Draft Genome Sequences of Four Different Strains Belonging to Leptospira interrogans Serovar Pomona Isolated from Mammals in the Island of Sardinia, Italy

Piredda, Ivana; Scarpa, Fabio; Sanna, Daria; Casu, Marco; Ponti, Maria Nicoletta; Chisu, Valentina

doi:10.1128/mra.00698-21

Cited by 4 publications

(5 citation statements)

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“…Reads were mapped against the reference genome NC_005336.1 (this genome is the only one branded as reference genome for ORFV in NCBI Virus portal) using an end-to-end read alignment (basic command line: bowtie2 [options]* -x <bt2-idx> {−1 <m1> −2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | b <bam>} -S [<sam>]). A de novo assembly was also performed to use an approach as complete as possible, using the software SPAdes v3.15.3 (Center for Algorithmic Biotechnology, St Petersburg, Russia) [ 27 ] (command line: --outdir out --cpus 6 --ram 30 --R1 fastq_r1.fastqsanger --R2 fastq_r2.fastqsanger --trim --namefmt contig%05d --depth 100 --nocorr --minlen 0 --mincov 2 --assembler spades) by following Scarpa et al [ 28 ] and Piredda et al [ 29 ]. Scaffolds were subsequently oriented with the reference genome NC_005336.1 by using Unipro UGENE v.35 (Unipro Center for Information Technologies, Novosibirsk, Russia) [ 30 ].…”

Section: Methodsmentioning

confidence: 99%

“…Seven whole genome sequences were obtained for ORFV in the present study. The whole dataset ( n = 26) was aligned using the Clustal Omega package [ 31 ] (available at ; accessed on 15 April 2022) after editing by means of Unipro UGENE v.35 [ 29 ], and subsequently deposited in GenBank (see Table 2 for accession numbers).…”

Section: Methodsmentioning

confidence: 99%

“…Seven whole genome sequences were obtained for ORFV in the present study. The whole dataset (n = 26) was aligned using the Clustal Omega package [31] (available at https://www.ebi.ac.uk/Tools/msa/clustalo/; accessed on 15 April 2022) after editing by means of Unipro UGENE v.35 [29], and subsequently deposited in GenBank (see Table 2 for accession numbers). These Sardinian sequences were included in a large dataset containing all the ORFV whole genomes available on GenBank to date (see Table 2 for details and references).…”

Section: Phylogeny Molecular Dating and Evolutionary Ratementioning

confidence: 99%

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A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ORF Virus through the Whole Genome Sequencing of the First Italian Strains

Coradduzza

Sanna

Scarpa

et al. 2022

Viruses

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Orf virus (ORFV) is distributed worldwide and is the causative agent of contagious ecthyma that mainly occurs in sheep and goats. This disease was reported for the first time at the end of 18th century in Europe but very little is currently known about the temporal and geographic origins of this virus. In the present study, the use of new Italian whole genomes allowed for better inference on the evolutionary history of ORFV. In accordance with previous studies, two genome types (S and G) were described for infection of sheep and goats, respectively. These two well-differentiated groups of genomes originated for evolutive convergence in the late 1800s in two different areas of the world (Europe for S type and Asia for G type), but it was only in the early 1900s that the effective size of ORFV increased among hosts and the virus spread across the whole European continent. The Italian strains which were sequenced in the present study were isolated on the Mediterranean island of Sardinian and showed to be exclusive to this geographic area. One of them is likely representative of the early European forms of ORFV which infected sheep and became extinct about one century ago. Such an ancient Sardinian strain may have reached the island simple by chance, where it quickly adapted to the new habitat.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Phylogeny Molecular Dating and Evolutionary Ratementioning

confidence: 99%

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A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ORF Virus through the Whole Genome Sequencing of the First Italian Strains

Coradduzza

Sanna

Scarpa

et al. 2022

Viruses

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“…Recent studies in which pathogenic and intermediate strains of Leptospira have been isolated from clinical samples indicated that the disease is wide-spread among wildlife and domestic mammals on the island [16][17][18]. Whole-genome sequencing obtained from pathogenic Leptospira strains isolated from the two urine samples and all kidney samples had 100% identity with the deposited sequences in NCBI GenBank under BioProject accession number PRJNA731636 [36]. Furthermore, when the nucleotide sequence from environment strains isolated was compared with the other published genome sequences of Leptospira, we found a nucleotide similarity of 98.08% with the genomospecies L. vanthielii (NZ_RQHF00000000.1).…”

Section: Discussionmentioning

confidence: 99%

Co-Infection by Leptospira montravelensis and Leptospira interrogans Serovar Pomona in Urine Samples of Donkeys and Pigs in Sardinia, Italy

Piredda

Bertoldi

Pedditzi

et al. 2023

Animals

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Saprophytic leptospires are spirochetes enclosed within the non-pathogenic clade of the genus Leptospira, which in turn is subdivided into two subclades S1 and S2. To date, the microorganisms included in these subclades have been isolated from the environment in various parts of the world, and are believed to have no known animal reservoirs. After a case of Leptospira interrogans serovar Pomona was notified to the owner of a farm in Sardinia, all of the farm animals (11 pigs and 3 donkeys) were examined for the presence of Leptospira. Sera of all tested animals resulted positive for antibodies to Leptospira using a microscopic agglutination test (MAT). Moreover, nine (82%) kidney samples from pigs and three urine samples collected from donkeys (100%) tested positive for Leptospira DNA after qPCR. Results obtained after MLST analysis and sequencing of rrs, rpoB, and secY genes, performed on six Leptospira strains isolated in culture, revealed the presence of the genomospecies L. interrogans serovar Pomona in the kidney samples. Conversely, whole-genome sequencing combined with mean nucleotide identity revealed the presence of the saprophytic L. montravelensis in the urine samples. Our results report, for the first time, the isolation of a saprophytic species from mammalian urine, suggesting a new ecological specialization for these bacteria, with a possible transition from free-living to a symbiotic lifestyle. Further studies will have to be conducted to understand the evolution of virulence of these bacteria, potential infectivity, and possible public health implications.

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“…Samples have been sequenced through the WGS technique on the MiSeq platform by BMR Genomics in Padua, Italy, generating paired end reads 2 × 300 (Illumina, San Diego, California, Stati Uniti). The resulting FASTQ files were checked for quality using the tool fastQC from the FASTX-Toolkit v0.7 [35]; assembly with reference and de novo were performed with Bowtie 2 v2.4.2 (Johns Hopkins University, Baltimore, MD, USA) [36,37] and SPAdes v3.15.3 (Center for Algorithmic Biotechnology, St. Petersburg, Russia) [38] following Scarpa et al [39] and Piredda et al [40]. Scaffolds were aligned with the reference genome NC_005336.1 using Unipro UGENE v.35 (Unipro Center for Information Technologies, Novosibirsk, Russia) [41].…”

Section: Viral Dna Extraction Sequencing and Genome Assemblymentioning

confidence: 99%

The Global Evolutionary History of Orf Virus in Sheep and Goats Revealed by Whole Genomes Data

Coradduzza,

Scarpa,

Rocchigiani

et al. 2024

Viruses

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Orf virus (ORFV) belongs to the genus Parapoxvirus (Poxviridae family). It is the causative agent of contagious ecthyma (CE) that is an economically detrimental disease affecting small ruminants globally. Contagious ecthyma outbreaks are usually reported in intensive breeding of sheep and goats but they have also been reported in wildlife species. Notably, ORFV can infect humans, leading to a zoonotic disease. This study aims to elucidate the global evolutionary history of ORFV genomes in sheep and goats, including the first genomes from Central America in the analyses. In comparison to the last study on ORFV whole genomes, the database now includes 11 more sheep and goat genomes, representing an increase of 42%. The analysis of such a broader database made it possible to obtain a fine molecular dating of the coalescent time for ORFV S and G genomes, further highlighting the genetic structuring between sheep and goat genomes and corroborating their emergence in the latter half of 20th century.

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Draft Genome Sequences of Four Different Strains Belonging to Leptospira interrogans Serovar Pomona Isolated from Mammals in the Island of Sardinia, Italy

Cited by 4 publications

References 5 publications

A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ORF Virus through the Whole Genome Sequencing of the First Italian Strains

A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ORF Virus through the Whole Genome Sequencing of the First Italian Strains

Co-Infection by Leptospira montravelensis and Leptospira interrogans Serovar Pomona in Urine Samples of Donkeys and Pigs in Sardinia, Italy

The Global Evolutionary History of Orf Virus in Sheep and Goats Revealed by Whole Genomes Data

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