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)

Cell Migration: A Physically Integrated Molecular Process

The European Position Paper on Rhinosinusitis and Nasal Polyps 2020 is the update of similar evidence based position papers published in 2005 and 2007 and 2012. The core objective of the EPOS2020 guideline is to provide revised, up-to-date and clear evidence-based recommendations and integrated care pathways in ARS and CRS. EPOS2020 provides an update on the literature published and studies undertaken in the eight years since the EPOS2012 position paper was published and addresses areas not extensively covered in EPOS2012 such as paediatric CRS and sinus surgery. EPOS2020 also involves new stakeholders, including pharmacists and patients, and addresses new target users who have become more involved in the management and treatment of rhinosinusitis since the publication of the last EPOS document, including pharmacists, nurses, specialised care givers and indeed patients themselves, who employ increasing self-management of their condition using over the counter treatments. The document provides suggestions for future research in this area and offers updated guidance for definitions and outcome measurements in research in different settings. EPOS2020 contains chapters on definitions and classification where we have defined a large number of terms and indicated preferred terms. A new classification of CRS into primary and secondary CRS and further division into localized and diffuse disease, based on anatomic distribution is proposed. There are extensive chapters on epidemiology and predisposing factors, inflammatory mechanisms, (differential) diagnosis of facial pain, allergic rhinitis, genetics, cystic fibrosis, aspirin exacerbated respiratory disease, immunodeficiencies, allergic fungal rhinosinusitis and the relationship between upper and lower airways. The chapters on paediatric acute and chronic rhinosinusitis are totally rewritten. All available evidence for the management of acute rhinosinusitis and chronic rhinosinusitis with or without nasal polyps in adults and children is systematically reviewed and integrated care pathways based on the evidence are proposed. Despite considerable increases in the amount of quality publications in recent years, a large number of practical clinical questions remain. It was agreed that the best way to address these was to conduct a Delphi exercise . The results have been integrated into the respective sections. Last but not least, advice for patients and pharmacists and a new list of research needs are included. The full document can be downloaded for free on the website of this journal: http://www.rhinologyjournal.com.

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European Position Paper on Rhinosinusitis and Nasal Polyps 2020

While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.

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MetaSPAdes: A new versatile metagenomic assembler

Comparative genomics demonstrated that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving. This process is most evident for bacterial pathogens where the majority contain prophages or phage remnants integrated into the bacterial DNA. Many prophages from bacterial pathogens encode virulence factors. Two situations can be distinguished: Vibrio cholerae, Shiga toxin-producing Escherichia coli, Corynebacterium diphtheriae, and Clostridium botulinum depend on a specific prophage-encoded toxin for causing a specific disease, whereas Staphylococcus aureus, Streptococcus pyogenes, and Salmonella enterica serovar Typhimurium harbor a multitude of prophages and each phage-encoded virulence or fitness factor makes an incremental contribution to the fitness of the lysogen. These prophages behave like “swarms” of related prophages. Prophage diversification seems to be fueled by the frequent transfer of phage material by recombination with superinfecting phages, resident prophages, or occasional acquisition of other mobile DNA elements or bacterial chromosomal genes. Prophages also contribute to the diversification of the bacterial genome architecture. In many cases, they actually represent a large fraction of the strain-specific DNA sequences. In addition, they can serve as anchoring points for genome inversions. The current review presents the available genomics and biological data on prophages from bacterial pathogens in an evolutionary framework.

Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion

Background Cardiac device-related endocarditis has emerged as a serious complication in the era of advanced medical technology. Pacemaker related infections are rare and life-threatening with incidence from 0.06% to 7% and high mortality rate (30-35%). Diagnosis is hard, frequently delayed and could be even missed due to poor clinical findings. The average delay in diagnosis is 5.5 month. We report a case of the late-onset of pacemaker lead endocarditis caused by S. epidermidis successfully treated with open heart surgery. Case report Patient with persistent high fever for 11 month and suspicion for infective endocarditis was admitted in Cardiovascular Institute. No clinical signs of endocarditis were observed. TTE revealed large vegetation 30 × 17 mm attached to the atrial electrodes with high embolic potential. This finding was verified by transesophageal echocardiography (TEE), although CT scan did not reveal vegetation. Blood cultures were negative. A sternotomy with cardiopulmonary bypass was performed and electrodes were extracted with large vegetation. Intraoperative finding revealed large thrombus with vegetation around pacemaker leads. Cultures of the electrodes and vegetation revealed Staphylococcus epidermidis. Surgery was followed up with antibiotic treatment for 6 weeks. He has been followed up for the next 2 years, and without complications. Conclusion The absence of criteria for endocarditis and negative blood cultures should not keep the physician from ruling out lead endocarditis. This complication carries high risk of mortality if left untreated.

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A rare case of pacemaker lead endocarditis successfully treated with open heart surgery.

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Vancomycin-resistant Enterococcus faecium high-resolution typing by core genome multilocus sequence typing.

High-risk lineages among Extended-Spectrum β-Lactamase Escherichia coli from extraintestinal infections in Maputo Central Hospital, Mozambique.

This issue of the Journal of Infection in Developing Countries is a celebration of 50 years of dedicated infectious disease research by Professor Giovanni Fadda. As an internationally renowned microbiologist, Professor Fadda was dedicated to the fight against tuberculosis. Throughout his career, he worked in developing countries establishing laboratories for the identification of mycobacteria. He was one of the first scientists to help JIDC in its initial steps, and he is a key member of the mentoring committee of the journal.
On 31 October 2011, Professor Giovanni Fadda, full professor of microbiology at the Catholic University of the Sacred Heart in Rome, retired after 50 years of studies and research in the field of general and clinical microbiology. Professor Fadda was born in Tempio Pausania, Sardinia, Italy, in 1938. He achieved the degree of medical doctor in Parma with distinction in 1963 under the guidance of Professor Antonio Sanna, a pioneer of microbiology in Italy. He then obtained specialties in microbiology (1965) and in Pathology (1967) and since 1971 he has been appointed as professor of microbiology in the Universities of Parma and Sassari. From 1978 to1985 he served as Chief of the Clinical Laboratory of the Regional General Hospital of Sassari. Professor Fadda was subsequently promoted full professor of microbiology at the University of Sassari (1986-1995).

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In honor of Professor Giovanni Fadda: a fighter against tuberculosis.

Abstract Enterobacter spp. are important nosocomial pathogens responsible of a wide variety of infections, mainly due to Extended Spectrum β-Lactamase (ESBL) producing isolates, constituting a global public health issue in terms of clinical treatment and infection control, especially in low-income countries, where last-line treatment is often unavailable and there is weak nosocomial surveillance. In this study, we conducted a phenotypic and molecular characterization of 8 clinical Enterobacter spp. strains, isolated from patient’s blood in three hospitals in Mozambique. Isolates were identified by MALDI-TOF and antimicrobial Susceptibility Testing was performed by VITEK 2 system. Half of isolates were analyzed by PCR for β-lactamases genes, other isolates by Whole Genome Sequencing. We identified all isolates as Enterobacter cloacae complex (ECC), those from Maputo Central Hospital were polyclonal, multidrug resistant (5/8), and ESBL producers (50%), carrying bla CTX-M-15 and different assortment of bla SHV-12 , bla TEM-1B and bla OXA-1 , and AmpCs bla CMH-3 , bla ACT-7 and bla ACT-9 genes. Resistance determinants linked to fluoroquinolone ( aac(6')Ib-cr and qnrB1 ) and others antimicrobials were also found. Notably, one isolate showed phenotypically resistance to colistin, while another colistin susceptible isolate carried a silent mcr-9 gene. ECC nosocomial surveillance is urgently needed to contain and prevent the dissemination of ESBLs producing clones, and mcr-9 spread to other Enterobacteriaceae. 

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Polyclonal emergence of MDR Enterobacter cloacae complex isolates producing multiple extended spectrum beta-lactamases at Maputo Central Hospital, Mozambique

Salvatore Rubino

Papers

A rare case of pacemaker lead endocarditis successfully treated with open heart surgery.

Vancomycin-resistant Enterococcus faecium high-resolution typing by core genome multilocus sequence typing.

High-risk lineages among Extended-Spectrum β-Lactamase Escherichia coli from extraintestinal infections in Maputo Central Hospital, Mozambique.

In honor of Professor Giovanni Fadda: a fighter against tuberculosis.

Polyclonal emergence of MDR Enterobacter cloacae complex isolates producing multiple extended spectrum beta-lactamases at Maputo Central Hospital, Mozambique