Historical, current, and emerging tools for identification and serotyping of Shigella.

The Shigella genus includes serious foodborne disease etiologic agents, with 4 species and 54 serotypes. Identification at species and serotype levels is a crucial task in microbiological laboratories. Nevertheless, the genetic similarity between Shigella spp. and Escherichia coli challenges the correct identification and serotyping of Shigella spp., with subsequent negative repercussions on surveillance, epidemiological investigations, and selection of appropriate treatments. For this purpose, multiple techniques have been developed historically ranging from phenotype-based methods and single or multilocus molecular techniques to whole-genome sequencing (WGS). To facilitate the selection of the most relevant method, we herein provide a global overview of historical and emerging identification and serotyping techniques with a particular focus on the WGS-based approaches. This review highlights the excellent discriminatory power of WGS to more accurately elucidate the epidemiology of Shigella spp., disclose novel promising genomic targets for surveillance methods, and validate previous well-established methods.

Microbial Culturomics Application for Global Health: Noncontiguous Finished Genome Sequence and Description of Pseudomonas massiliensis Strain CB-1T sp. nov. in Brazil.

Culturomics is a new postgenomics field that explores the microbial diversity of the human gut coupled with taxono-genomic strategy. Culturomics, and the microbiome science more generally, are anticipated to transform global health diagnostics and inform the ways in which gut microbial diversity contributes to human health and disease, and by extension, to personalized medicine. Using culturomics, we report in this study the description of strain CB1T ( = CSUR P1334 = DSM 29075), a new species isolated from a stool specimen from a 37-year-old Brazilian woman. This description includes phenotypic characteristics and complete genome sequence and annotation. Strain CB1T is a gram-negative aerobic and motile bacillus, exhibits neither catalase nor oxidase activities, and presents a 98.3% 16S rRNA sequence similarity with Pseudomonas putida. The 4,723,534 bp long genome contains 4239 protein-coding genes and 74 RNA genes, including 15 rRNA genes (5 16S rRNA, 4 23S rRNA, and 6 5S rRNA) and 59 tRNA genes. Strain CB1T was named Pseudomonas massiliensis sp. nov. and classified into the family Pseudomonadaceae. This study demonstrates the usefulness of microbial culturomics in exploration of human microbiota in diverse geographies and offers new promise for incorporating new omics technologies for innovation in diagnostic medicine and global health.

Molecular identification of lice from pre-Columbian mummies.

BACKGROUND: Three distinctly different lineages of head and body lice are known to parasitize humans. One lineage includes head and body lice and is currently worldwide in distribution (type A). The other 2 (types B and C) include only head lice and are geographically restricted. It was hypothesized that head louse phylotypes were exchanged only recently, after European exploration and colonization (after Columbus). METHODS: To determine which louse type or types were found in the Americas before European colonization, we used polymerase chain reaction in 2 laboratories to amplify DNA from 2 genes (Cytb and Cox1) belonging to 1000-year-old lice collected from Peruvian mummies. RESULTS: Only the worldwide type (type A) was found. Therefore, this phylotype was worldwide before European colonization, as type A lice were common in Europe, Africa, and Asia. CONCLUSIONS: The findings of this study show that several phylotypes of head lice have coexisted for centuries in humans and support the claim that type A lice were present in the Americas before the time of Columbus.