Surveillance for severe acute respiratory infections (SARI) in hospitals in the WHO European region - an exploratory analysis of risk factors for a severe outcome in influenza-positive SARI cases.

BACKGROUND: The 2009 H1N1 pandemic highlighted the need to routinely monitor severe influenza, which lead to the establishment of sentinel hospital-based surveillance of severe acute respiratory infections (SARI) in several countries in Europe. The objective of this study is to describe characteristics of SARI patients and to explore risk factors for a severe outcome in influenza-positive SARI patients. METHODS: Data on hospitalised patients meeting a syndromic SARI case definition between 2009 and 2012 from nine countries in Eastern Europe (Albania, Armenia, Belarus, Georgia, Kazakhstan, Kyrgyzstan, Romania, Russian Federation and Ukraine) were included in this study. An exploratory analysis was performed to assess the association between risk factors and a severe (ICU, fatal) outcome in influenza-positive SARI patients using a multivariate logistic regression analysis. RESULTS: Nine countries reported a total of 13,275 SARI patients. The majority of SARI patients reported in these countries were young children. A total of 12,673 SARI cases (95%) were tested for influenza virus and 3377 (27%) were laboratory confirmed. The majority of tested SARI cases were from Georgia, the Russian Federation and Ukraine and the least were from Kyrgyzstan. The proportion positive varied by country, season and age group, with a tendency to a higher proportion positive in the 15+ yrs age group in six of the countries. ICU admission and fatal outcome were most often recorded for influenza-positive SARI cases aged > 15 yrs. An exploratory analysis using pooled data from influenza-positive SARI cases in three countries showed that age > 15 yrs, having lung, heart, kidney or liver disease, and being pregnant were independently associated with a fatal outcome. CONCLUSIONS: Countries in Eastern Europe have been able to collect data through routine monitoring of severe influenza and results on risk factors for a severe outcome in influenza-positive SARI cases have identified several risk groups. This is especially relevant in the light of an overall low vaccination uptake and antiviral use in Eastern Europe, since information on risk factors will help in targeting and prioritising vulnerable populations.

Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph.

Alteromonas macleodii is a marine gammaproteobacterium with widespread distribution in temperate or tropical waters. We describe three genomes of isolates from surface waters around Europe (Atlantic, Mediterranean and Black Sea) and compare them with a previously described deep Mediterranean isolate (AltDE) that belongs to a widely divergent clade. The surface isolates are quite similar, the most divergent being the Black Sea (BS11) isolate. The genomes contain several genomic islands with different gene content. The recruitment of very similar genomic fragments from metagenomes in different locations indicates that the surface clade is globally abundant with little effect of geography, even the AltDE and the BS11 genomes recruiting from surface samples in open ocean locations. The finding of CRISPR protospacers of AltDE in a lysogenic phage in the Atlantic (English Channel) isolate illustrates a flow of genetic material among these clades and a remarkably wide distribution of this phage.

Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea.

The genetic diversity of 19 strains belonging to Alteromonas macleodii isolated from different geographic areas (Pacific and Indian Ocean, and different parts of the Mediterranean Sea) and at different depths (from the surface down to 3500 m) has been studied. Fragments of the 16S rRNA gene, the internal transcribed spacer (ITS) between 16S and 23S rDNA genes, the gyrB and the rpoB genes, have been sequenced for each strain. Amplified fragment length polymorphisms were used to characterize similarity at the level of the whole genome. Most of the diversity reflected the existence of a cluster of strains isolated from deep Mediterranean waters and two isolates from the Black Sea. Particularly the isolates from the deep sites were consistently different from all the others indicating the existence of a specific ecotype adapted to these conditions. Amplification of gyrB gene and ITS directly from DNA retrieved from deep Mediterreanean waters and one Atlantic sample showed that presence of this deep-sea ecotype is widespread and is not a product of culture bias. On the other hand, strains isolated from surface tropical waters showed a remarkable level of resemblance to the first isolate of this species obtained from Hawaii in 1972. The results indicate the existence of both lineages of global distribution and ecotypes adapted to specific conditions such as deep or more diluted (the Black Sea) waters.

Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea.

A slightly creamy, melanogenic, gram-negative, aerobic bacterium was isolated from seawater sample collected in the Karadag Natural Reserve of the Eastern Crimea, the Black Sea. The novel organism was chemoorganotrophic, had no obligate requirement in NaCl, tolerated to 12% NaCl, grew between 10 and 45 degrees C, was slightly alkaliphilic, and was not able to degrade starch, gelatin, agar, and Tween 80. 16S rRNA gene sequence-based analyses of the new organism revealed that Oceanimonas doudoroffii ATCC 27123T, Oceanimonas baumanii ATCC 700832T, and Oceanisphaera litoralis DSM 15406T were the closest relatives (similarity around 97%-96%). The G + C content of the DNA of the strain 31-13T was 55.5mol%. Phosphatidylethanolamine (49.0%), phosphatidylglycerol (41.8%), and diphosphatidylglycerol (9.2%) were the predominant phospholipids. The major fatty acids were 16:0 (24.1%), 16:1omega7 (40.3%), and 18:1omega7 (29.2%). On the basis of the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the bacterium be classified as a novel species; the name Oceanimonas smirnovii sp. nov. is proposed. The type strain is 31-13T (UCM B-11076T = LMG 22147T = ATCC BAA-899T).

Marinomonas pontica sp. nov., isolated from the Black Sea.

A Gram-negative, polarly flagellated bacterium was isolated from a sea-water sample collected from the Karadag Natural Reserve of the Eastern Crimea and characterized to clarify its taxonomic position. 16S rRNA gene sequence-based phylogenetic analysis of this novel organism revealed Marinomonas vaga, Marinomonas communis, Marinomonas mediterranea, Marinomonas primoryensis and 'Marinomonas protea' as its closest relatives (similarity 95-97 %). The G+C content of the DNA was 46.5 mol%. The organism grew between 4 and 33 degrees C, tolerated 10 % NaCl, was slightly alkaliphilic and was not able to degrade starch, gelatin, agar or Tween 80. Phosphatidylethanolamine (53.4 %) and phosphatidylglycerol (46.6 %) were the predominant phospholipids. The major fatty acids were 16 : 0 (15.5 %), 16 : 1omega7 (26.7 %) and 18 : 1omega7 (47.1 %). The phylogenetic, genetic and physiological properties of the organism placed it within a novel species, proposed as Marinomonas pontica sp. nov., the type strain of which is 46-16T (=LMG 22531T=KMM 3492T=UCM 11075T).