different resistance that must be known to guide physicians to effective antibiotic therapy. The resistances acquired can affect most of the molecules used in anaerobic infections, although in most cases the strains are frequently sensitive to penicillin-beta-lactamase inhibitor associations (and especially piperacillin tazobactam), carbapenems and metronidazole. However, the demonstration of multiresistant strains among the Bacteroides of the fragilis group, which is very frequently involved in infections, the clinical failures associated with these strains, and the evolution of resistance for certain antibiotics, shows that, as for enterobacteriaceae during in recent decades, the situation is changing. It is therefore essential to test the susceptibility of isolated strains in critical clinical situations and for the most resistant species. For the most resistant strains, the use of other antibiotic classes (oxazolidinones, new cyclins) should then be considered.
L’étude des bactéries anaérobies connaît un regain d’intérêt du fait de la description de leur importance dans les microbiotes et dans les processus infectieux. De nombreux outils commercialisés ...(milieux de transport, géloses et bouillons, systèmes assurant l’anaérobiose) permettent à ce jour leur culture à partir des échantillons cliniques. La spectrométrie de masse de type MALDI-TOF, éventuellement complétée par le séquenéage de l’ARN 16S, a révolutionné leur identification, y compris pour des espèces d’isolement moins fréquent, et diminué considérablement le délai de rendu des résultats. Les techniques phénotypiques conventionnelles, s’appuyant sur une série de tests facilement utilisables en routine et peu coûteux (microscopie, tests biochimiques rapides et taxodisques) permettent d’identifier les principaux genres d’importance clinique et parfois les espèces mais impliquent un délai de réponse de 48 h Étant donné l’évolution de la résistance aux antibiotiques de certaines bactéries (Bacteroides, Parabacteroides, Prevotella, cocci à Gram positif anaérobie) il est souhaitable de tester leur sensibilité surtout dans le cadre d’infections monomicrobiennes ou d’infections mixtes impliquant des bactéries potentiellement résistantes. Les techniques de routine facilement utilisables et flexibles reposent actuellement essentiellement sur les bandelettes imprégnées d’un gradient d’antibiotique. La méthode de référence (dilution en gélose) est réservée aux laboratoires spécialisés.
Role of medical biology laboratory in the microbiological diagnosis of anaerobic bacteria
There is a renewed interest in the study of anaerobes bacteria because of their role in microbiota and in infectious processes. Various commercially available systems (transport media, solid culture media and broth, systems providing suitable anaerobic environment) allow to isolate anaerobic bacteria successfully from clinical specimens. The use of matrix-assisted laser desorption/ionization timeof-flight mass spectrometry, eventually supplemented by 16S rRNA gene sequencing, has revolutionized identification of anaerobes, with quickly and accurately results even for unusual anaerobes. Conventional phenotypic techniques based on routinely usable and cost-effective tests (microscopy, rapid biochemical tests and special potency antibiotic disks) lead to an identification of main clinically relevant anaerobes at the genus level and sometimes at the species level but is time consuming. Because significative change in resistance patterns of many anaerobes (Bacteroides, Parabacteroides, Prevotella, anaerobe Gram positif cocci), antimicrobial susceptibility testing (AST) is recommended, especially in the case of monomicrobial infections or mixed infections incriminating potentially resistant bacteria. Methodology for easy and flexible routine AST of anaerobic bacteria is essentially based to date on the use of gradient strips. Agar dilution, considered as the reference standard for AST remains reserved for specialized laboratories.
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