Draft Genome Sequences of Six Actinobacillus pleuropneumoniae Serotype 8 Brazilian Clinical Isolates: Insight into New Applications

Pereira, Monalessa Fábia; Rossi, Ciro César; Carvalho, Fabíola Marques de; Almeida, Luiz Gonzaga Paula de; Souza, Rangel Celso; Vasconcelos, Ana Tereza Ribeiro de; Bazzolli, Denise Mara Soares

doi:10.1128/genomea.01585-14

Cited by 8 publications

(11 citation statements)

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“…pleuropneumoniae Serotype 8. The set of clusters of the coding DNA sequences (CDS) predicted for A. pleuropneumoniae serotype 8 was based on the seven genomes of clinical isolates taken from pig farms, six from Brazil [21] and one from the United Kingdom [22]. In this analysis, the CD-HIT v.4.6.1 program [24,25] was used to consider an identity threshold of 0.85 to cluster the CDS.…”

Section: Determination Of Protein-coding Sequence Set In Amentioning

confidence: 99%

“…Over the years, A. pleuropneumoniae serotype 8 has been neglected in identification studies due to failures in serotyping techniques, and as a result, genomic studies involving this serotype are nonexistent. Although recent studies have showed a wide distribution of this serotype in several regions, such as the United Kingdom [17,18], North America [19], and Brazil [20], just recently A. pleuropneumoniae serotype 8 genome sequence was available [21,22].…”

Section: Introductionmentioning

confidence: 99%

“…Clinical isolates from A. pleuropneumoniae serotype 8 have virulence complexity [9], but no specific information on genotypic variability is available so far. Then, this study is the first to describe A. pleuropneumoniae serotype 8 genomic from comparative analysis between A. pleuropneumoniae serotype 8 genomes (clinical isolates: Brazilian origin [21], one of English origin [22]) and twelve genomes of different serotypes of A. pleuropneumoniae deposited in databases.…”

Section: Introductionmentioning

confidence: 99%

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Comparative Genomics of Actinobacillus pleuropneumoniae Serotype 8 Reveals the Importance of Prophages in the Genetic Variability of the Species

Prado

Silva

Crispim

et al. 2020

International Journal of Genomics

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Actinobacillus pleuropneumoniae is the etiologic agent of porcine pleuropneumonia. Currently, there are 18 different serotypes; the serotype 8 is the most widely distributed in the United States, Canada, United Kingdom, and southeastern Brazil. In this study, genomes of seven A. pleuropneumoniae serotype 8 clinical isolates were compared to the other genomes of twelve serotypes. The analyses of serotype 8 genomes resulted in a set of 2352 protein-coding sequences. Of these sequences, 76.6% are present in all serotypes, 18.5% are shared with some serotypes, and 4.9% were differential. This differential portion was characterized as a series of hypothetical and regulatory protein sequences: mobile element sequence. Synteny analysis demonstrated possible events of gene recombination and acquisition by horizontal gene transfer (HGT) in this species. A total of 30 sequences related to prophages were identified in the genomes. These sequences represented 0.3 to 3.5% of the genome of the strains analyzed, and 16 of them contained complete prophages. Similarity analysis between complete prophage sequences evidenced a possible HGT with species belonging to the family Pasteurellaceae. Thus, mobile genetic elements, such as prophages, are important components of the differential portion of the A. pleuropneumoniae genome and demonstrate a central role in the evolution of the species. This study represents the first study done to understand the genome of A. pleuropneumoniae serotype 8.

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Section: Determination Of Protein-coding Sequence Set In Amentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative Genomics of Actinobacillus pleuropneumoniae Serotype 8 Reveals the Importance of Prophages in the Genetic Variability of the Species

Prado

Silva

Crispim

et al. 2020

International Journal of Genomics

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“…The sequences of the final sRNA candidates were also searched by BLASTn in the other 11 serotype reference genomes available of A. pleuropneumoniae and in the genomes of six Brazilian clinical isolates (Pereira et al 2015a) to investigate their distribution among the species. In addition, 33 genomes of 14 other Pasteurellaceae species, whose complete genomes are available from Genbank, were also searched (Supplemental Table S4).…”

Section: In Silico Identification Of Srnasmentioning

confidence: 99%

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Rossi

Bossé

et al. 2016

RNA

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Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.

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“…A further 14.5% of the tested isolates had tet (B) genes that appeared to be associated with plasmid sequences ( Bossé et al, 2017 ). Wgs for six Brazilian isolates also indicate the presence of tet (B) associated with plasmid sequences in four of these isolates ( Pereira et al, 2015 ). As small plasmids often appear to be common amongst members of the Pasteurellaceae ( Michael et al, 2018 ), the aim of this study was to identify the tet (B) plasmids present in these sequenced isolates of A. pleuropneumoniae .…”

Section: Introductionmentioning

confidence: 99%

Evidence of Illegitimate Recombination Between Two Pasteurellaceae Plasmids Resulting in a Novel Multi-Resistance Replicon, pM3362MDR, in Actinobacillus pleuropneumoniae

Silva

et al. 2018

Front. Microbiol.

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Evidence of plasmids carrying the tetracycline resistance gene, tet(B), was found in the previously reported whole genome sequences of 14 United Kingdom, and 4 Brazilian, isolates of Actinobacillus pleuropneumoniae. Isolation and sequencing of selected plasmids, combined with comparative sequence analysis, indicated that the four Brazilian isolates all harbor plasmids that are nearly identical to pB1001, a plasmid previously found in Pasteurella multocida isolates from Spain. Of the United Kingdom isolates, 13/14 harbor plasmids that are (almost) identical to pTetHS016 from Haemophilus parasuis. The remaining United Kingdom isolate, MIDG3362, harbors a 12666 bp plasmid that shares extensive regions of similarity with pOV from P. multocida (which carries blaROB-1, sul2, and strAB genes), as well as with pTetHS016. The newly identified multi-resistance plasmid, pM3362MDR, appears to have arisen through illegitimate recombination of pTetHS016 into the stop codon of the truncated strB gene in a pOV-like plasmid. All of the tet(B)-carrying plasmids studied were capable of replicating in Escherichia coli, and predicted origins of replication were identified. A putative origin of transfer (oriT) sequence with similar secondary structure and a nic-site almost identical to that of RP4 was also identified in these plasmids, however, attempts to mobilize them from an RP4-encoding E. coli donor strain were not successful, indicating that specific conjugation machinery may be required.

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Draft Genome Sequences of Six Actinobacillus pleuropneumoniae Serotype 8 Brazilian Clinical Isolates: Insight into New Applications

Cited by 8 publications

References 8 publications

Comparative Genomics of Actinobacillus pleuropneumoniae Serotype 8 Reveals the Importance of Prophages in the Genetic Variability of the Species

Comparative Genomics of Actinobacillus pleuropneumoniae Serotype 8 Reveals the Importance of Prophages in the Genetic Variability of the Species

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Evidence of Illegitimate Recombination Between Two Pasteurellaceae Plasmids Resulting in a Novel Multi-Resistance Replicon, pM3362MDR, in Actinobacillus pleuropneumoniae

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