Resequencing and characterization of the first Corynebacterium pseudotuberculosis genome isolated from camel

Background

Corynebacterium pseudotuberculosis is a zoonotic Gram-positive bacterial pathogen known to cause different diseases in many mammals, including lymph node abscesses in camels. Strains from biovars equi and ovis of C. pseudotuberculosis can infect camels. Comparative genomics could help to identify features related to host adaptation, and currently strain Cp162 from biovar equi is the only one from camel with a sequenced genome.

Methods

In this work, we compared the quality of three genome assemblies of strain Cp162 that used data from the DNA sequencing platforms SOLiD v3 Plus, IonTorrent PGM, and Illumina HiSeq 2500 with an optical map and investigate the unique features of this strain. For this purpose, we applied comparative genomic analysis on the different Cp162 genome assembly versions and included other 129 genomes from the same species.

Results

Since the first version of the genome, there was an increase of 88 Kbp and 121 protein-coding sequences, a decrease of pseudogenes from 139 to 53, and two inversions and one rearrangement corrected. We identified 30 virulence genes, none associated to the camel host, and the genes rpob2 and rbpA predicted to confer resistance to rifampin. In comparison to 129 genomes of the same species, strain Cp162 has four genes exclusively present, two of them code transposases and two truncated proteins, and the three exclusively absent genes lysG, NUDIX domain protein, and Hypothetical protein. All 130 genomes had the rifampin resistance genes rpob2 and rbpA. Our results found no unique gene that could be associated with tropism to camel host, and further studies should include more genomes and genome-wide association studies testing for genes and SNPs.

Mass Spectrometry Applications to Study Human Microbiome

Microbiotas are an adaptable component of ecosystems, including human ecology. Microorganisms influence the chemistry of their specialized niche, such as the human gut, as well as the chemistry of distant surroundings, such as other areas of the body. Metabolomics based on mass spectrometry (MS) is one of the primary methods for detecting and identifying small compounds generated by the human microbiota, as well as understanding the functional significance of these microbial metabolites. This book chapter gives basic knowledge on the kinds of untargeted mass spectrometry as well as the data types that may be generated in the context of microbiome study. While data analysis remains a barrier, the emphasis is on data analysis methodologies and integrative analysis, particularly the integration of microbiome sequencing data. Mass spectrometry (MS)-based techniques have resurrected culture methods for studying the human gut microbiota, filling in the gaps left by high-throughput sequencing methods in terms of culturing minor populations.

Environmental Biofilms from an Urban Community in Salvador, Brazil, Shelter Previously Uncharacterized Saprophytic Leptospira

Biofilms are complex microecosystems with valuable ecological roles that can shelter a variety of microorganisms. Spirochetes from the genus Leptospira have been observed to form biofilms in vitro, in rural environments, and in the kidneys of reservoir rats. The genus Leptospira is composed of pathogenic and non-pathogenic species, and the description of new species is ongoing due to the advent of whole genome sequencing. Leptospires have increasingly been isolated from water and soil samples. To investigate the presence of Leptospira in environmental biofilms, we collected three distinct samples of biofilms formed in an urban setting with poor sanitation: Pau da Lima, in Salvador, Bahia, Brazil. All biofilm samples were negative for the presence of pathogenic leptospires via conventional PCR, but cultures containing saprophytic Leptospira were identified. Whole genomes were generated and analyzed for twenty isolates obtained from these biofilms. For species identification, we used digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analysis. The obtained isolates were classified into seven presumptive species from the saprophytic S1 clade. ANI and dDDH analysis suggest that three of those seven species were new. Classical phenotypic tests confirmed the novel isolated bacteria as saprophytic Leptospira. The isolates presented typical morphology and ultrastructure according to scanning electron microscopy and formed biofilms under in vitro conditions. Our data indicate that a diversity of saprophytic Leptospira species survive in the Brazilian poorly sanitized urban environment, in a biofilm lifestyle. We believe our results contribute to a better understanding of Leptospira biology and ecology, considering biofilms as natural environmental reservoirs for leptospires.

Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil

Background

The COVID-19 pandemic had a major impact on indigenous populations. Understanding the viral dynamics within this population is essential to create targeted protection measures.

Methods

A total of 204 SARS-CoV-2 positive samples collected between May 2020 and November 2021 from an indigenous area in Mato Grosso do Sul (MS), Midwestern Brazil, were screened. Samples were submitted to whole genome sequencing using the Nanopore sequencing platform. Clinical, demographic, and phylogenetic data were analyzed.

Results

We found the co-circulation of six main SARS-CoV-2 lineages in the indigenous population, with the Zeta lineage being the most prevalent (27.66%), followed by B.1.1 (an ancestral strain) (20.21%), Gamma (14.36%) and Delta (13.83%). Other lineages represent 45.74% of the total. Our phylogenetic reconstruction indicates that multiple introduction events of different SARS-CoV-2 lineages occurred in the indigenous villages in MS. The estimated indigenous population mortality rate was 1.47%. Regarding the ethnicity of our cohort, 64.82% belong to the Guarani ethnicity, while 33.16% belong to the Terena ethnicity, with a slightly higher prevalence of males (53.43%) among females. Other ethnicities represent 2.01%. We also observed that almost all patients (89.55%) presented signs and symptoms related to COVID-19, being the most prevalent cough, fever, sore throat, and headache.

Discussion

Our results revealed that multiple independent SARS-CoV-2 introduction events had occurred through time, probably due to indigenous mobility, since the villages studied here are close to urban areas in MS. The mortality rate was slightly below of the estimation for the state in the period studied, which we believe could be related to the small number of samples evaluated, the underreporting of cases and deaths among this population, and the inconsistency of secondary data available for this study.

Conclusion

In this study, we showed the circulation of multiple SARS-CoV-2 variants in this population, which should be isolated and protected as they belong to the most fragile group due to their socioeconomic and cultural disparities. We reinforce the need for constant genomic surveillance to monitor and prevent the spread of new emerging viruses and to better understand the viral dynamics in these populations, making it possible to direct specific actions.

Draft Genome Sequence of Seven Pigmented Strains of Xanthomonas citri pv. anacardii, the Causal Agent of Cashew Angular Spot

Cashew (Anacardium occidentale) angular leaf spot is caused by pigmented and non-pigmented strains of Xanthomonas citri pv. anacardii, which have been isolated from infected plants in Brazil. The disease symptoms can be observed in leaves, stems, and fruits. Given that infection in young fruits results in fruits unsuitable for commercialization, angular leaf spot represents a serious threat to the cashew crop in Brazil. Here, we report the genomic sequencing of seven pigmented strains of X. citri pv. anacardii, obtained from the leaves of cashew trees from São Paulo state, Brazil, in 2009. The construction of the libraries was carried out according to the manufacturer, and whole-genome sequencing was performed using the Illumina HiSeq 2500 platform. Genome size, number of coding sequences, largest contig length, and N50 ranged from 4,996,984 to 5,003,485 bp, 4,621 to 4,643 bp, 212,513 to 362,232 bp, and 113,582 to 141,003 bp, respectively. GC content and RNA numbers were 64.68% and 54, respectively, for all strains. ANIm and dDDH analyses showed values above 99.5 and 92.1% among these strains and the non-pigmented pathotype strain of X. citri pv. anacardii (IBSBF2579PT). A maximum likelihood tree built with 2,708 core genes grouped all X. citri pv. anacardii strains in the same clade, with a 100% bootstrap. These resources will contribute in a relevant way to help understand the ecological, taxonomic, evolutionary, pathogenicity, and virulence aspects of X. citri pv. anacardii, which will be useful for the study and development of techniques for managing cashew angular leaf spot.

Genomic Characterization of Aeromonas veronii Provides Insights into Taxonomic Assignment and Reveals Widespread Virulence and Resistance Genes throughout the World

Aeromonas veronii is a Gram-negative bacterial species that causes disease in fish and is nowadays increasingly recurrent in enteric infections of humans. This study was performed to characterize newly sequenced isolates by comparing them with complete genomes deposited at the NCBI (National Center for Biotechnology Information). Nine isolates from fish, environments, and humans from the São Francisco Valley (Petrolina, Pernambuco, Brazil) were sequenced and compared with complete genomes available in public databases to gain insight into taxonomic assignment and to better understand virulence and resistance profiles of this species within the One Health context. One local genome and four NCBI genomes were misidentified as A. veronii. A total of 239 virulence genes were identified in the local genomes, with most encoding adhesion, motility, and secretion systems. In total, 60 genes involved with resistance to 22 classes of antibiotics were identified in the genomes, including mcr-7 and cphA. The results suggest that the use of methods such as ANI is essential to avoid misclassification of the genomes. The virulence content of A. veronii from local isolates is similar to those complete genomes deposited at the NCBI. Genes encoding colistin resistance are widespread in the species, requiring greater attention for surveillance systems.

Genomic insights into the c-di-GMP signaling and biofilm development in the saprophytic spirochete Leptospira biflexa

C-di-GMP is a bacterial second messenger with central role in biofilm formation. Spirochete bacteria from Leptospira genus present a wide diversity, with species of medical importance and environmental species, named as saprophytic. Leptospira form biofilms in the rat's reservoir kidneys and in the environment. Here, we performed genomic analyses to identify enzymatic and effector c-di-GMP proteins in the saprophytic biofilm-forming species Leptospira biflexa serovar Patoc. We identified 40 proteins through local alignments. Amongst them, 16 proteins are potentially functional diguanylate cyclases, phosphodiesterases, or hybrid proteins. We also identified nine effectors, including PilZ proteins. Enrichment analyses suggested that c-di-GMP interacts with cAMP signaling system, CsrA system, and flagella assembly regulation during biofilm development of L. biflexa. Finally, we identified eight proteins in the pathogen Leptospira interrogans serovar Copenhageni that share high similarity with L. biflexa c-di-GMP-related proteins. This work revealed proteins related to c-di-GMP turnover and cellular response in Leptospira and their potential roles during biofilm development.

Characterization and Association of Rips Repertoire to Host Range of Novel Ralstonia solanacearum Strains by In Silico Approaches

Ralstonia solanacearum species complex (RSSC) cause several phytobacteriosis in many economically important crops around the globe, especially in the tropics. In Brazil, phylotypes I and II cause bacterial wilt (BW) and are indistinguishable by classical microbiological and phytopathological methods, while Moko disease is caused only by phylotype II strains. Type III effectors of RSSC (Rips) are key molecular actors regarding pathogenesis and are associated with specificity to some hosts. In this study, we sequenced and characterized 14 newly RSSC isolates from Brazil's Northern and Northeastern regions, including BW and Moko ecotypes. Virulence and resistance sequences were annotated, and the Rips repertoire was predicted. Confirming previous studies, RSSC pangenome is open as α≅0.77. Genomic information regarding these isolates matches those for R. solanacearum in NCBI. All of them fit in phylotype II with a similarity above 96%, with five isolates in phylotype IIB and nine in phylotype IIA. Almost all R. solanacearum genomes in NCBI are actually from other species in RSSC. Rips repertoire of Moko IIB was more homogeneous, except for isolate B4, which presented ten non-shared Rips. Rips repertoire of phylotype IIA was more diverse in both Moko and BW, with 43 common shared Rips among all 14 isolates. New BW isolates shared more Rips with Moko IIA and Moko IIB than with other public BW genome isolates from Brazil. Rips not shared with other isolates might contribute to individual virulence, but commonly shared Rips are good avirulence candidates. The high number of Rips shared by new Moko and BW isolates suggests they are actually Moko isolates infecting solanaceous hosts. Finally, infection assays and Rips expression on different hosts are needed to better elucidate the association between Rips repertoire and host specificities.

Co-culturing fructophilic lactic acid bacteria and yeast enhanced sugar metabolism and aroma formation during cocoa beans fermentation

Glucose and fructose are the main fermentable sugars in cocoa pulp. During fermentation, glucose is consumed within 48-72 h and fructose only after 120 h, mainly associated with the preferential use of glucose by microorganisms. In the first stage of this study, the complete genome sequence of a lactic acid bacterium with high fructose consumption capacity (Lactobacillus plantarum LPBF35) was reported. The notable genomic features of L. plantarum LPBF35 were the presence of alcohol/acetaldehyde dehydrogenase gene and improved PTS system, confirming its classification as a "facultatively" fructophilic bacterium. Subsequently, this bacterium was introduced into cocoa fermentation process in single and mixed cultures with Pediococcus acidilactici LPBF66 or Pichia fermentans YC5.2. Community composition by Illumina-based amplicon sequencing and viable counts indicated suppression of wild microflora in all treatments. At the beginning of the fermentation processes, cocoa pulp consisted of approximately 73.09 mg/g glucose and 73.64 mg/g fructose. The L. plantarum LPBF35 + P. fermentans YC5.2 process showed the lowest levels of residual sugars after 72 h of fermentation (7.89 and 4.23 mg/g, for fructose and glucose, respectively), followed by L. plantarum LPBF35 + Ped. acidilactici LPBF66 (8.85 and 6.42 mg/g, for fructose and glucose, respectively), single L. plantarum LPBF35 treatment (4.15 and 10.15 mg/g, for fructose and glucose, respectively), and spontaneous process (22.25 and 14.60 mg/g, for fructose and glucose, respectively). The positive interaction between L. plantarum LPBF35 and P. fermentans YC5.2 resulted in an improved formation of primary (ethanol, lactic acid, and acetic acid) and secondary (2-methyl-1-butanol, isoamyl acetate, and ethyl acetate) metabolites during fermentation. The primary metabolites accumulated significantly in cocoa beans fermented by P. fermentans YC5.2 + L. plantarum LPBF35, causing important reactions of color development and key flavor molecules formation. The results of this study suggest that fructophilic lactic acid bacteria and yeast is a microbial consortium that could improve sugar metabolism and aroma formation during cocoa beans fermentation.

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.

Pan-genomic approach shows insight of genetic divergence and pathogenic-adaptation of Pasteurella multocida

Pasteurella multocida is a gram-negative, non-motile bacterial pathogen, which is associated with chronic and acute infections as snuffles, pneumonia, atrophic rhinitis, fowl cholera and hemorrhagic septicemia. These diseases affect a wide range of domestic animals, leading to significant morbidity and mortality and causing significant economic losses worldwide. Due to the interest in deciphering the genetic diversity and process adaptive between P. multocida strains, this work aimed was to perform a pan-genome analysis to evidence horizontal gene transfer and positive selection among 23 P. multocida strains isolated from distinct diseases and hosts. The results revealed an open pan-genome containing 3585 genes and an accessory genome presenting 1200 genes. The phylogenomic analysis based on the presence/absence of genes and islands exhibit high levels of plasticity, which reflects a high intraspecific diversity and a possible adaptive mechanism responsible for the specific disease manifestation between the established groups (pneumonia, fowl cholera, hemorrhagic septicemia and snuffles). Additionally, we identified differences in accessory genes among groups, which are involved in sugar metabolism and transport systems, virulence-related genes and a high concentration of hypothetical proteins. However, there was no specific indispensable functional mechanism to decisively correlate the presence of genes and their adaptation to a specific host/disease. Also, positive selection was found only for two genes from sub-group hemorrhagic septicemia, serotype B. This comprehensive comparative genome analysis will provide new insights of horizontal gene transfers that play an essential role in the diversification and adaptation mechanism into P. multocida species to a specific disease.

Complete Genome Sequence of Xanthomonas citri pv. anacardii Strain IBSBF2579 from Brazil

The bacterium Xanthomonas citri pv. anacardii is the agent of angular leaf spot of the cashew tree (Anacardium occidentale L.). The complete genome sequencing of the strain IBSBF2579 was done on an Illumina HiSeq 2500 platform. The de novo assembly of the X. citri pv. anacardii strain IBSBF2579 genome yielded 133 contigs, with a size of 5,329,247 bp and a G+C content of 64.03%. The prediction was performed by GeneMarkS and the automatic annotation by Rapid Annotations using Subsystems Technology (RAST), with 4,406 identified genes.

Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002

Background

Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements.

Results

In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions.

Conclusion

In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2673-7) contains supplementary material, which is available to authorized users.

The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains

Corynebacterium pseudotuberculosis is a facultative intracellular pathogen and the causative agent of several infectious and contagious chronic diseases, including caseous lymphadenitis, ulcerative lymphangitis, mastitis, and edematous skin disease, in a broad spectrum of hosts. In addition, Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic, and singleton analyses revealed close relationships among pathogenic corynebacteria, the clonal-like behavior of C. pseudotuberculosis and slow increases in the sizes of pan-genomes. According to extrapolations based on the pan-genomes, core genomes and singletons, the C. pseudotuberculosis biovar ovis shows a more clonal-like behavior than the C. pseudotuberculosis biovar equi. Most of the variable genes of the biovar ovis strains were acquired in a block through horizontal gene transfer and are highly conserved, whereas the biovar equi strains contain great variability, both intra- and inter-biovar, in the 16 detected pathogenicity islands (PAIs). With respect to the gene content of the PAIs, the most interesting finding is the high similarity of the pilus genes in the biovar ovis strains compared with the great variability of these genes in the biovar equi strains. Concluding, the polymerization of complete pilus structures in biovar ovis could be responsible for a remarkable ability of these strains to spread throughout host tissues and penetrate cells to live intracellularly, in contrast with the biovar equi, which rarely attacks visceral organs. Intracellularly, the biovar ovis strains are expected to have less contact with other organisms than the biovar equi strains, thereby explaining the significant clonal-like behavior of the biovar ovis strains.

Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation sequencing technology

The Actinobacteria, Corynebacterium pseudotuberculosis strain P54B96, a nonmotile, non-sporulating and a mesophile bacterium, was isolated from liver, lung and mediastinal lymph node lesions in an antelope from South Africa. This strain is interesting in the sense that it has been found together with non-tuberculous mycobacteria (NTMs) which could nevertheless play a role in the lesion formation. In this work, we describe a set of features of C. pseudotuberculosis P54B96, together with the details of the complete genome sequence and annotation. The genome comprises of 2.34 Mbp long, single circular genome with 2,084 protein-coding genes, 12 rRNA, 49 tRNA and 62 pseudogenes and a G+C content of 52.19%. The analysis of the genome sequence provides means to better understanding the molecular and genetic basis of virulence of this bacterium, enabling a detailed investigation of its pathogenesis.

Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production

Corynebacterium pseudotuberculosis is the causative agent of several veterinary diseases in a broad range of economically important hosts, which can vary from caseous lymphadenitis in sheep and goats (biovar ovis) to ulcerative lymphangitis in cattle and horses (biovar equi). Existing vaccines against C. pseudotuberculosis are mainly intended for small ruminants and, even in these hosts, they still present remarkable limitations. In this study, we present the complete genome sequence of C. pseudotuberculosis biovar equi strain 258, isolated from a horse with ulcerative lymphangitis. The genome has a total size of 2,314,404 bp and contains 2088 predicted protein-coding regions. Using in silico analysis, eleven pathogenicity islands were detected in the genome sequence of C. pseudotuberculosis 258. The application of a reverse vaccinology strategy identified 49 putative antigenic proteins, which can be used as candidate vaccine targets in future works.

The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome

Background

Pan-genomic studies aim, for instance, at defining the core, dispensable and unique genes within a species. A pan-genomics study for vaccine design tries to assess the best candidates for a vaccine against a specific pathogen. In this context, rather than studying genes predicted to be exported in a single genome, with pan-genomics it is possible to study genes present in different strains within the same species, such as virulence factors. The target organism of this pan-genomic work here presented is Corynebacterium pseudotuberculosis, the etiologic agent of caseous lymphadenitis (CLA) in goat and sheep, which causes significant economic losses in those herds around the world. Currently, only a few antigens against CLA are known as being the basis of commercial and still ineffective vaccines. In this regard, the here presented work analyses, in silico, five C. pseudotuberculosis genomes and gathers data to predict common exported proteins in all five genomes. These candidates were also compared to two recent C. pseudotuberculosis in vitro exoproteome results.

Results

The complete genome of five C. pseudotuberculosis strains (1002, C231, I19, FRC41 and PAT10) were submitted to pan-genomics analysis, yielding 306, 59 and 12 gene sets, respectively, representing the core, dispensable and unique in silico predicted exported pan-genomes. These sets bear 150 genes classified as secreted (SEC) and 227 as potentially surface exposed (PSE). Our findings suggest that the main C. pseudotuberculosis in vitro exoproteome could be greater, appended by a fraction of the 35 proteins formerly predicted as making part of the variant in vitro exoproteome. These genomes were manually curated for correct methionine initiation and redeposited with a total of 1885 homogenized genes.

Conclusions

The in silico prediction of exported proteins has allowed to define a list of putative vaccine candidate genes present in all five complete C. pseudotuberculosis genomes. Moreover, it has also been possible to define the in silico predicted dispensable and unique C. pseudotuberculosis exported proteins. These results provide in silico evidence to further guide experiments in the areas of vaccines, diagnosis and drugs. The work here presented is the first whole C. pseudotuberculosis in silico predicted pan-exoproteome completed till today.