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Bacterial small RNAs have emerged as crucial regulators in complex networks controlling diverse phenotypes. Two groups, Mediati et al. and McKellar et al., have leveraged CLASH technology and the global regulatory potential of RNase III to build a rich landscape of RNA interactions in Staphylococcus aureus, revealing post-transcriptional control of virulence and new mechanistic themes for exploration.

Streptococcus suis, a ubiquitous bacterial colonizer in pigs, has recently extended host range to humans, leading to a global surge of deadly human infections and three large outbreaks since 1998. To better understand the mechanisms for the emergence of cross‐species transmission and virulence in human, we have sequenced 366 S. suis human and pig isolates from 2005 to 2016 and performed a large‐scale phylogenomic analysis on 1,634 isolates from 14 countries over 36 years. We show the formation of a novel human‐associated clade (HAC) diversified from swine S. suis isolates. Phylogeographic analysis identified Europe as the origin of HAC, coinciding with the exportation of European swine breeds between 1960s and 1970s. HAC is composed of three sub‐lineages and contains several healthy‐pig isolates that display high virulence in experimental infections, suggesting healthy‐pig carriers as a potential source for human infection. New HAC‐specific genes are identified as promising markers for pathogen detection and surveillance. Our discovery of a human‐associated S. suis clade provides insights into the evolution of this emerging human pathogen and extend our understanding of S. suis epidemics worldwide., The increasing incidences of human infections caused by Streptococcus suis indicate that this bacterium may undergo adaptive evolution in humans. In this study, a novel clade of S. suis strongly associated with human infections was identified.

RNA-binding proteins (RBPs) function in all aspects of RNA processes including stability, structure, export, localization and translation, and control gene expression at the posttranscriptional level. To investigate the roles of RBPs and their direct RNA ligands in vivo, recent global approaches combining RNA immunoprecipitation and deep sequencing (RIP-seq) as well as UV-cross-linking (CLIP-seq) have become instrumental in dissecting RNA-protein interactions. However, the computational analysis of these high-throughput sequencing data is still challenging. Here, we provide a computational pipeline to analyze CLIP-seq and RIP-seq datasets. This generic analytic procedure may help accelerate the identification of direct RNA-protein interactions from high-throughput RBP profiling experiments in a variety of bacterial species.

Bacteria express many small RNAs for which the regulatory roles in pathogenesis have remained poorly understood due to a paucity of robust phenotypes in standard virulence assays. Here we use a generic 'dual RNA-seq' approach to profile RNA expression simultaneously in pathogen and host during Salmonella enterica serovar Typhimurium infection and reveal the molecular impact of bacterial riboregulators. We identify a PhoP-activated small RNA, PinT, which upon bacterial internalization temporally controls the expression of both invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity causes pervasive changes in coding and noncoding transcripts of the host. Interspecies correlation analysis links PinT to host cell JAK-STAT signalling, and we identify infection-specific alterations in multiple long noncoding RNAs. Our study provides a paradigm for a sensitive RNA-based analysis of intracellular bacterial pathogens and their hosts without physical separation, as well as a new discovery route for hidden functions of pathogen genes.

Thirty-eight cows in a herd were determined to be positive for bovine tuberculosis (TB). The bacterial isolation and characterization with multiplex PCR identified six Mycobacterium tuberculosis isolates. The Mycobacterium bovis and M. tuberculosis infection induced comparable pathology in cattle in both gross pathology and histopathology based on the qualitative assessment of the sampled lung tissues. The spoligotyping demonstrated that cow M. tuberculosis isolates belonged to Beijing family strains. Meanwhile, the isolates from tuberculosis patients hospitalized in the local hospitals were assessed. No M. bovis strains were identified in 186 human isolates. Eighty-two percent (153/186) of M. tuberculosis isolates were Beijing-family strains. The 12 loci MIRU genotyping revealed that the first three prevalent patterns were 2232-2517-3533, 2233-2517-3533, and 2223-2517-3533. The bovine M. tuberculosis isolates were the third dominant MIRU pattern. The further 16 loci MIRU-VNTR assay confirmed that the bovine M. tuberculosis strains shared the same pattern suggesting there was a common source causing cow infection and an epidemiological link between cow and human M. tuberculosis infection. On the other hand, the retrospective investigation for the past three years' cases of TB patients from local hospitals revealed 0.34% (17/5011) prevalence of M. bovis infection in local people. In conclusion, in TB high-burden countries like China where bovine and human TB coexists, the fact that cattle maintain both M. bovis and M. tuberculosis would be a potential challenge to both Stop TB Plan of humans and bovine TB eradication scheme.

This study aimed to establish human IFN-gamma (hIFN-gamma) in vitro release assay and to apply it in diagnosis of human tuberculosis. Human IFN-gamma gene was cloned and expressed in Escherichia coli. The recombinant hIFN-gamma was purified and used as immunogen to immunize mice and rabbits respectively. Monoclonal and polyclonal antibodies were respectively developed and a sandwich ELISA was established. The heparized whole blood from 111 active tuberculosis patients and 292 clinical healthy controls were collected. The blood was stimulated with tuberculosis specific fused antigen ESAT-6/CFP-10 and the plasma was collected for IFN-gamma detection. The sensitivity for tuberculosis diagnosis was 95.5%, whereas the positive detection rate for the healthy controls was 16.7%. There was a significant difference between the patients and healthy controls (P0.01) indicating that this assay had a high sensitivity and specificity, and thus could be promising in tuberculosis diagnosis.

Mycobacterial interspersed repetitive unit (MIRU) typing has been found to allow rapid, reliable, high-throughput genotyping of Mycobacterium tuberculosis, and may represent a feasible approach to study M. tuberculosis molecular epidemiology. To evaluate the use of MIRU typing in discriminating M. tuberculosis strains, isolates from 105 patients in Wuhan City, China, were genotyped by this method as compared to spoligotyping. MIRU typing identified 55 types that defined 21 clusters and 34 unique isolates. The discriminatory power was high [Hunter–Gaston discriminatory index (HGDI), 0.97]. Spoligotyping showed that 86 (81.9 %) of 105 isolates belonged to the Beijing family genotype. For Beijing family and non-Beijing strains, the discriminatory power of MIRU was high (HGDI, 0.95 and 0.98, respectively). Among the alleles of the MIRU loci for the Beijing family, only locus 26 was highly discriminative, but for non-Beijing strains, loci 10, 16 and 26 were highly discriminative. MIRU typing is a simple and fast method which may be used for preliminary screening of M. tuberculosis isolates in China.