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)

After the incursion of bluetongue virus (BTV) into European Mediterranean countries in 1998, vaccination was used in an effort to minimize direct economic losses to animal production, reduce virus circulation and allow safe movements of animals from endemic areas. Vaccination strategies in different countries were developed according to their individual policies, the geographic distribution of the incurring serotypes of BTV and the availability of appropriate vaccines. Four monovalent modified live virus (MLV) vaccines were imported from South Africa and subsequently used extensively in both cattle and sheep. MLVs were found to be immunogenic and capable of generating strong protective immunity in vaccinated ruminants. Adverse side effects were principally evident in sheep. Specifically, some vaccinated sheep developed signs of clinical bluetongue with fever, facial oedema and lameness. Lactating sheep that developed fever also had reduced milk production. More severe clinical signs occurred in large numbers of sheep that were vaccinated with vaccine combinations containing the BTV-16 MLV, and the use of the monovalent BTV-16 MLV was discontinued as a consequence. Abortion occurred in <0.5% of vaccinated animals. The length of viraemia in sheep and cattle that received MLVs did not exceed 35 days, with the single notable exception of a cow vaccinated with a multivalent BTV-2, -4, -9 and -16 vaccine in which viraemia persisted at least 78 days. Viraemia of sufficient titre to infect Culicoides insects was observed transiently in MLV-vaccinated ruminants, and natural transmission of MLV strains has been confirmed. An inactivated vaccine was first developed against BTV-2 and used in the field. An inactivated vaccine against BTV-4 as well as a bivalent vaccine against serotypes 2 and 4 were subsequently developed and used in Corsica, Spain, Portugal and Italy. These inactivated vaccines were generally safe although on few occasions reactions occurred at the site of inoculation. Two doses of these BTV inactivated vaccines provided complete, long-lasting immunity against both clinical signs and viraemia, whereas a single immunization with the BTV-4 inactivated vaccine gave only partial reduction of viraemia in vaccinated cattle when challenged with the homologous BTV serotype. Additional BTV inactivated vaccines are currently under development, as well as new generation vaccines including recombinant vaccines.

Vaccines against bluetongue in Europe

Recombinant canarypox virus vaccine co-expressing genes encoding the VP2 and VP5 outer capsid proteins of bluetongue virus induces high level protection in sheep.

Active circulation of bluetongue vaccine virus serotype-2 among unvaccinated cattle in central Italy

In summer 2000, bluetongue (BT) infection was reported in Italy and caused a widespread epidemic involving a total of ten southern and central regions and is still in progress after three years. From the date of the first case (18 August 2000) to 14 May 2001, when the lowpoint in the first epidemic curve was reached, a total of 310,234 animals in 6,869 flocks of three regions had been involved. From 15 May 2001 to 14 April 2002, when a second epidemic wave swept through central and southern Italy, a total of 323,635 animals in 6,807 flocks in seven regions were involved. During 2000 and 2001 virtually no susceptible ruminants were vaccinated. On 11 May 2001, the Italian Ministry of Health ordered the vaccination of all susceptible domestic ruminant species (i.e. sheep, goats, cattle and water buffalo) in the infected and surrounding areas. The vaccination strategy stemmed from a risk assessment that demonstrated the possibility of such a strategy preventing most of the direct economic losses and decreasing the level of virus circulation. Vaccination of the target populations commenced in January 2002. In July 2002, when the new epidemic peak was reached, the percentage of vaccinated populations varied between the regions with direct consequences on the spread of BT. The relationship between vaccination coverage of the target populations and animal losses due to disease and virus circulation, and as detected by the sentinel surveillance system, was analysed. The effectiveness of the vaccination campaign in limiting virus circulation and consequently indirect losses due to animal movement restrictions was analysed and evaluated. At the end of 2002, a second risk assessment led to the authorization of the movement of vaccinated animals from infected areas (where at least 80% of the susceptible population was vaccinated) directly to slaughter in unvaccinated areas free from infection. This risk assessment also generated new criteria to define zones where animal movement restrictions should be applied. Following the second vaccination campaign (January to May 2003), a third risk assessment was performed and the results from vaccination trials performed in controlled and in field conditions studied. These studies indicated that procedures to move vaccinated breeding animals from zones where infection exists to unvaccinated infection free zones could be contemplated.

Bluetongue in Italy: Part II.

A group of 44 sheep was vaccinated with the bivalent modified-live vaccine against bluetongue virus (BTV) serotype 2 (BTV-2) and BTV-9 to evaluate viraemia and antibody kinetics. Blood samples were taken from the sheep three times a week for two months and screened for the presence of BTV and for antibody using the competitive enzyme-linked immunosorbent assay (c-ELISA) and the virus neutralisation (VN) test. Intravenous egg inoculation, followed by two blind passages in Vero cells, was used to isolate BTV-2 and BTV-9 from the ethylene-diaminetetra-acetic acid (EDTA) blood samples; virus titres were also determined in the viraemic animals. BTV was detected in the blood of 39 sheep between day 3 and day 24 post vaccination (pv). Viraemia peaked on day 7 pv with average titres of 10(5.3)TCID50/ml. Antibodies were first detected in the c-ELISA on day 6 pv and by day 16, all sheep were seropositive. Only 36 of the 44 inoculated sheep developed virus-neutralising antibodies against both BTV-2 and BTV-9 while 4 were positive to BTV-2 only; neutralising antibodies were not detected in the 4 remaining animals. Antibody titres were very low and unstable and often bordered on the negative/positive threshold.

Virological and serological response of sheep following field vaccination with bivalent modified-live vaccine against bluetongue virus serotypes 2 and 9.

Bartonellae are emerging vector-borne pathogens distributed worldwide that can cause various clinical symptoms in humans and animals, ranging from a mild flu-like illness to more severe manifestations such as endocarditis, myocarditis, arthritis, hepatitis, and arthralgia. Numerous mammalian species, including domestic animals such as dogs, cats, as well as humans, serve as reservoir hosts for various Bartonella species. The vectors play a central role in the transmission of these bacteria and pets and their ectoparasites can pose a serious risk of zoonoses. This paper reviews selected literature on important bartonellosis of dogs, cats, and humans with notes on transmission, vectors, pathogenesis, and diagnosis.

Bartonella infections in humans dogs and cats.

Monophasic variant of Salmonella enterica subspecies enterica serovar Typhimurium (monophasic S. Typhimurium), with antigenic structure 1,4,[5],12:i:-, appears to be of increasing importance in Europe. In Italy, monophasic S. Typhimurium represented the third most frequent Salmonella serovar isolated from human cases between 2004 and 2008. From June 2013 to October 2014, a total of 206 human cases of salmonellosis were identified in Abruzzo region (Central Italy). Obtained clinical isolates characterised showed S. Typhimurium 1,4,[5],12:i:- with sole resistance to nalidixic acid, which had never been observed in Italy in monophasic S. Typhimurium, neither in humans nor in animals or foods. Epidemiological, microbiological and environmental investigations were conducted to try to identify the outbreak source. Cases were interviewed using a standardised questionnaire and microbiological tests were performed on human as well as environmental samples, including samples from fruit and vegetables, pigs, and surface water. Investigation results did not identify the final vehicle of human infection, although a link between the human cases and the contamination of irrigation water channels was suggested.

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Outbreak of unusual Salmonella enterica serovar Typhimurium monophasic variant 1,4 [5],12:i:-, Italy, June 2013 to September 2014.

Ectoparasitic insects play a major role in veterinary medicine. Fleas infest man and animals and are the most frequent external parasites of companion animals worldwide. Some species are known to be vectors of zoonotic pathogens. Dogs and cats may play an important role either as reservoir of some of the pathogens or as transport vehicles for infected eas between their natural reservoirs and human beings, thus playing a crucial step in the transmission cycle of ea-borne diseases. This article reviews relevant literature on morphology, classi cation, host speci city, geographical distribution, and seasonality of eas infesting dogs and cats in order to improve their timely identi cation, prevention, and control.

Fleas of dog and cat: species, biology and flea-borne diseases.

In response to complaints of the potential side-effects of the bivalent live-modified vaccine used to control the spread of bluetongue (BT) virus (BTV) serotypes 2 and 9 in Italy, a study was conducted to determine the effects of immunisation on milk production. Thirty-four Comisana cross-bred sheep were vaccinated with the bivalent BTV-2/BTV-9 modified-live vaccine produced by Onderstepoort Biological Products in South Africa; six animals served as unvaccinated controls. All animals were bled twice a week for two months and the presence and titres of BTV in the blood determined. The somatic cell count, pH, fat, protein and lactose content of the milk, as well as the quantity of the milk produced, were also measured. Vaccine virus was isolated from vaccinated animals between day 3 and day 20 post vaccination (pv) with peak titres observed on days 3 and 6 pv for BTV-2 and BTV-9, respectively. Milk production declined in the vaccinated group between days 8 and 14 pv, with the greatest decrease on day 9 pv. No differences were observed in the somatic cell count and pH, or in the milk fat, protein and lactose content.

Stefania Salucci

Papers

Virological and serological response of sheep following field vaccination with bivalent modified-live vaccine against bluetongue virus serotypes 2 and 9.

Bartonella infections in humans dogs and cats.

Outbreak of unusual Salmonella enterica serovar Typhimurium monophasic variant 1,4 [5],12:i:-, Italy, June 2013 to September 2014.

Fleas of dog and cat: species, biology and flea-borne diseases.

Field vaccination of sheep with bivalent modified-live vaccine against bluetongue virus serotypes 2 and 9: effect on milk production.