Eubiosis and dysbiosis: the two sides of the microbiota.

The microbial ecosystem of the gastrointestinal tract is characterized by a great number of microbial species living in balance by adopting mutualistic strategies. The eubiosis/dysbiosis condition of the gut microbiota strongly influences our healthy and disease status. This review briefly describes microbiota composition and functions, to then focus on eubiosis and dysbiosis status: the two sides of the microbiota.

Possible antiviral effect of ciprofloxacin treatment on polyomavirus BK replication and analysis of non-coding control region sequences.

Acute renal dysfunction (ARD) is a common complication in renal transplant recipients. Multiple factors contribute to ARD development, including acute rejection and microbial infections. Many viral infections after kidney transplantation result from reactivation of "latent" viruses in the host or from the graft, such as the human Polyomavirus BK (BKV). We report the case of a 39 year-old recipient of a 2nd kidney graft who experienced BKV reactivation after a second episode of acute humoral rejection. A 10-day treatment with the quinolone antibiotic ciprofloxacin was administered with an increase of immunosuppressive therapy despite the active BKV replication. Real Time PCR analysis performed after treatment with ciprofloxacin, unexpectedly showed clearance of BK viremia and regression of BK viruria. During the follow-up, BK viremia persisted undetectable while viruria decreased further and disappeared after 3 months.BKV non-coding control region sequence analysis from all positive samples always showed the presence of archetypal sequences, with two single-nucleotide substitutions and one nucleotide deletion that, interestingly, were all representative of the subtype/subgroup I/b-1 we identified by the viral protein 1 sequencing analysis.We report the potential effect of the quinolone antibiotic ciprofloxacin in the decrease of the BKV load in both blood and urine.

Klebsiella pneumoniae ST258 producing KPC-3 identified in italy carries novel plasmids and OmpK36/OmpK35 porin variants.

A carbapenemase-resistant Klebsiella pneumoniae strain, clone ST258 producing KPC-3, was fully characterized. The entire plasmid content was investigated, thereby identifying plasmids of the IncFII(k) (two of them similar to pKPQIL and pKPN3, respectively), IncX, and ColE types, carrying a formidable set of resistance genes against toxic compounds, metals, and antimicrobial drugs and a novel iron(III) uptake system.

Retrospective case-control analysis of patients with staphylococcal infections receiving daptomycin or glycopeptide therapy.

Glycopeptides have been considered the antimicrobials of choice for serious meticillin-resistant Staphylococcus aureus (MRSA) and meticillin-resistant coagulase-negative staphylococci (MR-CoNS) infections for several years. Daptomycin is a new option for the treatment of these infections, including those exhibiting reduced susceptibility to glycopeptides. The aim of this study was to compare glycopeptides and daptomycin for the treatment of infections caused by MRSA or MR-CoNS. Data for 106 patients with bloodstream infections (bacteraemia or infective endocarditis) or skin and soft-tissue infections (SSTIs) were retrospectively reviewed, of which 43 were treated with daptomycin (DAP group) and 63 were treated with vancomycin or teicoplanin (GLYCO group). Patients included in the two comparison groups were homogeneous in terms of age, risk factors and clinical severity. Aetiology was mainly represented by MRSA in both groups, followed by various species of MR-CoNS. Daptomycin was used more frequently in patients with central venous catheter-associated bacteraemia or pacemaker-associated infection. Patients with SSTIs included in the GLYCO group had a longer mean duration of antibiotic therapy (18.2 days vs. 14.6 days; P=0.009) and a longer mean length of hospital stay (28.2 days vs. 19.6 days; P=0.01) compared with those included in the DAP group. A longer mean duration of antibiotic therapy was also observed in patients with bloodstream infections receiving glycopeptide therapy (25.6 days vs. 18 days; P=0.004). In conclusion, the good clinical efficacy of daptomycin is associated with a more rapid resolution of the clinical syndrome and a reduced length of hospitalisation. This latter aspect may have important pharmacoeconomic implications, promoting the use of daptomycin in the clinical setting.

An ertapenem-resistant extended-spectrum-beta-lactamase-producing Klebsiella pneumoniae clone carries a novel OmpK36 porin variant.

Carbapenem-resistant Klebsiella pneumoniae caused an outbreak in a hospital in Rome, Italy. The clinical isolates were tested by antimicrobial susceptibility testing, pulsed-field gel electrophoresis, multilocus sequence typing, plasmid typing, and ß-lactamase identification. The OmpK35 and OmpK36 porins were analyzed by SDS-PAGE, and their genes were amplified and sequenced. Complementation experiments were performed using a recombinant unrelated ompK36 gene. An ertapenem-resistant and imipenem- and meropenem-susceptible clone was identified and assigned to the sequence type 37 lineage by MLST; it carried SHV-12 and CTX-M-15 ESBLs, did not produce the OmpK35 due to a nonsense mutation, and expressed a novel OmpK36 variant (OmpK36V). This variant showed two additional amino acids located within the L3 internal loop, one of the highly conserved domains of the protein. Two isolates of the same clone also exhibited resistance to imipenem and meropenem, due to the loss of OmpK36 expression by a nonsense mutation occurring in the ompK36V variant gene. These were the first carbapenem-resistant K. pneumoniae isolates identified within the hospital. Screening for the ompK36V gene of unrelated K. pneumoniae isolates derived from patients from 2006 to 2009 demonstrated the high frequency of this gene variant as well as its association with ertapenem resistance, reduced susceptibility to meropenem, and susceptibility to imipenem.

Molecular Characterization of Stenotrophomonas maltophilia isolates from cystic fibrosis patients and the hospital environment.

OBJECTIVES: To ascertain whether cystic fibrosis (CF) patients are colonized or infected with unique or multiple strains of Stenotrophomonas maltophilia; to understand whether some strains colonize or infect more than 1 patient, indicating clonal spread; and to explore the molecular heterogeneity of hospital water isolates and their correlation with clinical isolates. SETTING: The regional CF center of Policlinico "Umberto I" of Rome, Italy. METHODS: The study was carried out on a random sample of S. maltophilia isolates (n = 110) collected from CF patients (n = 50) during the period 2002-2005 and on 24 water isolates obtained during a monitoring program in the first 6 months of 2005. Home environmental samplings were not performed. All isolates, which were recovered from cultures of specimens obtained in both inpatient and outpatient settings, were genotyped with DNA macrorestriction analysis with the restriction enzyme XbaI and pulsed-field gel electrophoresis. RESULTS: One-third of the patients with repeated episodes of S. maltophilia infection or colonization hosted more than 1 strain. A potential transmission, defined as the isolation of the same strain in 2 or more patients, occurred 5 times, showing a frequency of potential transmission episodes slightly higher than previously reported. Water, taps, and sinks of the different rooms of the CF center tended to be persistently colonized with the same strain of S. maltophilia, with no correlation between clinical and water-associated isolates. CONCLUSIONS: The study does not provide sufficient data to conclude definitively that isolation of colonized or infected CF patients and control of hospital water systems contamination would be beneficial infection control measures. Epidemiologic analytical studies that correlate the presence of S. maltophilia with clinical outcomes are strongly needed.

Diagnosis of neurological herpesvirus infections: real time PCR in cerebral spinal fluid analysis.

Human herpesviruses (HHVs) cause many serious acute and persistent central nervous system (CNS) disorders. Because these infections manifest with various, often non-specific, symptoms and signs, and because specific therapy is often available, accurate diagnosis is essential. Cerebrospinal fluid (CSF) from 146 patients with acute meningitis or meningoencephalitis and 9 with "other neurological disorders" were analyzed by using an automatic system for nucleic acid extraction and quantitative real-time polymerase chain reaction (PCR) for herpes simplex 1 and 2 (HSV-1, HSV-2), Epstein-Barr virus (EBV), human cytomegalovirus (HCMV), herpesvirus-6 (HHV-6), and varicella-zoster virus (VZV). HHVs DNA was detected in 52 of 155 (33.5%) analyzed samples. In 39 CSF samples from patients with meningoencephalitis we found: VZV in 13, HSV-1 in 12, EBV in 6, HHV-6 in 4, and HSV-2 in 4. Co-infections of EBV and HSV-2, HSV-1 and HSV-2, HSV-1 and VZV were also disclosed in four cases. In addition, two patients with Guillain-Barré syndrome had HCMV and one showed HHV6 positivity, two patients with myelitis / polymyeloradiculitis had VZV and HCMV respectively, HHV-6 DNA was found in one patient with lateral amyotrophic sclerosis. Three CSF specimens from HIV-infected patients with CNS complications had HHV-6 or EBV DNA. Moreover quantitative data were also correlated to clinical conditions to obtain more information on the virus aetiopathogenic role.

Molecular epidemiology of Escherichia coli producing extended-spectrum beta-lactamases isolated in Rome, Italy.

Escherichia coli strains producing extended-spectrum beta-lactamases (ESBLs) are a major problem in many different hospitals worldwide, causing outbreaks as well as sporadic infections. The prevalence of Escherichia coli ESBL producers was analyzed in a surveillance study performed on the population attending the Policlinico Umberto I, the largest university hospital in Rome, Italy. We also investigated genotypes, pathogenicity islands, and plasmids in the ESBL-positive E. coli isolates as further markers that are useful in describing the epidemiology of the infections. In this survey, 163 nonreplicate isolates of Escherichia coli were isolated from patients from 86 different wards, and 28 were confirmed as ESBL producers. A high prevalence (26/28) of CTX-M-15 producers was observed within the bacterial population circulating in this hospital, and the dissemination of this genetic trait was associated with the spread of related strains; however, these do not have the characteristics of a single epidemic clone spreading. The dissemination was also linked to horizontal transfer among the prevalent E. coli genotypes of multireplicon plasmids showing FIA, FIB, and FII replicons in various combinations, which are well adapted to the E. coli species. The analysis of related bacteria suggests a probable interpatient transmission occurring in several wards, causing small outbreaks.

Outbreak of Acinetobacter baumannii producing the carbapenem-hydrolyzing oxacillinase OXA-58 in Rome, Italy.

In this study 45 epidemic and sporadic isolates of Acinetobacter baumannii were investigated by antimicrobial resistance, integron identifications and genotyping. Isolates were genotyped by random amplified polymorphism (RAPD) DNA and pulsed-field gel electrophoresis (PFGE). Four different RAPD patterns were observed among the isolates of our collection, further discerned in six PFGE types. Two prevalent genotypes were identified, one corresponding to a carbapenem resistant epidemic clone, causing an outbreak at the intensive care unit of a hospital of Rome. Two class 1 integrons, carrying different gene cassette arrays, were identified among the two prevalent genotypes. Nucleotide analysis of the integron-variable regions revealed the presence of the aacA4, orfO, bla(OXA-20), and aacC1, orfX, orfX', aadA1 gene cassette arrays, respectively. All the carbapenem resistant strains analyzed in this study carried the bla (OXA-58) gene located on plasmids.

Inhibition of Epstein Barr Virus LMP1 gene expression in B lymphocytes by antisense oligonucleotides: uptake and efficacy of lipid-based and receptor-mediated delivery systems.

Epstein Barr Virus (EBV), is associated with an increasing number of lymphoid and epithelial malignancies. Among the genes expressed by EBV during latency, LMP1 plays a key role for growth transformation and immortalization of B lymphocytes. We have previously shown that antisense oligonucleotides (ONs) directed to LMP1 mRNA, effectively suppressed LMP1 gene expression and substantially reduced proliferation of the infected cells. The use of antisense phosphodiester oligonucleotides as therapeutic agents is limited by inefficient cellular uptake and intracellular transport to the target mRNA. We tested the ability of three cationic carriers internalized by different pathways, to increase the delivery of anti-LMP1-ON to their site of action in EBV-infected B lymphocytes. We report here that liposomes, dendrimers or transferrin-polylysine-conjugated ON were internalized by the cells at an extent several fold higher than that of the naked oligomers. However, only the delivery system exploiting the transferrin receptor pathway of internalization, was able to vectorize biologically active antisense LMP1-ON.

Emerging cystic fibrosis pathogens: incidence and antimicrobial resistance.

We examined the frequency of isolation and the antimicrobial resistance of Burkholderia cepacia complex, Stenotrophomonas maltophilia and Achromobacter xylosoxidans in cystic fibrosis patients from 2000 to 2004. Strains susceptibility to tobramycin, piperacillin/tazobactam, imipenem, gentamicin, ciprofloxacin and ceftazidime was determined by disc diffusion assay. B. cepacia complex showed a very high resistance also to ciprofloxacin reaching 100% in 2004. S. maltophilia and A. xvylosoxidans showed high rates of antimicrobial resistance both aminoglycoside and ciprofloxacin. It is very important to monitor the percentage of isolation of these species over time to verify strains resistance to antibiotics and also to test new combinations of antimicrobial agents.

Application of real time PCR in post transplant monitoring of cytomegalovirus infection: comparison with other diagnostic approaches.

Immunosuppressive status in solid organ transplant recipients is often related to the reactivation of Human Cytomegalovirus (HCMV) infection that remains one of the major causes of morbidity and mortality. Therefore, the early detection of HCMV followed by infection monitoring is important to institute prompt and appropriate treatment. In recent years good results have been obtained by HCMV DNA amplification methods; qualitative and quantitative approaches have shown good sensitivity and specificity, but they often require post-PCR manipulation that adds time to the analysis and may lead to contamination problems. Recently, Real Time PCR (RT-PCR) has been proposed in HCMV DNA analysis as a valid method for its good sensitivity and rapidity. In the present study, twenty-five solid organ transplant recipients were analyzed for HCMV diagnosis; 60 peripheral blood leukocytes and 120 plasma samples were tested by RT-PCR and the results compared to those obtained by a qualitative Nested PCR and a quantitative DNA enzyme immunoassay.

Early evidence of lymphoproliferative disorder: post-transplant monitoring of Epstein-Barr infection in adult and pediatric patients.

Transplant patients are at high risk of post-transplant lymphoproliferative disorder (PTLD). A strong correlation between Epstein-Barr virus (EBV) and PTLD is observed in pediatric patients with primary infection after transplant. Because many patients have responded to reversal of immunosuppressive therapy, an early identification of EBV is essential for the reduction of immunosuppression and/or introduction of antiviral therapy to prevent PTLD. Polymerase chain reaction (PCR) is a specific and sensitive method to identify EBV DNA in blood. The aim of our study was to establish a protocol for monitoring EBV infection in transplanted patients for early identification those at high risk of PTLD. Viral presence in peripheral blood leukocytes (PBL) and serum samples was revealed by Nested PCR; positive specimens were quantified with Real Time PCR (RT-PCR). DNA in PBL was observed in 12 cases and 6 showed EBV in sera. Quantitative analysis showed a wide range of EBV DNA copies in leukocytes that were higher than in sera. Two patients displayed high viral load values in both PBL and sera associated with clinical evidence of PTLD. Our data suggest that the study of the EBV load represents an essential approach in the diagnosis of PTLD and the analysis of serum samples could provide useful information in the post-transplant monitoring of high-risk patients.

Surveillance and infection control in an intensive care unit.

OBJECTIVE: To evaluate the effect of an infection control program on the incidence of hospital-acquired infection (HAI) and associated mortality. DESIGN: Prospective study. SETTING: A 2000-bed, university-affiliated hospital in Italy. PATIENTS: All patients admitted to the general intensive care unit (ICU) for more than 48 hours between January 2000 and December 2001. METHODS: The infection control team (ICT) collected data on the following from all patients: demographics, origin, diagnosis, severity score, underlying diseases, invasive procedures, HAI, isolated microorganisms, and antibiotic susceptibility. INTERVENTIONS: Regular ICT surveillance meetings were held with ICU personnel. Criteria for invasive procedures, particularly central venous catheters (CVCs), were modified. ICU care was restricted to a team of specialist physicians and nurses and ICU antimicrobial therapy policies were modified. RESULTS: Five hundred thirty-seven patients were included in the study (279 during 2000 and 258 in 2001). Between 2000 and 2001, CVC exposure (82.8% vs 71.3%; P < .05) and mechanical ventilation duration (11.2 vs 9.6 days) decreased. The HAI rate decreased from 28.7% in 2000 to 21.3% in 2001 (P < .05). The crude mortality rate decreased from 41.2% in 2000 to 32.9% in 2001 (P < .05). The most commonly isolated microorganisms were nonfermentative gram-negative organisms and staphylococci (particularly MRSA). Mortality was associated with infection (relative risk, 2.11; 95% confidence interval, 1.72-2.59; P < .05). CONCLUSION: Routine surveillance for HAI, coupled with new measures to prevent infections and a revised policy for antimicrobial therapy, was associated with a reduction in ICU HAls and mortality.

Inter-laboratory comparison of qualitative and quantitative detection of hepatitis C (HCV) virus RNA in diagnostic virology: a multicentre study (MS) in Italy.

BACKGROUND: The importance of the standardisation of nucleic acid amplification technology (NAT) assays for the detection of hepatitis C virus RNA is well known today, as many studies carried out in different European countries attest. The results of a previous study performed in Italy (J. Clin. Virol. 1 (2003) 83) by the Italian Society of Clinical Microbiology (AMCLI) showed that the use of external reference standards and of multicentre collaborative studies significantly improves laboratory performance for the qualitative evaluation of HCV RNA. OBJECTIVES: the AMCLI organised a new study on the standardisation of both the qualitative and the quantitative evaluation of HCV RNA with NAT in order to improve the implementation of the diagnostic methods for HCV RNA detection. STUDY DESIGN: seventeen diagnostic centres of major Italian Hospitals participated in this quality control study. The study consisted of testing three panels, each made up of 10 coded samples including negative and positive samples. Positive samples contained four levels of HCV RNA (genotype 1). RESULTS AND CONCLUSION: Seven out of 510 qualitative results obtained were incorrect (1.4%), two false negative and five false positive. The results gave a sensitivity of 99.5% and a specificity of 95.8%. Regarding quantitative tests, the geometric mean (GM) and standard deviation (S.D.) could be calculated only for the three highest HCV RNA levels. The percentage of results within the range of GM +/- 0.5 log(10) varied from 91% to 100%. Some laboratories had some difficulty in the exact quantification of the lowest (3.00 log IU/ml) as well as of the highest viral levels (6.35 log IU/ml) values, very near to the limits of the dynamic range of the assays. The comparison of the results of this study with that previously carried out one confirms that a regular participation in external quality assessment (EQA) assures the achievement of a high proficiency level in the diagnosis of HCV infection.

Multicentre Italian Study Group (MISG) for the standardisation of hepatitis C virus (HCV) PCR.

BACKGROUND: Several studies on standardisation of NAT assays for diagnosis of hepatitis C virus (HCV) infection have been carried out in European countries. In fact the widespreading use of nucleic acid amplification technology (NAT) in diagnostic centres for the evaluation of the HCV infection, requires the application of reference external standards to control laboratory performance; but up to date they are not routinely used. OBJECTIVES: Fifteen diagnostic centres of major Italian Hospitals participated to a quality control study for the standardisation of polymerase chain reaction (PCR)-based HCV-RNA detection, organised by the Committee for the Study of Biotechnology (CoSBio) of the Italian Society of Clinical Microbiology (AMCLI). All the participant centres (PC) used commercial assays, automated or semi-automated. STUDY DESIGN: The study was performed in four rounds. Altogether each centre received 14 reference negative and 22 reference positive sera. The range of copies number per ml of the reference positive sera was 10(4)-10(7). RESULTS AND CONCLUSIONS: Considering the 540 samples tested, 4.54% of false negative (FN) and 4.28% of false positive (FP) results were reported. Thereafter the sensitivity and the specificity were 95.65 and 95.89%, respectively. The errors were distributed among seven out of the 15 PCs. The percentage of FP results was uniformly distributed in each shipment, whereas FN results emerged with the sera at lower HCV genome copies number. The analysis of the data obtained suggests that FP as well as FN results may be attributable to errors or to others problems of laboratories. To improve the performance of Italian, as well as of laboratories throughout the world, the use of external reference standards in multicentre collaborative studies will be required.

Protective features of monoclonal antibodies to Escherichia coli during experimental infection of mice with homologous and heterologous serotypes of E. coli.

Murine monoclonal antibodies (MAbs) MT1F and ARM1-4, recognising proteins on the surface of untreated Escherichia coli O6:K-, protected 100% of mice challenged intraperitoneally with 2 x LD50 of the same strain. MAb MT1F protected 70% of animals challenged with 2 x LD50 of E. coli O111:B4, whereas ARM1-4 gave complete protection. Lower survival was observed in mice given either MAb and challenged with E. coli O128:K-, with values ranging from 30 to 42%. However, the protection afforded against E. coli O111:B4 and E. coli O128:K- was significantly improved when the mice were pre-treated with a mixture of the two MAbs. Control mice, pre-treated with unrelated ascitic fluid and challenged with any of the E. coli serotypes, showed 100% mortality and organ histological lesions resembling those of the early stages of septic shock. The mice had high levels of circulating endotoxin and tumour necrosis factor-alpha (TNF-alpha) at 90 min after challenge. In contrast, mice treated with MAbs and surviving the infection displayed moderate histological lesions, enhanced bacterial clearance and lower serum levels of TNF-alpha, despite circulating endotoxin levels that were higher than in the control group. Protection by the MAbs was probably due to the prevention of the bacterial spread to organs and of the cascade of events leading to septic shock. This occurred in spite of the presence of high levels of circulating endotoxin.