CHARACTERISTICS OF BRUCELLAPHAGE

Investigating the mechanism of rough phenotype in a naturally attenuated Brucella strain: insights from whole genome sequencing

Objective

Brucellosis, a significant zoonotic disease, not only impacts animal health but also profoundly influences the host immune responses through gut microbiome. Our research focuses on whole genome sequencing and comparative genomic analysis of these Brucella strains to understand the mechanisms of their virulence changes that may deepen our comprehension of the host immune dysregulation.

Methods

The Brucella melitensis strain CMCC55210 and its naturally attenuated variant CMCC55210a were used as models. Biochemical identification tests and in vivo experiments in mice verified the characteristics of the strain. To understand the mechanism of attenuation, we then performed de novo sequencing of these two strains.

Results

We discovered notable genomic differences between the two strains, with a key single nucleotide polymorphism (SNP) mutation in the manB gene potentially altering lipopolysaccharide (LPS) structure and influencing host immunity to the pathogen. This mutation might contribute to the attenuated strain's altered impact on the host's macrophage immune response, overing insights into the mechanisms of immune dysregulation linked to intracellular survival. Furthermore, we explore that manipulating the Type I restriction-modification system in Brucella can significantly impact its genome stability with the DNA damage response, consequently affecting the host's immune system.

Conclusion

This study not only contributes to understanding the complex relationship between pathogens, and the immune system but also opens avenues for innovative therapeutic interventions in inflammatory diseases driven by microbial and immune dysregulation.

Protective efficacy of attenuated Salmonella Typhimurium strain expressing BLS, Omp19, PrpA, or SOD of Brucella abortus in goats

Background

Attenuated Salmonella strain can be used as a vector to transport immunogens to the host antigen-binding sites.

Objectives

The study aimed to determine the protective efficacy of attenuated Salmonella strain expressing highly conserved Brucella immunogens in goats.

Methods

Goats were vaccinated with Salmonella vector expressing individually lipoprotein outer-membrane protein 19 (Omp19), Brucella lumazine synthase (BLS), proline racemase subunit A (PrpA), Cu/Zn superoxide dismutase (SOD) at 5 × 10⁹ CFU/mL and challenge of all groups was done at 6 weeks after vaccination.

Results

Among these vaccines inoculated at 5 × 10⁹ CFU/mL in 1 mL, Omp19 or SOD showed significantly higher serum immunoglobulin G titers at (2, 4, and 6) weeks post-vaccination, compared to the vector control. Interferon-γ production in response to individual antigens was significantly higher in SOD, Omp19, PrpA, and BLS individual groups, compared to that in the vector control (all p < 0.05). Brucella colonization rate at 8 weeks post-challenge showed that most vaccine-treated groups exhibited significantly increased protection by demonstrating reduced numbers of Brucella in tissues collected from vaccinated groups. Real-time polymerase chain reaction revealed that Brucella antigen expression levels were reduced in the spleen, kidney, and parotid lymph node of vaccinated goats, compared to the non-vaccinated goats. Besides, treatment with vaccine expressing individual antigens ameliorated brucellosis-related histopathological lesions.

Conclusions

These results delineated that BLS, Omp19, PrpA, and SOD proteins achieved a definite level of protection, indicating that Salmonella Typhimurium successfully delivered Brucella antigens, and that individual vaccines could differentially elicit an antigen-specific immune response.

Isolation and genome analysis of a lytic Pasteurella multocida Bacteriophage PMP-GAD-IND

Currently used alum precipitated and oil adjuvant vaccines against HS caused by Pasteurella multocida B:2, have side effects and short-lived immunity, leading to regular catastrophic outbreaks in bovines in Asian subcontinent. The need for the development of an improved vaccine with longer immunity and the ability to differentiate between vaccinated and infected is essential. Pasteurella phage isolated in present study belongs to family Siphoviridae. PMP-GAD-IND phage exhibited lytic activity against vaccine strain (P52) as well as several field strains of P. multocida (B:2), and fowl cholera agent (P. multocida A:1).The phage has a double stranded DNA (dsDNA) with a genome of 46 335 bp. The complete genome sequence of the Pasteurella multocida phage has been deposited in Gen Bank with accession no: KY203335. PMP-GAD-IND being a lytic phage with broad activity range has a potential to be used in therapy against multidrug resistant P. multocida infections.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present work is a part of research for the development of an improved phage lysate marker vaccine and a companion DIVA assay against haemorhagic septicaemia. This study describes the isolation and genome analysis of PMP-GAD-IND a lytic Pasteurella multocida bacteriophage.

Highly Sensitive Bacteriophage-Based Detection of Brucella abortus in Mixed Culture and Spiked Blood

For decades, bacteriophages (phages) have been used for Brucella species identification in the diagnosis and epidemiology of brucellosis. Traditional Brucella phage typing is a multi-day procedure including the isolation of a pure culture, a step that can take up to three weeks. In this study, we focused on the use of brucellaphages for sensitive detection of the pathogen in clinical and other complex samples, and developed an indirect method of Brucella detection using real-time quantitative PCR monitoring of brucellaphage DNA amplification via replication on live Brucella cells. This assay allowed the detection of single bacteria (down to 1 colony-forming unit per milliliter) within 72 h without DNA extraction and purification steps. The technique was equally efficient with Brucella abortus pure culture and with mixed cultures of B. abortus and α-proteobacterial near neighbors that can be misidentified as Brucella spp., Ochrobactrum anthropi and Afipia felis. The addition of a simple short sample preparation step enabled the indirect phage-based detection of B. abortus in spiked blood, with the same high sensitivity. This indirect phage-based detection assay enables the rapid and sensitive detection of live B. abortus in mixed cultures and in blood samples, and can potentially be applied for detection in other clinical samples and other complex sample types.

Whole genome sequence comparison of ten diagnostic brucellaphages propagated on two Brucella abortus hosts

Background

Recently the genome sequences of two brucellaphages, isolated in Georgia (Tb) and Mexico (Pr) were reported revealing pronounced sequence homogeneity and the presence of two major indels discriminating the two phages. Subsequent genome sequencing of six diagnostic brucellaphages: Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C phages identified three major genetic groups. However, the propensity for fine-scale genetic variability of diverse brucellaphages grown on multiple hosts within a single Brucella species remains unknown.

Methods

We sequenced the complete genomes of ten brucellaphages following initial propagation on B. abortus strain 141 and after subsequent propagation on B. abortus strain S19. All brucellaphages were isolated and propagated at the Eliava Institute including the original Tb phage. Genomic libraries were quantified using the Qbit and sheared on the Covaris M220. QC for fragmentation was performed on the BioAnalyzer 2100. DNA libraries were prepared using an Illumina Paired-End protocol and sequenced on the Illumina MiSeq. Sequence analysis was performed using Geneious and MEGA software.

Results

Comparative whole genome sequence analysis revealed genetic homogeneity consistent with previously published data as well as multiple nucleotide variations. Genomic changes as a result of passages were observed in similar genes and predominantly occurred at identical sites in separate phages. Multiple instances of within-sample genetic heterogeneity were observed often at shared genomics positions across phages. Positive selection was detected in the tail collar protein gene. We also identified a Staphylothermus marinus F1-like CRISPR spacer and sequences orthologous to both prophage antirepressors of Brucella spp. and intergenic sequences encoded by Ochrobactrum anthropi.

Conclusion

We surveyed whole genome level diversity in phage lytic for B. abortus as they are propagated on alternate vaccine strains within the species. Our data extend previous results indicating select variable hotspots and broad genomic homogeneity as well as multiple common polymorphisms and within-sample variation. These data also provide additional genomes for future reference in comparative studies involving the molecular evolution and host specificity of brucellaphages.

Comparative whole genome analysis of six diagnostic brucellaphages

Whole genome sequencing of six diagnostic brucellaphages, Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C, was followed with genomic comparisons including recently described genomes of the Tb phage from Mexico (TbM) and Pr phage to elucidate genomic diversity and candidate host range determinants. Comparative whole genome analysis revealed high sequence homogeneity among these brucellaphage genomes and resolved three genetic groups consistent with defined host range phenotypes. Group I was composed of Tb and Fz phages that are predominantly lytic for Brucella abortus and Brucella neotomae; Group II included Bk, R/C, and Pr phages that are lytic mainly for B. abortus, Brucella melitensis and Brucella suis; Group III was composed of Wb and S708 phages that are lytic for B. suis, B. abortus and B. neotomae. We found that the putative phage collar protein is a variable locus with features that may be contributing to the host specificities exhibited by different brucellaphage groups. The presence of several candidate host range determinants is illustrated herein for future dissection of the differential host specificity observed among these phages.

Comparative genomic analysis of two brucellaphages of distant origins

Here, we present the first complete genome sequence of brucellaphage Tbilisi (Tb) and compared it with that of Pr, a broad host-range brucellaphage recently isolated in Mexico. The genomes consist of 41,148 bp (Tb) and 38,253 bp (Pr), they differ mainly in the region encoding structural proteins, in which the genome of Tb shows two major insertions. Both genomes share 99.87% nucleotide identity, a high percentage of identity among phages isolated at so globally distant locations and temporally different occasions. Sequence analysis revealed 57 conserved ORFs, three transcriptional terminators and four putative transcriptional promoters. The co-occurrence of an ORF encoding a putative DnaA-like protein and a putative oriC-like origin of replication was found in both brucellaphages genomes, a feature not described in any other phage genome. These elements suggest that DNA replication in brucellaphages differs from other phages, and might resemble that of bacterial chromosomes.

Molecular characterization of Tb, a new approach for an ancient Brucellaphage

Tb (Tbilisi), the reference Brucellaphage strain, was classified as a member of the Podoviridae family with icosahedral capsids (57 ± 2 nm diameter) and short tails (32 ± 3 nm long). Brucellaphage DNA was double stranded and unmethylated; its molecular size was 34.5 kilobase pairs. Some sequences were found through RAPD analysis, TA cloning technology, and structural proteins were observed by using SDS-PAGE. Thus, the results have laid the foundation for the wider use of Brucellaphage’s basic mechanisms and practical applications.

Phenotypic alterations in the colonial morphology of Brucella abortus due to a bacteriophage carrier state

Jones, Lois M. (University of Wisconsin, Madison), C. R. McDuff, and J. B. Wilson. Phenotypic alterations in the colonial morphology of Brucella abortus due to a bacteriophage carrier state. J. Bacteriol. 83:860-866. 1962.-In the course of examining a number of Brucella cultures with a brucellaphage, it was observed that B. abortus cultures of intermediate colonial morphology, which had a blue-gray colonial appearance, were not lysed within 24 hr; in 48 hr they had developed sticky white growth in the area of the phage drop. When this growth was streaked on agar plates, both white and blue-gray colonies developed. White colonies which were sticky always carried phage and upon restreaking always gave rise to both white and blue-gray colonies. White colonies which were not sticky were rough and phage resistant. Blue-gray colonies produced only blue-gray colonies, did not carry phage, and were similar to the parent in their response to phage. When sticky white colonies were incubated for 6 hr or more in phage antiserum, all phage was eliminated and only blue-gray colonies developed. It was believed that the sticky white colonies were carrier clones in which lysis was delayed until after cell division, thus resulting in the establishment of a colony containing some phage-free progeny. With the accumulation of phage, the colony became sticky. This effect may be caused by the action of bacteriophage enzymes on the cell walls. Brucellaphage had an extremely slow rate of adsorption on a culture of intermediate colonial morphology. A phage mutant which was more strongly lytic for cultures of intermediate colonial morphology was selected from the original phage. The adsorption rate of this phage was more rapid and the latent period shorter. A serological difference between phages could not be demonstrated.

Determination of stability of Brucella abortus RB51 by use of genomic fingerprint, oxidative metabolism, and colonial morphology and differentiation of strain RB51 from B. abortus isolates from bison and elk

Brucella abortus RB51 and isolates from cattle, bison, and elk were characterized by pulsed-field gel electrophoresis and standard techniques for biotyping Brucella species, which included biochemical, morphological, and antigenic techniques, phage susceptibility, and antibiotic resistance. The objectives were to ascertain the stability of RB51 and to differentiate RB51 from other brucellae. Genomic restriction endonuclease patterns produced by pulsed-field gel electrophoresis demonstrated a unique fingerprint for RB51 relative to other brucellae. Comparisons of the oxidative metabolic profiles of RB51 after time in vivo (14 weeks) and in vitro (75 passages) showed no change in characteristic patterns of oxygen uptake on selected amino acid and carbohydrate substrates. Strain RB51 was biotyped as a typical rough B. abortus biovar 1 (not strain 19) after animal passage or a high number of passages in vitro and remained resistant to rifampin or penicillin and susceptible to tetracycline. No reactions with A or M antiserum or with a monoclonal antibody to the O antigen of Brucella lipopolysaccharides were detected; however, RB51 agglutinated with R antiserum. The results indicate that the genomic fingerprint and rough colonial morphology of RB51 are stable characteristics and can be used to differentiate this vaccine strain from Brucella isolates from cattle, bison, and elk.

Isolation and characterization of a bacteriophage for Vibrio fetus

Bacteriophages were isolated from 22 of 38 strains of Vibrio fetus by an enrichment process, utilizing the donor and host strains growing together in fluid thioglycollate medium. One phage, V-45, isolated by the conventional lawn-spot method, was characterized by stability in broth, growth kinetics, and morphology. It was sensitive to rapid thermal inactivation, chloroform, and pH values above 6.5. Calcium was required for phage replication and stability in broth. Magnesium provided the best protection against thermal inactivation at 50 C in the pH range of 6.5 to 7.5. The minimum latent period was 135 min, rise time was 75 min, and average burst size was 35 plaque-forming units per infected cell. Phage V-45 resembled Bradley's morphological group B, having a long tail without contractile sheath. Dimensions were: head, about 50 nm; tail, about 7 by 240 nm; and tail lumen, 2 to 3 nm.

Phage typing reactions on Brucella species

The nature of the phage typing reactions on Brucella species was determined by rates of adsorption and infection, one-step growth experiments, and susceptibility to lysis from without. The highest rates of adsorption and infection were obtained on smooth B. abortus cultures, and large clear plaques were produced. One or a few phage particles per B. neotomae cell killed about one-half of the cells, but some went through an infective cycle and released mature phage that resulted in production of small clear plaques. With B. suis, more phage particles per cell were required to kill, replication did not occur, and plaques were not observed. Still greater numbers of phage particles were required to cause some inhibition of growth of B. melitensis lawns. Rough Brucella cultures and species, such as B. ovis and B. canis, were not affected by the highest concentrations of phage. B. abortus cultures of intermediate colonial morphology adsorbed phage, but only a few infected cells (after a delayed latent period) released mature phage. An infected culture or colony appeared normal until spontaneous phage mutants appeared which could penetrate the cell wall more effectively than the parent phage. The mutant phage multiplied more rapidly, and the colony changed to a sticky white form.

Spontaneous mutation and recombination among brucellaphages

Merz, George S. (University of Wisconsin, Madison), and Joe B. Wilson. Spontaneous mutation and recombination among brucellaphages. J. Bacteriol. 91:2356-2361. 1966.-Two plaque morphology variants, as seen on Brucella abortus 544A, termed c (for clear plaque) and lc (for late-clearing plaque) were isolated from stocks of wild-type brucellaphage and from colonies of B. abortus 544A which had undergone an alteration in colonial morphology associated with the establishment of the phage carrier state. Single-burst experiments showed that the phage variants arise by spontaneous mutation of the wild-type phage during its replication on B. abortus strain R19. Two-factor crosses of independently occurring c mutant phages showed the presence of wild-type recombinants among the progeny. Control experiments showed that there are no strong selective forces against either wild-type or c mutant phage inherent in the cross-procedure. Other control experiments ruled out the possibility that wild-type phage in the cross-progeny resulted from either back mutation of the c mutants or the presence of wild-type phage among the input c mutants.

PRODUCTION AND CHARACTERIZATION OF BRUCELLA SPHEROPLASTS

Hines, William D. (University of Chicago, Chicago, Ill.), Bob A. Freeman, and Gary R. Pearson . Production and characterization of Brucella spheroplasts. J. Bacteriol. 87: 438–445. 1964.—Spheroplasts of Brucella were induced by glycine, penicillin, and a combination of the two. These spheroplasts lacked cell-wall endotoxin but did react with antiserum prepared against cell wall and against whole cells. Phase-contrast photomicrographs and electron micrographs are presented, which show no morphological difference between the protoplasts produced by penicillin and by glycine. The glycine and glycine-penicillin spheroplasts were osmotically sensitive, would not reproduce, and only a small percentage reverted to the bacillary form. Penicillin spheroplasts would not reproduce and were not osmotically sensitive. Penicillin spheroplasts showed significant reversion when induced by low concentrations of penicillin, but the rate of reversion decreased with increasing antibiotic concentration. Penicillin and glycine spheroplasts adsorbed brucellaphage at a reduced rate compared with normal Brucella , but spheroplasts produced by the combined action of penicillin and glycine failed to demonstrate brucellaphage adsorption.