The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/pdf

Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance

Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

/pdf/detection-of-2019-novel-coronavirus-2019-ncov-by-real-time-5an3azdech.pdf

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR.

Objectives
Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. Thus, the current challenge is to extract the relevant information from the large amount of generated data.

/pdf/identification-of-acquired-antimicrobial-resistance-genes-3jqc4799a3.pdf

Identification of acquired antimicrobial resistance genes

Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.

Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance

Food authentication is a rapidly growing field driven by increasing public awareness of food quality and safety. Foods containing herbs are particularly prone to industrial fraud and adulteration. Several methodologies are currently used to evaluate food authenticity. DNA-based technologies have increased focus, with DNA barcoding the most widely used. DNA barcoding is based on the sequencing and comparison of orthologous DNA regions from all species in a sample, but the approach is limited by its low resolution to distinguish closely-related species. Here we developed a customised database and bioinformatics pipeline (Herbs Authenticity - GitHub) to identify herbal ingredients implemented as a metagenomics approach for plant-derived product authenticity testing. We evaluated the accuracy of the method by using publicly available plant genomes and databases to allow the construction of our customised database barcodes, which were also complemented with entries from publicly available resources (iBOL and ENA). The pipeline performance was then tested with new 47 de novo partly sequenced whole plant genomes or barcodes as query sequences. Our results show that using our mapping algorithm with the customised barcode database correctly identifies the main components of a wide range of plant-derived samples, albeit with variable additional noise across samples depending on the tested samples and barcodes. Our result also show that at the current stage the usefulness of metagenomics is limited by the availability of reference sequences and the needed sequencing depth. However, this method shows promise for evaluating the authenticity of different herbal products provided that the method is further refined to increase the qualitative and quantitative accuracy.

Evaluating the usefulness of next-generation sequencing for herb authentication

External quality assurance system (EQAS) for identification of mastitis pathogens in Denmark from 2006 to 2011

Characterization of Staphylococcus aureus from bovine mastitis

A resistencia crescente das bacterias patogenicas aos antimicrobianos tem causado preocupacao, em todo o mundo, de que uso generalizado de agentes antimicrobianos na producao animal possa promover o desenvolvimento de bacterias resistentes ou de genes da resistencia que possam ser transferidos para bacterias que causam doenca no homem. No interesse da saude do consumidor e da saude animal e humana os Ministerios da Agricultura e das Pescas, e da Saude da Dinamarca em 1995 pediram ao Laboratorio Veterinario Dinamarques, a Agencia Dinamarquesa para a Alimentacao, e ao “Statens Serum Institut” para colaborarem na vigilância e investigacao da resistencia antimicrobiana.

Vigilância da resistência aos antimicrobianos no homem, nos produtos alimentares e no gado na Dinamarca

Citation: Schlundt J and Aarestrup FM (2017) Commentary: Benefits and risks of antimicrobial use in food-producing animals. In a recent general attempt to review literature related to documentation of policy changes in the area of antimicrobial use in agriculture we have read the article by Hao et al. (2014) and have found it full of flaws and misinterpretations. We cannot comment on all but would like to address some claims specifically focusing on the effects of banning antimicrobial growth promoters in Denmark. The claims put forward in the review are all based on references, but they seem to be selected to reflect a perspective by the pharmaceutical industry. The authors claim that morbidity rate of enteric infections increased by 600%. We have been unable to find these figures in the two references cited. The authors also cite a review for an increase in mortality among piglets from 2.7 to 3.5% comparing only the years immediately before and after then ban. We have previously analyzed these data on mortality and productivity in much more detail (Aarestrup et al., 2010). Looking at longer term trend data clearly suggest that Danish piglets in the period around the ban (1998) had a general increase in mortality probably unrelated to the ban and actually immediately after the ban an increase in average daily gain. Longer term data also shows that the mortality increase changed to a decrease by 2002 and has continued to drop since. In a paper published in Food Control (Wielinga et al., 2014) we suggest that the continued improvement in productivity in the Danish pig sector is partially explained by improved animal management through increased veterinary oversight (while veterinarians in Denmark since 1995 were legally banned from making a direct profit from sales of antimicrobials). The authors also claim that the ban of AGP resulted in a compensatory increase in the use of therapeutic antimicrobials. Once again the authors oversimplify the situation by just selecting 2 years to make their point. The overall consumption of antimicrobial agents in the Danish pig production has fluctuated over time and in the same time-period the production of pigs has increased by almost 50%, which naturally influences consumption. More detailed data and adjustments to productivity are provided in Aarestrup (2015). The authors also cite a Danish study (Heuer et al., 2001) for the claim that the population of Campylobacter in broilers fed without antimicrobials was threefold …

/pdf/commentary-benefits-and-risks-of-antimicrobial-use-in-food-8xy91wswu6.pdf

Frank Møller Aarestrup

Papers

Evaluating the usefulness of next-generation sequencing for herb authentication

External quality assurance system (EQAS) for identification of mastitis pathogens in Denmark from 2006 to 2011

Characterization of Staphylococcus aureus from bovine mastitis

Vigilância da resistência aos antimicrobianos no homem, nos produtos alimentares e no gado na Dinamarca

Commentary: Benefits and risks of antimicrobial use in food-producing animals