The MALDIxin test is an accurate, rapid, cost-effective and scalable method that represents a major advance in the diagnosis of polymyxin resistance by directly assessing lipid A modifications in intact bacteria.

SUMMARY Fibrin sealant is used to close perforated or preperforated corneal ulcers. In addition to the usual advantages of cyanoacrylates it is degraded physiologically and provides a good support for corneal healing. Corneal grafting can be avoided when contraindicated or postponed when conditions allow. This technique has been successful in nine eyes of eight patients.

Supplementary figure legends.Supplementary Fig. 1 Number of antibiotic resistance genes (ARG) according to the phylogenetic group among E. coli ST410 isolates. The horizontal lines in the boxes represent the median number of ARG associated to the three clades: Basal (n=22); FQR clade (n=92) and OXA-181 subclade (n=41). The box boundaries represent the first and third quartiles of the distribution and box-plot whiskers span 1.5 times the interquartile range of the distribution. Outliers are denoted as black dots outside whiskers. Statistical significances were tested with a one-sided Wilcoxon rank-sum test. ***, P < 0.001. Supplementary Fig. 2. Recombination events in isolates of the E. coli ST410 FQR clade. Phylogeny of the E. coli ST410 FQR clade (left). On the right side, the recombined blocks identified by Gubbins 1 are highlighted in red when they occurred in an internal branch and affect more than one isolate and in blue when they occurred in a terminal branch affecting a single isolate. The core genome of E. coli ST410 FQR strains is represented above the figure and annotated genes correspond to the limits of major recombination events. Supplementary Fig. 3. Phylogeny and mutations in non-redundant CP-Ec isolates of ST167, ST101 and ST156. ML phylogenies were estimated as for Fig. 1, using 5,843, 21,810, and 18,746 non-recombinant SNPs for a. Ec ST167, rooted with the ST10 strain MG1655 (NC_00913) b. Ec ST101, and c. Ec ST156 respectively, both rooted with the ST1128 strain IAI1 (NC_011741). 14 distantly related non-CP-Ec ST156 isolates have been removed from the phylogenetic analysis. Branch tips indicates the presence and the type of carbapenemase according to the figure key on the left. On the right side of the tree are represented, from left to right: blaCTX-M ESBL, gyrA and parC QRDR mutations, mutations in the ftsI gene, and genetic events affecting ompF and ompC according to the figure key at the bottom. SNPs in the dcw region are represented by small vertical red bars. Genes from the dcw locus are indicated by arrows and the ftsI gene in red. Black arrowheads indicate isolates used as reference for SNPs mapping in the dcw gene cluster.

We investigated unusual carbapenemase-producing Enterobacter cloacae complex isolates (n = 8) in the novel sequence type (ST) 873, which caused nosocomial infections in 2 hospitals in France. Whole-genome sequence typing showed the 1-year persistence of the epidemic strain, which harbored a blaVIM-4 ST1-IncHI2 plasmid, in 1 health institution and 2 closely related strains harboring blaCTX-M-15 in the other. These isolates formed a new subgroup in the E. hormaechei metacluster, according to their hsp60 sequences and phylogenomic analysis. The average nucleotide identities, specific biochemical properties, and pangenomic and functional investigations of isolates suggested isolates of a novel species that had acquired genes associated with adhesion and mobility. The emergence of this novel Enterobacter phylogenetic lineage within hospitals should be closely monitored because of its ability to persist and spread.

With the dissemination of carbapenemase-producing (CPE) strains worldwide, carbapenem-hydrolyzing enzymes are increasingly reported among isolates of, the first hospital and community-acquired opportunistic pathogen. Here, we have performed an epidemiological survey of carbapenemase-producing (CP-) isolates received at the French National Reference Centre (F-NRC) in 2012 and 2013. Antimicrobial susceptibilities for last-resort antibiotics and antimicrobial compounds commonly used to treat urinary tract infections were determined by broth microdilution. Clonal relationship was assessed using repetitive sequence-based PCR (rep-PCR) and multilocus sequence typing (MLST). From this collection of 140 carbapenemase-producing isolates, 74% produced an OXA-48-like carbapenemase and 21% produced an NDM carbapenemase. A link with a foreign country was suspected for 37% of infected/colonized patients. Most of the isolates were from screening (56%) and from urine samples (26%). Colistin, fosfomycin, and nitrofurantoin possessed the most consistent activity, with 100%, 95%, and 96% isolates susceptible, respectively. A wide diversity of carbapenemase-producing isolates has been found (50 different sequence types [STs]). The most prevalent clones were (i) sequence type 38 (ST38) producing OXA-48 ( = 21), a clone linked to Turkey and North African countries, (ii) ST-90 producing OXA-204 ( = 9), which was responsible for an outbreak related to a contaminated duodenoscope, and (iii) ST-410 producing OXA-181 ( = 5), which was recovered from patients of different geographical origins. These specific clones might be considered high-risk clones for the dissemination of carbapenemases in The wide diversity of STs, combined with the increasing number of CP- isolates received by the F-NRC, suggests a likely dissemination of CP- isolates in the community.

We evaluated the usefulness of a serum Aspergillus PCR assay for the diagnosis and prognosis of invasive aspergillosis in a study involving 941 patients for a total of 5146 serum samples. Fifty-one patients had proven/probable aspergillosis. We compared galactomannan (GM), PCR and mycologic analysis of pulmonary samples in both neutropenic and nonneutropenic patients. PCR performed in serum yielded 66.7% sensitivity, 98.7% specificity, 75.6% positive predictive value and 98.0% negative predictive value, while the GM index yielded 78.4% sensitivity, 87.5% specificity, 27% positive predictive value and 98.6% negative predictive value. The inclusion of PCR in the European Organization for Research and Treatment of Cancer (EORTC) and the Mycosis Study Group (MSG) mycologic criteria permitted the reclassification of nine other cases from possible to probable aspergillosis and increased the sensitivity to 71.7%. Combining the GM index with serum PCR increased the detection rate of invasive aspergillosis with 88.2% sensitivity. PCR was systematically negative in 16 patients with noninvasive forms of aspergillosis (namely aspergilloma and chronic aspergillosis). Remaining PCR positive after a period of 14 to 20 days of treatment was related to poor outcome at 30 and 90 days. Our results also indicate that, unlike the determination of the GM index, the initial fungus load as determined by PCR was highly predictive of 90-day mortality, with the rate of the latter being 15.8% for patients with <150 copies/mL vs. 73.2% for patients at or above that cutoff (p <0.0001). Therefore, PCR appears to be a powerful and interesting tool for the identification of patients with invasive aspergillosis who might benefit from more intense care.

The rCIM is a rapid (less than 3 h), cheap and accurate test for the detection of CPEs, which can be implemented in low-resource settings, making it a useful tool for microbiology laboratories.

BackgroundThere is an urgent need for accurate and rapid diagnostic tests to identify carbapenemase producing enterobacteria (CPE). Here, we have evaluated the Carbapenem Inactivation Method (CIM) test to detect CPEs from cultured colonies.MethodsA total of 256 enterobacterial isolates were used to evaluate the performance of the CIM in comparison to Carba NP test and molecular detection used a reference method. Ninety three well-characterized isolates (including 29 non-CPE and 63 CPEs of worldwide origin) with decreased susceptibility to at least one carbapenem were used to (i) evaluate the efficacy of CIM test and (ii) to compare it to the Carba NP test. We also tested different carbapenems to determine the best substrate for this test. Finally, the CIM test was then evaluated prospectively against 164 isolates referred to the French National Reference Center (NRC) for Antimicrobial Resistance from may 2016 to july 2016.ResultsBased on the results of this retrospective study, sensitivity and specificity of the CIM and the Carba NP test were 92.1% and 100%, respectively. We demonstrated that the meropenem was the best substrate to perform the CIM test since sensitivity and specificity were 81.1% and 100% using ertapenem disk, and 100% and 65,6% using imipenem disk, and respectively. Taking in account the results of retrospective and prospective studies, CIM and Carba NP tests have similar sensitivity, specificity, positive predictive value and negative predictive values being 96.3%, 98.9%, 99.0% and 98.4% for the CIM test versus 96.9%, 100%, 100% and 100% for the Carba NP test.ConclusionsOur results confirm that the CIM test may be a useful tool for the reliable confirmation of carbapenemase-activity in enterobacterial isolates, especially in clinical microbiological laboratories with limited resources, no trained personnel, and no specialized equipment.