Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction

To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E. coli population that may function as reservoirs of the mcr-1 gene, the largest of which was linked to ST10, a sequence type known for its ubiquity in human faecal samples and in food samples. No genotypic clustering by geographical origin or isolation source was observed. Amongst a total of 13 plasmid incompatibility types, the IncI2, IncX4 and IncHI2 plasmids accounted for more than 90% of MGEs carrying the mcr-1 gene. We observed significant geographical clustering with regional spread of IncHI2 plasmids in Europe and IncI2 in Asia. These findings point towards promiscuous spread of the mcr-1 gene by efficient horizontal gene transfer dominated by a limited number of plasmid incompatibility types

New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam.

Nontyphoidal Salmonella (NTS), particularly Salmonella enterica serovar Typhimurium, is among the leading etiologic agents of bacterial enterocolitis globally and a well-characterized cause of invasive disease (iNTS) in sub-Saharan Africa. In contrast, S Typhimurium is poorly defined in Southeast Asia, a known hot spot for zoonotic disease with a recently described burden of iNTS disease. Here, we aimed to add insight into the epidemiology and potential impact of zoonotic transfer and antimicrobial resistance (AMR) in S Typhimurium associated with iNTS and enterocolitis in Vietnam. We performed whole-genome sequencing and phylogenetic reconstruction on 85 human (enterocolitis, carriage, and iNTS) and 113 animal S Typhimurium isolates isolated in Vietnam. We found limited evidence for the zoonotic transmission of S Typhimurium. However, we describe a chain of events where a pandemic monophasic variant of S Typhimurium (serovar I:4,[5],12:i:- sequence type 34 [ST34]) has been introduced into Vietnam, reacquired a phase 2 flagellum, and acquired an IncHI2 multidrug-resistant plasmid. Notably, these novel biphasic ST34 S Typhimurium variants were significantly associated with iNTS in Vietnamese HIV-infected patients. Our study represents the first characterization of novel iNTS organisms isolated outside sub-Saharan Africa and outlines a new pathway for the emergence of alternative Salmonella variants into susceptible human populations.IMPORTANCESalmonella Typhimurium is a major diarrheal pathogen and associated with invasive nontyphoid Salmonella (iNTS) disease in vulnerable populations. We present the first characterization of iNTS organisms in Southeast Asia and describe a different evolutionary trajectory from that of organisms causing iNTS in sub-Saharan Africa. In Vietnam, the globally distributed monophasic variant of Salmonella Typhimurium, the serovar I:4,[5],12:i:- ST34 clone, has reacquired a phase 2 flagellum and gained a multidrug-resistant plasmid to become associated with iNTS disease in HIV-infected patients. We document distinct communities of S Typhimurium and I:4,[5],12:i:- in animals and humans in Vietnam, despite the greater mixing of these host populations here. These data highlight the importance of whole-genome sequencing surveillance in a One Health context in understanding the evolution and spread of resistant bacterial infections

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates with detailed clinical phenotypes from pigs and humans from the United Kingdom and Vietnam. Here, we show that isolates associated with disease contain substantially fewer genes than non-clinical isolates, but are more likely to encode virulence factors. Human disease isolates are limited to a single-virulent population, originating in the 1920 s when pig production was intensified, but no consistent genomic differences between pig and human isolates are observed. There is little geographical clustering of different S. suis subpopulations, and the bacterium undergoes high rates of recombination, implying that an increase in virulence anywhere in the world could have a global impact over a short timescale.Peer reviewe

Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security

Acetylcholinesterase Inhibitory Activities of Essential Oils from Vietnamese Traditional Medicinal Plants

Essential oils are promising as environmentally friendly and safe sources of pesticides for human use. Furthermore, they are also of interest as aromatherapeutic agents in the treatment of Alzheimer’s disease, and inhibition of the enzyme acetylcholinesterase (AChE) has been evaluated as an important mechanism. The essential oils of some species in the genera Callicarpa, Premna, Vitex and Karomia of the family Lamiaceae were evaluated for inhibition of electric eel AChE using the Ellman method. The essential oils of Callicarpa candicans showed promising activity, with IC50 values between 45.67 and 58.38 μg/mL. The essential oils of Callicarpa sinuata, Callicarpa petelotii, Callicarpa nudiflora, Callicarpa erioclona and Vitex ajugifolia showed good activity with IC50 values between 28.71 and 54.69 μg/mL. The essential oils Vitex trifolia subsp. trifolia and Callicarpa rubella showed modest activity, with IC50 values of 81.34 and 89.38, respectively. trans-Carveol showed an IC50 value of 102.88 µg/mL. Molecular docking and molecular dynamics simulation were performed on the major components of the studied essential oils to investigate the possible mechanisms of action of potential inhibitors. The results obtained suggest that these essential oils may be used to control mosquito vectors that transmit pathogenic viruses or to support the treatment of Alzheimer’s disease

Essential Oils from Vietnamese Asteraceae for Environmentally Friendly Control of Aedes Mosquitoes

Mosquitoes, in addition to being a biting nuisance, are vectors of several pathogenic viruses and parasites. As a continuation of our work identifying abundant and/or invasive plant species in Vietnam for use as ecologically friendly pesticidal agents, we obtained the essential oils of Blumea lacera, Blumea sinuata, Emilia sonchifolia, Parthenium hysterophorus, and Sphaeranthus africanus; analyzed the essential oils using gas chromatographic techniques; and screened the essential oils for mosquito larvicidal activity against Aedes aegypti and Aedes albopictus. The most active larvicidal essential oils were B. sinuata, which was rich in thymohydroquinone dimethyl ether (29.4%), (E)-β-caryophyllene (19.7%), α-pinene (8.8%), germacrene D (7.8%), and α-humulene (4.3%), (24-h LC50 23.4 and 29.1 μg/mL) on Ae. aegypti and Ae. albopictus, respectively, and Emilia sonchifolia, dominated by 1-undecene (41.9%) and germacrene D (11.0%), (24-h LC50 30.1 and 29.6 μg/mL) on the two mosquito species. The essential oils of P. hysterophorus and S. africanus were also active against mosquito larvae. Notably, B. sinuata, P. hysterophorus, and S. africanus essential oils were not toxic to the non-target water bug, Diplonychus rusticus. However, E. sonchifolia essential oil showed insecticidal activity (24-h LC50 48.1 μg/mL) on D. rusticus. Based on these results, B. sinuata, P. hysterophorus, and S. africanus essential oils appear promising for further investigations

Author Correction: Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction (Scientific Reports, (2017), 7, 1, (15364), 10.1038/s41598-017-15539-7)

In the original version of this Article, Martin C. J. Bootsma, Perry J. van Genderen, Abraham Goorhuis, Martin Grobusch, Nicky Molhoek, Astrid M. L. Oude Lashof, Ellen E. Stobberingh & Henri A. Verbrugh were incorrectly listed as the COMBAT consortium. This error has now been corrected in the HTML and PDF versions of the Article, and in the accompanying supplementary material

Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (dataset - High-Throughput sequencing)

The raw sequence reads generated from Illumina High-Throughput sequencing have been deposited in the Sequence Read Archive