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

Bacterial cell shape regulation: testing of additional predictions unique to the two-competing-sites model for peptidoglycan assembly and isolation of conditional rod-shaped mutants from some wild-type cocci

The two-competing-sites model for peptidoglycan assembly for bacterial cell shape regulation suggests that in rods, bacterial cell shape depends on the balance between two reactions (sites), one responsible for lateral wall elongation and the other responsible for septum formation. The two reactions compete with each other so that no lateral wall can be formed during septum formation and vice versa. When the site for lateral wall elongation overcomes that for septum formation, long rods or filaments are formed and cell division may be blocked. When the reaction leading to septum formation is hyperactive compared with the other, coccobacilli or cocci are formed. Other bacteria carry only one site for peptidoglycan assembly and can grow only as cocci. The two-competing-sites model predicts that two different types of cocci exist (among both morphology mutants and wild-type strains); one carries only the site for septum formation, whereas the other also carries the site for lateral wall elongation, the former site predominating over the latter. As a consequence of the inhibition (by antibiotics or by mutations) of septum formation in wild-type cocci of various species and in coccoid morphology mutants, some cocci are expected to undergo transition to rod shape and others are not. We have evaluated these predictions and show that they are in agreement. In fact, we found that among wild-type cocci belonging to 13 species, those of 6 species formed rods, whereas the remaining organisms maintained their coccal shape when septa were inhibited by antibiotics. Some coccoid morphology mutants of rod-shaped bacteria underwent coccus-to-rod transition after septum inhibition by antibiotics, whereas others maintained their coccal shape. When a mutation that causes septum inhibition was expressed in a morphology mutant of Klebsiella pneumoniae grown as a coccus, transition to rod shape was observed. A total of 914 mutants unable to form colonies at 42 degrees C were isolated from the coccoid species mentioned above. Between 75 and 95% of the mutants isolated from the species that formed rods when septum formation was inhibited by antibiotics but none of those isolated from the others underwent coccus-to-rod transition upon incubation at the nonpermissive temperature

Identification of a gene (arpU) controlling muramidase-2 export in Enterococcus hirae

Muramidase-2 of Enterococcus hirae is a 74-kDa peptidoglycan hydrolase that plays a role in cell wall growth and division. To study its regulation, we isolated a mutant defective in muramidase-2 release under certain growth conditions. This mutant had cell walls which apparently lacked 74-kDa muramidase-2 but which accumulated two proteolytic fragments of 32 and 43 kDa, which exhibited muramidase-2 activity in the membrane fraction. By complementation cloning, we identified a 2.6-kb fragment of the E. hirae chromosome containing a gene cluster coding for proteins of 58 to 137 amino acids. One of these genes (arpU), which encoded a 15.9-kDa protein, was shown to complement the defect of the A9 mutant in trans. We propose that this gene may be involved in the regulation of muramidase-2 export

Mechanisms of resistance of enterococci to beta-lactam antibiotics

Two mechanisms are responsible for resistance of enterococci to beta-lactam antibiotics: alterations of penicillin-binding proteins and production of a beta-lactamase. The latter has been found in a few clinical isolates of Enterococcus faecalis, whereas the former appears to account for resistance in most strains. A correlation has been established between the amount of a particular penicillin-binding protein which has a low affinity for penicillin and the level of resistance. The higher activity of some penicillins, as compared to cephalosporins, has been related to the relatively higher affinity for these penicillins of the penicillin-binding protein involved in the mechanism of resistance. Alterations in the autolytic enzyme pattern have been associated with the paradoxical response to bactericidal activity of penicillin often exhibited by Enterococcus faecalis clinical isolates

Influenza del fattore sigma RpoS sulla sopravvivenza di Escherichia coli in stato vitale ma non coltivabile

Valutazione dell'influenza di Rpos o fattore sigma alternativo sula capacit\ue0 di sopravvivenza di Escserichia coli in presenza di situazioni di stress ambientale. E' stato indotto lo stato VBNC in vari mutanti di E.coli difettivi in rpoS: si \ue8 valutata la cinetica di acquisizione delo stato VBNC e la possibilit\ue0 di "rivitalizzazione" rispetto ai ceppi selvaggi. I mutanti RpoS-difettivi muoiono pi\uf9 rapidamente e presentano una capacit\ue0 di ricrescita molto pi\uf9 scarsa rispetto ai ceppi progentori, indicando un probabile ruolo di rpoS nella fase di entrata e mantenimento dello stato VBN

Peptidoglycan synthesis and its fine chemical composition in dividing and not dividing Klebsiella pneumoniae cocci

Peptidoglycan synthesis and its fine chemical composition were studied in dividing and in non-dividing Klebsiella pneumoniae cocci and compared with rods. The beta-lactam mecillinam, a specific inhibitor of lateral wall elongation which causes rod-to-sphere transition in rods, showed 50% inhibition of the peptidoglycan in normal rods of the parent Mir A12 only if added at an early stage of the cell cycle and no effect if added later or during septation. In the rods of the mutant Mir M7, mecillinam was shown to inhibit 50% of peptidoglycan synthesis until rods become cocci, and thereafter to be absolutely devoid of effects. On the contrary, piperacillin, a specific inhibitor of septum formation, was active on all strains regardless of their cell shape, only if added at 20 and removed at 40 min of the cell cycle. As regards the analysis of peptidoglycan fine chemical composition, bacteria dividing as cocci showed alterations in the muropeptide composition consisting in a 50-fold increase in the tetramer family. This alteration was not seen in the cocci that did not divide as such. These results confirm our previous claim that septum formation and lateral wall elongation are mutually exclusive in normal rods and that septum formation requires the synthesis of a peptidoglycan of different chemical composition

In vitro adhesion to human cells by viable but nonculturable Enterococcus faecalis

The ability of viable but nonculturable (VBNC) Enterococcus faecalis to adhere to Caco-2 and Girardi heart cultured cells and to urinary tract epithelial cells (ECs) was studied. Enterococci were harvested during the vegetative growth phase (early exponential and stationary), in the VBNC state, and after recovery of the ability to divide. VBNC bacteria maintained their adherence capability but the efficiency of attachment was reduced by about 50 to 70%, depending on the target cell employed. The decrease was transient, since enterococci that regained their culturability showed adherence values similar to those observed for actively growing cells. Analysis of the invasive properties of E. faecalis revealed that the VBNC state caused a decrease in the number of bacteria that entered the cultured HEK cells as a result of the reduction in the number of adhering bacteria. These results highlight the importance of studies of the VBNC phenomenon, with respect to both microbial survival in the environment and the impact on human health

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