Genomic insights into the origin of farming in the ancient Near East

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 BC, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia

Intraguild predation and partial consumption of blue sharks Prionace glauca

The top-down effects of predators on ecosystem structure and dynamics have been studied increasingly. However, the nature and consequence of trophic interactions between upper-trophic-level predators have received considerably less attention. This is especially the case in marine systems due to the inherent challenges of studying highly mobile marine species. Here we describe the first documentation of asymmetrical intraguild predation by a pinniped predator on a mid-sized predatory shark. The report is based on direct observations in South African waters, in which free-swimming blue sharks Prionace glauca were captured and partially consumed by Cape fur seals Arctocephalus pusillus pusillus. These observations are important not just for understanding the interactions between these two species but more broadly for their implications in understanding the trophic ecology of pinnipeds, many populations of which have increased while numerous shark populations have declined.Keywords: belly-biting, pinnipeds, trophic interaction

Diagnosis, management and prevention of Candida auris in hospitals: position statement of the Australasian Society for Infectious Diseases

Candida auris is an emerging drug-resistant yeast responsible for hospital outbreaks. This statement reviews the evidence regarding diagnosis, treatment and prevention of this organism and provides consensus recommendations for clinicians and microbiologists in Australia and New Zealand. C. auris has been isolated in over 30 countries (including Australia). Bloodstream infections are the most frequently reported infections. Infections have crude mortality of 30-60%. Acquisition is generally healthcare-associated and risks include underlying chronic disease, immunocompromise and presence of indwelling medical devices. C. auris may be misidentified by conventional phenotypic methods. Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry or sequencing of the internal transcribed spacer regions and/or the D1/D2 regions of the 28S ribosomal DNA are therefore required for definitive laboratory identification. Antifungal drug resistance, particularly to fluconazole, is common, with variable resistance to amphotericin B and echinocandins. Echinocandins are currently recommended as first-line therapy for infection in adults and children ≥2 months of age. For neonates and infants <2 months of age, amphotericin B deoxycholate is recommended. Healthcare facilities with C. auris should implement a multimodal control response. Colonised or infected patients should be isolated in single rooms with Standard and Contact Precautions. Close contacts, patients transferred from facilities with endemic C. auris or admitted following stay in overseas healthcare institutions should be pre-emptively isolated and screened for colonisation. Composite swabs of the axilla and groin should be collected. Routine screening of healthcare workers and the environment is not recommended. Detergents and sporicidal disinfectants should be used for environmental decontamination

Search and Contain: Impact of an Integrated Genomic and Epidemiological Surveillance and Response Program for Control of Carbapenemase-producing Enterobacterales

BACKGROUND: Multiresistant organisms (MROs) pose a critical threat to public health. Population-based programs for control of MROs such as carbapenemase-producing Enterobacterales (CPE) have emerged and evaluation is needed. We assessed the feasibility and impact of a statewide CPE surveillance and response program deployed across Victoria, Australia (population 6.5 million). METHODS: A prospective multimodal intervention including active screening, carrier isolation, centralized case investigation, and comparative pathogen genomics was implemented. We analyzed trends in CPE incidence and clinical presentation, risk factors, and local transmission over the program's first 3 years (2016-2018). RESULTS: CPE case ascertainment increased over the study period to 1.42 cases/100 000 population, linked to increased screening without a concomitant rise in active clinical infections (0.45-0.60 infections/100 000 population, P = .640). KPC-2 infection decreased from 0.29 infections/100 000 population prior to intervention to 0.03 infections/100 000 population in 2018 (P = .003). Comprehensive case investigation identified instances of overseas community acquisition. Median time between isolate referral and genomic and epidemiological assessment for local transmission was 11 days (IQR, 9-14). Prospective surveillance identified numerous small transmission networks (median, 2; range, 1-19 cases), predominantly IMP and KPC, with median pairwise distance of 8 (IQR, 4-13) single nucleotide polymorphisms; low diversity between clusters of the same sequence type suggested genomic cluster definitions alone are insufficient for targeted response. CONCLUSIONS: We demonstrate the value of centralized CPE control programs to increase case ascertainment, resolve risk factors, and identify local transmission through prospective genomic and epidemiological surveillance; methodologies are transferable to low-prevalence settings and MROs globally

A qualitative investigation of the views of primary care dentists on participating in prospective studies in the North-West of England

Background: There is a poor understanding of to how to recruit and involve primary care dentists in clinical trials. Aim: To use a qualitative paradigm to explore the views of primary care dentists towards participating in clinical trials and develop an understanding of the factors that facilitate and prevent their involvement. Design, setting, subjects and methods: An iterative approach was undertaken using a focus group (n = 6) followed by phased semi-structured interviews (n = 18). Data were analysed using thematic analysis and constant comparative analysis. Findings: The semi-structured interviews generated nine codes which were organised into three themes: technical issues for trials in primary dental care, practical issues for research in primary dental care and primary care dentists as research consumers. Overall, primary care dentists had a poor understanding of research methodology and clinical research. Barriers to participation included loss of clinical freedom and control, practice disruption, patient welfare, staff workload, financial loss and time. Conclusions: Barriers to primary dental care research need to be overcome through appropriate protocols, funding, training and support. Joint working of primary dental care teams and academic researchers is essential, along with a constructive and open dialogue, if clinical trials are to be successfully undertaken in a practice environment. © 2011 Macmillan Publishers Limited. All rights reserved

Search and contain: Impact of an integrated genomic and epidemiological surveillance and response program for control of carbapenemase-producing Enterobacterales

Background: Multi-resistant organisms (MROs) pose a critical threat to public health. Population-based programs for control of MROs such as Carbapenemase-producing Enterobacterales (CPE) have emerged and evaluation is needed. We assess the feasibility and impact of a state-wide CPE surveillance and response program deployed in December 2015 across Victoria, Australia (population 6.5 million). Methods: A prospective multi-modal intervention including active screening, carrier isolation, centralised case investigation and comparative pathogen genomics was implemented. We analyze trend in CPE incidence and clinical presentation, risk factors and local transmission over the program’s first three years (January 2016 to December 2018). Results: CPE case ascertainment increased over the study period to 1.42 cases/100,000 population, linked to increased screening without a concomitant rise in active clinical infections (0.45-0.60 infections/100,000 population, p=0.640). KPC-2 infection decreased from 0.29 infections/100,000 population prior to intervention to 0.03 infections/100,000 population in 2018 (p=0.003). Comprehensive case investigation identified putative overseas community acquisition. Median time between isolate referral and initial genomic and epidemiological assessment for local transmission was 11 days (IQR 9-14). Prospective surveillance identified numerous small transmission networks (median 2, range 1-19 cases), predominantly IMP and KPC, with median pairwise distance of 8 (IQR 4-13) single nucleotide polymorphisms; low diversity between clusters of the same sequence type suggested genomic cluster definitions alone are insufficient for targeted response. Conclusions: We demonstrate the value of centralised CPE control programs to increase case ascertainment, resolve risk factors and identify putative local transmission through prospective genomic and epidemiological surveillance; methodologies are transferable to low-prevalence settings and MROs globally.</p