Analysis of the Genomics and Mouse Virulence of an Emergent Clone of Streptococcus dysgalactiae Subspecies equisimilis.

Streptococcus dysgalactiae subsp. equisimilis is a bacterial pathogen that is increasingly recognized as a cause of severe human infections. Much less is known about the genomics and infection pathogenesis of S. dysgalactiae subsp. equisimilis strains compared to the closely related bacterium Streptococcus pyogenes. To address these knowledge deficits, we sequenced to closure the genomes of seven S. dysgalactiae subsp. equisimilis human isolates, including six that were emm type stG62647. Recently, for unknown reasons, strains of this emm type have emerged and caused an increasing number of severe human infections in several countries. The genomes of these seven strains vary between 2.15 and 2.21 Mbp. The core chromosomes of these six S. dysgalactiae subsp. equisimilis stG62647 strains are closely related, differing on average by only 495 single-nucleotide polymorphisms, consistent with a recent descent from a common progenitor. The largest source of genetic diversity among these seven isolates is differences in putative mobile genetic elements, both chromosomal and extrachromosomal. Consistent with the epidemiological observations of increased frequency and severity of infections, both stG62647 strains studied were significantly more virulent than a strain of emm type stC74a in a mouse model of necrotizing myositis, as assessed by bacterial CFU burden, lesion size, and survival curves. Taken together, our genomic and pathogenesis data show the strains of emm type stG62647 we studied are closely genetically related and have enhanced virulence in a mouse model of severe invasive disease. Our findings underscore the need for expanded study of the genomics and molecular pathogenesis of S. dysgalactiae subsp. equisimilis strains causing human infections. IMPORTANCE Our studies addressed a critical knowledge gap in understanding the genomics and virulence of the bacterial pathogen Streptococcus dysgalactiae subsp. equisimilis. S. dysgalactiae subsp. equisimilis strains are responsible for a recent increase in severe human infections in some countries. We determined that certain S. dysgalactiae subsp. equisimilis strains are genetically descended from a common ancestor and that these strains can cause severe infections in a mouse model of necrotizing myositis. Our findings highlight the need for expanded studies on the genomics and pathogenic mechanisms of this understudied subspecies of the Streptococcus family.

MONOCYTIC MYELOID-DERIVED SUPPRESSOR CELL EXPANSION AFTER CARDIAC SURGERY WITH CARDIOPULMONARY BYPASS INDUCES LYMPHOCYTE DYSFUNCTION.

ABSTRACT: Cardiac surgery with cardiopulmonary bypass (CPB) is associated with an immune paresis that predisposes to the development of postoperative infections and sepsis. Among factors responsible for CPB-induced immunosuppression, circulating myeloid-derived suppressor cells (MDSCs) have been found to induce early lymphocyte apoptosis and lymphocyte proliferation inhibition. However, the mechanisms involved are not fully understood. In this study, we found that the main lymphocyte subsets decreased significantly 24 h after cardiac surgery with CBP. As expected, cardiac surgery with CPB induced a monocytic MDSC expansion associated with an increased T-cell apoptosis and decreased proliferation capacity. Noteworthy, granulocytic MDSCs remain stable. Myeloid-derived suppressor cell depletion restored the ability of T-cell to proliferate ex vivo . After CPB, indoleamine 2,3-dioxygenase activity and IL-10 plasma level were increased such as programmed death-ligand 1 monocytic expression, whereas plasma level of arginine significantly decreased. Neither the inhibition of indoleamine 2,3-dioxygenase activity nor the use of anti-programmed death-ligand 1 or anti-IL-10 blocking antibody restored the ability of T-cell to proliferate ex vivo . Only arginine supplementation restored partially the ability of T-cell to proliferate.

A recurrent prosthetic joint infection caused by Erysipelothrix rhusiopathiae: case report and literature review.

Prosthetic knee joint infection caused by Erysipelothrix rhusiopathiae is uncommon and only one case of recurrent infection has previously been described. Here, we describe the case of a 77-year-old male patient who was admitted to the teaching hospital of Rennes (France) with bilateral and nocturnal gonalgia evolving for 1 month. He had bilateral knee prosthesis 10 years ago, and a history of large B-cell lymphoma in remission. A diagnosis of infective endocarditis, with prosthetic knee infection, was made, with positive cultures of synovial fluids and blood; colonies of E. rhusiopathiae were identified by MALDI-TOF MS. Initial treatment involved debridement, implant retention surgery and intravenous amoxicillin (12 g day-1) for 6 weeks with gentamicin 3 mg kg-1 day-1 added for the first 4 days. One year later, a second episode of E. rhusiopathiae infection occurred, suggesting a recurrence or reinfection due to the same bacterial species. The patient was finally cured after a two-stage exchange with a cemented articulated spacer and a 3 month course of amoxicillin (12 g day-1, iv). Different characteristics of E. rhusiopathiae infection were discussed, with a review of all cases of prosthetic joint infections caused by Erysipelothrix species. This case highlights the need for a long-term survey of patients, and a good knowledge of their environment to avoid any risk of reinfection.

Cerebral nocardiosis in a patient treated with pembrolizumab: a first case report.

BACKGROUND: Checkpoints inhibitors (CPIs) are increasingly used for the treatment of several malignancies. The most common side effects are Immune Related Adverse Events, while infectious complications are rare, especially cerebral nocardiosis. CASE PRESENTATION: Here, we report the first clinical case of a cerebral nocardiosis revealed after seizure in a patient treated by pembrolizumab for a metastatic lung cancer, in the absence of any additional immunosuppressive therapy or risk factors for cerebral nocardiosis. The extended evaluation including a brain CT-scan did not reveal any lesion before pembrolizumab. Nevertheless, the 3-month delay between the start of Pembrolizumab and the diagnosis of cerebral nocardiosis suggests that the infection occurred prior to the CPI. Unfortunately, the patient died during treatment for cerebral nocardiosis, while the lung cancer tumor mass had decreased by 80% after the sixth cycle of pembrolizumab. CONCLUSIONS: This case report emphasizes that clinicians should consider diagnoses other than metastasis in a patient with a brain mass and metastatic cancer treated with CPI, such as opportunistic infections or IRAE.

Clinical value of serology for the diagnosis of strongyloidiasis in travelers and migrants: A 4-year retrospective study using the Bordier IVD® Strongyloides ratti ELISA assay.

Strongyloides stercoralis serology is a sensitive method for strongyloidiasis diagnosis, but it is prone to cross-reactions with other helminthiases. This four-year retrospective study aimed at estimating the performance of the Bordier IVD® Strongyloides ratti ELISA assay in a non-endemic country (France). The study included all patients tested for strongyloidiasis in our center between 2015 and 2019, by both serology and stool examination. Cases were defined using an algorithm considering serological results, microscopic examination of stools, and other biological, clinical or epidemiological data. The study included 805 stools from 341 patients (70% migrants, 20% travelers, 10% without travel to a highly endemic area). Thirty patients (8.8%) had positive serology, 9 had microscopically proven strongyloidiasis, and 11 and 10 were classified as probable and possible strongyloidiasis, respectively. Performances of microscopy and serology were compared, considering proven and probable strongyloidiasis as true infections. The sensitivity, specificity, positive predictive value and negative predictive value of serology were 100%, 97%, 67% and 100%, respectively, and those of microscopic examination of stools were 45% (p < 0.01), 100% (p < 0.01), 100% (p = 0.079) and 96% (p < 0.001), respectively. Eosinophilia did not help in discriminating true-positive from false-positive results. Overall, these results underline the high value of the S. stercoralis serologic assay, compared to stool examination. The systematic use of this technique for screening purposes in travelers or migrants, or before onset of immunosuppressive therapy, could help to improve patient management and epidemiological knowledge.

TITLE: Utilité clinique de la sérologie pour le diagnostic de la strongyloïdose chez les voyageurs et les migrants : une étude rétrospective de 4 ans utilisant le test ELISA Strongyloides ratti Bordier IVD®. ABSTRACT: La sérologie de Strongyloides stercoralis est une méthode sensible pour le diagnostic de la strongyloïdose, mais elle est sujette à des réactions croisées avec d'autres helminthes. Cette étude rétrospective sur 4 ans visait à estimer les performances du test ELISA Strongyloides ratti Bordier IVD® dans un pays non endémique (la France). L'étude a inclus tous les patients testés pour la strongyloïdose dans notre centre entre 2015 et 2019, à la fois par sérologie et examen des selles. La définition des cas a été faite à l'aide d'un algorithme tenant compte des résultats sérologiques, de l'examen microscopique des selles et d'autres données biologiques, cliniques ou épidémiologiques. L'étude a inclus 805 selles de 341 patients (70 % de migrants, 20 % de voyageurs, 10 % sans voyage dans une zone de forte endémie). Trente patients (8,8 %) avaient une sérologie positive, 9 avaient une strongyloïdose prouvée au microscope, et 11 et 10 ont été classés respectivement comme strongyloïdose probable et possible. Les performances de la microscopie et de la sérologie ont été comparées, en considérant les strongyloïdoses avérées et probables comme de véritables infections. La sensibilité, la spécificité, la valeur prédictive positive et la valeur prédictive négative de la sérologie étaient de 100 %, 97 %, 67 % et 100 %, respectivement, et celles de l'examen microscopique des selles étaient de 45 % (p < 0,01), 100 % (p < 0,01), 100 % (p = 0,079) et 96 % (p < 0,001), respectivement. L'éosinophilie n'a pas aidé à distinguer les vrais positifs des faux positifs. Dans l'ensemble, ces résultats soulignent la valeur élevée du test sérologique de S. stercoralis, par rapport à l'examen des selles. L'utilisation systématique de cette technique à des fins de dépistage chez les voyageurs ou les migrants, ou avant le début d'un traitement immunosuppresseur, pourrait contribuer à améliorer la prise en charge des patients et les connaissances épidémiologiques.

The emergence of Staphylococcus aureus as the primary cause of cardiac device-related infective endocarditis.

BACKGROUND: Increasing use of cardiovascular implantable electronic devices (CIED), as permanent pacemakers (PPM), implantable cardioverter defibrillators (ICD), or cardiac resynchronization therapy (CRT), is associated with the emergence of CIED-related infective endocarditis (CIED-IE). We aimed to characterize CIED-IE profile, temporal trends, and prognostic factors. METHODS: CIED-IE diagnosed at Rennes University Hospital during years 1992-2017 were identified through computerized database, and included if they presented all of the following: (1) clinical signs of infection; (2) microbiological documentation through blood and/or CIED lead cultures; (3) lead or valve vegetation, or definite IE according to Duke criteria. Data were retrospectively extracted from medical charts. The cohort was categorized in three periods: 1992-1999, 2000-2008, and 2009-2017. RESULTS: We included 199 patients (51 women, 148 men, median age 73 years [interquartile range, 64-79]), with CIED-IE: 158 PPMs (79%), 24 ICD (12%), and 17 CRT (9%). Main pathogens were coagulase-negative staphylococci (CoNS: n = 86, 43%), Staphylococcus aureus (n = 60, 30%), and other Gram-positive cocci (n = 28, 14%). Temporal trends were remarkable for the decline in CoNS (P = 0.002), and the emergence of S. aureus as the primary cause of CIED-IE (24/63 in 2009-2017, 38%). Factors independently associated with one-year mortality were chronic obstructive pulmonary disease (COPD: hazard ratio 3.84 [1.03-6.02], P = 0.03), left-sided endocarditis (HR 2.25 [1.09-4.65], P = 0.03), pathogens other than CoNS (HR 3.16 [1.19-8.39], P = 0.02), and CIED removal/reimplantation (HR 0.41 [0.20-0.83], P = 0.01). CONCLUSIONS: S. aureus has emerged as the primary cause of CIED-IE. Left-sided endocarditis, COPD, pathogens other than CoNS, and no CIED removal/reimplantation are independent risk factors for one-year mortality.

Ventriculitis: A Severe Complication of Central Nervous System Infections.

BACKGROUND: Ventriculitis, a dreaded complication of brain abscess, meningitis, and various neurosurgical procedures, has attracted limited attention in the medical literature. METHODS: This is a retrospective, single-center study. We screened the medical files of all patients who had a brain imaging report that included the word "ventriculitis" during years 2005-2019. Only patients with clinical, microbiological, and imaging features of ventriculitis were included. Data were collected through a standardized questionnaire. RESULTS: Ninety-eight patients fulfilled inclusion criteria: 42 women and 56 men, and the median age was 60 years (interquartile range, 48-68). The primary mechanism for ventriculitis was classified as follows: brain abscess (n = 29, 29.6%), meningitis (n = 27, 27.6%), intraventricular catheter-related (n = 17, 17.3%), post-neurosurgery (n = 13, 13.3%), and hematogenous (n = 12, 12.2%). The main neuroimaging features were intraventricular pus (n = 81, 82.7%), ependymal enhancement (n = 70, 71.4%), and intraventricular loculations (n = 15, 15.3%). The main pathogens were streptococci (n = 44, 44.9%), Gram-negative bacilli (n = 27, 27.6%), and staphylococci (n = 15, 15.3%). In-hospital and 1-year mortality rates were 30.6% (n = 30) and 38.8% (n = 38), respectively. Neurological sequelae were reported in 34 of 55 (61.8%) survivors, including cognitive impairment (n = 11), gait disturbances (n = 9), paresis (n = 7), behavior disorder (n = 6), and epilepsy (n = 5). On multivariate analysis, age >65 years, Glasgow Coma Scale score <13 at initial presentation, status epilepticus, hydrocephalus, and positive cerebrospinal fluid culture were associated with 1-year mortality. We built a scoring system to stratify patients with ventriculitis into low risk (12.5%), intermediate risk (36.5%), and high risk (71.4%) of death. CONCLUSIONS: Ventriculitis is a severe complication of brain abscess, meningitis, or neurosurgery, with an in-hospital mortality rate of 30% and neurological sequelae in 60% of survivors.

A prospective survey of Streptococcus pyogenes infections in French Brittany from 2009 to 2017: Comprehensive dynamic of new emergent emm genotypes.

Streptococcus pyogenes or group A Streptococcus (GAS) causes diseases ranging from uncomplicated pharyngitis to life-threatening infections. It has complex epidemiology driven by the diversity, the temporal and geographical fluctuations of the circulating strains. Despite the global burden of GAS diseases, there is currently no available vaccination strategy against GAS infections. This study, based on a longitudinal population survey, aimed to understand the dynamic of GAS emm types and to give leads to better recognition of underlying mechanisms for the emergence of successful clones. From 2009 to 2017, we conducted a systematic culture-based diagnosis of GAS infections in a French Brittany population with a prospective recovery of clinical data. The epidemiological analysis was performed using emm typing combined with the structural and functional cluster-typing system for all the recovered strains. Risk factors for the invasiveness, identified by univariate analysis, were computed in a multiple logistic regression analysis, and the only independent risk factor remaining in the model was the age (OR for the entire range [CI95%] = 6.35 [3.63, 11.10]; p<0.0001). Among the 61 different emm types identified, the most prevalent were emm28 (16%), emm89 (15%), emm1 (14%), and emm4 (8%), which accounted for more than 50% of circulating strains. During the study period, five genotypes identified as emm44, 66, 75, 83, 87 emerged successively and belonged to clusters D4, E2, E3, and E6 that were different from those gathering "Prevalent" emm types (clusters A-C3 to 5, E1 and E4). We previously reported significant genetic modifications for emm44, 66, 83 and 75 types resulting possibly from a short adaptive evolution. Herein we additionally observed that the emergence of a new genotype could occur in a susceptible population having specific risk factors or probably lacking a naturally-acquired cluster-specific immune cross-protection. Among emergent emm types, emm75 and emm87 tend to become prevalent with a stable annual incidence and the risk of a clonal expansion have to be considered.

In vitro activity of eravacycline and mechanisms of resistance in enterococci.

Eravacycline (ERC), the first fluorocycline, is a new tetracycline with superior activity to tigecycline (TGC) against many bacterial species. This work aimed to determine the in vitro activity of ERC compared with other tetracyclines against enterococcal clinical isolates and to analyse corresponding resistance mechanisms. A collection of 60 enterococcal strains was studied: 54 epidemiologically unrelated clinical isolates (46 Enterococcus faecium and 8 Enterococcus faecalis) including 42 vancomycin-resistant enterococci (VRE) (33 vanA and 9 vanB), 3 in vitro TGC-resistant mutants (E. faecium AusTig, HMtig1 and HMtig2) and 3 reference wild-type strains (E. faecium Aus0004 and HM1070, E. faecalis ATCC 29212). In vitro susceptibility was determined using Etest strips (for ERC) or by broth microdilution (for TGC, doxycycline, minocycline and tetracycline). Resistance genes [tet(M), tet(L), tet(O) and tet(S)] were screened by PCR for TGC- and/or ERC-resistant strains as well as sequencing of the rpsJ gene (encoding ribosomal protein S10). MIC50/90 values were 0.016/0.08, ≤0.03/0.5, 4/32, 8/16 and 32/>32 mg/L for ERC, TGC, doxycycline, minocycline and tetracycline, respectively. According to EUCAST guidelines, nine strains were categorised as resistant to TGC (MIC, 0.5-8 mg/L), including four E. faecium vanA(+) strains also resistant to ERC (MIC, 0.19-1.5 mg/L). These four strains all possessed at least one mutation in rpsJ and two tet determinants: tet(M) + tet(L) (n = 2); and tet(M) + tet(S) (n = 2). Although ERC has excellent in vitro activity against enterococci (including VRE), emergence of resistance is possible due to combined mechanisms (rpsJ mutations + tet genes).

Performance of commercial methods for linezolid susceptibility testing of Enterococcus faecium and Enterococcus faecalis.

BACKGROUND: Linezolid-resistant enterococci (LRE) causing infections that are challenging to treat are rising, highlighting the need for reliable screening of LRE clinical isolates. OBJECTIVES: To evaluate the ability of the broth microdilution (BMD) method for LRE detection and to assess the performance of seven commercially available techniques for linezolid susceptibility testing. METHODS: A collection of 100 clinical isolates (80 Enterococcus faecium and 20 Enterococcus faecalis), including 20 optrA-positive isolates, 17 poxtA-positive isolates and 1 optrA/poxtA-positive E. faecium isolate, were studied. MICs were determined after 18 h [Day 1 (D1)] and 42 h [Day 2 (D2)] of incubation and interpreted following EUCAST and CLSI guidelines, which currently provide different interpretative breakpoints. Performance of commercial techniques was compared with BMD results. RESULTS: MIC50/D1 and MIC50/D2 were both 8 mg/L, while MIC90/D1 and MIC90/D2 were 16 and 32 mg/L, respectively. MICD1 values for poxtA-positive isolates were lower than those for optrA-positive isolates. Proportions of susceptible isolates at D1 and D2 were 48% and 41%, respectively, according to EUCAST breakpoints and 35% and 13%, respectively, according to CLSI criteria (the proportions of isolates categorized as intermediate following CLSI recommendations were 13% and 28% at D1 and D2, respectively). Percentage susceptibility assessed by the commercially available techniques was always higher. The four commercial methods allowing MIC determination provided an overall essential agreement of ≥90% at D1. Categorical agreement and error rates were generally improved at D2. CONCLUSIONS: Non-automated methods (Sensititre and UMIC) and, to a lesser extent, gradient strip Etest appear to show an acceptable correlation with the BMD reference method for the detection of isolates with low MICs of linezolid after prolonged incubation.

Complete Genome Sequences of Two Strains of Streptococcus pyogenes Belonging to an Emergent Clade of the Genotype emm89 in Brittany, France.

The frequency of infections due to Streptococcus pyogenes M/emm89 strains is increasing, presumably due to the emergence of a genetically distinct clone. We sequenced two emm89 strains isolated in Brittany, France, in 2009 and 2010 from invasive and noninvasive infections, respectively. Both strains belong to a newly emerged emm89 clade 3 clone.

Emergence of optrA-mediated linezolid resistance in enterococci from France, 2006-16.

OBJECTIVES: To describe the epidemiological trend of linezolid-resistant enterococci (LRE) collected in France from 2006 to 2016 and to extensively characterize LRE isolates. METHODS: The National Reference Center for Enterococci (NRC-Enc) received enterococcal isolates suspected to be VRE and/or LRE from all French hospitals between 2006 and 2016. LRE isolates were phenotypically characterized and their genomes were entirely sequenced by Miseq (Illumina). Transfer of linezolid resistance was attempted by filter mating experiments. RESULTS: Out of 3974 clinical isolates of enterococci received at the NRC-Enc over the period, 9 (0.2%) were LRE (MICs 8 to >32 mg/L), including 6 Enterococcus faecium and 3 Enterococcus faecalis. This overall prevalence significantly increased over the study period, reaching 0.8% in 2016. The five LRE isolated before 2016 were vanA-positive E. faecium whereas strains isolated in 2016 (one E. faecium and three E. faecalis) were susceptible to vancomycin. None of these isolates was part of an outbreak, while E. faecium strains were assigned to four different STs [17 (1), 80 (3), 412 (1) and 650 (1)] and all three E. faecalis belonged to ST480. Except for the strain isolated in 2010, all LRE were positive for optrA, which was located on plasmids (5/8) or in the chromosome (3/8). Plasmid transfer of optrA was successful in three cases. CONCLUSIONS: There has been a significant increase in the prevalence of LRE in France over time; this is due to the spread of optrA among E. faecium and E. faecalis human clinical isolates (VRE or not).

Performance comparison of new Veris and Xpert random access HIV-1 RNA quantification assays.

BACKGROUND: Recent systems for Human Immunodeficiency Virus 1 (HIV-1) viral load (VL) monitoring allow one-by-one analysis and fast turn-around-time for results. VL measurement on two rapid recently commercialized systems, GeneXpert (Cepheid) and Veris (Beckman Coulter) was compared to classical methods. METHODS: Plasma specimen from HIV-1 (group M) positive patients (n = 129) initially quantified with Abbott RealTime HIV-1 and Generic HIV-VL Biocentric assays were retrospectively tested with GeneXpert and Veris. RESULTS: Valid results on all techniques were obtained for 116/129 specimens composed of 89 Abbott quantifiable VL (38 B, 51 non-B subtypes) [range: 2.09-7.20 log cp/mL] and 27 plasma (9 B, 18 non-B) with Abbott-VL below the limit of quantification (LLQ). All techniques showed good correlation and agreement with a lowest Spearman correlation coefficient of 0.86. Compared to Abbott, the mean bias was 0.35 (95% CI: 0.25-0.45), 0.44 (0.36-0.53) and - 0.04 (- 0.13-0.05) for Biocentric, Beckman and Cepheid, respectively. A difference over 0.5 log cp/mL between VL-quantification of the same sample was observed for 19, 9 and 6 samples with Biocentric, Beckman and Cepheid, respectively. No influence of HIV-1 subtypes on VL was identified. Among 29 samples below LLQ on Abbott, only one was detected and quantified with the Veris assay (38 cp/mL), none with Cepheid. CONCLUSION: Both random access systems from Cepheid and Beckman appear well designed for quantifying plasma HIV-1 VL, are easy to handle, fast and fully automated. The slight observed differences suggest to follow the current guidelines recommending the use of the same technique over time for patient viral load monitoring.

Full Sequencing and Genomic Analysis of Three emm75 Group A Streptococcus Strains Recovered in the Course of an Epidemiological Shift in French Brittany.

While the incidence and invasiveness of type emm75 group A Streptococcus (GAS) infections increased in French Brittany during 2013, we sequenced and analyzed the genomes of three independent strains isolated in 2009, 2012, and 2014, respectively. In this short-term evolution, genomic analysis evidenced mainly the integration of new phages encoding virulence factors.