Comparative Genomics Analysis of Two Different Virulent Bovine Pasteurella multocida Isolates

Exploring the intricacies of Pasteurella multocida dynamics in high-altitude livestock and its consequences for bovine health: A personal exploration of the yak paradox

Pasturella multocida (P. multocida), a gram-negative bacterium, has long been a focus of interest in animal health because of its capacity to cause different infections, including hemorrhagic septicemia. Yaks, primarily found in high-altitude environments, are among the several livestock animals affected by these bacteria. Yaks are essential to the socioeconomic life of the people who depend on them since they are adapted to the cold and hypoxic conditions of highland environments. Nevertheless, these terrains exhibit a greater incidence of P. multocida despite the severe environmental complications. This predominance has been linked to the possible attenuation of the yak's immunological responses in such circumstances and the evolution of some bacterial strains to favor survival in the respiratory passages of the animals. Moreover, these particular strains threaten other cattle populations that interact with yaks, which might result in unanticipated outbreaks in areas previously thought to be low risk. Considering these findings, designing and executing preventative and control strategies suited explicitly for these distinct biological environments is imperative. Through such strategies, yaks' health will be guaranteed, and a larger bovine population will be safeguarded against unanticipated epidemics. The current review provides thorough insights that were previously dispersed among several investigations. Its distinct method of connecting the ecology of yaks with the dynamics of infection offers substantial background information for further studies and livestock management plans.

RACK1 mediates NLRP3 inflammasome activation during Pasteurella multocida infection

Pasteurella multocida is a gram-negative bacterium that causes serious diseases in a wide range of animal species. Inflammasomes are intracellular multimolecular protein complexes that play a critical role in host defence against microbial infection. Our previous study showed that bovine P. multocida type A (PmCQ2) infection induces NLRP3 inflammasome activation. However, the exact mechanism underlying PmCQ2-induced NLRP3 inflammasome activation is not clear. Here, we show that NLRP3 inflammasome activation is positively regulated by a scaffold protein called receptor for activated C kinase 1 (RACK1). This study shows that RACK1 expression was downregulated by PmCQ2 infection in primary mouse peritoneal macrophages and mouse tissues, and overexpression of RACK1 prevented PmCQ2-induced cell death and reduced the numbers of adherent and invasive PmCQ2, indicating a modulatory role of RACK1 in the cell death that is induced by P. multocida infection. Next, RACK1 knockdown by siRNA significantly attenuated PmCQ2-induced NLRP3 inflammasome activation, which was accompanied by a reduction in the protein expression of interleukin (IL)-1β, pro-IL-1β, caspase-1 and NLRP3 as well as the formation of ASC specks, while RACK1 overexpression by pcDNA3.1-RACK1 plasmid transfection significantly promoted PmCQ2-induced NLRP3 inflammasome activation; these results showed that RACK1 is essential for NLRP3 inflammasome activation. Furthermore, RACK1 knockdown decreased PmCQ2-induced NF-κB activation, but RACK1 overexpression had the opposite effect. In addition, the immunofluorescence staining and immunoprecipitation results showed that RACK1 colocalized with NLRP3 and that NEK7 and interacted with these proteins. However, inhibition of potassium efflux significantly attenuated the RACK1-NLRP3-NEK7 interaction. Our study demonstrated that RACK1 plays an important role in promoting NLRP3 inflammasome activation by regulating NF-κB and promoting NLRP3 inflammasome assembly.

The important role of NLRP6 inflammasome in Pasteurella multocida infection

Pasteurella multocida (P. multocida) can cause severe respiratory disease in cattle, resulting in high mortality and morbidity. Inflammasomes are multiprotein complexes in the cytoplasm that recognize pathogens and play an important role in the host defense against microbial infection. In this study, the mechanism of P. multocida-induced NLRP6 inflammasome activation was investigated in vitro and in vivo. Firstly, P. multocida induced severe inflammation with a large number of inflammatory cells infiltrating the lungs of WT and Nlrp6^−/− mice. Nlrp6^−/− mice were more susceptible to P. multocida infection and they had more bacterial burden in the lungs. Then, the recruitment of macrophages and neutrophils in the lungs was investigated and the results show that the number of immune cells was significantly decreased in Nlrp6^−/− mice. Subsequently, NLRP6 was shown to regulate P. multocida-induced inflammatory cytokine secretion including IL-1β and IL-6 both in vivo and in vitro while TNF-α secretion was not altered. Moreover, NLRP6 was found to mediate caspase-1 activation and ASC oligomerization, resulting in IL-1β secretion. Furthermore, NLRP6 inflammasome mediated the gene expression of chemokines including CXCL1, CXCL2 and CXCR2 which drive the activation of NLRP3 inflammasomes. Finally, NLRP3 protein expression was detected to be abrogated in P. multocida-infected Nlrp6^−/− macrophages, indicating the synergic effect of NLRP6 and NLRP3. Our study demonstrates that NLRP6 inflammasome plays an important role in the host against P. multocida infection and contributes to the development of immune therapeutics against P. multocida.

Mexican Strains of Anaplasma marginale: A First Comparative Genomics and Phylogeographic Analysis

The One Health approach looks after animal welfare and demands constant monitoring of the strains that circulate globally to prevent outbreaks. Anaplasma marginale is the etiologic agent of bovine anaplasmosis and is endemic worldwide. This study aimed to analyze, for the first time, the genetic diversity of seven Mexican strains of A. marginale and their relationship with other strains reported. The main features of A. marginale were obtained by characterizing all 24 genomes reported so far. Genetic diversity and phylogeography were analyzed by characterizing the msp1a gene and 5′-UTR microsatellite sequences and constructing a phylogenetic tree with 540 concatenated genes of the core genome. The Mexican strains show 15 different repeat sequences in six MSP1a structures and have phylogeographic relationships with strains from North America, South America, and Asia, which confirms they are highly variable. Based on our results, we encourage the performance of genome sequencing of A. marginale strains to obtain a high assembly level of molecular markers and the performance of extensive phylogeographic analysis. Undoubtedly, genomic surveillance helps build a picture of how a pathogen changes and evolves in geographical regions. However, we cannot discard the study of relationships pathogens establish with ticks and how they have co-evolved to establish themselves as a successful transmission system.

Comparative genome analysis of Pasteurella multocida serogroup B:2 strains causing haemorrhagic septicaemia (HS) in bovines

Pasteurella multocida, a Gram-negative bacterium with ubiquitous nature, is known to affect wide range of host species worldwide with varied clinical manifestations including haemorrhagic septicaemia (HS) in bovines. Although, HS causing P. multocida strains were identified and characterized by conventional tools and PCR assays, diverse strains are indistinguishable by these tools in the face of disease outbreaks. In this study, draft genomes of three virulent P. multocida serotype B:2 strains (NIVEDIPm32, NIVEDIPm34 and NIVEDIPm35) were analyzed following whole genome sequencing, assembly, annotation and compared them with existing global genomes (n = 43) of bovine origin in the database. Three draft genomes of NIVEDIPm strains consisted of 40-52 contigs with GC content of ∼40.4%. The genome size and predicted genes content was ∼2.3 Mb and 2181-2189, respectively. Besides, the presence of various mobile genetic elements, antimicrobial resistance genes and biofilm related genes suggested their vital roles in virulence; further, adaptation to the host immune system as well as host pathogen interaction. Multi locus sequence analysis based on RIRDC scheme showed the presence of ST122 in all the three strains. wgMLST based phylogenic analysis suggested that HS causing Indian virulent field strains differed geographically and showed diversity from existing HS vaccine strain P52. The phylogenetic tree revealed that North Indian strains share high similarity with strains of Pakistan than South Indian Strain. Notably, a high divergence of SNPs between the HS causing circulating virulent strains of India and current HS vaccine strain P52 suggested an imminent need for relook in to HS vaccination strategy for livestock in India.

Bacterioplankton community indicators for seasonal variation in a fragmented subtropical river

In this study, spatiotemporal investigations were conducted along five cascade dams in the main channel of the North River of China during 2019 to explore bacterioplankton community indicators of water environments in a fragmented, highly regulated river. Bacterioplankton communities were good bioindicators of temporal variation in river environments, especially when considering the bacterial class level. Specifically, the most dominant bacterial classes (Gammaproteobacteria, Oxyphotobacteria, and Actinobacteria) and sub-dominant bacterial classes (Bacteroidia, Betaproteobacteria, and Acidimicrobiia) exhibited obvious temporal variation. Rainfall, water temperature (WT), water transparency (SD), and pH were all highly associated with temporal variation. In contrast, bacterioplankton indicators of spatial variation were limited to individual dominant bacterial classes for individual study periods, while rainfall, total phosphorus (TP), and pH were also associated with spatial variation. Clustering of bacterioplankton community compositions revealed that temporal differences were much stronger than spatial differences, which is consistent with most environmental parameters exhibiting obvious temporal differences, but minimal spatial differences. A possible reason for these observations could be that river fragmentation caused by cascade dams weakened spatial differences in communities, with WT, rainfall, and river runoff playing key roles in these patterns. In conclusion, bacterioplankton communities were good bioindicators of water environments in the fragmented river ecosystem of this study and their temporal variation was more apparent than their spatial variation.

The Critical Role of Potassium Efflux and Nek7 in Pasteurella multocida-Induced NLRP3 Inflammasome Activation

Pasteurella multocida is a zoonotic pathogen causing respiratory infection in different animal species such as cattle, sheep, pigs, chickens and humans. Inflammasome is a complex assembled by multiple proteins in the cytoplasm and plays an important role in the host defense against microbial infection. Bovine Pasteurella multocida type A (PmCQ2) infection induces NLRP3 inflammasome activation and IL-1β secretion, but the mechanism of PmCQ2-induced activation of NLRP3 inflammasome is still unknown. Therefore, the underlying mechanism was investigated in this study. The results showed that potassium efflux mediated PmCQ2-induced IL-1β secretion and blocking potassium efflux attenuated PmCQ2-induced caspase-1 activation and ASC oligomerization. Furthermore, NIMA-related kinase 7 (Nek7) was also involved in PmCQ2-induced caspase-1 activation and IL-1β secretion. In addition, PmCQ2 infection promoted Nek7-NLRP3 interaction, which is dependent on potassium efflux. In conclusion, our results indicate the critical role of potassium efflux and Nek7 in Pasteurella multocida-induced NLRP3 inflammasome activation, which provides useful information about Pasteurella multocida-induced host immune response.

A single point mutation in the hyaC gene affects Pasteurella multocida serovar A capsule production and virulence

Pasteurella multocida (P. multocida) is a Gram-negative bacterium which causes diseases in poultry, livestock, and humans, resulting in huge economic losses. P. multocida serovar A CQ6 (PmCQ6) is a naturally occurring attenuated strain with a thin capsule. Thus, we aimed to explore why this strain is less virulent and produces less capsule compared with P. multocida serovar A strain CQ2 (PmCQ2). Analysis of capsular polysaccharide synthesis genes in PmCQ6 revealed that, compared with PmCQ2, there was only a single point mutation in the initiation codon sequence of the hyaC gene. To test whether this point mutation caused capsular deficiency and reduced virulence, we rescued this hyaC mutation and observed a restoration of capsule production and higher virulence. Transcriptome analysis showed that the hyaC point mutation led to a downregulation of capsule synthesis and/or iron utilization related-genes. Taken together, the results indicate that the start codon mutation of hyaC is an important factor affecting the capsule synthesis and virulence of PmCQ6.

Transcriptomic Analysis of High- and Low-Virulence Bovine Pasteurella multocida in vitro and in vivo

Pasteurella multocida is a gram-negative opportunistic pathogen that causes various diseases in poultry, livestock, and humans, resulting in huge economic losses. Pasteurella multocida serotype A CQ6 (PmCQ6) is a naturally occurring attenuated strain, while P. multocida serotype A strain CQ2 (PmCQ2) is a highly virulent strain isolated from calves. Compared with PmCQ2, it was found that bacterial loads and tissue lesions of lung tissue significantly decreased and survival rates significantly improved in mice infected with PmCQ6 by intranasal infection. However, comparative genome analysis showed that the similarity between the two strains is more than 99%. To further explore the virulence difference mechanism of PmCQ2 and PmCQ6, transcriptome sequencing analysis of the two strains was performed. The RNA sequencing analysis of PmCQ2 and PmCQ6 showed a large number of virulence-related differentially expressed genes (DEGs) in vivo and in vitro. Among them, 38 virulence-related DGEs were significantly up-regulated due to PmCQ6 infection, while the number of PmCQ2 infection was 46, much more than PmCQ6. In addition, 18 virulence-related DEGs (capsule, iron utilization, lipopolysaccharide, and outer membrane protein-related genes) were up-regulated in PmCQ2 infection compared to PmCQ6 infection, exhibiting a higher intensive expression level in vivo. Our findings indicate that these virulence-related DEGs (especially capsule) might be responsible for the virulence of PmCQ2 and PmCQ6, providing prospective candidates for further studies on pathogenesis.

Transcriptomic Analysis of Chicken Lungs Infected With Avian and Bovine Pasteurella multocida Serotype A

Pasteurella multocida (P. multocida) is a common animal pathogen responsible for many animal diseases. Strains from different hosts exhibit disparate degrees of effect in other species. Here, we characterize an avian P. multocida serogroup A strain (PmQ) showing high lethality to chickens and a bovine P. multocida serogroup A strain (PmCQ2) with no lethality to chickens. We used RNA-seq to profile the transcriptomes of chicken lungs infected with PmQ and PmCQ2. A total of 1,649 differentially expressed genes (DEGs) due to PmQ infection (831 upregulated genes and 818 downregulated genes) and 1427 DEGs (633 upregulated genes and 794 downregulated genes) due to PmCQ2 infection were identified. Functional analysis of these DEGs demonstrated that the TNF signaling pathway, the toll-like receptor signaling pathway, complement and coagulation cascades, and cytokine–cytokine receptor interaction were both enriched in PmQ and PmCQ2 infection. STAT and apoptosis signaling pathways were uniquely enriched by PmQ infection, and the NOD-like receptor signaling pathway was enriched only by PmCQ2 infection. Cell-type enrichment analysis of the transcriptomes showed that immune cells, including macrophages and granulocytes, were enriched in both infection groups. Collectively, our study profiled the transcriptomic response of chicken lungs infected with P. multocida and provided valuable information to understand the chicken responses to P. multocida infection.

Pathogenomics insights for understanding Pasteurella multocida adaptation

Pasteurella multocida is an important veterinary pathogen able to infect a wide range of animals in a broad spectrum of diseases. P. multocida is a complex microorganism in relation to its genomic flexibility, host adaptation and pathogenesis. Epidemiological analysis based on multilocus sequence typing, serotyping, genotyping, association with virulence genes and single nucleotide polymorphisms (SNPs), enables assessment of intraspecies diversity, phylogenetic and strain-specific relationships associated with host predilection or disease. A high number of sequenced genomes provides us a more accurate genomic and epidemiological interpretation to determine whether certain lineages can infect a host or produce disease. Comparative genomic analysis and pan-genomic approaches have revealed a flexible genome for hosting mobile genetic elements (MGEs) and therefore significant variation in gene content. Moreover, it was possible to find lineage-specific MGEs from the same niche, showing acquisition probably due to an evolutionary convergence event or to a genetic group with infective capacity. Furthermore, diversification selection analysis exhibits proteins exposed on the surface subject to selection pressures with an interstrain heterogeneity related to their ability to adapt. This article is the first review describing the genomic relationship to elucidate the diversity and evolution of P. multocida.

High- and low-virulent bovine Pasteurella multocida induced differential NLRP3 inflammasome activation and subsequent IL-1β secretion

Pasteurella multocida is a gram-negative bacterial pathogen, which causes a large number of diseases in mammals, birds and human. Although the bacterium has been known for decades, the pathogenesis and the mechanisms of P. multocida induced host immunity are poorly understood. Recently, we have reported that nucleotide-binding oligomerization domain-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome plays an important role in caspase-1 activation and IL-1β secretion in macrophages infected with P. multocida. In this study, the inflammasome activation and IL-1β secretion were further demonstrated by using high- and low-virulent bovine P. multocida isolates. The results showed that, comparing with macrophages infected with the high-virulent PmCQ2 isolates, the low-virulent PmCQ6 induced higher levels of NLRP3 transcription, caspase-1 activation and mature IL-1β secretion. Furthermore, the capsule of the high-virulent PmCQ2 was much thicker than that of low-virulent PmCQ6, which indicating that capsular thickness might influence the bacteria colonization and NLRP3 inflammasome activation. The results suggested that differences in maturation of IL-1β in macrophages upon high- and low- virulent P. multocida infection are critically dependent on the differential activation of NLRP3 inflammasome. This study provided more understanding for the host immune responses induced by P. multocida and further extended the knowledge of P. multocida virulence from the view of host innate immunity.

Differences in pathogenicity and virulence-associated gene expression among Pasteurella multocida strains with high and low virulence in a lung tissue model

Pasteurella multocida capsular type A can cause a pulmonary infection, leading to serious pecuniary losses in cattle. The heterogeneity of infection outcome of P. multocida strains showing different virulence may be related to divergent expression of virulence genes. In this study, we compared the transcriptional response of virulence-associated genes in high (PMPAN001) and low (PMPAN007) virulence P. multocida capsular type A strains in lung tissues and in vitro. These clinical isolates differ in their organ bacterial loads, mRNA abundance of the same virulence genes between lung and culture medium, and extent of lung damage. Among the eight virulence-associated genes (fimA, tbpA, exbD, fur, oma87, pmHAS, nanH, and tonB), seven genes showed higher expression in lung compared with in vitro at 16 h (P ≤ 0.05) in PMPAN001, but not in PMPAN007. FimA, exbD, fur, oma87, pmHAS, and tonB gene transcripts showed significantly higher expression in PMPAN001 than in PMPAN007 in the lung tissues at 16 h post-infection (P ≤ 0.05). Specially, the virulence gene, nanH, in both strains was associated with poor expression in vitro and lung tissue (mean relative mRNA abundance values < 0.6). Strain PMPAN001 had a higher proliferation rate in vivo than strain PMPAN007. The bacterial loads of PMPAN001 in the organs increased from 12 h post-infection, with maximum bacteria count ranging from 1 million to 20 million/mg. In addition, lungs treated with PMPAN001 produced serious and extensive lesions marked with inflammation at 20 h. Overall, our results reveal that the highly expressed virulence-associated genes, fimA, exbD, fur, oma87, pmHAS, and tonB can be used as markers for assessing the virulence of P. multocida capsular type A strains.

l-Serine Lowers the Inflammatory Responses during Pasteurella multocida Infection

Pasteurella multocida causes a variety of infectious diseases in various species of mammals and birds, resulting in enormous economic loss to the modern livestock and poultry industry. However, the mechanism of host-pathogen interaction is unclear. Here, we found that l-serine levels were significantly decreased in murine lungs infected with P. multocida.

Pasteurella multocida causes a variety of infectious diseases in various species of mammals and birds, resulting in enormous economic loss to the modern livestock and poultry industry. However, the mechanism of host-pathogen interaction is unclear. Here, we found that l-serine levels were significantly decreased in murine lungs infected with P. multocida. Exogenous l-serine supplementation significantly increased the survival rate of mice and decreased the colonization of P. multocida in the lungs of mice. Notably, l-serine decreased the macrophage- and neutrophil-mediated inflammatory responses in mice during P. multocida infection.

Pasteurella multocida: Genotypes and Genomics

Pasteurella multocida is a highly versatile pathogen capable of causing infections in a wide range of domestic and wild animals as well as in humans and nonhuman primates. Despite over 135 years of research, the molecular basis for the myriad manifestations of P. multocida pathogenesis and the determinants of P. multocida phylogeny remain poorly defined. The current availability of multiple P. multocida genome sequences now makes it possible to delve into the underlying genetic mechanisms of P. multocida fitness and virulence. Using whole-genome sequences, the genotypes, including the capsular genotypes, lipopolysaccharide (LPS) genotypes, and multilocus sequence types, as well as virulence factor-encoding genes of P. multocida isolates from different clinical presentations can be characterized rapidly and accurately. Putative genetic factors that contribute to virulence, fitness, host specificity, and disease predilection can also be identified through comparative genome analysis of different P. multocida isolates. However, although some knowledge about genotypes, fitness, and pathogenesis has been gained from the recent whole-genome sequencing and comparative analysis studies of P. multocida, there is still a long way to go before we fully understand the pathogenic mechanisms of this important zoonotic pathogen. The quality of several available genome sequences is low, as they are assemblies with relatively low coverage, and genomes of P. multocida isolates from some uncommon host species are still limited or lacking. Here, we review recent advances, as well as continuing knowledge gaps, in our understanding of determinants contributing to virulence, fitness, host specificity, disease predilection, and phylogeny of P. multocida.

PamulDB: a comprehensive genomic resource for the study of human- and animal-pathogenic Pasteurella multocida

Pasteurella multocida can infect a wide range of host, including humans and animals of economic importance. Genomics studies on the pathogen have produced a large amount of omics data, which are deposited in GenBank but lacks a dedicated and comprehensive resource for further analysis and integration so that need to be brought together centrally in a coherent and systematic manner. Here we have collected the genomic data for 176 P. multocida strains that are categorized into 11 host groups and 9 serotype groups, and developed the open-access P. multocida Database (PamulDB) to make this resource readily available. The PamulDB implements and integrates Chado for genome data management, Drupal for web content management, and bioinformatics tools like NCBI BLAST, HMMER, PSORTb and OrthoMCL for data analysis. All the P. multocida genomes have been further annotated for search and analysis of homologous sequence, phylogeny, gene ontology, transposon, protein subcellular localization and secreted protein. Transcriptomic data of P. multocida are also selectively adopted for gene expression analysis. The PamulDB has been developing and improving to better aid researchers with identifying and classifying of pathogens, dissecting mechanisms of the pathogen infection and host response.

OmpA protein sequence-based typing and virulence-associated gene profiles of Pasteurella multocida isolates associated with bovine haemorrhagic septicaemia and porcine pneumonic pasteurellosis in Thailand

Background

Pasteurella multocida is a Gram-negative bacterium that causes economically significant infections of a broad range of animal species. Pneumonic and septicaemic pasteurellosis caused by this bacterium remain important problems in pigs, cattle, and water buffaloes in Thailand. The aim of this study was to characterise the virulence-associated gene profiles and to develop an OmpA molecular typing scheme for classifying 191 bovine and porcine isolates of P. multocida collected between 1989 and 2012 in Thailand using polymerase chain reactions (PCRs), nucleotide sequencing, and sequence and structural bioinformatics analyses.

Results

PCR screening successfully characterised the profiles of 25 virulence-associated genes in all isolates. The gene profiles separated these isolates into bovine and porcine clusters based on eight genes (hgbB, hsf1, tadD, nanH, pfhA, plpE, pmHAS, and tbpA). Phylogenetic analyses of the nucleotide and protein sequences corresponding to the ompA gene, which encodes a major outer membrane surface protein, showed two major bovine and porcine clusters. Structural prediction and analysis of the dN/dS ratio revealed four hypervariable extracellular loops of the OmpA transmembrane domains. These four loops were used to develop an OmpA typing scheme. This scheme classified 186 isolates into five major loop sequence types (LST8, LST12, LST15, LST18, and LST19), consistent with the phylogenetic results. The loop regions of the bovine isolates were predicted to be more antigenic than those of the porcine isolates. Thus, molecular evolution of the OmpA proteins could be used to classify P. multocida isolates into different capsular types, host types, and, possibly, pathogenicity levels.

Conclusions

Together with the virulence-associated gene profiles, the typing reported in this work provides a better understanding of P. multocida virulence. Effective monitoring and potential strain-specific subunit vaccines could be developed based on these loop oligopeptides.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-017-1157-6) contains supplementary material, which is available to authorized users.