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To the Editor: Previously, we reported the use of whole-genome sequencing to investigate a putative methicillin-resistant Staphylococcus aureus (MRSA) outbreak in 2011 in the special care baby unit (SCBU) at the Cambridge University Hospitals National Health Service Foundation Trust (CUH) in the United Kingdom (1). The report identified 26 related cases of infection with or asymptomatic carriage of MRSA and showed that transmission occurred within the SCBU, between mothers on a postnatal ward, and in the community; the outbreak apparently resolved at the end of 2011. The outbreak strain, sequence type (ST) 2371, was of a novel multilocus ST related to the dominant hospital-associated lineage in the UK (ST22, EMRSA-15), but unlike most ST22 strains, this strain was Panton-Valentine leucocidin–positive (2). Since then, ST2371 has been identified as a prevalent communityassociated MRSA clone in Southern India, and sporadic isolates have also been detected by whole-genome sequencing of MRSA in Denmark (3–5) ; The study was supported by grants from the UKCRC Translational Infection Research (TIR) 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 a Healthcare Infection Society Major Research Grant; and by Wellcome Trust grant number 098051 awarded to the Wellcome Trust Sanger Institute.

[cat] Utilitzem un conjunt de mètriques del paisatge per estudiar l'evolució a llarg termini seguida en una típica zona costanera del Mediterrani des de 1850 fins a 2005, que mostren una greu deterioració del medi ambient entre 1950 i 2005. Les principals forces motores d'aquesta degradació del paisatge han estat el creixement urbà experimentat a les antigues zones agrícoles situades a les planes litorals, juntament amb l'abandonament i la reforestació dels vessants dels pujols interceptats per àrees residencials de baixa densitat, carreteres i altres infraestructures lineals. Duem a terme una anàlisi estadística de redundància (RDA) amb la finalitat d'identificar els que considerem com alguns agents rectors socioeconòmics i polítics d'última instància d'aquests impactes ambientals. Els resultats confirmen les nostres hipòtesis interpretatives, que són que: 1) els canvis en les cobertes i usos del sòl determinen canvis en les propietats dels paisatge, tant estructurals com funcionals; 2) aquests canvis no es produeixen per atzar, sinó que estan relacionats amb factors geogràfics i forces socioeconòmiques i polítiques. ; [eng] We use a set of landscape metrics to study the long-term environmental transformation of a typical coastal Mediterranean area from 1850 to 2005. Our figures show a dramatic environmental deterioration between 1950 and 2005. The main proximate drivers of this landscape degradation are the effects of urban sprawl on former agricultural areas located in the coastal plains, together with the abandonment and reforestation of hilly slopes intercepted by low-density residential areas, highways, and other linear infrastructures. We carry out a statistical redundancy analysis (RDA) to identify certain ultimate socioeconomic and political drivers of these environmental impacts. The results confirm our interpretive hypothesis that: 1) land cover changes determine changes in landscape properties, both structural and functional; 2) these changes are not at random, but related to geographical endowments and socioeconomic or political drivers.

BACKGROUND: The spread of USA300 methicillin-resistant Staphylococcus aureus (MRSA) across the United States resulted in an epidemic of infections. In Europe, only sporadic cases or small clusters of USA300 infections are described, and its prevalence in England is unknown. We conducted prospective surveillance for USA300 in the east of England. METHODS: We undertook a 12-month prospective observational cohort study of all individuals with MRSA isolated from community and hospital samples submitted to a microbiology laboratory. At least 1 MRSA isolate from each individual underwent whole-genome sequencing. USA300 was identified on the basis of sequence analysis, and phylogenetic comparisons were made between these and USA300 genomes from the United States. RESULTS: Between April 2012 and April 2013, we sequenced 2283 MRSA isolates (detected during carriage screening and in clinical samples) from 1465 individuals. USA300 was isolated from 24 cases (1.6%). Ten cases (42%) had skin and soft tissue infection, and 2 cases had invasive disease. Phylogenetic analyses identified multiple introductions and household transmission of USA300. CONCLUSIONS: Use of a diagnostic laboratory as a sentinel for surveillance has identified repeated introductions of USA300 in eastern England in 2012-2013, with evidence for limited transmission. Our results show how systematic surveillance could provide an early warning of strain emergence and dissemination. ; This work was supported by grants from the UK Clinical Research Collaboration 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 a Healthcare Infection Society Major Research Grant (to Prof. Peacock), and by Wellcome Trust grant number 098051 awarded to the Wellcome Trust Sanger Institute. MST is a Wellcome Trust Clinical PhD Fellow. MET is a Clinician Scientist Fellow, supported by the Academy of Medical Sciences and the Health Foundation, and by the National Institute for Health Research Cambridge Biomedical Research Centre. ; This is the final version of the article. It first appeared from Oxford University Press via https://doi.org/10.1093/infdis/jiw166

BackgroundMandatory reporting of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSI) has occurred in England for over 15years. Epidemiological information is recorded, but routine collection of isolates for characterisation has not been routinely undertaken. Ongoing developments in whole-genome sequencing (WGS) have demonstrated its value in outbreak investigations and for determining the spread of antimicrobial resistance and bacterial population structure. Benefits of adding genomics to routine epidemiological MRSA surveillance are unknown.AimTo determine feasibility and potential utility of adding genomics to epidemiological surveillance of MRSA.MethodsWe conducted an epidemiological and genomic survey of MRSA BSI in England over a 1-year period (1 October 2012--30 September 2013).ResultsDuring the study period, 903 cases of MRSA BSI were reported; 425 isolates were available for sequencing of which, 276 (65%) were clonal complex (CC) 22. Addition of 64 MRSA genomes from published outbreak investigations showed that the study genomes could provide context for outbreak isolates and supported cluster identification. Comparison to other MRSA genome collections demonstrated variation in clonal diversity achieved through different sampling strategies and identified potentially high-risk clones e.g. USA300 and local expansion of CC5 MRSA in South West England.ConclusionsWe demonstrate the potential utility of combined epidemiological and genomic MRSA BSI surveillance to determine the national population structure of MRSA, contextualise previous MRSA outbreaks, and detect potentially high-risk lineages. These findings support the integration of epidemiological and genomic surveillance for MRSA BSI as a step towards a comprehensive surveillance programme in England. ; This work was supported by grants from the UK Clinical Research Collaboration 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); and the Wellcome Trust (to Prof. Parkhill [Grant 098051], Prof. Peacock). MST is a Wellcome Trust Clinical PhD Fellow at the University of Cambridge. MET is a Clinician Scientist Fellow, supported by the Academy of Medical Sciences and the Health Foundation, and by the National Institute for Health Research Cambridge Biomedical Research Centre. FC is supported by the Wellcome Trust (201344/Z/16/Z).

Using 894 phylogenetically diverse genomes of the Mycobacterium tuberculosis complex (MTBC), we simulated in silico the ability of the Hain Lifescience GenoType MTBC to differentiate the causative agents of tuberculosis. We propose a revised interpretation of this assay to reflect its strengths (e.g. it can distinguish some strains of M. canettii and variants of M. bovis that are not intrinsically resistant to pyrazinamide) and limitations (e.g. M. orygis cannot be differentiated from M. africanum). This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

$\textbf{Background:}$ Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant $\textit{Staphylococcus aureus}$ (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Whole-genome sequencing (WGS) has been used successfully to understand MRSA epidemiology and transmission in hospitals and has the potential to identify transmission between these and LTCF. $\textbf{Methods:}$ Two prospective observational studies of MRSA carriage were conducted in LTCF in England and Ireland. MRSA isolates were whole-genome sequenced and analyzed using established methods. Genomic data were available for MRSA isolated in the local healthcare systems (isolates submitted by hospitals and general practitioners). $\textbf{Results:}$ We sequenced a total of 181 MRSA isolates from the two study sites. The majority of MRSA were multilocus sequence type (ST)22. WGS identified one likely transmission event between residents in the English LTCF and three putative transmission events in the Irish LTCF. WGS also identified closely related isolates present in colonized Irish residents and their immediate environment. Based on phylogenetic reconstruction, closely related MRSA clades were identified between the LTCF and their healthcare referral network, together with putative MRSA acquisition by LTCF residents during hospital admission. $\textbf{Conclusions:}$ These data confirm that MRSA is transmitted between residents of LTCF and is both acquired and transmitted to others in referral hospitals and beyond. Our data present compelling evidence for the importance of environmental contamination in MRSA transmission, reinforcing the importance of environmental cleaning. The use of WGS in this study highlights the need to consider infection control in hospitals and community healthcare facilities as a continuum. ; UKCRC Translational Infection Research (TIR) Initiative, Medical Research Council (Grant ID: G1000803), Biotechnology and Biological Sciences Research Council, National Institute for Health Research, Chief Scientist Office of the Scottish Government Health Directorate, Hospital Infection Society (Major Research Grant), Wellcome Trust (Grant ID: 098051), Academy of Medical Sciences, Health Foundation, National Institute for Health Research Cambridge Biomedical Research Centre ; This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13073-016-0353-5

In this study, using the Hain GenoType MTBDRsl assays (versions 1 and 2), we found that some nonsynonymous and synonymous mutations in gyrA in Mycobacterium tuberculosis result in systematic false-resistance results to fluoroquinolones by preventing the binding of wild-type probes. Moreover, such mutations can prevent the binding of mutant probes designed for the identification of specific resistance mutations. Although these mutations are likely rare globally, they occur in approximately 7% of multidrug-resistant tuberculosis strains in some settings. ; Funding Agencies|Swedish Heart and Lung Foundation; Marianne and Marcus Wallenberg Foundation; Wellcome Trust [201344/Z/16/Z]; NIHR Oxford Biomedical Research Centre; NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance [HPRU-2012-10041]; Health Innovation Challenge Fund [T5-358, HICF-T5-342, WT098600]; German Center for Infection Research (DZIF); European Union TB-PAN-NET [FP7-223681]; PathoNgenTrace [278864]; UK Department of Health; Pacific Biosciences, Inc.; Illumina, Inc.; Colciencias; Hain Lifescience

A screening of more than 1,500 drug-resistant strains of Mycobacterium tuberculosis revealed evolutionary patterns characteristic of positive selection for three alanine racemase (Alr) mutations. We investigated these mutations using molecular modeling, in vitro MIC testing, as well as direct measurements of enzymatic activity, which demonstrated that these mutations likely confer resistance to D-cycloserine. ; Funding Agencies|University of Otago; Health Research Council; Maurice Wilkins Centre; European Union [FP7-278864-2]; German Center for Infection Research (DZIF); Fundacao para a Ciencia e a Tecnologia, Portugal [UID/Multi/04413/2013, SFRH/BPD/100688/2014, SFRH/BPD/95406/2013]; Wellcome Trust [201344/Z/16/Z]; Medical Research Council UK [MR/K000551/1, MR/M01360X/1, MR/N010469/1]; Indian Council of Medical Research, New Delhi; L2 Diagnostics LLC, New Haven; Pacific Biosciences, Inc.; Illumina, Inc.; European Society of Mycobacteriology; Hain Lifescience; UK Department of Health [HICF-T5-342, WT098600]; Wellcome Trust