Genetic diversity of Haemophilus parasuis from sick and healthy pigs

Poljak, Zvonimir; Gallant, Jackie; Chalmers, Gabhan; Nicholson, Vivian M.; Soltes, Glenn; MacInnes, Janet I.

doi:10.1016/j.vetmic.2013.07.028

“…186 The positive rates of most of the PVMs were similar among serovars (4, 5, 12, 13 and 187 14) which were dominated by isolates in clade Ⅰ and among serovars (1, 2 and 7) which were Manuscript to be reviewed 258 2014). Our study was also consistent with another report, in which serovar 5, 13, 14 were found 259 only in cluster I and serovar 2 was only found in cluster Ⅱ (Boerlin et al, 2013). 260 Systemic isolates were most frequently seen in serovar 13 in this study.…”

supporting

confidence: 92%

“…No strong correlation between clinical phenotype and 250 iscR-based phylogeny or PVMs profiles was observed in this study. 251The relationship between serotype and other typing methods has been evaluated(Turni 252 and Blackall, 2010;Ma et al, 2016;Zhao et al, 2018), but correlation were only been identified 253 in a few reports(Boerlin et al, 2013; Howell et al, 2014). In this study, isolates of serovar 4, 5,254 and 14 were found predominantly distributed in clade I, and those of serovar 12 and 13 were 255 mostly found in clade Ⅰ, while those of serovar1, 2 and 7 were predominantly in clade Ⅱ.…”

mentioning

confidence: 99%

Peer Review #2 of "Association between iscR-based phylogeny, serovars and potential virulence markers of Haemophilus parasuis (v0.2)"

2019

0

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Haemophilus parasuis is an economically important bacterial pathogen of swine. Extensive genetic and phenotypic heterogeneity among H.parasuis strains have been observed, which hinders the deciphering of the population structure and its association with clinical virulence. In this study, two highly divergent clades were defined according to iscR-based phylogeny analysis of 148 isolates. Clear separation of serovars and potential virulence markers (PVMs) were observed between the two clades, which are indicative of independent evolution of the two lineages. Previously suggested virulence factors showed no correlation with clinical virulence, and were probably clade or serovar specific genes emerged during different stage of evolution. PVMs profiles varied widely among isolates in the same serovar. Higher strain diversity in respect of PVMs was found for isolates from multi-strain infected farms than those from single strain infected ones, which indicates that multi-strain infection in one farm may increase the frequency of gene transfer in H.parasuis. Systemic isolates were more frequently found in serovar 13 and serovar 12, while no correlation between clinical virulence and iscR-based phylogeny was observed. It shows that iscR is a reliable marker for studying population structure of H.parasuis, while other factors should be included to avoid the interference of gene exchange of iscR between isolates. The two lineages of H.parasuis may have undergone independent evolution, but show no difference in clinical virulence. Wide distribution of systemic isolates across the entire population poses new challenge for development of vaccine with better cross-protection. Our study provides new information for better deciphering the population structure of H.parasuis, which helps understanding the extreme diversity within this pathogenic bacterium. PeerJ reviewing PDF | (2018:12:33889:2:0:NEW 8 Apr 2019) Manuscript to be reviewed 1 2 Association between iscR-based phylogeny, serovars and potential virulence markers of 3 Haemophilus parasuis 4 5 Abstract 18 Haemophilus parasuis is an economically important bacterial pathogen of swine. 19 Extensive genetic and phenotypic heterogeneity among H.parasuis strains have been observed, PeerJ reviewing PDF | (2018:12:33889:2:0:NEW 8 Apr 2019)Manuscript to be reviewed 20 which hinders the deciphering of the population structure and its association with clinical 21 virulence. 22 In this study, two highly divergent clades were defined according to iscR-based 23 phylogeny analysis of 148 isolates. Clear separation of serovars and potential virulence markers 24 (PVMs) were observed between the two clades, which are indicative of independent evolution of 25 the two lineages. Previously suggested virulence factors showed no correlation with clinical 26 virulence, and were probably clade or serovar specific genes emerged during different stage of 27 evolution. PVMs profiles varied widely among isolates in the same serovar. Higher strain 28 diversity in respect of PVMs was found for isolat...

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“…Results of current study on correlation between population structure and virulence were contradictory. H.parasuis strains in some sub-groups tend to be virulent (Ruiz et al, 2001;Olvera et al, 2006a;Olvera et al, 2006b;Wang et al, 2016), while no association between population structure and clinical virulence was found in others (Zehr et al, 2012;Boerlin et al, 2013;Howell et al, 2014). No strong correlation between clinical phenotype and iscR-based phylogeny or PVMs profiles was observed in this study.…”

Section: Discussioncontrasting

confidence: 47%

“…The relationship between serotype and other typing methods has been evaluated (Turni and Blackall, 2010;Ma et al, 2016;Zhao et al, 2018), but correlation were only been identified in a few reports (Boerlin et al, 2013;Howell et al, 2014). In this study, isolates of serovar 4, 5, and 14 were found predominantly distributed in clade I, and those of serovar 12 and 13 were mostly found in clade Ⅰ, while those of serovar1, 2 and 7 were predominantly in clade Ⅱ.…”

Section: Discussionmentioning

confidence: 59%

Peer Review #2 of "Association between iscR-based phylogeny, serovars and potential virulence markers of Haemophilus parasuis (v0.1)"

2019

0

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Haemophilus parasuis is an economically important bacterial pathogen of swine. Extensive genetic and phenotypic heterogeneity among H.parasuis strains have been observed, which hinders the deciphering of the population structure and its association with clinical virulence. In this study, two highly divergent clades were defined according to iscR-based phylogeny analysis of 148 isolates. Clear separation of serovars and potential virulence markers (PVMs) were observed between the two clades, which are indicative of independent evolution of the two lineages. Previously suggested virulence factors showed no correlation with clinical virulence, and were probably clade or serovar specific genes emerged during different stage of evolution. PVMs profiles varied widely among isolates in the same serovar. Higher strain diversity in respect of PVMs was found for isolates from multi-strain infected farms than those from single strain infected ones, which indicates that multi-strain infection in one farm may increase the frequency of gene transfer in H.parasuis. Systemic isolates were more frequently found in serovar 13 and serovar 12, while no correlation between clinical virulence and iscR-based phylogeny was observed. It shows that iscR is a reliable marker for studying population structure of H.parasuis, while other factors should be included to avoid the interference of gene exchange of iscR between isolates. The two lineages of H.parasuis may have undergone independent evolution, but show no difference in clinical virulence. Wide distribution of systemic isolates across the entire population poses new challenge for development of vaccine with better cross-protection. Our study provides new information for better deciphering the population structure of H.parasuis, which helps understanding the extreme diversity within this pathogenic bacterium.

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“…The presence of multiple isolates of H. parasuis, particularly in URT samples (27)(28)(29), is one of the major challenges in designing a prospective molecular tool for determining virulence. Current surveillance methods for other pathogens such as Actinobacillus pleuropneumoniae operate on an individual isolate level, where the detection of the bacterium initiates a more thorough investigation at the single-colony level to look for the presence of toxins (30,31).…”

Section: Discussionmentioning

confidence: 99%

“Pathotyping” Multiplex PCR Assay for Haemophilus parasuis: a Tool for Prediction of Virulence

Howell

¹

,

Weinert

²

,

Peters

³

et al. 2017

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Haemophilus parasuis is a diverse bacterial species that is found in the upper respiratory tracts of pigs and can also cause Glässer's disease and pneumonia. A previous pangenome study of H. parasuis identified 48 genes that were associated with clinical disease. Here, we describe the development of a generalized linear model (termed a pathotyping model) to predict the potential virulence of isolates of H. parasuis based on a subset of 10 genes from the pangenome. A multiplex PCR (mPCR) was constructed based on these genes, the results of which were entered into the pathotyping model to yield a prediction of virulence. This new diagnostic mPCR was tested on 143 field isolates of H. parasuis that had previously been whole-genome sequenced and a further 84 isolates from the United Kingdom from cases of H. parasuis-related disease in pigs collected between 2013 and 2014. The combination of the mPCR and the pathotyping model predicted the virulence of an isolate with 78% accuracy for the original isolate collection and 90% for the additional isolate collection, providing an overall accuracy of 83% (81% sensitivity and 93% specificity) compared with that of the "current standard" of detailed clinical metadata. This new pathotyping assay has the potential to aid surveillance and disease control in addition to serotyping data.

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Genetic diversity of Haemophilus parasuis from sick and healthy pigs

Cited by 15 publications

References 39 publications

Peer Review #2 of "Association between iscR-based phylogeny, serovars and potential virulence markers of Haemophilus parasuis (v0.2)"

Peer Review #2 of "Association between iscR-based phylogeny, serovars and potential virulence markers of Haemophilus parasuis (v0.2)"

Peer Review #2 of "Association between iscR-based phylogeny, serovars and potential virulence markers of Haemophilus parasuis (v0.1)"

“Pathotyping” Multiplex PCR Assay for Haemophilus parasuis: a Tool for Prediction of Virulence

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