An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes

Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST). Currently, there are little comparisons studies of these different analytical approaches. Our objective was to assess and compare different genomic methods that can be implemented in order to cluster isolates of L. monocytogenes.Methods: The clustering methods were evaluated on a collection of 207 L. monocytogenes genomes of food origin representative of the genetic diversity of the Anses collection. The trees were then compared using robust statistical analyses.Results: The backward comparability between conventional typing methods and genomic methods revealed a near-perfect concordance. The importance of selecting a proper reference when calling SNPs was highlighted, although distances between strains remained identical. The analysis also revealed that the topology of the phylogenetic trees between wgMLST and cgMLST were remarkably similar. The comparison between SNP and cgMLST or SNP and wgMLST approaches showed that the topologies of phylogenic trees were statistically similar with an almost equivalent clustering.Conclusion: Our study revealed high concordance between wgMLST, cgMLST, and SNP approaches which are all suitable for typing of L. monocytogenes. The comparable clustering is an important observation considering that the two approaches have been variously implemented among reference laboratories

Is combined cataract surgery associated with acute postoperative endophthalmitis? A nationwide study from 2005 to 2014

International audiencePURPOSE:To assess the incidence of acute postoperative endophthalmitis (POE) after cataract surgery combined with corneal, glaucoma or vitreoretinal surgical procedures from 2005 to 2014 in France.METHODS:In this cohort study, acute POE occurring within 6 weeks after surgery was identified by means of billing codes recorded in a national database in patients operated for cataract extraction with phacoemulsification, or corneal, glaucoma or vitreoretinal surgical procedures, either combined or stand-alone.RESULTS:From January 2005 to December 2014, up to 6 260 477 eyes underwent phacoemulsification cataract surgery as a single procedure and 115 468 eyes underwent phacoemulsification combined with corneal, glaucoma or vitreoretinal surgical procedures. The crude incidence of acute POE after stand-alone or combined cataract surgery was 0.102% and 0.149%, respectively. In multivariate Poisson analysis, combined surgery taken as a whole was at higher risk than cataract stand-alone surgery, with an adjusted incidence rate ratio (IRR) (95% CI) of 1.38 (1.11 to 1.70; p=0.0054). Glaucoma surgeries were associated with a lower acute POE incidence compared with phacoemulsification, conversely to vitreoretinal surgical procedures: IRR 0.63 (0.47 to 0.85; p<0.001) and IRR 1.78 (1.58 to 2.01; p<0.001), respectively.CONCLUSION:A higher incidence of acute POE after combined cataract surgery than after cataract surgery done as a stand-alone procedure was observed based on the French nationwide medical-administrative database. The incidence of acute POE after combined surgery was related to the type of surgery performed simultaneously with cataract extraction

Acta Ophthalmol

National audienc

JAMA Ophthalmol

Importance: The number of patients affected by retinal diseases treated with intravitreal injections (IVTs) has resulted in a rapidly growing number of procedures. One of the worst complications after these injections is endophthalmitis. Objective: To evaluate the incidence of acute endophthalmitis after IVTs of corticosteroids or anti-vascular endothelial growth factor (anti-VEGF) agents. Design, Setting, and Participants: This population-based cohort study included patients undergoing IVTs from January 1, 2012, through December 31, 2015, in France. Data were acquired from the French medical-administrative database (Systeme National d'Information Inter-Regime de l'Assurance Maladie), which collects hospitalization discharge abstracts and out-of-hospital care information for the whole country. Data were analyzed from March through July 2017. Exposures: Intravitreal injections of corticosteroid or anti-VEGF agents. Main Outcomes and Measures: Incidence of acute endophthalmitis within 6 weeks after IVT by means of billing codes from a national database. Results: During the study period, 1811977 IVTs of corticosteroids or anti-VEGF agents performed on 254927 patients (60.4% female; median age, 79 years [interquartile range, 70-85 years]) were analyzed. A total of 444 acute endophthalmitis cases (crude incidence, 0.0245%) were recorded. In multivariable analysis, which did not include adjustment for when the endophthalmitis occurred during the study period, the risk of endophthalmitis was lower in male patients (incidence rate ratio [IRR], 0.78; 95% CI, 0.63-0.96; P = .02), higher for corticosteroids than for anti-VEGF agents (IRR, 3.21; 95% CI, 2.33-4.44; P < .001), and higher for nonprefilled syringes of anti-VEGF medications than prefilled syringes for ranibizumab (IRR, 1.63; 95% CI, 1.15-2.30) and aflibercept (IRR, 1.82; 95% CI, 1.25-2.66; P < .001). Conclusions and Relevance: The findings from this study of a nationwide database appear to have confirmed the low incidence rate of acute endophthalmitis after IVTs of corticosteroids or anti-VEGF agents. Although an association may not necessarily indicate a cause and effect, the risk for acute endophthalmitis after IVTs appeared to be higher for corticosteroids compared with anti-VEGF agents, while a lower risk of endophthalmitis appeared to be found with prefilled syringes of anti-VEGF medications

Acta Ophthalmol

Purpose To report the incidence of acute postoperative endophthalmitis (POE) after macular surgery in France between 2006 and 2016 and to identify associated factors. Methods This retrospective database study included all hospital discharge records involving a surgical procedure for an epiretinal membrane or a macular hole in France from January 2006 to October 2016. Acute POE was identified by two codes in the tenth edition of the International Classification of Diseases within 42 days of a macular surgical procedure in the French national administrative database. Results In France, 152 034 macular surgical procedures for epiretinal membranes or macular holes were recorded from 1 January 2006 to 31 October 2016. Suspected acute POE was reported in 381 cases. The incidence of POE was 0.25% overall, 0.30% for epiretinal membrane surgery and 0.14% for macular hole surgery. In multivariable Poisson regression analysis, epiretinal membrane surgery was associated with POE [incidence rate ratio (IRR), 2.24; 95% CI, 1.62–3.11; p < 0.001]. For epiretinal membrane surgery, the 2010–2011 period was significantly associated with a higher risk of POE (IRR, 1.66; 95% CI, 1.13–2.42; p = 0.03). Conclusion The incidence of POE after macular surgery was 0.25% overall in France between 2006 and 2016 and twice higher for epiretinal membrane surgery than for macular hole surgery. For epiretinal surgery only, the incidence of POE was higher in 2010–2011 (period of the switch to transconjunctival vitrectomy) than in the rest of the study period

Epidemiology of acute endophthalmitis after intraocular procedures: a national database study

OBJECTIVE: To describe the causes of postoperative acute endophthalmitis at a national scale longitudinally. DESIGN: Cohort study from 2009 to 2018 in France. PARTICIPANTS: Patients diagnosed with acute endophthalmitis following intraocular procedures. METHODS: The French Medical-Administrative Database was used, endophthalmitis cases and intraocular procedures were identified by means of billing codes in all French hospitals and private practices. Main Outcomes and Measures: Incidence of acute endophthalmitis within 42 days of the procedure. RESULTS: From January 1, 2009 to October 31, 2018, 7522 cases of acute endophthalmitis occurred following 14 438 854 intraocular procedures. Most cases occurred after standalone cataract surgery (4808 cases for 7 316 077 procedures, 63.92%), followed by IVTs (1 296 cases for 5 455 631 IVTs, 17.23%), vitreoretinal surgery (698 for 442 263 procedures, 9.28%), anterior segment surgery (245 cases, 3.26%), combined cataract and vitreoretinal surgery (191 cases, 2.54%), cornea surgery (142 cases, 1.89%), and glaucoma surgery (80 cases, 1.06%). The overall incidence of acute endophthalmitis was 1 per 1920 procedures (0.0521% procedures, 95% CI, 0.0520-0.0522). The surgeries with the highest incidence of endophthalmitis were the scleral and globe surgery group, 0.1827% (95% CI, 0.1757-0.1898), followed by vitreoretinal surgery combined with cataract surgery, 0.1685% (95% CI, 0.1663-0.1706). The incidence of endophthalmitis after IVTs was stable over the study-period and patients were the oldest, 75.4 years (SD±12.0), P < 0.001. The onset of endophthalmitis following intravitreal procedures, after IVTs and vitreoretinal surgery, was shorter than for other procedures (P < 0.001). CONCLUSIONS: The profile of patients referred for acute endophthalmitis has been evolving over a decade, with a decrease in the raw number of endophthalmitis cases after cataract surgery as opposed to an increase in the number of patients presenting with endophthalmitis after IVTs

Metastatic Potential and Survival of Duodenal and Pancreatic Tumors in Multiple Endocrine Neoplasia Type 1

IF 9.203International audienceObjective: To assess the distant metastatic potential of duodeno-pancreatic neuroendocrine tumors (DP-NETs) in patients with MEN1, according to functional status and size.Summary Background Data: DP-NETs, with their numerous lesions and endocrine secretion-related symptoms, continue to be a medical challenge; unfortunately they can become aggressive tumors associated with distant metastasis, shortening survival. The survival of patients with large nonfunctional DP-NETs is known to be poor, but the overall contribution of DP-NETs to metastatic spread is poorly known.Methods: The study population included patients with DP-NETs diagnosed after 1990 and followed in the MEN1 cohort of the Groupe d’étude des Tumeurs Endocrines (GTE). A multistate Markov piecewise constant intensities model was applied to separate the effects of prognostic factors on 1) metastasis, and 2) metastasis-free death or 3) death after appearance of metastases.Results: Among the 603 patients included, 39 had metastasis at diagnosis of DP-NET, 50 developed metastases during follow-up, and 69 died. The Markov model showed that Zollinger-Ellison-related tumors (regardless of tumor size and thymic tumor pejorative impact), large tumors over 2 cm, and age over 40 years were independently associated with an increased risk of metastases. Men, patients over 40 years old and patients with tumors larger than 2 cm, also had an increased risk of death once metastasis appeared.Conclusions: DP-NETs of 2 cm in size or more, regardless of the associated secretion, should be removed to prevent metastasis and increase survival. Surgery for gastrinoma remains debatable

Author Correction: Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing (Nature Genetics, (2019), 51, 3, (414-430), 10.1038/s41588-019-0358-2)

An amendment to this paper has been published and can be accessed via a link at the top of the paper