Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700

Bacterial symbionts in oral niche use type VI secretion nanomachinery for fitness increase against pathobionts

Microbial ecosystems experience spatial and nutrient restrictions leading to the coevolution of cooperation and competition among cohabiting species. To increase their fitness for survival, bacteria exploit machinery to antagonizing rival species upon close contact. As such, the bacterial type VI secretion system (T6SS) nanomachinery, typically expressed by pathobionts, can transport proteins directly into eukaryotic or prokaryotic cells, consequently killing cohabiting competitors. Here, we demonstrate for the first time that oral symbiont Aggregatibacter aphrophilus possesses a T6SS and can eliminate its close relative oral pathobiont Aggregatibacter actinomycetemcomitans using its T6SS. These findings bring nearer the anti-bacterial prospects of symbionts against cohabiting pathobionts while introducing the presence of an active T6SS in the oral cavity.

Invasive Aggregatibacter infection: shedding light on a rare pathogen in a retrospective cohort analysis

Introduction. Aggregatibacter are Gram-negative, facultatively anaerobic rods or coccobacilli that are infrequently encountered as pathogens causing infection.Hypothesis/Gap Statement. The range of invasive infection that Aggregatibacter cause is poorly described. The pathogenicity of species such as Aggregatibacter segnis is debated.Aim. To identify invasive infection due to Aggregatibacter species in a large healthcare organization and to characterize clinical syndromes, co-morbidities and risk factors.Methodology. All microbiological samples positive for Aggregatibacter species were identified by conventional culture or 16S rRNA PCR between October 2017 and March 2021. Electronic records for all patients with positive samples were reviewed and the infection syndrome classified for patients with invasive disease.Results. Twenty-seven patients with invasive infection were identified, with a statistically significant difference in species-specific patterns of invasive infection (P=0.02) and a statistically significant association with residence in the 30 % most deprived households in the UK by postcode (P<0.01). The three most common co-morbidities were periodontitis or recent dental work (29.6%), cardiovascular disease (25.9%) and diabetes (18.5 %).Conclusion. We describe a novel association of Aggregatibacter segnis with skin and soft tissue infection. The propensity of the Aggregatibacter species to cause invasive infection at different body sites and be associated with deprivation is reported. Aggregatibacter actinomycetemcomitans bacteraemia was associated with infective endocarditis, and Aggregatibacter aphrophilus was implicated in severe appendicitis and noted to cause brain abscess. Areas warranting future research include exploring the risk-factors required for invasive infection and those that may determine the species-specific differences in patterns of invasive disease.

Aggregatibacter actinomycetemcomitans and Aggregatibacter aphrophilus in a Kenyan Maasai Adolescent Population and Inhibition of Leukotoxic Activity by Herbal Plants Used as Part of Oral Hygiene Procedures

BACKGROUND

A virulent genotype (JP2) of the periodonto-pathogen, Aggregatibacter actinomycetemcomitans (Aa), is widespread in North and West Africa, while its presence in East Africa has not been thoroughly investigated. This JP2 genotype is associated with periodontitis in adolescents and has a high leukotoxicity. The aim of the study was to examine the prevalence of Aa and its JP2 genotype, the prevalence of the oral, commensal Aggregatibacter aphrophilus in a Maasai adolescent population, and the effect of herbal plants for inhibition of leukotoxicity.

METHODS

A total of 284 adolescents from Maasai Mara, Kenya, underwent an oral examination and microbial sampling. The presence of Aa and A. aphrophilus was analyzed by quantitative PCR and cultivation (the 58 samples collected at the last day of field study). The collected Aa strains were characterized and leukotoxin promoter typed. Additionally, herbal plants commonly used for oral hygiene were assessed for the inhibition of leukotoxicity.

RESULTS AND CONCLUSIONS

The prevalence of Aa in stimulated whole saliva was high (71.8%), with the JP2 genotype detected in one individual, and A. aphrophilus in 99% of the sampled individuals. The commonly used herbal plant, Warburgia ugandensis, inactivated Aa leukotoxicity. The Aa virulence might be reduced through use of W. ugandensis and the high levels of A. aphrophilus.

An unusual case of aggregatibacter aphrophilus liver abscess

Liver abscess of oropharyngeal origin in an immunocompetent patient is a rare condition. Furthermore, microbiologic diagnosis of liver abscess can be challenging due to the tremendous diversity of the microorganisms implicated and culture difficulties under laboratory conditions. We report a case of a previously healthy 23-year-old male, who presented multiple liver abscesses, attributed to aggregatibacter aphrophilus, an obligatory oral gram-negative microorganism, that normally is a component of the commensal oral microbiota and non-virulent. The etiopathogenic microorganism was identified after needle aspiration of a liver abscess cavity. Treatment with broad-spectrum antimicrobials and percutaneous catheter drainage under computed tomography guidance of both abscesses, resulted in full recovery. A. aphrophilus represents a rare entity of liver abscess in healthy individuals and suggests that a pathogen of oropharyngeal origin should be suspected when an overt source of infection cannot be documented.

Role of OmpA1 and OmpA2 in Aggregatibacter actinomycetemcomitans and Aggregatibacter aphrophilus serum resistance

Aggregatibacter actinomycetemcomitans and Aggregatibacter aphrophilus belong to the HACEK group of fastidious Gram-negative organisms, a recognized cause of infective endocarditis. A. actinomycetemcomitans is also implicated in aggressive forms of periodontitis. We demonstrated that A. aphrophilus strains, as A. actinomycetemcomitans are ubiquitously serum resistant. Both species encode two Outer membrane protein A paralogues, here denoted OmpA1 and OmpA2. As their respective pangenomes contain several OmpA1 and OmpA2 alleles, they represent potential genotypic markers. A naturally competent strain of A. actinomycetemcomitans and A. aphrophilus, respectively were used to elucidate if OmpA1 and OmpA2 contribute to serum resistance. Whereas OmpA1 was critical for survival of A. actinomycetemcomitans D7SS in 50% normal human serum (NHS), serum resistant ompA1 mutants were fortuitously obtained, expressing enhanced levels of OmpA2. Similarly, OmpA1 rather than OmpA2 was a major contributor to serum resistance of A. aphrophilus HK83. Far-Western blot revealed that OmpA1^AA, OmpA2^AA, and OmpA1^AP can bind to C4-binding protein, an inhibitor of classical and mannose-binding lectin (MBL) complement activation. Indeed, ompA1 mutants were susceptible to these pathways, but also to alternative complement activation. This may at least partly reflect a compromised outer membrane integrity but is also consistent with alternative mechanisms involved in OmpA-mediated serum resistance.

Gene expression of bacterial collagenolytic proteases in root caries

Objective: It is unknown whether bacteria play a role in the collagen matrix degradation that occurs during caries progression. Our aim was to characterize the expression level of genes involved in bacterial collagenolytic proteases in root biofilms with and without caries. Method: we collected samples from active cavitated root caries lesions (RC, n = 30) and from sound root surfaces (SRS, n = 10). Total microbial RNA was isolated and cDNA sequenced on the Illumina Hi-Seq2500. Reads were mapped to 162 oral bacterial reference genomes. Genes encoding putative bacterial collagenolytic proteases were identified. Normalization and differential expression analysis was performed on all metatranscriptomes (FDR<10-3).

Result: Genes encoding collagenases were identified in 113 bacterial species the majority were peptidase U32. In RC, Streptococcus mutans and Veillonella parvula expressed the most collagenases. Organisms that overexpressed collagenolytic protease genes in RC (Log2FoldChange>8) but none in SRS were Pseudoramibacter alactolyticus [HMPREF0721_RS02020; HMPREF0721_RS04640], Scardovia inopinata [SCIP_RS02440] and Olsenella uli DSM7084 [OLSU_RS02990].

Conclusion: Our findings suggest that the U32 proteases may be related to carious dentine. The contribution of a small number of species to dentine degradation should be further investigated. These proteases may have potential in future biotechnological and medical applications, serving as targets for the development of therapeutic agents.

Phylogenomic and molecular demarcation of the core members of the polyphyletic pasteurellaceae genera actinobacillus, haemophilus, and pasteurella

The genera Actinobacillus, Haemophilus, and Pasteurella exhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses to clarify the phylogenetic and taxonomic boundary of these genera. We have identified large clusters of Actinobacillus, Haemophilus, and Pasteurella species which represent the “sensu stricto” members of these genera. We have identified 3, 7, and 6 conserved signature indels (CSIs), which are specifically shared by sensu stricto members of Actinobacillus, Haemophilus, and Pasteurella, respectively. We have also identified two different sets of CSIs that are unique characteristics of the pathogen containing genera Aggregatibacter and Mannheimia, respectively. It is now possible to demarcate the genera Actinobacillus sensu stricto, Haemophilus sensu stricto, and Pasteurella sensu stricto on the basis of discrete molecular signatures. The other members of the genera Actinobacillus, Haemophilus, and Pasteurella that do not fall within the “sensu stricto” clades and do not contain these molecular signatures should be reclassified as other genera. The CSIs identified here also provide useful diagnostic targets for the identification of current and novel members of the indicated genera.

The cell envelope proteome of Aggregatibacter actinomycetemcomitans

The cell envelope of gram-negative bacteria serves a critical role in maintenance of cellular homeostasis, resistance to external stress, and host-pathogen interactions. Envelope protein composition is influenced by the physiological and environmental demands placed on the bacterium. In this study, we report a comprehensive compilation of cell envelope proteins from the periodontal and systemic pathogen Aggregatibacter actinomycetemcomitans VT1169, an afimbriated serotype b strain. The urea-extracted membrane proteins were identified by mass spectrometry-based shotgun proteomics. The membrane proteome, isolated from actively growing bacteria under normal laboratory conditions, included 648 proteins representing 27% of the predicted open reading frames in the genome. Bioinformatic analyses were used to annotate and predict the cellular location and function of the proteins. Surface adhesins, porins, lipoproteins, numerous influx and efflux pumps, multiple sugar, amino acid and iron transporters, and components of the type I, II and V secretion systems were identified. Periplasmic space and cytoplasmic proteins with chaperone function were also identified. A total of 107 proteins with unknown function were associated with the cell envelope. Orthologs of a subset of these uncharacterized proteins are present in other bacterial genomes, whereas others are found exclusively in A. actinomycetemcomitans. This knowledge will contribute to elucidating the role of cell envelope proteins in bacterial growth and survival in the oral cavity.

Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans

The aim of this review is to provide a comprehensive update on the current classification and identification of Haemophilus and Aggregatibacter species with exclusive or predominant host specificity for humans. Haemophilus influenzae and some of the other Haemophilus species are commonly encountered in the clinical microbiology laboratory and demonstrate a wide range of pathogenicity, from life-threatening invasive disease to respiratory infections to a nonpathogenic, commensal lifestyle. New species of Haemophilus have been described (Haemophilus pittmaniae and Haemophilus sputorum), and the new genus Aggregatibacter was created to accommodate some former Haemophilus and Actinobacillus species (Aggregatibacter aphrophilus, Aggregatibacter segnis, and Aggregatibacter actinomycetemcomitans). Aggregatibacter species are now a dominant etiology of infective endocarditis caused by fastidious organisms (HACEK endocarditis), and A. aphrophilus has emerged as an important cause of brain abscesses. Correct identification of Haemophilus and Aggregatibacter species based on phenotypic characterization can be challenging. It has become clear that 15 to 20% of presumptive H. influenzae isolates from the respiratory tracts of healthy individuals do not belong to this species but represent nonhemolytic variants of Haemophilus haemolyticus. Due to the limited pathogenicity of H. haemolyticus, the proportion of misidentified strains may be lower in clinical samples, but even among invasive strains, a misidentification rate of 0.5 to 2% can be found. Several methods have been investigated for differentiation of H. influenzae from its less pathogenic relatives, but a simple method for reliable discrimination is not available. With the implementation of identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry, the more rarely encountered species of Haemophilus and Aggregatibacter will increasingly be identified in clinical microbiology practice. However, identification of some strains will still be problematic, necessitating DNA sequencing of multiple housekeeping gene fragments or full-length 16S rRNA genes.

Pasteurella multocida: from zoonosis to cellular microbiology

In a world where most emerging and reemerging infectious diseases are zoonotic in nature and our contacts with both domestic and wild animals abound, there is growing awareness of the potential for human acquisition of animal diseases. Like other Pasteurellaceae, Pasteurella species are highly prevalent among animal populations, where they are often found as part of the normal microbiota of the oral, nasopharyngeal, and upper respiratory tracts. Many Pasteurella species are opportunistic pathogens that can cause endemic disease and are associated increasingly with epizootic outbreaks. Zoonotic transmission to humans usually occurs through animal bites or contact with nasal secretions, with P. multocida being the most prevalent isolate observed in human infections. Here we review recent comparative genomics and molecular pathogenesis studies that have advanced our understanding of the multiple virulence mechanisms employed by Pasteurella species to establish acute and chronic infections. We also summarize efforts being explored to enhance our ability to rapidly and accurately identify and distinguish among clinical isolates and to control pasteurellosis by improved development of new vaccines and treatment regimens.

Genomic Stability of Aggregatibacter actinomycetemcomitans during Persistent Oral Infection in Human

The genome of periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits substantial variations in gene content among unrelated strains primarily due to the presence or absence of genomic islands. This study examined the genomic stability of A. actinomycetemcomitans during its persistent infection in the same host. Four pairs of A. actinomycetemcomitans strains, each pair isolated from an individual over time (0–10 years), were examined for their gains/losses of genes by whole genome sequencing, comparative genomic hybridization by microarray and PCR analysis. Possible effects due to genomic changes were further assessed by comparative transcriptome analysis using microarrays. The results showed that each pair of strains was clonally identical based on phylogenetic analysis of 150 core genes. A novel 24.1-Kb plasmid found in strain S23A was apparently lost in the sibling strain I23C. A 353-bp inversion affecting two essential genes of the serotype-specific gene cluster was found in the serotype antigen-nonexpressing strain I23C, while the same gene cluster was intact in the serotype-expressing sibling strain S23A. A 2,293-bp deletion affecting a gene encoding oxaloacetate decarboxylase and its neighbor region was found in strain SCC2302 but not in the sibling strain AAS4a. However, no evidence of gains or losses of genomic islands was found in the paired strains. Transcriptome profiles showed little or no difference in the paired strains. In conclusion, the genome of A. actinomycetemcomitans appears to be relatively stable during short-term infection. Several types of genomic changes were observed in the paired strains of A. actinomycetemcomitans recovered from the same subjects, including a mutation in serotype-specific gene cluster that may allow the bacteria to evade host immune response.

Differential gene expression in Ulva prolifera under low light and low temperature conditions

The past several years witnessed the increasing global interest in the marine green macroalga Ulva prolifera as it is a key causative species of the massive green tides successively occurring in the Yellow Sea. Accurate localization of the 'seed' source is one of the principal scientific concerns to be solved before it is possible to manage these algal blooms. It has been suggested that somatic cells of Ulva prolifera which settled in cold benthic sediments might serve as one of the major propagule banks. To identify the molecular mechanisms underlying this hypothesis, PCR-based suppression subtractive hybridization was employed to analyze the differential gene expression of Ulva prolifera under low light and low temperature conditions (matching the cold benthic sediments conditions, 6 °C, 30 μmol photons m(-2) s(-1)). 137 ESTs representing 88 unigenes (80 singletons and 8 contigs) were detected as being over-expressed, whereas 109 unigenes (96 singletons and 13 contigs) in 130 ESTs were found to be down-regulated in this study. BLASTX analysis revealed that 65 % of the over-expressed and 59 % of the down-regulated genes did not belong to any documented functionally annotated or hypothetical proteins in the public database. However, analysis of the functional defined sequences displayed (1) an obvious sign of senescence, (2) enhancements of the photosynthesis system and the pentose phosphate pathway, (3) slow-down of activities in a wide range of processes including the DNA replication, the transcription, the translation, the glycolysis, the citrate cycle and the pyruvate metabolism in Ulva prolifera cells under low light and low temperature conditions. This work disclosed some basic information of the molecular mechanisms of Ulva prolifera cells under low light and low temperature conditions and provides useful clues for future studies on the "seed" source of the massive green tides.

A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation

BACKGROUND

Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes.

FINDINGS

Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ~90% of 100 assemblies with < 10 scaffolds and ~95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%.

CONCLUSIONS

A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks.

6-10× pyrosequencing is a practical approach for whole prokaryote genome studies

Next generation 454 pyrosequencing technology for whole bacterial genome sequencing involves a deep sequencing strategy with at least 15-20× in depth proposed by official protocols but usually done with over 20× in practices. In this study, we carried out a comprehensive evaluation of quality of the de novo assemblies based on realistic pyrosequencing simulated data from 1480 prokaryote genomes and 7 runs of machine-generated data. Our results demonstrated that for most of the prokaryote genomes, 6-10× sequencing in qualified runs with 400 bp reads could produce high quality draft assembly (>98% genome coverage, <100 contigs with N50 size >100 kb, single base accuracy >99.99, indel error rate <0.01%, false gene loss/duplication rate <0.5%). Our study proves the power of low depth pyrosequencing strategy, which provides a cost-effective way for sequencing whole prokaryote genomes in a short time and enables further studies in microbial population diversity and comparative genomics.

Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis

Background

Aggregatibacter actinomycetemcomitans is genetically heterogeneous and comprises distinct clonal lineages that may have different virulence potentials. However, limited information of the strain-to-strain genomic variations is available.

Methodology/Principal Findings

The genome sequences of 11 A. actinomycetemcomitans strains (serotypes a-f) were generated de novo, annotated and combined with three previously sequenced genomes (serotypes a-c) for comparative genomic analysis. Two major groups were identified; serotypes a, d, e, and f, and serotypes b and c. A serotype e strain was found to be distinct from both groups. The size of the pangenome was 3,301 genes, which included 2,034 core genes and 1,267 flexible genes. The number of core genes is estimated to stabilize at 2,060, while the size of the pangenome is estimated to increase by 16 genes with every additional strain sequenced in the future. Within each strain 16.7–29.4% of the genome belonged to the flexible gene pool. Between any two strains 0.4–19.5% of the genomes were different. The genomic differences were occasionally greater for strains of the same serotypes than strains of different serotypes. Furthermore, 171 genomic islands were identified. Cumulatively, 777 strain-specific genes were found on these islands and represented 61% of the flexible gene pool.

Conclusions/Significance

Substantial genomic differences were detected among A. actinomycetemcomitans strains. Genomic islands account for more than half of the flexible genes. The phenotype and virulence of A. actinomycetemcomitans may not be defined by any single strain. Moreover, the genomic variation within each clonal lineage of A. actinomycetemcomitans (as defined by serotype grouping) may be greater than between clonal lineages. The large genomic data set in this study will be useful to further examine the molecular basis of variable virulence among A. actinomycetemcomitans strains.

Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.