The pathogenicity of the Streptococcus genus

Vitamin D and Streptococci: The Interface of Nutrition, Host Immune Response, and Antimicrobial Activity in Response to Infection

Streptococcus species are common causes of human infection. These Gram-positive, encapsulated bacterial pathogens infect diverse anatomic spaces, leading to infections including skin and soft tissue infection, endocarditis, pneumonia, meningitis, sinusitis, otitis media, chorioamnionitis, sepsis, and even death. Risk for streptococcal infection is highest in low- and middle-income countries where micronutrient deficiency is common. Epidemiological data reveal that vitamin D deficiency is associated with enhanced risk of streptococcal infection and cognate disease outcomes. Additionally, vitamin D improves antibacterial defenses by stimulating innate immune processes such as phagocytosis and enhancing production of reactive oxygen species (oxidative burst) and antimicrobial peptides (including cathelicidin and lactoferrin), which are important for efficient killing of bacteria. This review presents the most recent published work that studies interactions between the micronutrient vitamin D, the host immune system, and pathogenic streptococci as well as comparisons with other relevant infection models.

Potential role of the gut microbiota in neuromyelitis optica spectrum disorder: Implication for intervention

The gut microbiota plays an important role in the occurrence and development of neuroimmunological diseases. Neuromyelitis optica spectrum disorder (NMOSD) is an autoimmune disease of the central nervous system that is characterized by the peripheral production of the disease-specific serum autoantibody aquaporin-4 (AQP4)-IgG. Recently, accumulating evidence has provided insights into the associations of gut microbiota dysbiosis and intestinal mucosal barrier destruction with NMOSD, but the underlying pathogenesis remains unclear. Thus, a microbiota intervention might be a potential therapeutic strategy for NMOSD by regulating the gut microbiota, repairing the intestinal mucosal barrier, and modulating intestinal immunity and peripheral immunity.

Impact of Intestinal Microbiota on Growth and Feed Efficiency in Pigs: A Review

This review summarises the evidence for a link between the porcine intestinal microbiota and growth and feed efficiency (FE), and suggests microbiota-targeted strategies to improve productivity. However, there are challenges in identifying reliable microbial predictors of host phenotype; environmental factors impact the microbe–host interplay, sequential differences along the intestine result in segment-specific FE- and growth-associated taxa/functionality, and it is often difficult to distinguish cause and effect. However, bacterial taxa involved in nutrient processing and energy harvest, and those with anti-inflammatory effects, are consistently linked with improved productivity. In particular, evidence is emerging for an association of Treponema and methanogens such as Methanobrevibacter in the small and large intestines and Lactobacillus in the large intestine with a leaner phenotype and/or improved FE. Bacterial carbohydrate and/or lipid metabolism pathways are also generally enriched in the large intestine of leaner pigs and/or those with better growth/FE. Possible microbial signalling routes linked to superior growth and FE include increased intestinal propionate production and reduced inflammatory response. In summary, the bacterial taxa and/or metabolic pathways identified here could be used as biomarkers for FE/growth in pigs, the taxa exploited as probiotics or the taxa/functionality manipulated via dietary/breeding strategies in order to improve productivity in pigs.

Novel Type of Water-Soluble Photosensitizer from Trichoderma reesei for Photodynamic Inactivation of Gram-Positive Bacteria

Antimicrobial photodynamic therapy (APDT) is a promising alternative to traditional antibiotics for the treatment of bacterial infections, which inactivates a broad spectrum of bacteria. However, many traditional photosensitizers (PSs) are hydrophobic with poor water solubility and easy aggregation. On the other hand, some light sources such as ultraviolet (UV) have poor penetration and high cytotoxicity. Both issues lead to undesired photodynamic therapy efficacy. To overcome these issues, we develop a novel water-soluble natural PS (sorbicillinoids) obtained by microbial fermentation using recombinant filamentous fungus Trichoderma reesei. Sorbicillinoids could effectively generate singlet oxygen (¹O₂) under UV light irradiation and ultimately display photoinactivation activity on Gram-positive bacteria including Staphylococcus aureus, Bacillus subtilis, and Micrococcus luteus but not Gram-negative ones such as Escherichia coli and Proteus vulgaris. Sorbicillinoids were found to enter S. aureus but not E. coli. S. aureus treated with sorbicillinoids and UV light displayed high levels of intracellular reactive oxygen species (ROS), notable DNA photocleavage, and compromised cell semipermeability without overt cell membrane disruption, none of which was found in the treated E. coli. All these contribute to the sorbicillinoid-based photoinactivation of Gram-positive bacteria. Moreover, the dark toxicity and phototoxicity on mammalian cells or hemolysis activity of sorbicillinoids is negligible, showing its excellent biocompatibility. This study expands the utilization of UV light for surface sterilization to disinfection in solution. Therefore, sorbicillinoids, a type of secondary metabolite from fungus, have a promising future as a new PS for APDT using a nontoxic dose of UV irradiation.

5-Dodecanolide inhibits biofilm formation and virulence of Streptococcus pyogenes by suppressing core regulons of virulence

This study determined the antibiofilm and antivirulence potential of 5-Dodecanolide (DD) against an exclusive human pathogen Streptococcus pyogenes. Biofilm quantification assay showed antibiofilm efficacy of DD with maximum biofilm inhibition of 85% at 225 μg/mL concentration. Efficacy of antibacterial property of DD (225 μg/mL) was confirmed by CFU analysis and Alamar blue assay. Microscopic analyses evidently confirmed micro-colony formation, biofilm thickness and surface coverage were reduced upon DD treatment. In addition, based on the results of in vitro assays, it was noted that DD impaired the synthesis of surface hydrophobicity, slime, hyaluronic acid, hemolysin and protease production. Interestingly, DD increased the autoaggregation of S. pyogenes hence, facilitated enhanced recognition of clumped bacterial cells for innate immune clearance. The results were further validated by the reduced survival of DD treated S. pyogenes in healthy human blood. Consequently, based on the qPCR analysis DD altered the expression of core regulons srv, ropB, mga and genes associated with biofilm formation and virulence such as speB, dltA, srtB, sagA and slo. Hence, the overall results of the present study for the first time revealed the antibiofilm and antivirulence property of DD against clinically important pathogen S. pyogenes and further clinical investigations are required to assess the therapeutic use of DD.

Changes in Gut Microbial Community of Pig Feces in Response to Different Dietary Animal Protein Media

Beef, pork, chicken and milk are considered representative protein sources in the human diet. Since the digestion of protein is important, the role of intestinal microflora is also important. Despite this, the pure effects of meat and milk intake on the microbiome are yet to be fully elucidated. To evaluate the effect of beef, pork, chicken and milk on intestinal microflora, we observed changes in the microbiome in response to different types of dietary animal proteins in vitro. Feces were collected from five 6-week-old pigs. The suspensions were pooled and inoculated into four different media containing beef, pork, chicken, or skim milk powder in distilled water. Changes in microbial communities were analyzed using 16S rRNA sequencing. The feces alone had the highest microbial alpha diversity. Among the treatment groups, beef showed the highest microbial diversity, followed by pork, chicken, and milk. The three dominant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all the groups. The most abundant genera in beef, pork, and chicken were Rummeliibacillus, Clostridium, and Phascolarctobacterium, whereas milk was enriched with Streptococcus, Lactobacillus, and Enterococcus. Aerobic bacteria decreased while anaerobic and facultative anaerobic bacteria increased in protein-rich nutrients. Functional gene groups were found to be over-represented in protein-rich nutrients. Our results provide baseline information for understanding the roles of dietary animal proteins in reshaping the gut microbiome. Furthermore, growth-promotion by specific species/genus may be used as a cultivation tool for uncultured gut microorganisms.

Streptococcus catagoni sp. nov., isolated from the respiratory tract of diseased Chacoan peccaries (Catagonus wagneri)

Novel catalase-negative, Gram-stain-positive, beta-haemolytic, coccus-shaped organisms were isolated from Chacoan peccaries that died from respiratory disease. The initial API 20 Strep profiles suggested Streptococcus agalactiae with acceptable identification scores, but the 16S rRNA gene similarity (1548 bp) to available sequences of streptococci was below 98 %. Next taxa of the genus Streptococcus, displaying highest similarities to the strains from this study, were S. bovimastitidis NZ1587^T (97.5 %), S. iniae ATCC 29178^T (97.5 %), S. hongkongensis HKU30^T (97.4 %), S. parauberis DSM 6631^T (97.1 %), S. penaeicida CAIM 1838^T (97.1 %), S. pseudoporcinus DSM 18513^T (97.0 %), S. didelphis DSM 15616^T (96.6 %), S. ictaluri 707-05^T (96.6 %), S. uberis JCM 5709^T (96.5 %) and S. porcinus NCTC 10999^T (96.4 %). All other Streptococcus species had sequence similarities of below 96.4 %. A sodA gene as well as whole genome-based core genome phylogeny of three representative strains and 145 available Streptococcus genomes confirmed the unique taxonomic position. Interstrain average nucleotide identity (ANI) and amino acid identity (AAI) values were high (ANI >96 %; AAI 100%), but for other streptococci clearly below the proposed species boundary of 95-96 % (ANI <75 %; AAI <83 %). Results were confirmed by genome-to-genome distance calculations. Pairwise digital DNA-DNA hybridization estimates were high (>90 %) between the novel strains, but well below the species boundary of 70 % for closely related Streptococcus type strains (23.5-19.7 %). Phenotypic properties as obtained from extended biochemical profiles and MALDI-TOF mass spectrometry supported the outstanding rank. Based on the presented molecular and physiological data of the six strains, we propose a novel taxon for which we suggest the name Streptococcus catagoni sp. nov. with the type strain 99-1/2017^T (=DSM 110457^T=CCUG 74072^T) and five reference strains.

Eucalyptol inhibits biofilm formation of Streptococcus pyogenes and its mediated virulence factors

Introduction. Streptococcus pyogenes is a diverse virulent synthesis pathogen responsible for invasive systemic infections. Establishment of antibiotic resistance in the pathogen has produced a need for new antibiofilm agents to control the biofilm formation and reduce biofilm-associated resistance development.Aim. The present study investigates the in vitro antibiofilm activity of eucalyptol against S. pyogenes.Methodology. The antibiofilm potential of eucalyptol was assessed using a microdilution method and their biofilm inhibition efficacy was visualized by microscopic analysis. The biochemical assays were performed to assess the influence of eucalyptol on virulence productions. Real-time PCR analysis was performed to evaluate the expression profile of the virulence genes.Results. Eucalyptol showed significant antibiofilm potential in a dose-dependent manner without affecting bacterial growth. Eucalyptol at 300 µg ml^-1 (biofilm inhibitory concentration) significantly inhibited the initial stage of biofilm formation in S. pyogenes. However, eucalyptol failed to diminish the mature biofilms of S. pyogenes at biofilm inhibitory concentration and it effectively reduced the biofilm formation on stainless steel, titanium, and silicone surfaces. The biochemical assay results revealed that eucalyptol greatly affects the cell-surface hydrophobicity, auto-aggregation, extracellular protease, haemolysis and hyaluronic acid synthesis. Further, the gene-expression analysis results showed significant downregulation of virulence gene expression upon eucalyptol treatment.Conclusion. The present study suggests that eucalyptol applies its antibiofilm assets by intruding the initial biofilm formation of S. pyogenes. Supplementary studies are needed to understand the mode of action involved in biofilm inhibition.

Fingerprint Biometric System Hygiene and the Risk of COVID-19 Transmission

Biometric systems use scanners to verify the identity of human beings by measuring the patterns of their behavioral or physiological characteristics. Some biometric systems are contactless and do not require direct touch to perform these measurements; others, such as fingerprint verification systems, require the user to make direct physical contact with the scanner for a specified duration for the biometric pattern of the user to be properly read and measured. This may increase the possibility of contamination with harmful microbial pathogens or of cross-contamination of food and water by subsequent users. Physical contact also increases the likelihood of inoculation of harmful microbial pathogens into the respiratory tract, thereby triggering infectious diseases. In this viewpoint, we establish the likelihood of infectious disease transmission through touch-based fingerprint biometric devices and discuss control measures to curb the spread of infectious diseases, including COVID-19.

Lactoferrin: A Critical Mediator of Both Host Immune Response and Antimicrobial Activity in Response to Streptococcal Infections

Streptococcal species are Gram-positive bacteria responsible for a variety of disease outcomes including pneumonia, meningitis, endocarditis, erysipelas, necrotizing fasciitis, periodontitis, skin and soft tissue infections, chorioamnionitis, premature rupture of membranes, preterm birth, and neonatal sepsis. In response to streptococcal infections, the host innate immune system deploys a repertoire of antimicrobial and immune modulating molecules. One important molecule that is produced in response to streptococcal infections is lactoferrin. Lactoferrin has antimicrobial properties including the ability to bind iron with high affinity and sequester this important nutrient from an invading pathogen. Additionally, lactoferrin has the capacity to alter the host inflammatory response and contribute to disease outcome. This Review presents the most recent published work that studies the interaction between the host innate immune protein lactoferrin and the invading pathogen, Streptococcus.

Antibiotic Resistance-Susceptibility Profiles of Enterococcus faecalis and Streptococcus spp. From the Human Vagina, and Genome Analysis of the Genetic Basis of Intrinsic and Acquired Resistances

The spread of antibiotic resistance is a major public health concern worldwide. Commensal bacteria from the human genitourinary tract can act as reservoirs of resistance genes playing a role in their transfer to pathogens. In this study, the minimum inhibitory concentration of 16 antibiotics to 15 isolates from the human vagina, identified as Enterococcus faecalis, Streptococcus anginosus, and Streptococcus salivarius, was determined. Eight isolates were considered resistant to tetracycline, five to clindamycin and quinupristin-dalfopristin, and four to rifampicin. To investigate the presence of antimicrobial resistance genes, PCR analysis was performed in all isolates, and five were subjected to whole-genome sequencing analysis. PCR reactions identified tet(M) in all tetracycline-resistant E. faecalis isolates, while both tet(M) and tet(L) were found in tetracycline-resistant S. anginosus isolates. The tet(M) gene in E. faecalis VA02-2 was carried within an entire copy of the transposon Tn916. In S. anginosus VA01-10AN and VA01-14AN, the tet(M) and tet(L) genes were found contiguous with one another and flanked by genes encoding DNA mobilization and plasmid replication proteins. Amplification and sequencing suggested the lsaA gene to be complete in all E. faecalis isolates resistant to clindamycin and quinupristin-dalfopristin, while the gene contain mutations rendering to a non-functional LsaA in susceptible isolates. These results were subsequently confirmed by genome analysis of clindamycin and quinupristin-dalfopristin resistant and susceptible E. faecalis strains. Although a clinical breakpoint to kanamycin for S. salivarius has yet to be established, S. salivarius VA08-2AN showed an MIC to this antibiotic of 128 μg mL-1. However, genes involved in kanamycin resistance were not identified. Under the assayed conditions, neither tet(L) nor tet(M) from either E. faecalis or S. anginosus was transferred by conjugation to recipient strains of E. faecalis, Lactococcus lactis, or Lactobacillus plantarum. Nonetheless, the tet(L) gene from S. anginosus VA01-10AN was amplified by PCR, and cloned and expressed in Escherichia coli, to which it provided a resistance of 48-64 μg mL-1 to tetracycline. Our results expand the knowledge of the antibiotic resistance-susceptibility profiles of vaginal bacteria and provide the genetic basis of their intrinsic and acquired resistance.

A Review of the Effects of Natural Compounds, Medicinal Plants, and Mushrooms on the Gut Microbiota in Colitis and Cancer

The human gastrointestinal tract harbors a diverse array of microorganisms that play fundamental roles in health and disease. Imbalance in the gut microbiota, namely dysbiosis, can lead to various diseases, including cancer and gastrointestinal tract disorders. Approaches to improve gut dysbiosis, such as dietary intervention, intake of probiotics, and fecal microbiota transplantation are emerging strategies to treat these diseases. Various medicinal botanicals have reported anti-cancer and/or anti-inflammatory properties. Preclinical studies have illustrated that some of these natural products are also capable to modulate the gut microbiota, suggesting their use as possible alternative approach to improve gut dysbiosis and thereby assist diseases treatment. In this review article, we have summarized the current knowledge on the effects of natural compounds, medicinal plants, and mushrooms on the gut microbiota in various cancers and colitis in preclinical animal models. Challenges towards the clinical use of these medicinal botanicals as modulators of the gut microbiota in cancer and colitis treatment are also discussed.

Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus

Shotgun metagenomics is of great importance in order to understand the composition of the microbial community associated with a sample and the potential impact it may exert on its host. For clinical metagenomics, one of the initial challenges is the accurate identification of a pathogen of interest and ability to single out that pathogen within a complex community of microorganisms. However, in absence of an accurate identification of those microorganisms, any kind of conclusion or diagnosis based on misidentification may lead to erroneous conclusions, especially when comparing distinct groups of individuals. When comparing a shotgun metagenomic sample against a reference genome sequence database, the classification itself is dependent on the contents of the database. Focusing on the genus Streptococcus, we built four synthetic metagenomic samples and demonstrated that shotgun taxonomic profiling using the bacterial core genes as the reference database performed better in both taxonomic profiling and relative abundance prediction than that based on the marker gene reference database included in MetaPhlAn2. Additionally, by classifying sputum samples of patients suffering from chronic obstructive pulmonary disease, we showed that adding genomes of genomospecies to a reference database offers higher taxonomic resolution for taxonomic profiling. Finally, we show how our genomospecies database is able to identify correctly a clinical stool sample from a patient with a streptococcal infection, proving that genomospecies provide better taxonomic coverage for metagenomic analyses.

Repurposing the Streptococcus mutans CRISPR-Cas9 System to Understand Essential Gene Function

A recent genome-wide screen identified ~300 essential or growth-supporting genes in the dental caries pathogen Streptococcus mutans. To be able to study these genes, we built a CRISPR interference tool around the Cas9 nuclease (Cas9Smu) encoded in the S. mutans UA159 genome. Using a xylose-inducible dead Cas9Smu with a constitutively active single-guide RNA (sgRNA), we observed titratable repression of GFP fluorescence that compared favorably to that of Streptococcus pyogenes dCas9 (Cas9Spy). We then investigated sgRNA specificity and proto-spacer adjacent motif (PAM) requirements. Interference by sgRNAs did not occur with double or triple base-pair mutations, or if single base-pair mutations were in the 3' end of the sgRNA. Bioinformatic analysis of >450 S. mutans genomes allied with in vivo assays revealed a similar PAM recognition sequence as Cas9Spy. Next, we created a comprehensive library of sgRNA plasmids that were directed at essential and growth-supporting genes. We discovered growth defects for 77% of the CRISPRi strains expressing sgRNAs. Phenotypes of CRISPRi strains, across several biological pathways, were assessed using fluorescence microscopy. A variety of cell structure anomalies were observed, including segregational instability of the chromosome, enlarged cells, and ovococci-to-rod shape transitions. CRISPRi was also employed to observe how silencing of cell wall glycopolysaccharide biosynthesis (rhamnose-glucose polysaccharide, RGP) affected both cell division and pathogenesis in a wax worm model. The CRISPRi tool and sgRNA library are valuable resources for characterizing essential genes in S. mutans, some of which could prove to be promising therapeutic targets.

Harnessing bacterial interactions to manage infections: a review on the opportunistic pathogen Pseudomonas aeruginosa as a case example

During infections, bacterial pathogens can engage in a variety of interactions with each other, ranging from the cooperative sharing of resources to deadly warfare. This is especially relevant in opportunistic infections, where different strains and species often co-infect the same patient and interact in the host. Here, we review the relevance of these social interactions during opportunistic infections using the human pathogen Pseudomonas aeruginosa as a case example. In particular, we discuss different types of pathogen-pathogen interactions, involving both cooperation and competition, and elaborate on how they impact virulence in multi-strain and multi-species infections. We then review evolutionary dynamics within pathogen populations during chronic infections. We particuarly discuss how local adaptation through niche separation, evolutionary successions and antagonistic co-evolution between pathogens can alter virulence and the damage inflicted on the host. Finally, we outline how studying bacterial social dynamics could be used to manage infections. We show that a deeper appreciation of bacterial evolution and ecology in the clinical context is important for understanding microbial infections and can inspire novel treatment strategies.

Development of a reference data set for assigning Streptococcus and Enterococcus species based on next generation sequencing of the 16S-23S rRNA region

Background

Many members of Streptococcus and Enterococcus genera are clinically relevant opportunistic pathogens warranting accurate and rapid identification for targeted therapy. Currently, the developed method based on next generation sequencing (NGS) of the 16S-23S rRNA region proved to be a rapid, reliable and precise approach for species identification directly from polymicrobial and challenging clinical samples. The introduction of this new method to routine diagnostics is hindered by a lack of the reference sequences for the 16S-23S rRNA region for many bacterial species. The aim of this study was to develop a careful assignment for streptococcal and enterococcal species based on NGS of the 16S-23S rRNA region.

Methods

Thirty two strains recovered from clinical samples and 19 reference strains representing 42 streptococcal species and nine enterococcal species were subjected to bacterial identification by four Sanger-based sequencing methods targeting the genes encoding (i) 16S rRNA, (ii) sodA, (iii) tuf and (iv) rpoB; and NGS of the 16S-23S rRNA region.

Results

This study allowed obtainment and deposition of reference sequences of the 16S-23S rRNA region for 15 streptococcal and 3 enterococcal species followed by enrichment for 27 and 6 species, respectively, for which reference sequences were available in the databases. For Streptococcus, NGS of the 16S-23S rRNA region was as discriminative as Sanger sequencing of the tuf and rpoB genes allowing for an unambiguous identification of 93% of analyzed species. For Enterococcus, sodA, tuf and rpoB genes sequencing allowed for identification of all species, while the NGS-based method did not allow for identification of only one enterococcal species. For both genera, the sequence analysis of the 16S rRNA gene was endowed with a low identification potential and was inferior to that of other tested identification methods. Moreover, in case of phylogenetically related species the sequence analysis of only the intergenic spacer region was not sufficient enough to precisely identify Streptococcus strains at the species level.

Conclusions

Based on the developed reference dataset, clinically relevant streptococcal and enterococcal species can now be reliably identified by 16S-23S rRNA sequences in samples. This study will be useful for introduction of a novel diagnostic tool, NGS of the 16S-23S rRNA region, which undoubtedly is an improvement for reliable culture-independent species identification directly from polymicrobially constituted clinical samples.

Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis

Prophages (viral genomes integrated within a host bacterial genome) can confer various phenotypic traits to their hosts, such as enhanced pathogenicity. Here we analyse >1300 genomes of 70 different Streptococcus species and identify nearly 800 prophages and satellite prophages (prophages that do not encode their own structural components but rely on the bacterial host and another helper prophage for survival). We show that prophages and satellite prophages are widely distributed among streptococci in a structured manner, and constitute two distinct entities with little effective genetic exchange between them. Cross-species transmission of prophages is not uncommon. Furthermore, a satellite prophage is associated with virulence in a mouse model of Streptococcus pneumoniae infection. Our findings highlight the potential importance of prophages in streptococcal biology and pathogenesis.

Prophages are viral genomes integrated within bacterial genomes. Here, Rezaei Javan et al. identify nearly 800 prophages and satellite prophages in > 1300 Streptococcus genomes, and show that a satellite prophage is associated with virulence in a mouse model of pneumococcal infection.

The Pathogenic Factors from Oral Streptococci for Systemic Diseases

The oral cavity is suggested as the reservoir of bacterial infection, and the oral and pharyngeal biofilms formed by oral bacterial flora, which is comprised of over 700 microbial species, have been found to be associated with systemic conditions. Almost all oral microorganisms are non-pathogenic opportunistic commensals to maintain oral health condition and defend against pathogenic microorganisms. However, oral Streptococci, the first microorganisms to colonize oral surfaces and the dominant microorganisms in the human mouth, has recently gained attention as the pathogens of various systemic diseases, such as infective endocarditis, purulent infections, brain hemorrhage, intestinal inflammation, and autoimmune diseases, as well as bacteremia. As pathogenic factors from oral Streptococci, extracellular polymeric substances, toxins, proteins and nucleic acids as well as vesicles, which secrete these components outside of bacterial cells in biofilm, have been reported. Therefore, it is necessary to consider that the relevance of these pathogenic factors to systemic diseases and also vaccine candidates to protect infectious diseases caused by Streptococci. This review article focuses on the mechanistic links among pathogenic factors from oral Streptococci, inflammation, and systemic diseases to provide the current understanding of oral biofilm infections based on biofilm and widespread systemic diseases.

Indole-3-propionic acid inhibits gut dysbiosis and endotoxin leakage to attenuate steatohepatitis in rats

Microbial metabolites have emerged as critical components that mediate the metabolic effects of the gut microbiota. Here, we show that indole-3-propionic acid (IPA), a tryptophan metabolite produced by gut bacteria, is a potent anti-non-alcoholic steatohepatitis (NASH) microbial metabolite. Here, we demonstrate that administration of IPA modulates the microbiota composition in the gut and inhibits microbial dysbiosis in rats fed a high-fat diet. IPA induces the expression of tight junction proteins, such as ZO-1 and Occludin, and maintains intestinal epithelium homeostasis, leading to a reduction in plasma endotoxin levels. Interestingly, IPA inhibits NF-κB signaling and reduces the levels of proinflammatory cytokines, such as TNFα, IL-1β, and IL-6, in response to endotoxin in macrophages to repress hepatic inflammation and liver injury. Moreover, IPA is sufficient to inhibit the expression of fibrogenic and collagen genes and attenuate diet-induced NASH phenotypes. The beneficial effects of IPA on the liver are likely mediated through inhibiting the production of endotoxin in the gut. These findings suggest a protective role of IPA in the control of metabolism and uncover the gut microbiome and liver cross-talk in regulating the intestinal microenvironment and liver pathology via a novel dietary nutrient metabolite. IPA may provide a new therapeutic strategy for treating NASH.

A molecule made by beneficial microbes in the gut helps protect against a severe form of fatty liver disease by preventing bacterial toxins from leaking out of the intestines into the bloodstream. A research team in China led by Yu Li from the Shanghai Institute of Nutrition and Health (CAS) and Jian-Gao Fan from Xinhua Hospital (SJTU) showed in a rat model of non-alcoholic steatohepatitis that indole-3-propionic acid (IPA), a metabolite produced by gut bacteria, helps maintain the integrity of the intestinal inner lining. The more robust intestinal barrier ensures that bacterial toxins do not enter the bloodstream and eventually reach the liver, where they can trigger injury-inducing inflammation. The findings reveal an interaction between the gut microbiome and the liver, and suggest a role for IPA in the treatment of fatty liver disease.

Investigation of physicochemical composition and microbial communities in traditionally fermented vrum from Inner Mongolia

Mongolian traditionally fermented vrum is known for its functional characteristics, and indigenous microbial flora plays a critical role in its natural fermentation. However, studies of traditionally fermented vrum are still rare. In this study, we investigated the artisanal production of traditionally fermented vrum from Inner Mongolia. In general, its physicochemical composition was characterized by 34.5 ± 8% moisture, 44.9 ± 12.1% fat, 10.6 ± 3.2% protein, and 210 ± 102°T. The total lactic acid bacteria and yeast counts ranged from 50 to 2.8 × 10⁸ cfu/g and from 0 to 1.1 × 10⁶ cfu/g, respectively. We studied bacterial and fungal community structures in 9 fermented vrum; we identified 5 bacterial phyla represented by 11 genera (an average relative abundance >1%) and 8 species (>1%), and 3 fungal phyla represented by 8 genera (>1%) and 8 species (>1%). Relative abundance values showed that Lactococcus and Lactobacillus were the most common bacterial genera, and Dipodascus was the predominant fungal genus. This scientific investigation of the nutritional components, microbial counts, and community profiles in Mongolian traditionally fermented vrum could help to develop future functional biomaterials and probiotics.

Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing

Pathogen monitoring, detection and removal are essential to public health and outbreak management. Systems are in place for monitoring the microbial load of hospitals and public health facilities with strategies to mitigate pathogen spread. However, no such strategies are in place for ambulances, which are tasked with transporting at-risk individuals in immunocompromised states. As standard culturing techniques require a laboratory setting, and are time consuming and labour intensive, our approach was designed to be portable, inexpensive and easy to use based on the MinION third-generation sequencing platform from Oxford Nanopore Technologies. We developed a transferable sampling-to-analysis pipeline to characterize the microbial community in emergency medical service vehicles. Our approach identified over sixty-eight organisms in ambulances to the genera level, with a proportion of these being connected with health-care associated infections, such as Clostridium spp. and Staphylococcus spp. We also monitored the microbiome of different locations across three ambulances over time, and examined the dynamic community of microorganisms found in emergency medical service vehicles. Observed differences identified hot spots, which may require heightened monitoring and extensive cleaning. Through metagenomics analysis it is also possible to identify how microorganisms spread between patients and colonize an ambulance over time. The sequencing results aid in the development of practices to mitigate disease spread, while also providing a useful tool for outbreak prediction through ongoing analysis of the ambulance microbiome to identify new and emerging pathogens. Overall, this pipeline allows for the tracking and monitoring of pathogenic microorganisms of epidemiological interest, including those related to health-care associated infections.

Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow

Background

The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.

Results

Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.

The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.

Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.

Conclusions

Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1403-6) contains supplementary material, which is available to authorized users.

Urinary profiles associated with bacterial metabolites from asymptomatic pregnant women with at term or preterm premature rupture of membranes: a pilot study

Objective: Premature rupture of membranes (PROM) and preterm premature rupture of membranes (pPROM) are frequent conditions with a not fully understood multifactorial etiology. It has been suggested that infection may be the leading cause of pPROM. Metabolomics is nowadays recognized as a successful and versatile approach for the investigation of several pathological conditions, including pregnancy-related ones. However, collecting samples such as fetal fluids or placenta poses a limit on the clinical application of this strategy. Therefore, the aim of this study was to detect urinary metabolites that could be associated with bacterial infection in PROM and pPROM and to understand its role in these different conditions, using readily available samples such as urines.Methods: Urine samples were collected from pregnant women who experienced rupture of membranes: (1) at term (≥37 weeks) not in labor (NLPROM); (2) at term in labor (LPROM); (3) preterm (<37 weeks) not in labor (pPROM). Samples were analyzed using a GC-MS platform. Student's t-test, Pearson correlation coefficient, principal component analysis (PCA), and partial least squares discriminant analysis (PLS-DA) were applied to observe differences between groups.Results: Results showed that lactic acid, erythritol, and ethanolamine levels were significantly higher in pPROM than in PROM (NLPROM + LPROM considered as one single group). These three metabolites might be associated with bacterial infections since they derive from bacterial metabolic processes and environments.Conclusions: This study might be useful to understand the mechanisms underlying the etiology of pPROM and PROM, and urine samples might represent a useful and readily available sample to discriminate preterm high-risk women.

Isolation of Streptococcus agalactiae in a female llama (Lama glama) in South Tyrol (Italy)

BACKGROUND

Streptococcus agalactiae is pathogenic for both animals and humans. In dairy cattle it commonly causes mastitis, with great economic losses, and there is scientific evidence of mastitis, caseous lymphadenitis, contagious skin necrosis and purulent infections associated with S. agalactiae in camels (Camelus dromedarius) as well. In humans, it is a common component of the respiratory and gastrointestinal microflora, but it can also act as a pathogen, especially in elderly people and immunocompromised patients, as well as in pregrant women and newborns.

CASE PRESENTATION

A 10-year old non-pregnant female llama (Lama glama) was conferred to the Institute for Animal Health Control, in Bolzano for necropsy after sudden death. The animal had not shown unusual behaviour and had a low to normal nutritional condition (body condition score 2/5). The breeder had reported a chronic suppurative subcutaneous infection in the intermandibular area, resistant to therapy (therapy unknown). After necropsy, several samples were processed for histological, bacteriological and parasitological examinations.

CONCLUSIONS

This report describes, to the best of our knowledge, the first isolation of S. agalactiae in llamas (Lama glama). The animal came from a herd that counts approximately 200 South American camelids (llamas, alpacas) along with several horses, chicken, rabbits, cats and dogs; this farm offers services, such as trekking and pet therapy activities.

Lactobacillus reuteri F-9-35 Prevents DSS-Induced Colitis by Inhibiting Proinflammatory Gene Expression and Restoring the Gut Microbiota in Mice

Probiotics are considered to be a potential treatment for ulcerative colitis (UC). The aim of this study was to compare the preventive effect of a space flight-induced mutant L. reuteri F-9-35 and its wild type on UC in vivo. Female mice were randomly assigned to five groups: one normal and four colitic. Mice from colitis groups were daily gavaged with 0.2 mL 12% (w/v) skim milk containing the mutant or wild type (1 × 10¹¹ CFU/mL), skim milk alone or distilled water for the whole experiment period, starting 7 days before colitis induction. UC was induced by administrating mice with 3.5% (w/v) dextran sulfate sodium (DSS) in drinking water for 7 days, after which DSS was removed and maintained for 3 days as a recovery phase. The results showed that the mice fed with L. reuteri F-9-35 had less inflammatory phenotype according to macroscopic and histological analysis, reduced myeloperoxidase activity, and lower expression of proinflammatory genes (Tumor necrosis factor-α, cyclooxygenase-2 and interleukin-6) in colonic tissue compared with control. Furthermore, L. reuteri F-9-35 protected the mice from gut microbiota dysbiosis from DDS induced colitis. Neither wild type nor the milk alone had such beneficial effects. From above we conclude that L. reuteri F-9-35 has great potential in the prevention of UC as a dietary supplement.

PRACTICAL APPLICATION

Ulcerative colitis (UC) is the most common inflammatory bowel diseases and there is still a lack of safe and effective treatments. Consumption of L. reuteri F-9-35 may effective in preventing human UC.

Infectious Crystalline Keratopathy After Corneal Cross-linking

To report a rare case of infectious keratitis after collagen cross-linking (CXL) for keratoconus. A 20-year-old male patient underwent CXL for keratoconus in his right eye. Four weeks after the procedure, he reported blurred vision and redness with increasing pain in the treated eye. Ophthalmic examination revealed a corneal epithelial defect with corneal infiltrates that exhibited branching needle-like opacities. The patient was diagnosed with infectious crystalline keratopathy (ICK). Corneal scrapings and culture indicated the presence of Streptococcus sanguinis. The patient was successfully treated with fortified vancomycin and ceftazidime over several weeks. ICK is a potential post-operative complication of CXL that can lead to corneal scarring with a permanent reduction in visual acuity.

Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy

AIM

To investigate whether patients with refractory epilepsy and healthy infants differ in gut microbiota (GM), and how ketogenic diet (KD) alters GM.

METHODS

A total of 14 epileptic and 30 healthy infants were recruited and seizure frequencies were recorded. Stool samples were collected for 16S rDNA sequencing using the Illumina Miseq platform. The composition of GM in each sample was analyzed with MOTHUR, and inter-group comparison was conducted by R software.

RESULTS

After being on KD treatment for a week, 64% of epileptic infants showed an obvious improvement, with a 50% decrease in seizure frequency. GM structure in epileptic infants (P1 group) differed dramatically from that in healthy infants (Health group). Proteobacteria, which had accumulated significantly in the P1 group, decreased dramatically after KD treatment (P2 group). Cronobacter predominated in the P1 group and remained at a low level both in the Health and P2 groups. Bacteroides increased significantly in the P2 group, in which Prevotella and Bifidobacterium also grew in numbers and kept increasing.

CONCLUSION

GM pattern in healthy infants differed dramatically from that of the epileptic group. KD could significantly modify symptoms of epilepsy and reshape the GM of epileptic infants.

The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions

The functions of roughly a third of all proteins in Streptococcus pneumoniae, a significant human-pathogenic bacterium, are unknown. Using a yeast two-hybrid approach, we have determined more than 2,000 novel protein interactions in this organism. We augmented this network with meta-interactome data that we defined as the pool of all interactions between evolutionarily conserved proteins in other bacteria. We found that such interactions significantly improved our ability to predict a protein's function, allowing us to provide functional predictions for 299 S. pneumoniae proteins with previously unknown functions. IMPORTANCE Identification of protein interactions in bacterial species can help define the individual roles that proteins play in cellular pathways and pathogenesis. Very few protein interactions have been identified for the important human pathogen S. pneumoniae. We used an experimental approach to identify over 2,000 new protein interactions for S. pneumoniae, the most extensive interactome data for this bacterium to date. To predict protein function, we used our interactome data augmented with interactions from other closely related bacteria. The combination of the experimental data and meta-interactome data significantly improved the prediction results, allowing us to assign possible functions to a large number of poorly characterized proteins.

Respiratory Microbiome of Endangered Southern Resident Killer Whales and Microbiota of Surrounding Sea Surface Microlayer in the Eastern North Pacific

In the Salish Sea, the endangered Southern Resident Killer Whale (SRKW) is a high trophic indicator of ecosystem health. Three major threats have been identified for this population: reduced prey availability, anthropogenic contaminants, and marine vessel disturbances. These perturbations can culminate in significant morbidity and mortality, usually associated with secondary infections that have a predilection to the respiratory system. To characterize the composition of the respiratory microbiota and identify recognized pathogens of SRKW, exhaled breath samples were collected between 2006–2009 and analyzed for bacteria, fungi and viruses using (1) culture-dependent, targeted PCR-based methodologies and (2) taxonomically broad, non-culture dependent PCR-based methodologies. Results were compared with sea surface microlayer (SML) samples to characterize the respective microbial constituents. An array of bacteria and fungi in breath and SML samples were identified, as well as microorganisms that exhibited resistance to multiple antimicrobial agents. The SML microbes and respiratory microbiota carry a pathogenic risk which we propose as an additional, fourth putative stressor (pathogens), which may adversely impact the endangered SRKW population.

The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2

Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest chromosome, containing 1,731,838 bp. The annotation of its genome revealed the presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and 224 potential pseudogenes. A large number of pseudogenes were identified. This was also accompanied by the absence of pathogenic features suggesting evolution of strain ACA-DC 2 through genome decay processes, most probably due to adaptation to the milk ecosystem. Analysis revealed the existence of one complete lactose-galactose operon, several proteolytic enzymes, one exopolysaccharide cluster, stress response genes and four putative antimicrobial peptides. Interestingly, one CRISPR-cas system and one orphan CRISPR, both carrying only one spacer, were predicted indicating low activity or inactivation of the cas proteins. Nevertheless, four putative restriction-modification systems were determined that may compensate any deficiencies of the CRISPR-cas system. Furthermore, whole genome phylogeny indicated three distinct clades within S. thermophilus. Comparative analysis among selected strains representative for each clade, including strain ACA-DC 2, revealed a high degree of conservation at the genomic scale, but also strain specific regions. Unique genes and genomic islands of strain ACA-DC 2 contained a number of genes potentially acquired through horizontal gene transfer events, that could be related to important technological properties for dairy starters. Our study suggests genomic traits in strain ACA-DC 2 compatible to the production of dairy fermented foods.

Enzymology and Ultrastructure of the in situ Pellicle in Caries-Active and Caries-Inactive Patients

Aim: The present study aimed to evaluate the impact of caries activity on the key enzymes and the ultrastructure of the in situ pellicle. Methods: Pellicle formation was performed on bovine enamel slabs. Intraoral exposure (3, 30, and 120 min) was accomplished by 14 caries-active (DMFS: 22.7 ± 12.1) and 13 caries-inactive (DMFS: 1.5 ± 1.8) individuals. The enzyme activities (lysozyme, peroxidase, α-amylase, glycosyltransferase [GTF]) in the in situ pellicle and resting saliva of all participants were analyzed directly after oral exposure. In addition, a simultaneous visualization of these enzymes, extracellular glucans, and adherent bacteria was carried out. Fluorescent patterns were analyzed with fluorescence labeling and 4′,6-diamidino-2-phenylindole/concanavalin A staining. In addition, the distribution of GTF B, C, and D and the ultrastructure of the pellicle were examined by gold immunolabeling and transmission electron microscopy with selected samples. Results: Enzyme activities of amylase, peroxidase, lysozyme, and GTF were detected on all enamel slabs in an active conformation. Neither exposure time nor caries activity had an impact on the enzyme activities. Gold immunolabeling indicated that the pellicle of caries-active subjects tends to more GTF D molecules. The pellicles of caries-inactive and -active individuals revealed a similar ultrastructural pattern. Conclusion: The enzyme activities as well as the pellicle's ultrastructure are of high similarity in caries-active and -inactive subjects. Thereby, oral exposure time has no significant influence. This reflects a high uniformity during the initial phase of bioadhesion (3-120 min) concerning enzymatic functions. However, there is a tendency towards more GTF D in caries-active individuals.

Improved Differentiation of Streptococcus pneumoniae and Other S. mitis Group Streptococci by MALDI Biotyper Using an Improved MALDI Biotyper Database Content and a Novel Result Interpretation Algorithm

Reliable distinction of Streptococcus pneumoniae and viridans group streptococci is important because of the different pathogenic properties of these organisms. Differentiation between S. pneumoniae and closely related Sreptococcusmitis species group streptococci has always been challenging, even when using such modern methods as 16S rRNA gene sequencing or matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. In this study, a novel algorithm combined with an enhanced database was evaluated for differentiation between S. pneumoniae and S. mitis species group streptococci. One hundred one clinical S. mitis species group streptococcal strains and 188 clinical S. pneumoniae strains were identified by both the standard MALDI Biotyper database alone and that combined with a novel algorithm. The database update from 4,613 strains to 5,627 strains drastically improved the differentiation of S. pneumoniae and S. mitis species group streptococci: when the new database version containing 5,627 strains was used, only one of the 101 S. mitis species group isolates was misidentified as S. pneumoniae, whereas 66 of them were misidentified as S. pneumoniae when the earlier 4,613-strain MALDI Biotyper database version was used. The updated MALDI Biotyper database combined with the novel algorithm showed even better performance, producing no misidentifications of the S. mitis species group strains as S. pneumoniae All S. pneumoniae strains were correctly identified as S. pneumoniae with both the standard MALDI Biotyper database and the standard MALDI Biotyper database combined with the novel algorithm. This new algorithm thus enables reliable differentiation between pneumococci and other S. mitis species group streptococci with the MALDI Biotyper.

Management of Resistant, Atypical and Culture-negative Periprosthetic Joint Infections after Hip and Knee Arthroplasty

BACKGROUND

Periprosthetic joint infection (PJI) is a devastating complication following lower extremity total joint arthroplasty (TJA). It is a leading cause of morbidity and revision following TJA. As such, PJI is a significant driver of healthcare costs. The prevalence of PJI related to resistant and atypical organisms is increasing, and approximately 10-30% of PJIs are culture-negative. The purpose of this review is to summarize the current epidemiology, diagnostics, and management of PJI associated with resistant and atypical pathogens and of culture-negative PJIs.

METHODS

The published literature related to the epidemiology, diagnosis, and management of atypical, drug-resistant, and culture-negative PJI is reviewed.

RESULTS

The clinical diagnosis of PJI is often challenging, particularly when pathogens are fastidious or when antibiotics have been administered empirically. Molecular diagnostic studies, such as synovial α-defensin, may provide rapid, accurate identification of PJI, even in the setting of concurrent antibiotics administration or systemic inflammatory disease. Once PJI is diagnosed, two-stage exchange arthroplasty remains the gold standard for treating PJI with resistant microorganisms, since there is a high rate of treatment failure with irrigation and debridement and with one-stage exchange arthroplasty.

CONCLUSION

Additional research is needed to define the optimal treatment of PJIs associated with rare pathogens, such as fungi and mycobacteria. There is a need for inexpensive, reliable tests that rapidly detect specific microbial species and antimicrobial susceptibilities. Additional research is also required to define the specific organisms, clinical scenarios, surgical techniques, and antimicrobial regimens that allow for reproducible treatment success with prosthetic retention strategies.

Zincophorin - biosynthesis in Streptomyces griseus and antibiotic properties

Zincophorin is a polyketide antibiotic that possesses potent activity against Gram-positive bacteria, including human pathogens. While a number of total syntheses of this highly functionalized natural product were reported since its initial discovery, the genetic basis for the biosynthesis of zincophorin has remained unclear. In this study, the co-linearity inherent to polyketide pathways was used to identify the zincophorin biosynthesis gene cluster in the genome of the natural producer Streptomyces griseus HKI 0741. Interestingly, the same locus is fully conserved in the streptomycin-producing actinomycete S. griseus IFO 13350, suggesting that the latter bacterium is also capable of zincophorin biosynthesis. Biological profiling of zincophorin revealed a dose-dependent inhibition of the Gram-positive bacterium Streptococcus pneumoniae. The antibacterial effect, however, is accompanied by cytotoxicity. Antibiotic and cytotoxic activities were completely abolished upon esterification of the carboxylic acid group in zincophorin.

Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci

BACKGROUND

The genus Streptococcus is 1 of the dominant bacterial groups in human milk, but the taxonomic identification of some species remains difficult.

OBJECTIVE

The objective of this study was to investigate the discriminatory ability of different methods to identify streptococcal species in order to perform an assessment of the streptococcal diversity of human milk microbiota as accurately as possible.

METHODS

The identification of 105 streptococcal strains from human milk was performed by 16S rRNA, tuf, and sodA gene sequencing, phylogenetic analysis, and Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) mass spectrometry.

RESULTS

Streptococcus salivarius, Streptococcus mitis, and Streptococcus parasanguinis were the streptococcal dominant species in the human milk microbiota. Sequencing of housekeeping genes allowed the classification of 96.2% (16S rRNA), 84.8% ( sodA), and 88.6% ( tuf) of the isolates. Phylogenetic analysis showed 3 main streptococcal clusters corresponding with the mitis (73 isolates), salivarius (29), mutans (1)-pyogenic (2) groups, but many of the mitis group isolates (36) could not be assigned to any species. The application of the MALDI-TOF Bruker Biotyper system resulted in the identification of 56 isolates (53.33%) at the species level, but it could not discriminate between S pneumoniae and S mitis isolates, in contrast to the Vitek-MS system.

CONCLUSION

There was a good agreement among the different methods assessed in this study to identify those isolates of the salivarius, mutans, and pyogenic groups, whereas unambiguous discrimination could not be achieved concerning some species of the mitis group ( S mitis, S pneumoniae, S pseudopneumoniae, S oralis).

Regulatory RNAs in the Less Studied Streptococcal Species: From Nomenclature to Identification

Streptococcal species are Gram-positive bacteria involved in severe and invasive diseases in humans and animals. Although, this group includes different pathogenic species involved in life-threatening infections for humans, it also includes beneficial species, such as Streptococcus thermophilus, which is used in yogurt production. In bacteria virulence factors are controlled by various regulatory networks including regulatory RNAs. For clearness and to develop logical thinking, we start this review with a revision of regulatory RNAs nomenclature. Previous reviews are mostly dealing with Streptococcus pyogenes and Streptococcus pneumoniae regulatory RNAs. We especially focused our analysis on regulatory RNAs in Streptococcus agalactiae, Streptococcus mutans, Streptococcus thermophilus and other less studied Streptococcus species. Although, S. agalactiae RNome remains largely unknown, sRNAs (small RNAs) are supposed to mediate regulation during environmental adaptation and host infection. In the case of S. mutans, sRNAs are suggested to be involved in competence regulation, carbohydrate metabolism, and Toxin–Antitoxin systems. A new category of miRNA-size small RNAs (msRNAs) was also identified for the first time in this species. The analysis of S. thermophilus sRNome shows that many sRNAs are associated to the bacterial immune system known as CRISPR-Cas system. Only few of the other different Streptococcus species have been the subject of studies pointed toward the characterization of regulatory RNAs. Finally, understanding bacterial sRNome can constitute one step forward to the elaboration of new strategies in therapy such as substitution of antibiotics in the management of S. agalactiae neonatal infections, prevention of S. mutans dental caries or use of S. thermophilus CRISPR-Cas system in genome editing applications.

Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota

The genus Lactobacillus includes over 215 species that colonize plants, foods, sewage and the gastrointestinal tract (GIT) of humans and animals. In the GIT, Lactobacillus population can be made by true inhabitants or by bacteria occasionally ingested with fermented or spoiled foods, or with probiotics. This study longitudinally surveyed Lactobacillus species and strains in the feces of a healthy subject through whole genome sequencing (WGS) data-mining, in order to identify members of the permanent or transient populations. In three time-points (0, 670 and 700 d), 58 different species were identified, 16 of them being retrieved for the first time in human feces. L. rhamnosus, L. ruminis, L. delbrueckii, L. plantarum, L. casei and L. acidophilus were the most represented, with estimated amounts ranging between 6 and 8 Log (cells g(-1) ), while the other were detected at 4 or 5 Log (cells g(-1) ). 86 Lactobacillus strains belonging to 52 species were identified. 43 seemingly occupied the GIT as true residents, since were detected in a time span of almost 2 years in all the three samples or in 2 samples separated by 670 or 700 d. As a whole, a stable community of lactobacilli was disclosed, with wide and understudied biodiversity.

No Resistance to Penicillin, Cefuroxime, Cefotaxime, or Vancomycin in Pneumococcal Pneumonia

OBJECTIVES

Group B Streptococcus is a primary source of pneumonia, which is a leading cause of death worldwide. During the last few decades, there has been news of growing antibiotic resistance in group B streptococci to penicillin and different antibiotic agents. This clinical study retrospectively analyzes antimicrobial resistance in inpatients who were diagnosed with group B streptococcal pneumonia.

METHODS

All of the required information from inpatients who were identified to have group B streptococcal pneumonia was sourced from the database at the Department of Internal Medicine of HELIOS Clinic Wuppertal, Witten/Herdecke University, in Germany, from 2004-2014. Antimicrobial susceptibility testing was performed for the different antimicrobial agents that were regularly administered to these inpatients.

RESULTS

Sixty-six inpatients with a mean age of 63.3 ± 16.1 years (45 males [68.2%, 95% CI 60.0%-79.4%] and 21 females [31.8%, 95% CI 20.6%-43.0%]) were detected to have group B streptococcal pneumonia within the study period from January 1, 2004, to August 12, 2014. Group B Streptococcus had a high resistance rate to gentamicin (12.1%), erythromycin (12.1%), clindamycin (9.1%), and co-trimoxazole (3.0%), but it was not resistant to penicillin, cefuroxime, cefotaxime, or vancomycin (P < 0.0001).

CONCLUSION

No resistance to penicillin, cefuroxime, cefotaxime, or vancomycin was detected among inpatients with pneumonia caused by group B streptococci.

Zebrafish and Streptococcal Infections

Streptococcal bacteria are a versatile group of gram-positive bacteria capable of infecting several host organisms, including humans and fish. Streptococcal species are common colonizers of the human respiratory and gastrointestinal tract, but they also cause some of the most common life-threatening, invasive infections in humans and aquaculture. With its unique characteristics and efficient tools for genetic and imaging applications, the zebrafish (Danio rerio) has emerged as a powerful vertebrate model for infectious diseases. Several zebrafish models introduced so far have shown that zebrafish are suitable models for both zoonotic and human-specific infections. Recently, several zebrafish models mimicking human streptococcal infections have also been developed. These models show great potential in providing novel information about the pathogenic mechanisms and host responses associated with human streptococcal infections. Here, we review the zebrafish infection models for the most relevant streptococcal species: the human-specific Streptococcus pneumoniae and Streptococcus pyogenes, and the zoonotic Streptococcus iniae and Streptococcus agalactiae. The recent success and the future potential of these models for the study of host-pathogen interactions in streptococcal infections are also discussed.

Genome-wide analyses of small non-coding RNAs in streptococci

Streptococci represent a diverse group of Gram-positive bacteria, which colonize a wide range of hosts among animals and humans. Streptococcal species occur as commensal as well as pathogenic organisms. Many of the pathogenic species can cause severe, invasive infections in their hosts leading to a high morbidity and mortality. The consequence is a tremendous suffering on the part of men and livestock besides the significant financial burden in the agricultural and healthcare sectors. An environmentally stimulated and tightly controlled expression of virulence factor genes is of fundamental importance for streptococcal pathogenicity. Bacterial small non-coding RNAs (sRNAs) modulate the expression of genes involved in stress response, sugar metabolism, surface composition, and other properties that are related to bacterial virulence. Even though the regulatory character is shared by this class of RNAs, variation on the molecular level results in a high diversity of functional mechanisms. The knowledge about the role of sRNAs in streptococci is still limited, but in recent years, genome-wide screens for sRNAs have been conducted in an increasing number of species. Bioinformatics prediction approaches have been employed as well as expression analyses by classical array techniques or next generation sequencing. This review will give an overview of whole genome screens for sRNAs in streptococci with a focus on describing the different methods and comparing their outcome considering sRNA conservation among species, functional similarities, and relevance for streptococcal infection.

covR Mediated Antibiofilm Activity of 3-Furancarboxaldehyde Increases the Virulence of Group A Streptococcus

BACKGROUND

Group A streptococcus (GAS, Streptococcus pyogenes), a multi-virulent, exclusive human pathogen responsible for various invasive and non-invasive diseases possesses biofilm forming phenomenon as one of its pathogenic armaments. Recently, antibiofilm agents have gained prime importance, since inhibiting the biofilm formation is expected to reduce development of antibiotic resistance and increase their susceptibility to the host immune cells.

PRINCIPAL FINDINGS

The current study demonstrates the antibiofilm activity of 3Furancarboxaldehyde (3FCA), a floral honey derived compound, against GAS biofilm, which was divulged using crystal violet assay, light microscopy, and confocal laser scanning microscopy. The report is extended to study its effect on various aspects of GAS (morphology, virulence, aggregation) at its minimal biofilm inhibitory concentration (132μg/ml). 3FCA was found to alter the growth pattern of GAS in solid and liquid medium and increased the rate of auto-aggregation. Electron microscopy unveiled the increase in extra polymeric substances around cell. Gene expression studies showed down-regulation of covR gene, which is speculated to be the prime target for the antibiofilm activity. Increased hyaluronic acid production and down regulation of srtB gene is attributed to the enhanced rate of auto-aggregation. The virulence genes (srv, mga, luxS and hasA) were also found to be over expressed, which was manifested with the increased susceptibility of the model organism Caenorhabditis elegans to 3FCA treated GAS. The toxicity of 3FCA was ruled out with no adverse effect on C. elegans.

SIGNIFICANCE

Though 3FCA possess antibiofilm activity against GAS, it was also found to increase the virulence of GAS. This study demonstrates that, covR mediated antibiofilm activity may increase the virulence of GAS. This also emphasizes the importance to analyse the acclimatization response and virulence of the pathogen in the presence of antibiofilm compounds prior to their clinical trials.

Metagenomic sequencing reveals altered metabolic pathways in the oral microbiota of sailors during a long sea voyage

Seafaring is a difficult occupation, and sailors face higher health risks than individuals on land. Commensal microbiota participates in the host immune system and metabolism, reflecting the host's health condition. However, the interaction mechanisms between the microbiota and the host's health condition remain unclear. This study reports the influence of long sea voyages on human health by utilising a metagenomic analysis of variation in the microbiota of the buccal mucosa. Paired samples collected before and after a sea-voyage were analysed. After more than 120 days of ocean sailing, the oral microbial diversity of sailors was reduced by approximately 5 fold, and the levels of several pathogens (e.g., Streptococcus pneumonia) increased. Moreover, 69.46% of the identified microbial sequences were unclassified microbiota. Notably, several metabolic pathways were dramatically decreased, including folate biosynthesis, carbohydrate, lipid and amino acid pathways. Clinical examination of the hosts confirmed the identified metabolic changes, as demonstrated by decreased serum levels of haemoglobin and folic acid, a decreased neutrophil-to-lymphocyte ratio, and increased levels of triglycerides, cholesterol and homocysteine, which are consistent with the observed microbial variation. Our study suggests that oral mucosal bacteria may reflect host health conditions and could provide approaches for improving the health of sailors.

Glycosyltransferase-mediated Sweet Modification in Oral Streptococci

Bacterial glycosyltransferases play important roles in bacterial fitness and virulence. Oral streptococci have evolved diverse strategies to survive and thrive in the carbohydrate-rich oral cavity. In this review, we discuss 2 important biological processes mediated by 2 distinct groups of glycosyltransferases in oral streptococci that are important for bacterial colonization and virulence. The first process is the glycosylation of highly conserved serine-rich repeat adhesins by a series of glycosyltransferases. Using Streptococcus parasanguinis as a model, we highlight new features of several glycosyltransferases that sequentially modify the serine-rich glycoprotein Fap1. Distinct features of a novel glycosyltransferase fold from a domain of unknown function 1792 are contrasted with common properties of canonical glycosyltransferases. The second biological process we cover is involved in building sticky glucan matrix to establish cariogenic biofilms by an important opportunistic pathogen Streptococcus mutans through the action of a family of 3 glucosyltransferases. We focus on discussing the structural feature of this family as a glycoside hydrolase family of enzymes. While the 2 processes are distinct, they all produce carbohydrate-coated biomolecules, which enable bacteria to stick better in the complex oral microbiome. Understanding the making of the sweet modification presents a unique opportunity to develop novel antiadhesion and antibiofilm strategies to fight infections by oral streptococci and beyond.

Antipneumococcal activity of neuraminidase inhibiting artocarpin

Streptococcus (S.) pneumoniae is a major cause of secondary bacterial pneumonia during influenza epidemics. Neuraminidase (NA) is a virulence factor of both pneumococci and influenza viruses. Bacterial neuraminidases (NAs) are structurally related to viral NA and susceptible to oseltamivir, an inhibitor designed to target viral NA. This prompted us to evaluate the antipneumococcal potential of two NA inhibiting natural compounds, the diarylheptanoid katsumadain A and the isoprenylated flavone artocarpin. Chemiluminescence, fluorescence-, and hemagglutination-based enzyme assays were applied to determine the inhibitory efficiency (IC(50) value) of the tested compounds towards pneumococcal NAs. The mechanism of inhibition was studied via enzyme kinetics with recombinant NanA NA. Unlike oseltamivir, which competes with the natural substrate of NA, artocarpin exhibits a mixed-type inhibition with a Ki value of 9.70 μM. Remarkably, artocarpin was the only NA inhibitor (NAI) for which an inhibitory effect on pneumococcal growth (MIC: 0.99-5.75 μM) and biofilm formation (MBIC: 1.15-2.97 μM) was observable. In addition, we discovered that the bactericidal effect of artocarpin can reduce the viability of pneumococci by a factor of >1000, without obvious harm to lung epithelial cells. This renders artocarpin a promising natural product for further investigations.

The virulence of Streptococcus mutans and the ability to form biofilms

In some diseases, a very important role is played by the ability of bacteria to form multi-dimensional complex structure known as biofilm. The most common disease of the oral cavity, known as dental caries, is a top leader. Streptococcus mutans, one of the many etiological factors of dental caries, is a microorganism which is able to acquire new properties allowing for the expression of pathogenicity determinants determining its virulence in specific environmental conditions. Through the mechanism of adhesion to a solid surface, S. mutans is capable of colonizing the oral cavity and also of forming bacterial biofilm. Additional properties enabling S. mutans to colonize the oral cavity include the ability to survive in an acidic environment and specific interaction with other microorganisms colonizing this ecosystem. This review is an attempt to establish which characteristics associated with biofilm formation--virulence determinants of S. mutans--are responsible for the development of dental caries. In order to extend the knowledge of the nature of Streptococcus infections, an attempt to face the following problems will be made: Biofilm formation as a complex process of protein-bacterium interaction. To what extent do microorganisms of the cariogenic flora exemplified by S. mutans differ in virulence determinants "expression" from microorganisms of physiological flora? How does the environment of the oral cavity and its microorganisms affect the biofilm formation of dominant species? How do selected inhibitors affect the biofilm formation of cariogenic microorganisms?