Daptomycin Resistant Staphylococcus aureus Clinical Strain With Novel Non-synonymous Mutations in the mprF and vraS Genes:A New Insight Into Daptomycin Resistance

Objectives: Daptomycin (DAP) resistance in Staphylococcus aureus is uncommon but there are increasing reports of the emergence of resistance during DAP therapy. Most clinical DAP-resistant S. aureus isolates investigated carried mutations in the mprF gene. The aim of this study was to identify mutations between a clinical pair of methicillin-susceptible S. aureus (MSSA) isolates (DAP-susceptible and DAP-resistant). Additionally, the activity of genes previously associated with DAP resistance was assessed. Materials and Methods: Two MSSA isolates from patient with left-sided endocarditis were analyzed by whole genome sequencing (WGS) and reverse transcription-quantitative real-time PCR (RT-qPCR). The first isolate, DAP-susceptible, was obtained before initiation of treatment and the second isolate, DAP-resistant, was recovered after 4 weeks of DAP therapy. Results: Comparison of complete genomes of DAP-susceptible and its DAP-resistant variant identified two non-synonymous and one synonymous mutations. The non-synonymous mutations consisted of a S829L substitution in mprF and a T331I substitution in vraS. The RT-qPCR experiments revealed an increased expression of vraS, dltA, mprF, and sceD genes in DAP-resistant variant. Strikingly, the expression of dltA and mprF genes was significantly downregulated by DAP. Conclusion: The mprF and vraS genes were previously associated with DAP resistance, however, none of the mutations described in this study had been previously identified and linked to DAP resistance. Moreover, we provide a new insight into the DAP action on S. aureus, in which the expression of key genes in DAP resistance is decreased by the antibiotic

Microfluidic-Chip-Based Multiple-Locus Variable-Number Tandem-Repeat Fingerprinting with New Primer Sets for Methicillin-Resistant Staphylococcus aureus

The detection of outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) infections and a rapid and accurate identification of sources and routes of transmission should be conducted in hospital settings as early and swiftly as possible. In this study, we investigated the application potential of a new approach based on multiple-locus variable-number tandem-repeat fingerprinting (MLVF) and microfluidics technology for a rapid discrimination of MRSA lineages in outbreak settings. A total of 206 nonrepetitive MRSA isolates recovered from infected patients at the University Medical Center Groningen between 2000 and 2010 were tested. The results obtained by MLVF using microcapillary electrophoresis with newly designed primers were compared to those obtained by spa typing and multiple-locus variable-number tandem-repeat analysis (MLVA). The discriminatory power was 0.980 (107 patterns), 0.969 (85 allelic profiles), and 0.959 (66 types) for MLVF, MLVA, and spa typing, respectively. All methods tested showed a good concordance of results calculated by the adjusted Rand's coefficient method. Comparisons of data obtained by the three approaches allowed us to propose an 88% cutoff value for the similarity between any two MLVF patterns, which can be used in S. aureus epidemiological studies, including analyses of outbreaks and strain transmission events. Of the three tested methods, MLVF is the cheapest, fastest, and easiest to perform. MLVF applied to microfluidic polymer chips is a rapid, cheap, reproducible, and highly discriminating tool to determine the clonality of MRSA isolates and to trace the spread of MRSA strains over periods of many years. Although spa typing should be used due to its portability of data, MLVF has a high added value because it is more discriminatory

Carbapenemase-producing Enterobacteriaceaein Europe: assessment by national experts from 38 countries, May 2015

European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) working group collaborators: Koraqi A, Bino S, Hartl R, Apfalter P, Glupczynski Y, Jans B, Marković T, Dedeić- Ljubović A, Kojić D, Strateva T, Sabtcheva S, Butić I, Andrašević AT, Pieridou-Bagatzouni D, Panayiota M, Hrabák J, Žemličková H, Hammerum AM, Skov R, Ivanova M, Jalava J, Dortet L, Vaux S, Kaase M, Eckmanns T, Vatopoulos A, Giamarellou H, Tóth Á, Kurcz A, Hardarson H, Kristinsson K, Boo TW, Burns K, Carmeli Y, Pantosti A, Kurti A, Raka L, Balode A, Miciulevičienė J, Valintėlienė R, Perrin-Weniger M, Nestorova N, Borg M, Mijović G, Mugosa B, Meessen N, de Greeff S, Samuelsen Ø, Simonsen GS, Żabicka D, Hryniewicz W, Caniça M, Paiva JA, Kaftandzieva A, Memeti S, Damian M, Codita I, Jelesić Z, Stevanovic G, Nikš M, Schréterová E, Pirš M, Kolman J, Oteo J, Campos J, Giske CG, Sjöström K, Gür D, Ekmekci E, Wiuff C, Hopkins K, Woodford N, Cantón R, Friedrich AW, Gniadkowski M, Poirel L, Rossolini GM, Seifert H, Walsh T, Livermore D, Nordmann P.In 2012, the European Centre for Disease Prevention and Control (ECDC) launched the 'European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE)' project to gain insights into the occurrence and epidemiology of carbapenemase-producing Enterobacteriaceae (CPE), to increase the awareness of the spread of CPE, and to build and enhance the laboratory capacity for diagnosis and surveillance of CPE in Europe. Data collected through a post-EuSCAPE feedback questionnaire in May 2015 documented improvement compared with 2013 in capacity and ability to detect CPE and identify the different carbapenemases genes in the 38 participating countries, thus contributing to their awareness of and knowledge about the spread of CPE. Over the last two years, the epidemiological situation of CPE worsened, in particular with the rapid spread of carbapenem-hydrolysing oxacillinase-48 (OXA-48)- and New Delhi metallo-beta-lactamase (NDM)-producing Enterobacteriaceae. In 2015, 13/38 countries reported inter-regional spread of or an endemic situation for CPE, compared with 6/38 in 2013. Only three countries replied that they had not identified one single case of CPE. The ongoing spread of CPE represents an increasing threat to patient safety in European hospitals, and a majority of countries reacted by establishing national CPE surveillances systems and issuing guidance on control measures for health professionals. However, 14 countries still lacked specific national guidelines for prevention and control of CPE in mid-2015

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.

The correct interpretation of microbial sequencing data applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) genomes drawn from England, Northern Ireland, Wales, Scotland, and the Republic of Ireland over a decade. We sequenced 1013 MRSA submitted to the British Society for Antimicrobial Chemotherapy by 46 laboratories between 2001 and 2010. Each isolate was assigned to a regional healthcare referral network in England and was otherwise grouped based on country of origin. Phylogenetic reconstructions were used to contextualize MRSA outbreak investigations and to detect the spread of resistance. The majority of isolates (n = 783, 77%) belonged to CC22, which contains the dominant United Kingdom epidemic clone (EMRSA-15). There was marked geographic structuring of EMRSA-15, consistent with widespread dissemination prior to the sampling decade followed by local diversification. The addition of MRSA genomes from two outbreaks and one pseudo-outbreak demonstrated the certainty with which outbreaks could be confirmed or refuted. We identified local and regional differences in antibiotic resistance profiles, with examples of local expansion, as well as widespread circulation of mobile genetic elements across the bacterial population. We have generated a resource for the future surveillance and outbreak investigation of MRSA in the United Kingdom and Ireland and have shown the value of this during outbreak investigation and tracking of antimicrobial resistance.We are grateful for assistance from the library construction, sequencing and core informatics teams at the Wellcome Trust Sanger Institute. We acknowledge David Harris and Martin Aslett for their help in submitting the sequenced isolates to public databases. The study was supported by grants from the UKCRC Translational Infection Research Initiative, and the Medical Research Council (Grant Number G1000803) with contributions to the Grant from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate (to Prof. Peacock); by Wellcome Trust grant number 098051 awarded to the Wellcome Trust Sanger Institute; and by a Healthcare Infection Society Major Reasearch Grant. MET is a Clinician Scientist Fellow, supported by the Academy of Medical Sciences and the Health Foundation and the NIHR Cambridge Biomedical Research Centre. BGS was supported by Wellcome Trust grant number 089472. The study was approved by the University of Cambridge Human Biology Research Ethics Committee (reference HBREC.2013.05), and by the Cambridge University Hospitals NHS Foundation Trust Research and Development Department (reference A092869). Isolates were supplied by the BSAC Resistance Surveillance Project.This is the final version of the article. It first appeared from Cold Spring Harbor Laboratory Press via http://dx.doi.org/10.1101/gr.196709.11

Forecasting local hospital bed demand for COVID-19 using on-request simulations

For hospitals, realistic forecasting of bed demand during impending epidemics of infectious diseases is essential to avoid being overwhelmed by a potential sudden increase in the number of admitted patients. Short-term forecasting can aid hospitals in adjusting their planning and freeing up beds in time. We created an easy-to-use online on-request tool based on local data to forecast COVID-19 bed demand for individual hospitals. The tool is flexible and adaptable to different settings. It is based on a stochastic compartmental model for estimating the epidemic dynamics and coupled with an exponential smoothing model for forecasting. The models are written in R and Julia and implemented as an R-shiny dashboard. The model is parameterized using COVID-19 incidence, vaccination, and bed occupancy data at customizable geographical resolutions, loaded from official online sources or uploaded manually. Users can select their hospital's catchment area and adjust the number of COVID-19 occupied beds at the start of the simulation. The tool provides short-term forecasts of disease incidence and past and forecasted estimation of the epidemic reproductive number at the chosen geographical level. These quantities are then used to estimate the bed occupancy in both general wards and intensive care unit beds. The platform has proven efficient, providing results within seconds while coping with many concurrent users. By providing ad-hoc, local data informed forecasts, this platform allows decision-makers to evaluate realistic scenarios for allocating scarce resources, such as ICU beds, at various geographic levels.Comment: 23 pages, 3 figures. Code available at https://github.com/QUPI-IUK/Bed-demand-forecas

Hand hygiene improvement of individual healthcare workers: results of the multicentre PROHIBIT study

Hand hygiene; Intensive care; InterventionHigiene de manos; Cuidados intensivos; IntervenciónHigiene de mans; Cures intensives; IntervencióBackground Traditionally, hand hygiene (HH) interventions do not identify the observed healthcare workers (HWCs) and therefore, reflect HH compliance only at population level. Intensive care units (ICUs) in seven European hospitals participating in the “Prevention of Hospital Infections by Intervention and Training” (PROHIBIT) study provided individual HH compliance levels. We analysed these to understand the determinants and dynamics of individual change in relation to the overall intervention effect. Methods We included HCWs who contributed at least two observation sessions before and after intervention. Improving, non-changing, and worsening HCWs were defined with a threshold of 20% compliance change. We used multivariable linear regression and spearman’s rank correlation to estimate determinants for the individual response to the intervention and correlation to overall change. Swarm graphs visualized ICU-specific patterns. Results In total 280 HCWs contributed 17,748 HH opportunities during 2677 observation sessions. Overall, pooled HH compliance increased from 43.1 to 58.7%. The proportion of improving HCWs ranged from 33 to 95% among ICUs. The median HH increase per improving HCW ranged from 16 to 34 percentage points. ICU wide improvement correlated significantly with both the proportion of improving HCWs (ρ = 0.82 [95% CI 0.18–0.97], and their median HH increase (ρ = 0.79 [0.08–0.97]). Multilevel regression demonstrated that individual improvement was significantly associated with nurse profession, lower activity index, higher nurse-to-patient ratio, and lower baseline compliance. Conclusions Both the proportion of improving HCWs and their median individual improvement differed substantially among ICUs but correlated with the ICUs’ overall HH improvement. With comparable overall means the range in individual HH varied considerably between some hospitals, implying different transmission risks. Greater insight into improvement dynamics might help to design more effective HH interventions in the future.The study was funded by the European Commission 7th Framework Programme

Global Spread of Vancomycin-resistant Enterococcus faecium from Distinct Nosocomial Genetic Complex

Vancomycin-resistant enterococci (VRE) have caused hospital outbreaks worldwide, and the vancomycin-resistance gene (vanA) has crossed genus boundaries to methicillin-resistant Staphylococcus aureus. Spread of VRE, therefore, represents an immediate threat for patient care and creates a reservoir of mobile resistance genes for other, more virulent pathogens. Evolutionary genetics, population structure, and geographic distribution of 411 VRE and vancomycin-susceptible Enterococcus faecium isolates, recovered from human and nonhuman sources and community and hospital reservoirs in 5 continents, identified a genetic lineage of E. faecium (complex-17) that has spread globally. This lineage is characterized by 1) ampicillin resistance, 2) a pathogenicity island, and 3) an association with hospital outbreaks. Complex-17 is an example of cumulative evolutionary processes that improved the relative fitness of bacteria in hospital environments. Preventing further spread of this epidemic E. faecium subpopulation is critical, and efforts should focus on the early disclosure of ampicillin-resistant complex-17 strains