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.

Description of Chryseobacterium timonianum sp. nov., isolated from a patient with pneumonia.

Using a polyphasic taxonomic strategy, an aerobic, Gram-negative, non-motile, yellow pigmented rod isolated from a sputum sample of a patient with pneumonia was characterised. This bacterial strain, designated G972T, could not be identified by our systematic MALDI-TOF screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 98.57% sequence identity with that of Chryseobacterium indologenes 16777T, the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. The major cell fatty acids were identified as 13-methyl-tetradecanoic acid (61%), 3-hydroxy-heptadecanoic acid (16%) and 15-methyl-11-hexadecenoic acid (11%). D-glucose, D-mannose, aesculin, D-maltose, D-trehalose, and gentibiose are the main carbon source. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity values (ANI) of the strain G972T against genomes of the type strains of related species ranged between 18.9 and 32.8% and between 71.46 and 83.61%, respectively, thus confirming again the new species status of the strain. Here, we describe the characteristics of this organism, complete genome sequence and annotation. The 5,390,132 bp size genome contains 4867 protein-coding genes, 89 RNAs (three genes are 5S rRNA, one gene is 16S rRNA, one gene is 23S rRNA and 84 tRNAs) with 35.51% GC content. Finally, on the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we conclude that strain strain G972T (= DSM 103388T = CSUR P2233T) represents a novel species for which we propose the name Chryseobacterium timonianum. The 16S rRNA and genome sequences are available in GenBank database under accession numbers LT161886 and FJVD00000000.

Contemporary challenges and opportunities in the diagnosis and outbreak detection of multidrug-resistant infectious disease.

INTRODUCTION: The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunities for rapidly confronting infections caused by MDRB in the 21st century, including surveillance, detection, identification of resistance mechanisms, and action steps. Expert commentary: In this context, the first critical point for clinical microbiologists is to be able to rapidly detect an abnormal event, an outbreak and/or the spread of a MDRB with surveillance tools so that healthcare policies and therapies adapted to a new stochastic event that will certainly occur again in the future can be implemented.

Whole genome sequence to decipher the resistome of Shewanella algae, a multidrug-resistant bacterium responsible for pneumonia, Marseille, France.

UNLABELLED: We characterize and decipher the resistome and the virulence factors of Shewanella algae MARS 14, a multidrug-resistant clinical strain using the whole genome sequencing (WGS) strategy. The bacteria were isolated from the bronchoalveolar lavage of a hospitalized patient in the Timone Hospital in Marseille, France who developed pneumonia after plunging into the Mediterranean Sea. RESULTS: The genome size of S. algae MARS 14 was 5,005,710 bp with 52.8% guanine cytosine content. The resistome includes members of class C and D beta-lactamases and numerous multidrug-efflux pumps. We also found the presence of several hemolysins genes, a complete flagellum system gene cluster and genes responsible for biofilm formation. Moreover, we reported for the first time in a clinical strain of Shewanella spp. the presence of a bacteriocin (marinocin). CONCLUSION: The WGS analysis of this pathogen provides insight into its virulence factors and resistance to antibiotics.