MCR: modern colistin resistance

Recently, plasmid-mediated and, therefore, transferable bacterial polymyxin resistance was discovered in strains from both humans and animals. Such a trait may widely spread geographically, while simultaneously crossing microbial species barriers. This may ultimately render the “last resort” polymyxin antibiotics therapeutically useless. Colistin is currently used to treat infections caused by Gram-negative carbapenemase producers and colistin resistance may lead to practical pan-antibiotic resistance. We here analyzed the medical and diagnostic consequences of (emerging) colistin resistance and propose pathways toward adequate diagnostics for timely detection of both asymptomatic carriage and infection. Culture-based testing using chromogenic and selective media for screening clinical (and veterinary) specimens may constitute key tools for that purpose. Relevant molecular tests are also discussed

Correlation between phenotypic antibiotic susceptibility and the resistome in Pseudomonas aeruginosa

Genetic determinants of antibiotic resistance (AR) have been extensively investigated. High-throughput sequencing allows for the assessment of the relationship between genotype and phenotype. A panel of 672 Pseudomonas aeruginosa strains was analysed, including representatives of globally disseminated multidrug-resistant and extensively drug-resistant clones; genomes and multiple antibiograms were available. This panel was annotated for AR gene presence and polymorphism, defining a resistome in which integrons were included. Integrons were present in >70 distinct cassettes, with In5 being the most prevalent. Some cassettes closely associated with clonal complexes, whereas others spread across the phylogenetic diversity, highlighting the importance of horizontal transfer. A resistome-wide association study (RWAS) was performed for clinically relevant antibiotics by correlating the variability in minimum inhibitory concentration (MIC) values with resistome data. Resistome annotation identified 147 loci associated with AR. These loci consisted mainly of acquired genomic elements and intrinsic genes. The RWAS allowed for correct identification of resistance mechanisms for meropenem, amikacin, levofloxacin and cefepime, and added 46 novel mutations. Among these, 29 were variants of the oprD gene associated with variation in meropenem MIC. Using genomic and MIC data, phenotypic AR was successfully correlated with molecular determinants at the whole-genome sequence level

Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates

Silicon and chromium stable isotopic systematics during basalt weathering and lateritisation: A comparison of variably weathered basalt profiles in the Deccan Traps, India

Global biomass production is fundamentally affected by the hydrological cycling of elements at the Earth's surface. Continental weathering processes are the major source for most bio-essential elements in marine environments and therefore affect primary productivity. In addition, critical zone biomass depends on energy and chemical exchange reactions in weathering profiles. The latter reservoirs are in turn influenced by different climatic conditions that control weathering and pore water parameters like pH and Eh, which regulate mineral break down rates and dictate the mobility and mass flux of elements. Two Deccan Traps basalt weathering profiles of contrasting age and alteration intensity provide a natural laboratory for investigating the effects of rock alteration on Si and Cr and their isotopic. systematics. The Quaternary Chhindwara profile has progressed to a moderate degree of alteration (saprolite), while the Paleogene Bidar example displays an extremely altered laterite. The Chhindwara saprolite profile shows a near uniform Cr and Si concentration and isotopic composition, whereas the Bidar laterite profile is characterised by an intense loss of Si, a large enrichment of Cr within the most altered uppermost levels, and a wide range of Cr stable isotope ratios (-0.85 to 0.36 parts per thousand delta Cr-53/52). A co-variation between Si and Cr isotopes, as well as their co-variation with iron content, provides empirical evidence that iron redistribution within the profile has a large effect on Cr mobility and Si isotopic fractionation. Therefore, it is concluded that iron oxides exert a primary control over the isotopic composition of both Cr and Si in pore waters of laterites. Since laterite formation is promoted by tropical climates, the results of this study provide new evidence to suggest that the hydrological Cr and Si fluxes originating from continental weathering have changed in accordance with large-scale, deep time climate variation and continental plate configuration. An increased flux of Si and greater magnitude of Cr mobility and isotopic fractionation are possibly amplified under CO2-rich, greenhouse episodes and/or when large landmasses were tectonically arranged at near equatorial latitudes

Silicon isotope variations in the Earth and meteorites

A fluorhydric acid-free sample preparation method derived from Georg et al. [1] has been used to measure the natural variations of silicon isotope compositions in terrestrial (including 12 geological standard materials) and meteoritic bulk-rock samples. All measurements were done using a Neptune MC-ICPMS in medium resolution mode (m/Δm = 7000, peak-edge definition). Magnesium was used as internal standard for mass-bias drift correction. The δ30Si values are expressed relative to the NBS-28 silica standard. IRMM-17 reference material yields a δ30Si of -1.4‰ ± 0.05‰ (2SD, n=11) in agreement with previous data [2-3]. Long-term reproducibilities were obtained for BHVO-2 (δ30Si = -0.27‰ ± 0.08‰ (2SD, n=30)) and a in-house Si standard (δ30Si = -0.01‰ ± 0.07‰ (2SD, n=20)) on a 7 months time scale. Total variation of δ30Si in natural samples ranges from - 0.5‰ to -0.1‰. Comparison with δ29Si values shows that this isotopic fractionation is mass-dependent. A 0.2‰ isotopic variation occurs among terrestrial samples suggesting an enrichment in the heavier silicon isotopes as a function of magma differentiation, as initially hinted by Douthitt [4]. Terrestrial samples mean value (δ30SiEarth= -0.23‰) is heavier by about 0.24‰ in δ30Si compared to chondrites. This may be explained by silicon isotope fractionation during planetary accretion and/or differentiation

Comparative evaluation of a prototype chromogenic medium (ChromID CARBA) for detecting carbapenemase-producing Enterobacteriaceae in surveillance rectal swabs

Carbapenemase-producing Enterobacteriaceae (CPE) are an increasing problem worldwide, and rectal swab surveillance is recommended as a component of infection control programs. The performance of a prototype chromogenic medium (chromID CARBA) was evaluated and compared with media tested by four other screening methods: (i) overnight selective enrichment in 5 ml tryptic soy broth with a 10-μg ertapenem disk followed by plating onto MacConkey agar (CDC-TS), (ii) short selective enrichment in 9 ml brain heart infusion broth with a 10-μg ertapenem disk followed by plating onto chromID ESBL medium (ESBL-BH), (iii) direct plating onto chromID ESBL, and (iv) direct plating onto MacConkey agar supplemented with meropenem (1 μg/ml) (MCM). The screening methods were applied to detect CPE in 200 rectal swab specimens taken from different hospitalized patients. Identification and antimicrobial susceptibility were performed by the Vitek 2 system. Carbapenem MICs were checked by Etest. Carbapenemase production was confirmed using the modified Hodge test, combined-disk tests, and PCR assays. In total, 133 presumptive CPE strains were detected. Phenotypic and genotypic assays confirmed 92 strains to be CPE (56 KPC-positive Klebsiella pneumoniae, 29 VIM-positive K. pneumoniae, and 7 KPC-positive Enterobacter aerogenes strains) recovered from 73 patients, while the remaining 41 strains were confirmed to be CPE negative (19 ESBL producers and 22 nonfermenters). chromID CARBA, ESBL-BH, and chromID ESBL exhibited the highest sensitivity (92.4%), followed by CDC-TS and MCM (89.1%) (P = 0.631). The specificity was greater for chromID CARBA (96.9%) and ESBL-BH (93.2%) than for CDC-TS (86.4%), MCM (85.2%), and chromID ESBL (84.7%) (P = 0.014). In conclusion, chromID CARBA was found to be a rapid and accurate culture screening method for active CPE surveillance. Copyright © 2012, American Society for Microbiology. All Rights Reserved

ELECTROPHYSIOLOGICAL STUDY (VEP,BAEP) IN HIV-1 SEROPOSITIVE PATIENTS WITH AND WITHOUT AIDS

One hundred-twenty nine HIV-1 seropositive patients (39 females, 90 males) were studied by means of pattern visual evoked potential (VEP) and brainstem auditory evoked potential (BAEP) recording. Utilizing the criteria of the Centers for Disease Control the patients were clinically defined and then subdivided into four groups : group A included patients of category II (n : 11); group B patients of category III (n : 29); group C patients of category IVa and IVc2 (n : 55) and group D patients belonging to the other subgroups of category IV (n : 34). EP were altered in 26.35% of the entire group with a marked prevalence of BA EP alterations (21.7%) rather than of VEP (4.65%). A considerable amount of BA EP abnormalities (24.13%) were found in patients with persistent generalized lymphadenopathy (group B). A significant increase of BAEP mean interpeak latencies were observed in group B, C, D patients when compared with those of the control group. On the whole, EP were altered in 20.65% of the neurologically asymptomatic patients. EP alterations may precede any clinical manifestation and can be found during the earlier phases of HIV-1 infection

Population analysis of Escherichia coli isolates with discordant resistance levels by piperacillin-tazobactam broth microdilution and agar dilution testing

Population analysis was performed for 42 Escherichia coli isolates to determine whether heterogeneity of resistance was a factor in piperacillin-tazobactam category differences between agar dilution and broth microdilution. Of 20 isolates discordant between methods, 80% were heterogeneous. Of 22 isolates in agreement, 59% were homogeneous. Heterogeneity and homogeneity rates for those in agreement were significantly different from those that were discordant (P value, 0.010). Heterogeneity of resistance expression appears to be an important factor in category differences observed between broth microdilution and agar dilution for piperacillin-tazobactam. Copyrigh