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

Anti-quorum sensing and anti-biofilm activities of Pasteurella multocida strains

A total of 52 Pasteurella multocida strains of capsular serogroups (A, B and D) were screened for anti-quorum sensing activity against Chromobacterium violaceum. Of which, 12 strains of serogroups A were found to possess anti-quorum sensing activity. Inhibition activity was highest for strain NIVEDIPm9 and lowest for strain NIVEDIPm30 based on zone of pigment inhibition. Further, cell free extract of NIVEDIPm9 strain showed highest anti-biofilm activity in reference E. coli strain and concentration dependent degradation activity of C6-AHL molecule. In whole genome sequence annotation of NIVEDIPm9 strain predicted the presence of four metallo-β-lactamases (MBL) fold metallo-hydrolase proteins. In docking studies, MBL1 and MBL3 proteins showed high binding affinity with autoinduce signalling molecules AHL compound of OH-C10, binding energy value were -6.3 and -6.2 kcal/mol. Interaction study of VAF and quorum sensing molecules showed that OmpA and HgbA proteins were stimulated by all the ten molecules (C4-AHLs, C6-AHLs, C10-AHLs, C14-AHLs, 3-oxo-C10-AHLs, 3OH-C10-HSL, C8-HSL, C10-HSL, C12-HSL, C14-HSL), while toxA gene was stimulated by OH-C10-AHL molecule, sodC gene was stimulated by none. In conclusion, we described the anti-quorum sensing activities of diverse P. multocida strains causing Pasteurellosis in livestock.

Sero-Prevalence of Hemorrhagic Septicaemia in Cattle and Buffalo Population of Indian States Karnataka and Gujarat

Hemorrhagic septicemia (HS) is a highly contagious and fatal disease of cattle and buffaloes caused by P. multocida. Both conventional and molecular methods are applied in parallel for rapid diagnosis of HS outbreaks and the periodical surveillance strategy to identify risk areas for HS is ignored. The current cross-sectional study aimed to estimate sero-prevalence and associated risk factors for HS in cattle and buffaloes in non-vaccinated regions of two Indian states. HS surveillance was carried out through the multi-stage random sampling technique at different strata. The study employed a questionnaire incorporating host factors (species, breed, sex, age, and lactation) and demographic parameters (state, district, block/cluster and village/epiunits, and household). First, two Indian states known for high milk production were selected followed by two districts within each state, subsequently four clusters within each district, finally 5-10 epiunits within clusters and 5-8 households within clusters were randomly selected to collect cattle and buffalo samples. The chi-square/p values and maps were prepared to represent disease prevalence and to correlate disease risk factors at different strata. A total of 692 cattle and buffalo serum samples were sourced from two states of the country (Karnataka-285 and Gujarat-407). In the first strata, antibodies to P. multocida were high in Gujarat (14.49%, CI: 11.22-18.30) compared to Karnataka (3.85%, CI: 1.94-6.80) with significant (p < 0.0001) association between the states. In the second strata, one of the four districts investigated revealed the highest sero-prevalence (18.61%, CI: 13.81-24.24) with statistical significance (p = 0.01) between the districts. Among clusters, one out of eight clusters showed the highest sero-prevalence (23.02%, CI: 16.59-30.54) with statistical significance (p = 0.03) between the clusters in the third strata. At epiunit level (fourth strata), 9 out of 27 epiunits (33.33%) visited in Karnataka and 24 out of 29 epiunits sampled in Gujarat were sero-positive (82.75%) in iELISA. At the household level, out of 306 HH visited, 40 HH had at least one positive animal (13.07%) and the p value between HH in the two states was highly significant (p = 0.0002). Chi-square analysis did not find any association of HS sero-prevalence to species, age, and lactation. However, significantly higher (p < 0.05) sero-prevalence was recorded in indigenous cattle breeds (16.56%) compared to crossbreeds (6.59%). Various immunoprophylactics and antibiotic therapies are effective against HS, but inappropriate disease reporting and failure to implement adequate vaccination control measures are the gaps identified. The present study highlights the current scenario of HS sero-prevalence in two of the high milk-producing states of India, which will be useful for stakeholders for undertaking the implementation of surveillance and control strategies for the regions.

Role of biofilms in antimicrobial resistance of the bacterial bovine respiratory disease complex

An increase in chronic, non-responsive bovine respiratory disease (BRD) infections in North American feedlot cattle is observed each fall, a time when cattle are administered multiple antimicrobial treatments for BRD. A number of factors are responsible for BRD antimicrobial treatment failure, with formation of biofilms possibly being one. It is widely accepted that biofilms play a role in chronic infections in humans and it has been hypothesized that they are the default lifestyle of most bacteria. However, research on bacterial biofilms associated with livestock is scarce and significant knowledge gaps exist in our understanding of their role in AMR of the bacterial BRD complex. The four main bacterial species of the BRD complex, Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis are able to form biofilms in vitro and there is evidence that at least H. somni retains this ability in vivo. However, there is a need to elucidate whether their biofilm-forming ability contributes to pathogenicity and antimicrobial treatment failure of BRD. Overall, a better understanding of the possible role of BRD bacterial biofilms in clinical disease and AMR could assist in the prevention and management of respiratory infections in feedlot cattle. We review and discuss the current knowledge of BRD bacteria biofilm biology, study methodologies, and their possible relationship to AMR.

Emerging Approaches for Mitigating Biofilm-Formation-Associated Infections in Farm, Wild, and Companion Animals

The importance of addressing the problem of biofilms in farm, wild, and companion animals lies in their pervasive impact on animal health and welfare. Biofilms, as resilient communities of microorganisms, pose a persistent challenge in causing infections and complicating treatment strategies. Recognizing and understanding the importance of mitigating biofilm formation is critical to ensuring the welfare of animals in a variety of settings, from farms to the wild and companion animals. Effectively addressing this issue not only improves the overall health of individual animals, but also contributes to the broader goals of sustainable agriculture, wildlife conservation, and responsible pet ownership. This review examines the current understanding of biofilm formation in animal diseases and elucidates the complex processes involved. Recognizing the limitations of traditional antibiotic treatments, mechanisms of resistance associated with biofilms are explored. The focus is on alternative therapeutic strategies to control biofilm, with illuminating case studies providing valuable context and practical insights. In conclusion, the review highlights the importance of exploring emerging approaches to mitigate biofilm formation in animals. It consolidates existing knowledge, highlights gaps in understanding, and encourages further research to address this critical facet of animal health. The comprehensive perspective provided by this review serves as a foundation for future investigations and interventions to improve the management of biofilm-associated infections in diverse animal populations.

Spatial and temporal analysis of haemorrhagic septicaemia outbreaks in India over three decades (1987-2016)

Haemorrhagic septicaemia (HS) is an economically important disease affecting cattle and buffaloes and the livelihoods of small-holder farmers that depend upon them. The disease is caused by Gram-negative bacterium, Pasteurella multocida, and is considered to be endemic in many states of India with more than 25,000 outbreaks in the past three decades. Currently, there is no national policy for control of HS in India. In this study, we analysed thirty year (1987-2016) monthly data on HS outbreaks using different statistical and mathematical methods to identify spatial variability and temporal patterns (seasonality, periodicity). There was zonal variation in the trend and seasonality of HS outbreaks. Overall, South zone reported maximum proportion of the outbreaks (70.2%), followed by East zone (7.2%), Central zone (6.4%), North zone (5.6%), West zone (5.5%) and North-East zone (4.9%). Annual state level analysis indicated that the reporting of HS outbreaks started at different years independently and there was no apparent transmission between the states. The results of the current study are useful for the policy makers to design national control programme on HS in India and implement state specific strategies. Further, our study and strategies could aid in implementation of similar approaches in HS endemic tropical countries around the world.

Comparative genome analysis of Pasteurella multocida strains of porcine origin

Pasteurella multocida causes acute/chronic pasteurellosis in porcine, resulting in considerable economic losses globally. The draft genomes of two Indian strains NIVEDIPm17 (serogroup D) and NIVEDIPm36 (serogroup A) were sequenced. A total of 2182-2284 coding sequences (CDSs) were predicted along with 5-6 rRNA and 45-46 tRNA genes in the genomes. Multilocus sequence analysis and LPS genotyping showed the presence of ST50: genotype 07 and ST74: genotype 06 in NIVEDIPm17 and NIVEDIPm36, respectively. Pangenome analysis of 61 strains showed the presence of 1653 core genes, 167 soft core genes, 750 shell genes, and 1820 cloud genes. Analysis of virulence-associated genes in 61 genomes indicated the presence of nanB, exbB, exbD, ptfA, ompA, ompH, fur, plpB, fimA, sodA, sodC, tonB, and omp87 in all strains. The 61 genomes contained genes encoding tetracycline (54%), streptomycin (48%), sulphonamide (28%), tigecycline (25%), chloramphenicol (21%), amikacin (7%), cephalosporin (5%), and trimethoprim (5%) resistance. Multilocus sequence type revealed that ST50 was the most common (34%), followed by ST74 (26%), ST13 (24%), ST287 (5%), ST09 (5%), ST122 (3%), and ST07 (2%). Single-nucleotide polymorphism and core genome-based phylogenetic analysis clustered the strains into three major clusters. In conclusion, we described the various virulence factors, mobile genetic elements, and antimicrobial resistance genes in the pangenome of P. multocida of porcine origin, besides the rare presence of LPS genotype 7 in serogroup D.

Pan-genomic comparison of a potential solvent-tolerant alkaline protease-producing Exiguobacterium sp. TBG-PICH-001 isolated from a marine habitat

The identification and applicability of bacteria are inconclusive until comprehended with genomic repositories. Our isolate, Exiguobacterium sp. TBG-PICH-001 exhibited excellent halo- and organic solvent tolerance with simultaneous production of alkaline protease/s (0.512 IU/mL). The crude protease (1 IU) showed a 43.57% degradation of whey protein. The bulk proteins in the whey were hydrolyzed to smaller peptides which were evident in the SDS-PAGE profile. With such characteristics, the isolate became interesting for its genomic studies. The TBG-PICH-001 genome was found to be 3.14 Mb in size with 17 contigs and 47.33% GC content. The genome showed 3176 coding genes, and 2699 genes were characterized for their functionality. The Next-Generation-Sequencing of the genome identified only the isolate's genus; hence we attempted to delineate its species position. The genomes of the isolate and other representative Exiguobacterium spp. were compared based on orthologous genes (Orthovenn2 server). A pan-genomic analysis revealed the match of TBG-PICH-001 with 15 uncharacterized Exiguobacterium genomes at the species level. All these collectively matched with Exiguobacterium indicum, and the results were reconfirmed through phylogenetic studies. Further, the Exiguobacterium indicum genomes were engaged for homology studies rendering 11 classes of protease genes. Two putative proteases (Zinc metalloprotease and Serine protease) obtained from homology were checked for PCR amplification using genomic DNA of TBG-PICH-001 and other Exiguobacterium genomes. The results showed amplification only in the Exiguobacterium indicum genome. These protease genes, after sequencing, were matched with the TBG-PICH-001 genome. Their presence in its whole genome experimentally validated the study.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03796-5.

Genomic characterization and comparative genomic analysis of HS-associated Pasteurella multocida serotype B:2 strains from Pakistan

BACKGROUND

Haemorrhagic septicaemia (HS) is a highly fatal and predominant disease in livestock, particularly cattle and buffalo in the tropical regions of the world. Pasteurella multocida (P. multocida), serotypes B:2 and E:2, are reported to be the main causes of HS wherein serotype B:2 is more common in Asian countries including Pakistan and costs heavy financial losses every year. As yet, very little molecular and genomic information related to the HS-associated serotypes of P. multocida isolated from Pakistan is available. Therefore, this study aimed to explore the characteristics of novel bovine isolates of P. multocida serotype B:2 at the genomic level and perform comparative genomic analysis of various P. multocida strains from Pakistan to better understand the genetic basis of pathogenesis and virulence.

RESULTS

To understand the genomic variability and pathogenomics, we characterized three HS-associated P. multocida serotype B:2 strains isolated from the Faisalabad (PM1), Peshawar (PM2) and Okara (PM3) districts of Punjab, Pakistan. Together with the other nine publicly available Pakistani-origin P. multocida strains and a reference strain Pm70, a comparative genomic analysis was performed. The sequenced strains were characterized as serotype B and belong to ST-122. The strains contain no plasmids; however, each strain contains at least two complete prophages. The pan-genome analysis revealed a higher number of core genes indicating a close resemblance to the studied genomes and very few genes (1%) of the core genome serve as a part of virulence, disease, and defense mechanisms. We further identified that studied P. multocida B:2 strains harbor common antibiotic resistance genes, specifically PBP3 and EF-Tu. Remarkably, the distribution of virulence factors revealed that OmpH and plpE were not present in any P. multocida B:2 strains while the presence of these antigens was reported uniformly in all serotypes of P. multocida.

CONCLUSION

This study's findings indicate the absence of OmpH and PlpE in the analyzed P. multocida B:2 strains, which are known surface antigens and provide protective immunity against P. multocida infection. The availability of additional genomic data on P. multocida B:2 strains from Pakistan will facilitate the development of localized therapeutic agents and rapid diagnostic tools specifically targeting HS-associated P. multocida B:2 strains.

First report of whole genome sequence of septicemic Pasteurella multocida serovar B:2 'Soron' strain isolated from swine

Pig pasteurellosis, caused by Pasteurella multocida, is an acute infection that also has economic implications for pig farmers. We report the complete genome sequence of a P. multocida, serovar B:2 'Soron' strain isolated from the blood of a pig that had died of pasteurellosis in India. The isolate was not found to be haemorrhagic septicaemia (HS) specific B:2 by the PCR assay. The genome of 'Soron' strain is a single circular chromosome of 2,272,124 base pairs in length and contains 2014 predicted coding regions, 4 ribosomal RNA operons, and 52 tRNAs. It has 1812 protein-coding genes that were also found in reference sequence PmP52Vac. Phylogenetic analysis revealed that Pm_P52VAc and P. multocida 'Soron' serovar B:2 were clustered in different clades. Pasteurella multocida 'Soron' serovar B:2 was found to cluster with the same ancestor of Pm70, which is of avian origin. The genome was found to contain regions that encode proteins which may confer resistance to various antibiotics including cephalosporin, which is used to treat pasteurellosis. The isolate was also found to harbour a phage region. This strain represents a novel multi-locus sequence type (MLST) that has not been previously identified, as all of the alleles used for MLST were found, but did not match any of the alleles in the database with 100% nucleotide identity. The most closely related ST was ST221. This is the first whole-genome sequence from P. multocida serovar B:2 of pig origin.

Global commercialization and research of veterinary vaccines against Pasteurella multocida: 2015-2022 technological surveillance

BACKGROUND AND AIM

Pasteurella multocida can infect a multitude of wild and domesticated animals, bacterial vaccines have become a crucial tool in combating antimicrobial resistance (AMR) in animal production. The study aimed to evaluate the current status and scientific trends related to veterinary vaccines against Pasteurella multocida during the 2015-2022 period.

MATERIAL AND METHODS

The characteristics of globally marketed vaccines were investigated based on the official websites of 22 pharmaceutical companies. VOSviewer® 1.6.18 was used to visualize networks of coauthorship and cooccurrence of keywords from papers published in English and available in Scopus.

RESULTS

Current commercial vaccines are mostly inactivated (81.7%), adjuvanted in aluminum hydroxide (57.8%), and designed to immunize cattle (33.0%). Investigational vaccines prioritize the inclusion of attenuated strains, peptide fragments, recombinant proteins, DNA as antigens, aluminum compounds as adjuvants and poultry as the target species.

CONCLUSION

Despite advances in genetic engineering and biotechnology, there will be no changes in the commercial dominance of inactivated and aluminum hydroxide-adjuvanted vaccines in the short term (3-5 years). The future prospects for bacterial vaccines in animal production are promising, with advancements in vaccine formulation and genetic engineering, they have the potential to improve the sustainability of the industry. It is necessary to continue with the studies to improve the efficacy of the vaccines and their availability.

Whole-genome sequence analysis of Clostridium chauvoei isolated from clinical case of black quarter (BQ) from India

Black quarter (BQ) is an infectious disease affecting cattle and small ruminants worldwide caused by Gram-positive anaerobic bacterium Clostridium chauvoei. In this study, a draft genome sequence of C. chauvoei NIVEDIBQ1 strain isolated from clinical case of black quarter was analyzed. Sequence analysis indicated that genome had 2653 predicted coding DNA sequences, harbored numerous genes, mobile genetic elements for pathogenesis, and virulence factors. Computational analysis revealed that strain contained 30 virulence-associated genes. An intact genomic region highly similar to the Clostridium phage was present in the genome. Presence of CRISPR systems and the transposon components likely contribute to the genome plasticity. Strain encode diverse spectrum of degradative carbohydrate-active enzymes (CAZymes). Comparative SNP analysis revealed that the genomes of the C. chauvoei strains analyzed were highly conserved. Phylogenetic analysis of strains and available genome (n = 21) based on whole-genome multi-locus sequence typing (wgMLST) and core orthologous genes showed the clustering of strains into two different clusters suggesting geographical links.