Messages from the first International Conference on Clinical Metagenomics (ICCMg)

Abstract

Background: It has been suggested that prophages in the ST398 S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections. We carried out the first characterization of the various prophages carried by 76 ST398 bloodstream infection (BSI) isolates obtained over 9 years of observation. Results: Whole-genome sequencing of 22 representative isolates showed (1) the presence of the φ3-prophage and diverse genetic features typical of animal-associated isolates (i.e., SCCmec XI element, Tn916 transposon and non φ3-prophages) in a majority of BSI isolates, (2) one BSI isolate devoid of the φ3-prophage but otherwise similar to an animal-infecting isolate, (3) 35 prophages carrying numerous genes previously associated with virulence or immune evasion in animal models of staphylococcal infections. The analysis of prophage content in all 76 BSI isolates showed an increasing prevalence of polylysogeny over time. Overall, over the course of the last 10 years, the BSI isolates appear to have acquired increasing numbers of genetic features previously shown to contribute to bacterial adaptation and virulence in animal models of staphylococcal infections. Conclusions: We hypothesize that lysogeny has played a significant role in increasing the ability of the ST398 clone to cause infections in humans. Our findings highlight the risk that the ST398 lineage will increase its threat to public health by continuing to acquire virulence and/or multiple antibiotic-resistance genes from hospitalassociated clones of Staphylococcus aureus.

Diverticular Disease: a Gut Microbiota Perspective

“…However, in the foreseeable future, the management of many aspects of diverticular disease will take into consideration the intestinal microbiome. First, metagenomics is rapidly entering clinical practice, and many ongoing studies will contribute to define the reference standards for gut microbiota composition and the clinical significance of dysbiosis [4]. From this perspective, clinical profiling of the gut microbiota will allow a personalized management of several intestinal and extraintestinal diseases, including diverticulosis.…”

“…Recent studies have focused on the possible role of the gut microbiota. The emergence of culture-independent methods of microbial profiling has in fact improved the understanding of the extreme complexity of both fecal and mucosa-associated microbiota [3,4], highlighting its fundamental role in the onset and regulation of inflammation [5]. The pathophysiological role of the intestinal microbiota has been extensively studied for other gastrointestinal diseases, such as inflammatory bowel disease (IBD) [6] and colon cancer [7,8], and even for extraintestinal diseases, including metabolic syndrome [9], neurodegenerative diseases [10], kidney stones [11] and muscle-wasting disorders [12,13].…”

Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation

“…Though wet-laboratory workflows and data analysis pipelines combined with regulatory requirements are rapidly evolving, continued improvements are nonetheless needed. International conferences have recently been developed to discuss key aspects related to CMg [ 142 ]. Thus, as we move towards a CMg era, diagnostic laboratories should consider implementing the assay into practice particularly when standard microbiological testing fails to identify the putative pathogen.…”

Research Based on Multimodal Deep Feature Fusion for the Auxiliary Diagnosis Model of Infectious Respiratory Diseases

“…At present, the cause of 60% infectious diseases is still unclear [1]. Clinical metagenomics is a detection technology that uses high-throughput sequencing technology to clarify the classification and function of all microorganisms in a sample without relying on traditional microbial culture [2,3]. is technology can simultaneously detect bacteria, fungi, viruses, and parasites in the same sample without any bias and does not require specific amplification.…”