Proteomics boosts translational and clinical microbiology.

The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

Antibacterial and anti-biofilm effects of cathelicidin peptides against pathogens isolated from cystic fibrosis patients.

Six different cathelicidin-derived peptides were compared to tobramycin for antibacterial and anti-biofilm effects against S. aureus, P. aeruginosa, and S. maltophilia strains isolated from cystic fibrosis patients. Overall, SMAP-29, BMAP-28, and BMAP-27 showed relevant antibacterial activity (MIC(50) 4-8µg/ml), and in some cases higher than tobramycin. In contrast, indolicidin, LL-37, and Bac7(1-35) showed no significant antimicrobial activity (MIC(50)>32µg/ml). Killing kinetics experiments showed that in contrast to tobramycin the active cathelicidin peptides exert a rapid bactericidal activity regardless of the species tested. All three peptides significantly reduced biofilm formation by S. maltophilia and P. aeruginosa strains at 1/2× MIC, although at a lower extent than tobramycin. In addition, BMAP-28, as well as tobramycin, was also active against S. aureus biofilm formation. Preformed biofilms were significantly affected by bactericidal SMAP-29, BMAP-27 and BMAP-28 concentrations, although at a lesser extent than tobramycin. Overall, our results indicate the potential of some cathelicidin-derived peptides for the development of novel therapeutic agents for cystic fibrosis lung disease.

Molecular epidemiology of meticillin-resistant Staphylococcus aureus in Italian cystic fibrosis patients: a national overview.

BACKGROUND: The genetic background, transmissibility and virulence of MRSA have been poorly investigated in the cystic fibrosis (CF) population. The aim of this multicentre study was to analyse MRSA strains isolated from CF patients attending nine Italian CF care centres during a two-year period (2004-2005). All CF patients infected by MRSA were included. METHOD: Antibiotic susceptibility testing, SCCmec typing, Panton-Valentine Leukocidin (PVL) production, and Multi Locus Sequence Typing (MLST) analysis were carried out on collected isolates (one strain per patient). RESULTS: One hundred and seventy-eight strains isolated from 2360 patients attending the participating centres were analysed. We detected 56 (31.4%) SCCmec IV PVL-negative strains, with a resistance rate of 80.3% to clindamycin and of 14.5% to trimethoprim/sulphamethoxazole. MLST analysis showed that many isolates belonged to known epidemic lineages. The largest clone grouping of 29 isolates from 6 centres had the genetic background (ST8-MRSA-IV) of the American lineages USA300 and USA500, thus demonstrating the diffusion of these strains in a population considered at risk for hospital associated infections. CONCLUSIONS: Known MRSA epidemic clones such as USA600, USA800, USA1100, and UK EMRSA-3 were described for the first time in Italy. The diffusion of MRSA strains with high pathogenic potential in the CF population suggests that analysis of the MRSA strains involved in pulmonary infections of these patients is needed.

Pseudomonas aeruginosa infection in cystic fibrosis caused by an epidemic metallo-ß-lactamase-producing clone with a heterogeneous carbapenem resistance phenotype.

An epidemic IMP-13 metallo-ß-lactamase (MBL)-producing Pseudomonas aeruginosa clone, causing infections and even large outbreaks in Italian critical care settings, was detected in a young cystic fibrosis patient. In this patient, the chronic infection was sustained by distinct clonal sub-populations of the MBL-producing P. aeruginosa clone, either susceptible or resistant to carbapenems. These findings underscore the importance of infection prevention practices in cystic fibrosis settings and pose an important diagnostic and therapeutic challenge.

Subinhibitory concentrations of moxifloxacin decrease adhesion and biofilm formation of Stenotrophomonas maltophilia from cystic fibrosis.

Stenotrophomonas maltophilia is an emerging nosocomial bacterial pathogen that is currently isolated with increasing frequency from the airways of cystic fibrosis (CF) patients. In this study the effect of subinhibitory concentrations (subMICs) of moxifloxacin on adhesion, biofilm formation and cell-surface hydrophobicity of two strains of S. maltophilia isolated from CF patients were evaluated. Adhesion and biofilm formation assays were carried out on polystyrene and quantified by colony counts. Cell-surface hydrophobicity was determined by a test for adhesion to n-hexadecane. Moxifloxacin at 0.03x and 0.06x MIC caused a significant decrease in adhesion and biofilm formation by both strains tested. A significant reduction in cell-surface hydrophobicity following exposure to subMICs of moxifloxacin was observed for one strain only. The results of the present study provide an additional rationale for the use of moxifloxacin in CF patients and more generally in biofilm-related infections involving S. maltophilia.

Molecular characterization of virulence determinants of Stenotrophomonas maltophilia strains isolated from patients affected by cystic fibrosis.

Stenotrophomonas maltophilia is an emerging nosocomial bacterial pathogen which is currently isolated with increasing frequency from the airways of cystic fibrosis (CF) patients. In this study 13 S. maltophilia strains (11 isolated from the airways of independent CF patients, and two non-CF respiratory reference strains) have been characterized for the expression of several virulence-associated factors. In particular, the ability to form biofilm on abiotic surfaces has been determined and correlated with different features, such as motility, adherence and the ability to invade A549 respiratory epithelial cells. Moreover, the presence of a flagellum-associated gene as well as that of the StmPr1 gene, which encodes an extracellular protease, have been determined by Southern blot hybridization. Our data indicate that the different degree of biofilm formation exhibited by the 11 CF isolates does not correlate with motility, ability to adhere to and invade A549 cells, or with the presence of flagella. On the other hand, among the CF isolates the StmPr1 gene was found only in two strains, both able to establish chronic lung infections in CF patients. Moreover, only four of the strains analyzed show a temperature-independent antibiotic-resistance profile, suggesting either a different origin of these strains or an intervening adaptation to host tissues.

Transmission of Burkholderia cepacia complex: evidence for new epidemic clones infecting cystic fibrosis patients in Italy.

To analyze national prevalence, genomovar distribution, and epidemiology of the Burkholderia cepacia complex in Italy, 225 putative B. cepacia complex isolates were obtained from 225 cystic fibrosis (CF) patients attending 18 CF centers. The genomovar status of these isolates was determined by a polyphasic approach, which included whole-cell protein electrophoresis and recA restriction fragment length polymorphism (RFLP) analysis. Two approaches were used to genotype B. cepacia complex isolates: BOX-PCR fingerprinting and pulsed-field gel electrophoresis (PFGE) of genomic macrorestriction fragments. A total of 208 (92%) of 225 isolates belonged to the B. cepacia complex, with Burkholderia cenocepacia as the most prevalent species (61.1%). Clones delineated by PFGE were predominantly linked to a single center; in contrast, BOX-PCR clones were composed of isolates collected either from the same center or from different CF centers and comprised multiple PFGE clusters. Three BOX-PCR clones appeared of special interest. One clone was composed of 17 B. cenocepacia isolates belonging to recA RFLP type H. These isolates were collected from six centers and represented three PFGE clusters. The presence of insertion sequence IS 1363 in all isolates and the comparison with PHDC reference isolates identified this clone as PHDC, an epidemic clone prominent in North American CF patients. The second clone included 22 isolates from eight centers and belonged to recA RFLP type AT. The genomovar status of strains with the latter RFLP type is not known. Most of these isolates belonged to four different PFGE clusters. Finally, a third clone comprised nine B. pyrrocinia isolates belonging to recA RFLP type Se 13. They represented three PFGE clusters and were collected in three CF centers.

Group A streptococcal genotypes from pediatric throat isolates in Rome, Italy.

In a study assessing genetic diversity, 114 group A streptococcus (GAS) isolates were recovered from pediatric pharyngitis patients in Rome, Italy. These isolates comprised 22 different M protein gene (emm) sequence types, 14 of which were associated with a distinct serum opacity factor/fibronectin binding protein gene (sof) sequence type. Isolates with the same emm gene sequence type generally shared a highly conserved chromosomal macrorestriction profile. In three instances, isolates with dissimilar macrorestriction profiles had identical emm types; in each of these cases multilocus sequence typing revealed that isolates with the same emm type were clones having the same allelic profiles. Ninety-eight percent of the pharyngeal isolates had emm types previously found to be highly associated with mga locus gene patterns commonly found in pharyngeal GAS isolates.

Fatal pulmonary infection due to multidrug-resistant Mycobacterium abscessus in a patient with cystic fibrosis.

We report a case of fatal pulmonary infection caused by Mycobacterium abscessus in a young patient with cystic fibrosis, who underwent bipulmonary transplantation after a 1-year history of severe lung disease. Fifteen days after surgery he developed septic fever with progressive deterioration in lung function. M. abscessus, initially isolated from a pleural fluid specimen, was then recovered from repeated blood samples, suggesting a disseminated nature of the mycobacterial disease. Drug susceptibility testing assay, performed on two sequential isolates of the microorganism, showed a pattern of multidrug resistance. Despite aggressive therapy with several antimycobacterial drugs, including clarithromycin, the infection persisted, and the patient died.

Paecilomyces variotii peritonitis in an infant on automated peritoneal dialysis.

Fungal peritonitis is a serious complication of chronic peritoneal dialysis (CPD) and is frequently associated with CPD drop-out. Paecilomyces variotii, a common saprophytic fungus, rarely causes human infection. To date, only nine adult or adolescent patients with P. variotii peritonitis during continuous ambulatory peritoneal dialysis have been reported. In all patients, successful treatment required antifungal therapy and removal of the peritoneal catheter. We report the first case of P. variotii peritonitis in an infant on automated peritoneal dialysis successfully treated with combined intraperitoneal and oral fluconazole, without removal of the peritoneal catheter.

Fatal disseminated Nocardia farcinica infection in a renal transplant recipient.

Six years after a renal cadaver transplant, a 20-year-old girl developed multiple painful cutaneous abscesses and bilateral pneumonia secondary to Nocardia farcinica infection. Despite broad in vitro sensitivity to several antibiotic agents and aggressive medical treatment, the patient failed to respond and died after 10 weeks of therapy. We conclude that Nocardia farcinica is a very aggressive organism in immunocompromised patients and is often resistant to antimicrobial agents.

[Acute nonbacterial bronchopneumopathies in the 1st years of life. Diagnostic strategies and clinico-epidemiological peculiarities]. / Broncopenumopatie acute non batteriche nei primi anni di vita. Strategie diagnostiche e peculiarità clinico-epidemiologiche.

The authors summarise diagnostic strategies an clinical epidemiologic peculiarities of non-bacterial bronchopneumopathies in children. The role of classic viral agents (virus influenzal A-B, virus parainfluenza 2-3, RVS) is stressed without neglecting the role of other etiologic agents such as Chlamydia trachomatis, Mycoplasma pneumoniae and Pneumocystis carinii. The Authors point out the necessity of direct investigation (viral cultures, direct investigation in IF and ELISA, investigation with DNA probe use, etc.) and indirect serologic investigation to obtain the greatest possible accuracy an early diagnosis.