scholarly journals Comparative Genomics of 42 Arcanobacterium phocae Strains

Antibiotics ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 740
Author(s):  
Kirsi J. Aaltonen ◽  
Ravi Kant ◽  
Nanett Kvist Nikolaisen ◽  
Mikkel Lindegaard ◽  
Mirja Raunio-Saarnisto ◽  
...  
Keyword(s):  
Marine Mammals ◽  
Core Genome ◽  
Vaccine Development ◽  
Clinical Signs ◽  
Secreted Proteins ◽  
Clear Separation ◽  
Whole Genomes ◽  
Lung Infections ◽  
Arcanobacterium Phocae ◽  
Current Advice

For the last 13 years, the fur industry in Europe has suffered from epidemic spouts of a severe necrotizing pyoderma. It affects all species currently farmed for fur and causes animal welfare problems and significant losses to the farmers. The causative agent of this disease was identified as Arcanobacterium phocae. Previously, this bacterium has been isolated from seals and other marine mammals, apparently causing wound and lung infections. Attempts at antibiotic treatment have been unsuccessful and the current advice on preventing the disease is to cull all animals with clinical signs. This poses an urgent question regarding possible vaccine development, as well as the need for further understanding of the pathogenicity of this organism. This study compared the whole genomes of 42 A. phocae strains isolated from seals, blue foxes, finnraccoons, mink and otter. The sequences were created using the Illumina technology and annotations were done using the RAST pipeline. A phylogenetic analysis identified a clear separation between the seal strains and the fur-animal-derived isolates, but also indicated that the bacterium readily adapts to new environments and host species with reasonable diversity. A pan- and core-genome was created and analyzed for proteins. A further analysis identified several virulence factors as well as multiple putative and secreted proteins of special interest for vaccine development.

scholarly journals Live Attenuated African Swine Fever Viruses as Ideal Tools to Dissect the Mechanisms Involved in Cross-Protection

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1474
Author(s):  
Elisabeth Lopez ◽  
Juanita van Heerden ◽  
Laia Bosch-Camós ◽  
Francesc Accensi ◽  
Maria Jesus Navas ◽  
...  
Keyword(s):  
Vaccine Development ◽  
African Swine Fever Virus ◽  
Virulent Strain ◽  
Sequence Similarity ◽  
Clinical Signs ◽  
African Swine Fever ◽  
Cross Protection ◽  
Sub Saharan Africa ◽  
Genotype I ◽  
Genotype Ii

African swine fever (ASF) has become the major threat for the global swine industry. Furthermore, the epidemiological situation of African swine fever virus (ASFV) in some endemic regions of Sub-Saharan Africa is worse than ever, with multiple virus strains and genotypes currently circulating in a given area. Despite the recent advances on ASF vaccine development, there are no commercial vaccines yet, and most of the promising vaccine prototypes available today have been specifically designed to fight the genotype II strains currently circulating in Europe, Asia, and Oceania. Previous results from our laboratory have demonstrated the ability of BA71∆CD2, a recombinant LAV lacking CD2v, to confer protection against homologous (BA71) and heterologous genotype I (E75) and genotype II (Georgia2007/01) ASFV strains, both belonging to same clade (clade C). Here, we extend these results using BA71∆CD2 as a tool trying to understand ASFV cross-protection, using phylogenetically distant ASFV strains. We first observed that five out of six (83.3%) of the pigs immunized once with 106 PFU of BA71∆CD2 survived the tick-bite challenge using Ornithodoros sp. soft ticks naturally infected with RSA/11/2017 strain (genotype XIX, clade D). Second, only two out of six (33.3%) survived the challenge with Ken06.Bus (genotype IX, clade A), which is phylogenetically more distant to BA71∆CD2 than the RSA/11/2017 strain. On the other hand, homologous prime-boosting with BA71∆CD2 only improved the survival rate to 50% after Ken06.Bus challenge, all suffering mild ASF-compatible clinical signs, while 100% of the pigs immunized with BA71∆CD2 and boosted with the parental BA71 virulent strain survived the lethal challenge with Ken06.Bus, without almost no clinical signs of the disease. Our results confirm that cross-protection is a multifactorial phenomenon that not only depends on sequence similarity. We believe that understanding this complex phenomenon will be useful for designing future vaccines for ASF-endemic areas.

scholarly journals Role of African swine fever virus (ASFV) proteins EP153R and EP402R in reducing viral persistence and virulence from attenuated BeninΔDP148R

2021 ◽  
Author(s):  
Vlad Petrovan ◽  
Anusyah Rathakrishnan ◽  
Muneeb Islam ◽  
Lynnette Goatley ◽  
Katy Moffat ◽  
...  
Keyword(s):  
Virus Replication ◽  
Vaccine Development ◽  
African Swine Fever Virus ◽  
Clinical Signs ◽  
African Swine Fever ◽  
Viral Persistence ◽  
Fever Virus ◽  
Post Immunization

The limited knowledge on the role of many of the approximately 170 proteins encoded by African swine fever virus restricts progress towards vaccine development. In this study we investigated the effect of deleting combinations of different genes from a previously attenuated virus, BeninΔDP148R on: virus replication in macrophages, virus persistence and clinical signs post immunization, and induction of protection against challenge. Deletion of either EP402R or EP153R genes individually or in combination from BeninΔDP148R did not reduce virus replication in vitro. However, deletion of EP402R dramatically reduced viral persistence in vivo, whilst maintaining high levels of protection against challenge. The additional deletion of EP153R (BeninΔDP148RΔEP153RΔEP402R) further attenuated the virus and no viremia or clinical signs were observed post immunization. This was associated with decreased protection and detection of moderate levels of challenge virus in blood. Interestingly, the deletion of EP153R alone from BeninΔDP148R did not result in further virus attenuation and a slight increase in virus genome copies in blood was observed at different times post immunization when compared with BeninΔDP148R. These results show that EP402R and EP153R have a synergistic role in promoting viremia, however EP153R alone does not seem to have a major impact on virus levels in blood.

scholarly journals Microevolution ofStreptococcus agalactiaeST-261 from Australia Indicates Dissemination via Imported Tilapia and Ongoing Adaptation to Marine Hosts or Environment

2018 ◽  
Vol 84 (16) ◽  
Author(s):  
Minami Kawasaki ◽  
Jerome Delamare-Deboutteville ◽  
Rachel O. Bowater ◽  
Mark J. Walker ◽  
Scott Beatson ◽  
...  
Keyword(s):  
Streptococcus Agalactiae ◽  
Core Genome ◽  
Minimum Spanning Tree ◽  
Vaccine Development ◽  
The United States ◽  
Wild Fish ◽  
Clinical Isolates ◽  
Global Trade ◽  
Content Type ◽  
Wide Range

ABSTRACTStreptococcus agalactiae(group BStreptococcus[GBS]) causes disease in a wide range of animals. The serotype Ib lineage is highly adapted to aquatic hosts, exhibiting substantial genome reduction compared with terrestrial conspecifics. Here, we sequence genomes from 40 GBS isolates, including 25 isolates from wild fish and captive stingrays in Australia, six local veterinary or human clinical isolates, and nine isolates from farmed tilapia in Honduras, and compared them with 42 genomes from public databases. Phylogenetic analysis based on nonrecombinant core-genome single nucleotide polymorphisms (SNPs) indicated that aquatic serotype Ib isolates from Queensland were distantly related to local veterinary and human clinical isolates. In contrast, Australian aquatic isolates are most closely related to a tilapia isolate from Israel, differing by only 63 core-genome SNPs. A consensus minimum spanning tree based on core-genome SNPs indicates the dissemination of sequence type 261 (ST-261) from an ancestral tilapia strain, which is congruent with several introductions of tilapia into Australia from Israel during the 1970s and 1980s. Pangenome analysis identified 1,440 genes as core, with the majority being dispensable or strain specific, with non-protein-coding intergenic regions (IGRs) divided among core and strain-specific genes. Aquatic serotype Ib strains have lost many virulence factors during adaptation, but six adhesins were well conserved across the aquatic isolates and might be critical for virulence in fish and for targets in vaccine development. The close relationship among recent ST-261 isolates from Ghana, the United States, and China with the Israeli tilapia isolate from 1988 implicates the global trade in tilapia seed for aquaculture in the widespread dissemination of serotype Ib fish-adapted GBS.IMPORTANCEStreptococcus agalactiae(GBS) is a significant pathogen of humans and animals. Some lineages have become adapted to particular hosts, and serotype Ib is highly specialized to fish. Here, we show that this lineage is likely to have been distributed widely by the global trade in tilapia for aquaculture, with probable introduction into Australia in the 1970s and subsequent dissemination in wild fish populations. We report here the variability in the polysaccharide capsule among this lineage but identify a cohort of common surface proteins that may be a focus of future vaccine development to reduce the biosecurity risk in international fish trade.

scholarly journals Scrutinizing Coronaviruses Using Publicly Available Bioinformatic Tools: The Viral Structural Proteins as a Case Study

2021 ◽  
Vol 8 ◽  
Author(s):  
Sonia Beeckmans ◽  
Edilbert Van Driessche
Keyword(s):  
Structural Biology ◽  
Nucleocapsid Protein ◽  
Vaccine Development ◽  
Protein S ◽  
Structural Proteins ◽  
Molecular Graphics ◽  
Bioinformatic Tools ◽  
Life Threatening ◽  
Lung Infections

Since early 2020, the world suffers from a new beta-coronavirus, called SARS-CoV-2, that has devastating effects globally due to its associated disease, Covid-19. Until today, Covid-19, which not only causes life-threatening lung infections but also impairs various other organs and tissues, has killed hundreds of thousands of people and caused irreparable damage to many others. Since the very onset of the pandemic, huge efforts were made worldwide to fully understand this virus and numerous studies were, and still are, published. Many of these deal with structural analyses of the viral spike glycoprotein and with vaccine development, antibodies and antiviral molecules or immunomodulators that are assumed to become essential tools in the struggle against the virus. This paper summarizes knowledge on the properties of the four structural proteins (spike protein S, membrane protein M, envelope protein E and nucleocapsid protein N) of the SARS-CoV-2 virus and its relatives, SARS-CoV and MERS-CoV, that emerged few years earlier. Moreover, attention is paid to ways to analyze such proteins using freely available bioinformatic tools and, more importantly, to bring these proteins alive by looking at them on a computer/laptop screen with the easy-to-use but highly performant and interactive molecular graphics program DeepView. It is hoped that this paper will stimulate non-bioinformaticians and non-specialists in structural biology to scrutinize these and other macromolecules and as such will contribute to establishing procedures to fight these and maybe other forthcoming viruses.

scholarly journals Complete sequence analysis of human norovirus GII.17 detected in South Korea

2019 ◽  
Vol 147 ◽  
Author(s):  
H. Kim ◽  
Y. J. Won ◽  
L. H. Kang ◽  
A. R. Lee ◽  
J. I. Han ◽  
...  
Keyword(s):  
South Korea ◽  
Vaccine Development ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Prediction And Prevention ◽  
Whole Genomes ◽  
Novel Variant ◽  
Stool Samples ◽  
Norovirus Gii ◽  
Epidemiology Studies

AbstractNorovirus, a major cause of gastroenteritis in people of all ages worldwide, was first reported in South Korea in 1999. The most common causal agents of pediatric acute gastroenteritis are norovirus and rotavirus. While vaccination has reduced the pediatric rotavirus infection rate, norovirus vaccines have not been developed. Therefore, prediction and prevention of norovirus are very important. Norovirus is divided into genogroups GI–GVII, with GII.4 being the most prevalent. However, in 2012–2013, GII.17 showed a higher incidence than GII.4 and a novel variant, GII.P17-GII.17, appeared. In this study, 204 stool samples collected in 2013–2014 were screened by reverse transcriptase-polymerase chain reaction; 11 GI (5.39%) and 45 GII (22.06%) noroviruses were identified. GI.4, GI.5, GII.4, GII.6 and GII.17 were detected. The whole genomes of the three norovirus GII.17 were sequenced. The whole genome of GII.17 consists of three open reading frames of 5109, 1623 and 780 bp. Compared with 20 GII.17 strains isolated in other countries, we observed numerous changes in the protruding P2 domain of VP1 in the Korean GII.17 viruses. Our study provided genome information that might aid in epidemic prevention, epidemiology studies and vaccine development.

Pathology of Australian Native Wildlife

2009 ◽  
Author(s):  
Philip Ladds
Keyword(s):  
Marine Mammals ◽  
Clinical Signs ◽  
Pathological Changes ◽  
Rapid Access ◽  
Documented Information ◽  
Available Information

Pathology of Australian Native Wildlife brings together in one volume available information on the pathology of Australian native vertebrate wildlife, excluding fish. It provides rapid access to documented information on diseases in Australian wildlife, domiciled either in Australia or overseas. The book comprises 45 chapters, each detailing pathological changes caused by specific pathogens including viruses, bacteria, fungi, protozoa, helminths and ectoparasites, and other injurious agents and conditions such as toxins and neoplasia affecting terrestrial and marine mammals, birds, reptiles and amphibians. Although the aim is to describe morphological (gross and microscopic) changes, the author also indicates history and clinical signs, thus providing guidance as to which lesions should be specifically searched for, and what ancillary testing might be needed to confirm a diagnosis. Illustrated throughout with colour photographs, this will be the essential reference for veterinary pathologists and clinicians, as well as wildlife researchers, zoos, wildlife parks, environmentalists, conservationists and students. Awarded a 2010 Whitley Certificate of Commendation for Zoological Resource.

scholarly journals Treatment of naturally acquired demodectic mange with amitraz in two harbour seals (Phoca vitulina)

2015 ◽  
Vol 63 (3) ◽  
pp. 352-357 ◽  
Author(s):  
Kyoo-Tae Kim ◽  
Seung-Hun Lee ◽  
Dongmi Kwak
Keyword(s):  
Successful Treatment ◽  
Marine Mammals ◽  
Clinical Signs ◽  
Skin Lesions ◽  
Phoca Vitulina ◽  
Aetiological Agent ◽  
Harbour Seals ◽  
Causative Agents ◽  
Pure Cultures

Two male harbour seals (Phoca vitulina; 33 and 35 years old, respectively), housed since 2002 at a zoo for exhibition purposes, developed severe, multifocal and diffuse skin lesions. Skin scrapings and microscopy for parasites as well as pure cultures for bacteria and dermatophytes were carried out to identify the aetiological agent. Skin scrapings showed that lesions appearing on the seals were caused by an infestation of Demodex mites, which is uncommon in marine mammals, and were not due to other causative agents (parasites, bacteria or dermatophytes). Treatment with amitraz (0.01%) once a week for three weeks and with ampicillin (10 mg/kg SID per os) for six days eliminated the mites and resolved the clinical signs of demodectic mange in the harbour seals. The purpose of this report is to describe the successful treatment of naturally acquired demodectic mange with amitraz in harbour seals.

scholarly journals Erratum to: Nonclassically Secreted Proteins as Possible Antigens for Vaccine Development: A Reverse Vaccinology Approach

2015 ◽  
Vol 177 (5) ◽  
pp. 1199-1199 ◽  
Author(s):  
Mauricio de Alvarenga Mudadu ◽  
Viviane Carvalho ◽  
Sophie Yvette Leclercq
Keyword(s):  
Vaccine Development ◽  
Reverse Vaccinology ◽  
Secreted Proteins

scholarly journals Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Kirsi Aaltonen ◽  
Ravi Kant ◽  
Marjut Eklund ◽  
Mirja Raunio-Saarnisto ◽  
Lars Paulin ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Marine Mammals ◽  
Core Genome ◽  
Illumina Miseq ◽  
Emerging Pathogen ◽  
Pathogenic Potential ◽  
The Core ◽  
Poor Treatment ◽  
Different Strains ◽  
Fur Animals

Streptococcus halichoeri is an emerging pathogen with a variety of host species and zoonotic potential. It has been isolated from grey seals and other marine mammals as well as from human infections. Beginning in 2010, two concurrent epidemics were identified in Finland, in fur animals and domestic dogs, respectively. The fur animals suffered from a new disease fur animal epidemic necrotic pyoderma (FENP) and the dogs presented with ear infections with poor treatment response. S. halichoeri was isolated in both studies, albeit among other pathogens, indicating a possible role in the disease etiologies. The aim was to find a possible common origin of the fur animal and dog isolates and study the virulence factors to assess pathogenic potential. Isolates from seal, human, dogs, and fur animals were obtained for comparison. The whole genomes were sequenced from 20 different strains using the Illumina MiSeq platform and annotated using an automatic annotation pipeline RAST. The core and pangenomes were formed by comparing the genomes against each other in an all-against-all comparison. A phylogenetic tree was constructed using the genes of the core genome. Virulence factors were assessed using the Virulence Factor Database (VFDB) concentrating on the previously confirmed streptococcal factors. A core genome was formed which encompassed approximately half of the genes in Streptococcus halichoeri. The resulting core was nearly saturated and would not change significantly by adding more genomes. The remaining genes formed the pangenome which was highly variable and would still evolve after additional genomes. The results highlight the great adaptability of this bacterium possibly explaining the ease at which it switches hosts and environments. Virulence factors were also analyzed and were found primarily in the core genome. They represented many classes and functions, but the largest single category was adhesins which again supports the marine origin of this species.

Nonclassically Secreted Proteins as Possible Antigens for Vaccine Development: A Reverse Vaccinology Approach

2015 ◽  
Vol 175 (7) ◽  
pp. 3360-3370 ◽  
Author(s):  
Mauricio de Alvarenga Mudadu ◽  
Viviane Carvalho ◽  
Sophie Yvette Leclercq
Keyword(s):  
Vaccine Development ◽  
Reverse Vaccinology ◽  
Secreted Proteins
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