Developments in the use of genomics to guide natural product discovery and a recent emphasis on understanding the molecular mechanisms of microbiota-host interactions have converged on the discovery of small molecules from the human microbiome. Here, we review what is known about small molecules produced by the human microbiota. Numerous molecules representing each of the major metabolite classes have been found that have a variety of biological activities, including immune modulation and antibiosis. We discuss technologies that will affect how microbiota-derived molecules are discovered in the future and consider the challenges inherent in finding specific molecules that are critical for driving microbe-host and microbe-microbe interactions and understanding their biological relevance.

https://science.sciencemag.org/content/sci/349/6246/1254766.full.pdf

Small molecules from the human microbiota

Escherichia coli is a paradigm for a versatile bacterial species which comprises harmless commensal as well as different pathogenic variants with the ability to either cause intestinal or extraintestinal diseases in humans and many animal hosts. Because of this broad spectrum of lifestyles and phenotypes, E. coli is a well-suited model organism to study bacterial evolution and adaptation to different growth conditions and niches. The geno- and phenotypic diversity, however, also hampers risk assessment and strain typing. A marked genome plasticity is the key to the great variability seen in this species. Acquisition of genetic information by horizontal gene transfer, gene loss as well as other genomic modifications, like DNA rearrangements and point mutations, can constantly alter the genome content and thus the fitness and competitiveness of individual variants in certain niches. Specific gene subsets and traits have been correlated with an increased potential of E. coli strains to cause intestinal or extraintestinal disease. Intestinal pathogenic E. coli strains can be reliably discriminated from non-pathogenic, commensal, or from extraintestinal E. coli pathogens based on genome content and phenotypic traits. An unambiguous distinction of extraintestinal pathogenic E. coli and commensals is, nevertheless, not so easy, as strains with the ability to cause extraintestinal infection are facultative pathogens and belong to the normal flora of many healthy individuals. Here, we compare insights into phylogeny, geno-, and phenotypic traits of commensal and pathogenic E. coli. We demonstrate that the borderline between extraintestinal virulence and intestinal fitness can be blurred as improved adaptability and competitiveness may promote intestinal colonization as well as extraintestinal infection by E. coli.

E. coli as an all-rounder: the thin line between commensalism and pathogenicity.

Production of bioactive substances by intestinal bacteria as a basis for explaining probiotic mechanisms: Bacteriocins and conjugated linoleic acid

Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them

Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ-proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages.

/pdf/plasmid-flux-in-escherichia-coli-st131-sublineages-analyzed-2c7n1xcvw1.pdf

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

Background: Bacteriocin production is an important characteristic of E. coli strains of human origin. To date, 26 colicin and 9 microcin types have been analyzed on a molecular level allowing molecular detection of the corresponding genes. The production incidence of 29 bacteriocin types and E. coli phylogroups were tested in a set of 361 E. coli strains isolated from human urinary tract infections (UTI) and in 411 control strains isolated from feces of patients without bacterial gut infection. Results: Production of 17 and 20 individual bacteriocin types was found in the UTI and control strains, respectively. Microcin H47 encoding determinants were found more often among UTI strains compared to controls (37.9% and 27.0% respectively, p = 0.02) and strains producing microcin H47 belonged predominantly to phylogroup B2 when compared to other bacteriocin producers (67.4% and 36.7%, respectively; p < 0.0001). Producers of 3 or more identified bacteriocin types were more common in the UTI group (20.0% compared to 12.4% in controls, p = 0.03). In the UTI strains, there was a markedly higher number of those producing colicin E1 compared to controls (22.1% to 10.2%, respectively, p = 0.0008). Moreover, colicin E1 production was more common in the UTI bacteriocinogenic strains with multi-producer capabilities. As shown by Southern blotting, pColE1 DNA was not recognized by the ColIa probe and vice versa suggesting that pColE1 was independently associated with pColIa in UTI strains. Conclusion: E. coli strains isolated from human urinary tract infections showed increased incidence of microcin H47 and colicin E1 production, respectively. Moreover, colicin E1 itself appears to be a potentially important virulence factor of certain uropathogenic E. coli strains.

/pdf/bacteriocin-synthesis-in-uropathogenic-and-commensal-52lgqyze3l.pdf

Bacteriocin synthesis in uropathogenic and commensal Escherichia coli : colicin E1 is a potential virulence factor

A set of 415 clinical samples isolated from 294 patients suspected of having syphilis collected in the Czech Republic between 2004 and 2010 was tested for the presence of treponemal DNA. Standard serological tests showed that 197 patients were syphilis-seropositive and 97 patients were syphilis-seronegative. In each sample, PCR tests for polA (TP0105), tmpC (TP0319), TP0136, TP0548 and 23S rRNA genes were performed. Samples taken from 91 patients were PCR-positive. Molecular typing of treponemal DNA was based on the sequencing of TP0136, TP0548 and 23S rRNA genes. Treponemal DNA was typeable in samples taken from 64 PCR-positive patients and 9 different genotypes were found. The proportion of treponemal strains resistant to macrolide antibiotics was 37.3%. In the DNA samples taken from 39 patients, a parallel treponemal typing approved by Centers for Disease Control and Prevention was performed. The variants of arp and tpr genes appear to combine independently with sequence variants of TP0136, TP0548 and 23S rRNA genes.

Sequencing-based molecular typing of treponema pallidum strains in the Czech Republic: all identified genotypes are related to the sequence of the SS14 strain.

Using the Captia Select Syph-G enzyme-linked immunosorbent assay (ELISA), we analyzed the sera of 1,771 patients from a high-risk population attending sexually transmitted disease (STD) clinics. We focused on discrepancies between the results of the immunoglobulin G (IgG) ELISA and the Treponema pallidum hemagglutination (TPHA) test. We identified 57 patients (3.22%) with conflicting results in the IgG ELISA and TPHA test. In order to resolve these discrepancies, these patients' health records were reviewed and additional serological tests (rapid plasma reagin, IgM ELISA, fluorescent treponemal antibody absorption, and Western blotting) were performed. We subsequently diagnosed 22 of these 57 (38.6%) patients with late latent syphilis. None of the patients with discordant test results was diagnosed with early syphilis. We followed 35 of these 57 patients, analyzing two consecutive serum samples at 3 weeks and at 3 months. Discordant results persisted in 12 (33.3%) patients. We successfully resolved the test result discrepancies for 28 patients (80%) involved in follow-up. Captia SelectSyph-G ELISA showed a sensitivity of 99.0%, a specificity of 98.0%, and positive and negative predictive values of 99.3% and 97.2%, respectively. Based on the results of this study, we conclude that the Captia SelectSyph-G ELISA is a reliable tool for syphilis testing in a high-risk population and recommend the utilization of the Captia SelectSyph-G ELISA as a confirmatory test in at-risk patients.

Performance of CAPTIA SelectSyph-G Enzyme-Linked Immunosorbent Assay in Syphilis Testing of a High-Risk Population: Analysis of Discordant Results

Clarithromycin treatment failure in a patient with primary
syphilis is presented as a result of macrolide resistance of
Treponema pallidum.

Clarithromycin treatment failure due to macrolide resistance in Treponema pallidum in a patient with primary syphilis.

Treponema pallidum subspecies pallidum is the causative agent
of syphilis, a sexually transmitted disease that still
represents a major world health problem. Serology, the standard
laboratory method used for the diagnosis of syphilis, has
several limitations that preclude reliable diagnosis of
syphilis in some cases. Direct methods of syphilis diagnosis
are suboptimal because of low sensitivity and low specificity
(microscopy), or because of costly and delayed test results
(rabbit infectivity test). Recent status of PCR-based syphilis
diagnosis and molecular typing schemes are reviewed. PCR
detection of Treponema pallidum in various clinical samples
showed high sensitivity, specificity and potential for
molecular typing. PCR diagnosis is therefore considered an
important auxiliary laboratory test for syphilis. Typing of
Treponema pallidum strains isolated from patients will
stimulate epidemiological studies of syphilis and will allow
discrimination between re-infection and reactivation of
infection.

Zuzana Vališová

Papers

Bacteriocin synthesis in uropathogenic and commensal Escherichia coli : colicin E1 is a potential virulence factor

Sequencing-based molecular typing of treponema pallidum strains in the Czech Republic: all identified genotypes are related to the sequence of the SS14 strain.

Performance of CAPTIA SelectSyph-G Enzyme-Linked Immunosorbent Assay in Syphilis Testing of a High-Risk Population: Analysis of Discordant Results

Clarithromycin treatment failure due to macrolide resistance in Treponema pallidum in a patient with primary syphilis.

Diagnosis of syphilis by polymerase chain reaction and molecular typing of Treponema pallidum.