Mobilome analysis of Achromobacter spp. isolates from chronic and occasional lung infection in cystic fibrosis patients

Achromobacter spp. is an opportunistic pathogen that can cause lung infections in patients with cystic fibrosis (CF). Although a variety of mobile genetic elements (MGEs) carrying antimicrobial resistance genes have been identified in clinical isolates, little is known about the contribution of Achromobacter spp. mobilome to its pathogenicity. To provide new insights, we performed bioinformatic analyses of 54 whole genome sequences and investigated the presence of phages, insertion sequences (ISs), and integrative and conjugative elements (ICEs). Most of the detected phages were previously described in other pathogens and carried type II toxin-antitoxin systems as well as other pathogenic genes. Interestingly, the partial sequence of phage Bcep176 was found in all the analyzed Achromobacter xylosoxidans genome sequences, suggesting the integration of this phage in an ancestor strain. A wide variety of IS was also identified either inside of or in proximity to pathogenicity islands. Finally, ICEs carrying pathogenic genes were found to be widespread among our isolates and seemed to be involved in transfer events within the CF lung. These results highlight the contribution of MGEs to the pathogenicity of Achromobacter species, their potential to become antimicrobial targets, and the need for further studies to better elucidate their clinical impact

Toothbrushes may convey bacteria to the cystic fibrosis lower airways

Recent findings indicate that the oral cavity acts as a bacterial reservoir and might contribute to the transmission of bacteria to the lower airways. Control of a potentially pathogenic microbiota might contribute to prevent the establishment of chronic infection in cystic fibrosis. We evaluated the presence of CF microorganisms in saliva and toothbrushes of CF patients and verify their possible transmission to lower airways. Methods: We assessed the presence of P. aeruginosa, S. aureus, S. maltophilia, A. xylosoxidans, S. marcescens, and yeasts in saliva, toothbrushes and sputum of 38 CF patients and assessed the clonal identity of the strains occurring contemporary in multiple sites by PFGE. Results: At least one of the investigated species was isolated from 60 saliva samples and 23 toothbrushes. S. aureus was the most abundant species, followed by Candida spp. 31 patients contemporary had the same species in sputum and saliva/toothbrush: in most cases, clonal identity of the strains among the different sites was confirmed. Conclusion: Toothbrushes may be sources of oral contamination and might act as reservoirs favoring transmission of potentially pathogenic microorganisms from the environment to the oral cavity and eventually to the LAW. Oral hygiene and toothbrush care are important strategies to prevent CF lung infections

First IncHI2 Plasmid Carrying mcr-9.1, blaVIM-1, and Double Copies of blaKPC-3 in a Multidrug-Resistant Escherichia coli Human Isolate

We report a novel IncHI2 plasmid coharboring blaVIM-1, two copies of blaKPC-3, and mcr-9.1 resistance genes in a human Escherichia coli isolate of the new serogroup O188. The blaVIM-1 gene was included in a class 1 integron, mcr-9.1 in a cassette bracketed by IS903 and \u394IS1R, and blaKPC-3 in two copies within a new composite Tn4401-like transposon. The emergence of carbapenem and colistin resistance genes in a single plasmid is of great concern for upcoming clinical therapies

ScrInHeat: a computational approach for genomic screening of pathogenic factors in poorly studied bacteria

Background: The detection and identification of pathogenic factors (PFs) scattered across a genome can provide useful insights about the pathogenic potential of bacterial strains. Although very important, this process is often carried out in little depth, also due to a lack of tools that predict/identify potential pathogenic factors in poorly characterized species. We developed a collection of computational tools named ScrInHeat that allows to screen for PFs providing standardized annotation and visualization. Methods: ScrInHeat works through the following steps: building of PFs databases, screening of genomic assemblies/sets of proteins, integration of results, and generation of Gene Ontology (GO) annotated heatmaps for a simple results visualization. Its performance was evaluated through comparison against 3 freely available databases/tools with similar purpose: VFDB, PATRIC and ABRicate. Performances were compared using NCBI genomic assemblies of a well- and a poorly-characterized species, respectively Escherichia coli and Achromobacter xylosoxidans. Results: ScrInHeat was able to build reliable PFs databases when compared to the well-curated ones: although some PFs were not identified (62% content overlap), all the sequences within ScrInHeat database were truly related to pathogenicity. Moreover, when compared to the currently available A. xylosoxidans database, ScrInHeat could identify 148 additional PFs. ScrInHeat also offered cellular component, molecular function and biological process GO annotations while reducing the manual effort needed to filter and display results in the form of a heatmap. Conclusions: ScrInHeat proved to be a fast and versatile tool to identify PFs and readily visualize and interpret results with the support of GO annotations. Overall, it represents a new useful starting tool to study poorly characterized bacteria and aid microbiologists by prompting further characterization of putative PFs