Publications

4468

AbstractChlamydiae like Chlamydia trachomatis and Chlamydia psittaci are well-known human and animal pathogens. Yet, the chlamydiae are a much larger group of evolutionary ancient obligate intracellular bacteria that includes predominantly symbionts of protists and diverse animals. This makes them ideal model organisms to study evolutionary transitions from symbionts in microbial eukaryotes to pathogens of humans. To this end, comparative genome analysis has served as an important tool. Genome sequence data for many chlamydial lineages are, however, still lacking, hampering our understanding of their evolutionary history. Here, we determined the first high-quality draft genome sequence of the fish pathogen “Candidatus Clavichlamydia salmonicola”, representing a separate genus within the human and animal pathogenic Chlamydiaceae. The “Ca. Clavichlamydia salmonicola” genome harbors genes that so far have been exclusively found in Chlamydia species suggesting that basic mechanisms important for the interaction with chordate hosts have evolved stepwise in the history of chlamydiae. Thus, the genome sequence of “Ca. Clavichlamydia salmonicola” allows to constrain candidate genes to further understand the evolution of chlamydial virulence mechanisms required to infect mammals.

Huanglongbing (HLB) is one of the most destructive diseases in citrus, which imperils the sustainability of citriculture worldwide. The presumed causal agent of HLB, ‘<i>Candidatus</i> Liberibacter asiaticus’ (CLas) is a non-culturable phloem-limited α-proteobacterium transmitted by Asian citrus psyllids (ACP, <i>Diaphorina citri</i> Kuwayama). A widely adopted method for HLB diagnosis is based on quantitative real-time polymerase chain reaction (qPCR). Although HLB diagnostic qPCR provides high sensitivity and good reproducibility, it is limited by time-consuming DNA preparation from plant tissue or ACP and the requirement of proper lab instruments including a thermal cycler to conduct qPCR. In an attempt to develop a quick assay that can be deployed in the field for CLas detection, we developed a real-time loop-mediated isothermal amplification (rt-LAMP) assay by targeting the CLas five copy <i>nrd</i>B gene. The rt-LAMP assay using various plant sample types and psyllids successfully detected the <i>nrd</i>B target as low as ~2.6 Log<sub>10</sub> copies. Although the rt-LAMP assay was less sensitive than laboratory-based qPCR (detection limit ~10 copies), the data obtained with citrus leaf and bark and ACP showed that the rt-LAMP assay has >96% CLas detection rate, compared to that of laboratory-based qPCR. However, the CLas detection rate in fibrous roots was significantly decreased compared to qPCR due to low CLas titer in some root DNA sample. We also demonstrated that the rt-LAMP assay can be used with a crude leaf DNA extract which is fully deployable in the field for quick and reliable HLB screening.

‘Candidatus Liberibacter solanacearum’ (Lso) causes disease symptoms and economic losses in potato, tomato, and other solanaceous crops in North America. Lso is transmitted to plants by the potato psyllid, Bactericera cockerelli, which occurs as distinct haplotypes named western, central, and northwestern that differ in the presence or absence of the bacterial endosymbiont, Wolbachia. Previous work showed that all three vector haplotypes can transmit Lso, but it was not clear whether acquisition and transmission rates of Lso were equal among the haplotypes. The goal of our study was to compare Lso infection rates among psyllids of the western, central, and northwestern haplotypes. Using data collected from several years of periodic testing of Lso infection of laboratory-reared potato psyllid colonies, we showed that psyllids of the western and central haplotypes are more likely to harbor Lso than are psyllids of the northwestern haplotype. We then used greenhouse assays to demonstrate that psyllids of the northwestern haplotype are less likely to acquire and transmit Lso than those of the western haplotype. Lso infection rates corresponded with Wolbachia infection among the three psyllid haplotypes. The Wolbachia-infected central and western haplotypes were more likely to harbor and transmit Lso than the Wolbachia-free northwestern haplotype. Results demonstrate that potato psyllids of the western and central haplotypes pose a greater risk for spread of Lso in crops and suggest a pattern between infection with Lso and Wolbachia in potato psyllid.

IntroductionCandidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date.MethodsIn this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics.ResultsUsing Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples.ConclusionThis study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.