An Intronic Polypyrimidine-rich Element Downstream of the Donor Site Modulates Cystic Fibrosis Transmembrane Conductance Regulator Exon 9 Alternative Splicing *

Two intronic elements, a polymorphic TGmTn locus at the end of intron 8 and an intronic splicing silencer in intron 9, regulate aberrant splicing of human cystic fibrosis transmembrane conductance regulator (CFTR) exon 9. Previous studies (Pagani, F., Buratti, E., Stuani, C., Romano, M., Zuccato, E., Niksic, M., Giglio, L., Faraguna, D., and Baralle, F. E. (2000) J. Biol. Chem. 275, 21041–21047 and Buratti, E., Dork, T., Zuccato, E., Pagani, F., Romano, M., and Baralle, F. E. (2001) Embo J. 20, 1774–1784) have demonstrated that trans-acting factors that bind to these sequences, TDP43 and Ser/Arg-rich proteins, respectively, mediate splicing inhibition. Here, we report the identification of two polypyrimidine-binding proteins, TIA-1 and polypyrimidine tract-binding protein (PTB), as novel players in the regulation of CFTR exon 9 splicing. In hybrid minigene experiments, TIA-1 induced exon inclusion, whereas PTB induced exon skipping. TIA-1 bound specifically to a polypyrimidine-rich controlling element (PCE) located between the weak 5′-splice site (ss) and the intronic splicing silencer. Mutants of the PCE polypyrimidine motifs did not bind TIA-1 and, in a splicing assay, did not respond to TIA-1 splicing enhancement. PTB antagonized in vitro TIA-1 binding to the PCE, but its splicing inhibition was independent of its binding to the PCE. Recruitment of U1 small nuclear RNA to the weak 5′-ss by complementarity also induced exon 9 inclusion, consistent with the facilitating role of TIA-1 in weak 5′-ss recognition by U1 small nuclear ribonucleoprotein. Interestingly, in the presence of a high number of TG repeats and a low number of T repeats in the TGmTn locus, TIA-1 activated a cryptic exonic 3′-ss. This effect was independent of both TIA-1 binding to the PCE and U1 small nuclear RNA recruitment to the 5′-ss. Moreover, it was abolished by deletion of either the TG or T sequence. These data indicate that, in CFTR exon 9, TIA-1 binding to the PCE recruits U1 small nuclear ribonucleoprotein to the weak 5′-ss and induces exon inclusion. The TIA-1-mediated alternative usage of the 3′-splice sites, which depends on the composition of the unusual TGmTn element, represents a new mechanism of splicing regulation by TIA-1

Usefulness of Microscan System panels with EUCAST clinical breakpoints to evaluate the antimicrobial susceptibility of ß-lactamase producing- Gram negative isolates

The study aimed to evaluate the ability of NBC45, NBC46 and NB40 Microscan (MS) panels, updated to 2010 EUCAST breakpoints, to identify at species level and to correctly define the susceptibility to ß-lactams of 61 ß-lactamases (BLs) producing Gram-negative isolates. A collection of 73 fully identified strains was analyzed: 21 Klebsiella spp., 17 E. coli, 15 P. mirabilis, 9 A. baumannii (Ab), 7 P. aeruginosa and 4 Enterobacter spp.. 61/73 were BLs and/or carbapenemases producers: 15 were CTX-M-1/-2/-14/-15 positive, and among them two were also VIM-1 positive. Four were TEM-52/-92, 3 PER-1, 2 SHV-12/-18 and 6 CMY-16 producers, while 11 were KPC-2/-3, 9 OXA-51/-58/-23, 8 VIM-1 and 2 IMP-13 positive. One K. oxytoca K-1 iper-producer, 11 non-BL producers/ATCC control strains and a OprD2 porin lacking P. aeruginosa were also included. All isolates were identified by Api-20E and VITEK-2 System and antibiotic susceptibilities were obtained by broth microdilution method. Resistance genes were identified by PCR and sequencing. All 73 isolates were correctly identified and a complete agreement for susceptibility patterns was observed for both ATCC control strains and non-BL clinical isolates. MS failed to detect a BL/Extended-Spectrum-ß-Lactamase (ESâL) production in 5/61 cases: any ESßL alert was detected using NBC46 panel for 3/15 CTX-M positive strains and 2 VIM-1/CTX-M-15 producing K. pneumoniae isolates. Intermediate resistance to cefoxitin (MIC 16 mg/L), susceptibility to cefepime (MIC 8 mg/L for ertapenem (ETP), according to previously results. All VIM-1 producers resulted intermediate/resistant to imipenem (IP) and meropenem (MP); decreased MIC values were observed in 2/8 cases. Carbapenem MICs >8 mg/L were detected for IP-13 P. aeruginosa producers; 6/9 OXA carbapenemases- producing Ab showed IP MIC >8 mg/L and 3/6 MP MIC >8 mg/L. 3/9 Ab OXA-58/-51 producers, tested using NB40 panel, were intermediate or resistant to doripenem and meropenem. Regarding the detection of BLs overall agreement between MS and reference methods was 91.9%. Carbapenems MIC values resulted a fold lower than previously determined. Nevertheless using 2010 EUCAST breakpoints for ETP, MP and IP was possible to detect all carbapenemases- producers. MS System represents a useful tool to perform identification of BL- producing Gram negative bacteria

Growth in glucose-based medium and exposure to subinhibitory concentrations of imipenem induce biofilm formation in a multidrug-resistant clinical isolate of Acinetobacter baumannii

<p>Abstract</p> <p>Background</p> <p><it>Acinetobacter baumannii </it>is emerging as an important nosocomial pathogen. Multidrug resistance, as well as ability to withstand environmental stresses, makes eradication of <it>A. baumannii </it>difficult, particularly from hospital settings.</p> <p>Results</p> <p>Over a six-year period, 73 isolates of <it>A. baumannii </it>were collected from infected patients in two hospitals in Italy. While 69 out of the 73 isolates displayed identical multidrug antibiotic resistance pattern, they were susceptible to carbapenems. Genetic profiles of these 69 isolates, determined by Pulsed Field Gel Electrophoresis (PFGE), indicated that they were genetically related and could be clustered in a specific clone, called SMAL. We tested the ability of the SMAL clone to form biofilm, an important determinant for bacterial colonization of the human host and for persistence in the hospital environment. Biofilm formation by <it>A. baumannii </it>SMAL, measured as surface adhesion to polystyrene, is strongly affected by growth conditions, being impaired in rich growth media such as LB, while being favoured in glucose-based medium. Surface adhesion in glucose-based media is inhibited by treatment with cellulase, suggesting that it depends on production of cellulose or of a chemically related extracellular polysaccharide. Exposure of <it>A. baumannii </it>SMAL to subinhibitory concentrations of imipenem resulted in biofilm stimulation and increased production of iron uptake proteins. Growth in iron-supplemented medium also stimulated surface adhesion, thus suggesting that increased intracellular iron concentrations might act as an environmental signal for biofilm formation in <it>A. baumannii </it>SMAL.</p> <p>Conclusions</p> <p>Our results indicate that exposure to subinhibitory concentrations of imipenem can stimulate biofilm formation and induce iron uptake in a pathogenic strain of <it>A. baumannii</it>, with potential implications on antibiotic susceptibility and ability to persist in the human host.</p

Evidence for Cortical Functional Changes in Patients With Migraine and White Matter Abnormalities on Conventional and Diffusion Tensor Magnetic Resonance Imaging

Background— In this study, we used functional MRI (fMRI) to investigate the pattern of cortical activations after a simple motor task in patients with migraine and white matter (WM) abnormalities on conventional MRI scans of the brain. We also investigated whether the extent of brain activations was correlated with WM structural pathology measured using diffusion tensor (DT) MRI. Methods— From 15 right-handed patients with migraine and 15 sex- and age-matched, right-handed healthy volunteers, we obtained the following: (1) fMRI (repetitive flexion-extension of the last 4 fingers of the right hand), (2) dual-echo turbo spin echo scans, and (3) pulsed-gradient spin-echo echo-planar sequence to calculate DT-MRI maps. fMRI analysis was performed using SPM99 and cluster detection. We measured the volume, the average mean diffusivity ( ), and the average fractional anisotropy of all lesions seen on the dual-echo scans. histograms of the normal-appearing WM were also produced. Results— Compared with healthy volunteers, migraine patients had a larger relative activation of the contralateral primary sensorimotor cortex ( P =0.01) and a rostral displacement of the supplementary motor area ( P =0.03). The shapes of the curves reflecting the time course for fMRI signal intensity changes were similar between migraine patients and controls for all of the cortical areas we studied. Compared with healthy subjects, migraine patients had significantly lower histogram peak height of the normal-appearing WM histogram ( P =0.02), which was found to be correlated with the extent of displacement of the supplementary motor area ( r =−0.80, P <0.001). Conclusions— This study suggests that functional cortical changes occur in patients with migraine and brain MRI abnormalities and that they might be secondary to the extent of subcortical structural damage

Splicing Factors Induce Cystic Fibrosis Transmembrane Regulator Exon 9 Skipping through a Nonevolutionary Conserved Intronic Element

In monosymptomatic forms of cystic fibrosis such as congenital bilateral absence of vas deferens, variations in the TG(m) and T(n) polymorphic repeats at the 3' end of intron 8 of the cystic fibrosis transmembrane regulator (CFTR) gene are associated with the alternative splicing of exon 9, which results in a nonfunctional CFTR protein. Using a minigene model system, we have previously shown a direct relationship between the TG(m)T(n) polymorphism and exon 9 splicing. We have now evaluated the role of splicing factors in the regulation of the alternative splicing of this exon. Serine-arginine-rich proteins and the heterogeneous nuclear ribonucleoprotein A1 induced exon skipping in the human gene but not in its mouse counterpart. The effect of these proteins on exon 9 exclusion was strictly dependent on the composition of the TG(m) and T(n) polymorphic repeats. The comparative and functional analysis of the human and mouse CFTR genes showed that a region of about 150 nucleotides, present only in the human intron 9, mediates the exon 9 splicing inhibition in association with exonic regulatory elements. This region, defined as the CFTR exon 9 intronic splicing silencer, is a target for serine-arginine-rich protein interactions. Thus, the nonevolutionary conserved CFTR exon 9 alternative splicing is modulated by the TG(m) and T(n) polymorphism at the 3' splice region, enhancer and silencer exonic elements, and the intronic splicing silencer in the proximal 5' intronic region. Tissue levels and individual variability of splicing factors would determine the penetrance of the TG(m)T(n) locus in monosymptomatic forms of cystic fibrosis

Colistin resistance in KPC-producing Klebsiella pneumoniae strains from a high specialization rehabilitation facility

The worldwide rapid spread of KPC carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) represents an increasing problem in clinical settings. Reports on KPC-Kp epidemic spread in Italian hospitals began to appear since 2010; colistin (COL) represents one of the few remaining therapeutic options available for the treatment of such multi drug-resistant (MDR) pathogens. Here we report the presence and diffusion of COL resistant KPC-Kp isolates from a High Specialization Rehabilitation Facility located in Northern Italy. Species identification and antimicrobial susceptibilities were obtained by NBC46/NM40 Microscan panels (Siemens); imipenem, meropenem and ertapenem MICs were also evaluated by Etest and broth microdilution method; blaKPC-like genes PCR were performed. PFGE (XbaI) was used to investigate clonal relatedness; epidemiological data were collected from the hospital database. Seventy-five carbapenem-resistant K. pneumoniae isolates were collected from the Fondazione S. Maugeri hospital during the period January-June 2011. Seven out of 75 MDR KPC-Kp isolates by Microscan System showed COL resistance (MIC >2 mg/L). Among them, 5/7 were collected from coma and 2/7 from cardiology and rehabilitation cardiology wards. Most of these strains were from urine (5/7); the remaining 2/7 were from blood and bronco-alveolar lavage. The 85.7% of the strains showed susceptibility to tigecycline and fosfomycin; 71.4% only to gentamicina, 28.5% to trimethoprim/sulfamethoxazole and 14.2% to amikacin. The PFGE profiles obtained analyzing 5/7 isolates from patients hospitalized from almost 10 days, showed clonal relatedness between 4/5 isolates, thus confirming the high epidemic potential of almost one KPC-Kp clinical strain collected from 4 different wards.The emergence of COL resistance in KPC-Kp, dramatically reduces the available therapeutic options. These results underline the ability of a COL resistant KPC-producing clone to rapidly spread within this Rehabilitation Facility

Occurrence of two Norovirus outbreaks in the same cafeteria in one week

In October 2017, two outbreaks of gastroenteritis (GE) occurred among patrons of a cafeteria in Italy in one week. Virological and bacteria investigations on stool samples, environment and food were conducted to identify the infectious agents and the possible source of infection. Forty-five cases occurred in the two outbreaks, including 13 laboratory-confirmed cases of norovirus GI. Nine staff members were interviewed, six were confirmed positive for NoV GI and 3 experienced GE symptoms. Bacteria faecal indicators and other bacteria pathogens were not detected in either environmental swab samples or food. A low level of NoV GII was detected in two environmental swab samples. The same GI.6 strain was identified in cases related to both outbreaks, suggesting a common source of infection. Since the two outbreaks occurred in one week, the NoV contamination could have persisted in the cafeteria. Furthermore, virological investigation revealed confirmed cases among food handlers who had worked at the cafeteria between and during the two outbreaks. Several studies highlighted the importance of excluding symptomatic food handlers to prevent contamination of foods and environment

Evaluation of two commercially available methods used for the rapid detection of ESBL-producing strains

Detection of ESBL production by Enterobacteriaceae remains a challenge for microbiologists. Although recent changes in the breakpoints of third-generation cephalosporins decreased the likelihood of reporting ESBL producers as susceptible to these compounds, ESBL detection is of interest for prevention of dissemination of ESBL-producers by cross-transmission and for epidemiological purpose. The aim of this study was to evaluate the sensitivity and the specificity of two commercial methods suitable for rapid ESBL-detection in Gram negative bacilli: the ChromID ESBL medium (bioMérieux) and the Cica-ß-Test (Mast Group, Merseyde, UK). 121 Enterobacteriaceae collected between February 2008 and April 2009 at the Laboratory Analysis IRCCS Humanitas were tested for ESBL-production by PhoenixTM, E-test (ESBL reference test), ChromID ESBL medium and Cica-β-Test. ChromID showed 100% of sensitivity and specificity for the screening of ESBL in E. coli; lower values of specificity were found in the case of P. mirabilis (81%) and Klebsiella spp. (92%). The Cica-β-Test always showed high specificity levels, but the poor sensitivity found for both E. coli (90%), P. mirabilis (73%) and Klebsiella spp. (85%), discourages its use for screening of ESBL in Gram negative bacilli from blood-cultures. Rapid identification of ESBL producers is of interest to implement hygiene precautions. In that case, using a very sensitive primary test is of major interest

Multicenter Evaluation of the C6 Lyme ELISA Kit for the Diagnosis of Lyme Disease

Lyme disease (LD), caused by infection with Borrelia burgdorferi, is the most common tick-borne infection in many regions of Eurasia. Antibody detection is the most frequently used laboratory test, favoring a two-step serodiagnostic algorithm; immunoenzymatic detection of antibodies to C6 has been shown to perform similarly to a standard two-step workflow. The aim of this study was the performance evaluation of the C6 Lyme ELISA kit compared to a standard two-step algorithm in three laboratories located in the northeastern region of Italy which cater to areas with different LD epidemiology. A total of 804 samples were tested, of which 695 gave concordant results between C6 testing and routine workflow (564 negative, 131 positive). Wherever available, clinical presentation and additional laboratory tests were analyzed to solve discrepancies. The C6 based method showed a good concordance with the standard two-step algorithm (Cohen's κ = 0.619), however, the distribution of discrepancies seems to point towards a slightly lower specificity of C6 testing, which is supported by literature and could impact on patient management. The C6 ELISA, therefore, is not an ideal stand-alone test; however, if integrated into a two-step algorithm, it might play a part in achieving a sensitive, specific laboratory diagnosis of LD