Genomic characterisation of Escherichia coli isolates co-producing NDM-5 and OXA-1 from hospitalised patients with invasive infections.

OBJECTIVES: Carbapenems are one of the last-report therapeutic choices to treat infections due to multidrug-resistant (MDR) micro-organisms. For this reason, the spread of carbapenemase-producing Enterobacteriaceae represents a serious health-public problem. Here we describe isolates co-producing blaNDM-5 and blaOXA-1. METHODS: Three Escherichia coli isolates obtained from patients with invasive infections were analysed by phenotypic antibiotic susceptibility testing and whole-genome sequencing (WGS). RESULTS: All of the isolates were resistant to carbapenems, most ß-lactam antibiotics, piperacillin/tazobactam, amoxicillin/clavulanic acid and ciprofloxacin, remaining susceptible to amikacin, fosfomycin, colistin and tigecycline. The isolates belonged to sequence types ST44, ST405 and ST167 and co-harboured the blaNDM-5 and blaOXA-1 genes. Two of the isolates also harboured extended-spectrum ß-lactamase (ESBL) genes (blaCTX-M-15 and blaTEM-1b). The blaNDM-5 gene was probably carried chromosomally even if different plasmids were identified. Various virulence genes were also identified. CONCLUSION: Our results highlight that continuous surveillance is essential to monitor the spread of clinically important MDR pathogens.

In vitro inhibitory effect of two commercial probiotics on chromogenic actinomycetes.

PURPOSE: Black extrinsic discoloration is a common clinical and aesthetic problem. This study aims to evaluate the potential in vitro antagonistic activity of two commercial probiotics, Streptococcus salivarius M18 and Lactobacillus reuteri ProDentis, against microorganisms associated with black stains. METHODS: Streptococcus salivarius M18 and Lactobacillus reuteri were tested against Aggregatibacter actinomycetemcomitans and Actinomyces naeslundiiusing their cell-free fermentative broth in a planktonic growth inhibition test. RESULTS: Both probiotic cell-free supernatants showed the ability to reduce the pathogenic bacteria growth in a dose-dependent way. Streptococcus salivarius M18 showed a stronger antimicrobial activity than Lactobacillus reuteri ProDentis against the two indicator strains used. A. naeslundi was less susceptible to the probiotic activity of both S. salivarius and L. reuteri compared to A. actinomycetemcomitans. CONCLUSIONS: The obtained results demonstrate a potent antagonistic ability of probiotics to reduce the growth of microorganisms associated with black tooth stains. Therefore, these strains could be evaluated for a therapeutic use against dental pigmentations.

Correlation between tcdB gene PCR cycle threshold and severe Clostridium difficile disease.

A retrospective study, including all samples tested for Clostridium difficile from 2015 to 2018, was conducted. 222 and 199 patients were respectively classified as having a mild/moderate or severe disease. A CT ≤ 26 was significantly associated with severe disease. Furthermore, low CT values were significantly associated to older patients and leukocytosis.

Invasive Candidiasis in Brescia, Italy: Analysis of Species Distribution and Antifungal Susceptibilities During Seven Years.

The aims of this study were to evaluate the epidemiology of nosocomial candidemia in a large teaching hospital in Brescia, Italy, and the in vitro antifungal susceptibility of isolates. We analyzed 196 isolates causing fungemia in patients admitted in our hospital, between January 2009 and December 2015. Strains were identified by VITEK 2 and MALDI-TOF MS. MICs were determined by Sensititre Yeast OneTM. The resistance was defined by using the revised CLSI breakpoints/epidemiological cutoff values to assign susceptibility or wild type to systemic antifungal agents. Most infections were caused by Candida albicans (60%), Candida parapsilosis (15%), Candida glabrata (12%) and Candida tropicalis (6%). The susceptibility rate for fluconazole was 96.5%. Non-Candida species isolates exhibited full susceptibilities to echinocandins according to CLSI breakpoints. Amphotericin B demonstrated excellent activity against all Candida species. Local epidemiological and antifungal susceptibility studies are necessary in order to improve empirical treatment guidelines.

Emergence of the first levofloxacin-resistant strains of Streptococcus agalactiae isolated in Italy.

Of 901 group B streptococcus strains analyzed, 13 (1.4%) were resistant to levofloxacin (MICs of >32 µg/ml for seven isolates, 2 µg/ml for four isolates, and 1.5 µg/ml for four isolates). Mutations in the quinolone resistance-determining regions (QRDRs) of gyrase and topoisomerase IV were identified. A double mutation involving the Ser-81 change to Leu for gyrA and the Ser-79 change to Phe or to Tyr for parC was linked to a high level of fluoroquinolone resistance. In addition, two other mutational positions in parC were observed, resulting in an Asp-83-to-Tyr substitution and an Asp-83-to-Asn substitution. Different mutations were also observed in gyrB, with unknown significance. Most levofloxacin-resistant GBS strains were of serotype Ib and belonged to sequence type 19 (ST19) and clonal complex 19 (CC-19). Most of them exhibited the epsilon gene.

Prevalence of multidrug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa in an Italian hospital.

The severity and extent of disease caused by multidrug-resistant organisms (MDROs) varies by the population(s) affected and the institution(s) at which these organisms are found; therefore, preventing and controlling MDROs are extremely important. A retrospective study of patients who were infected with Acinetobacter baumannii or Pseudomonas aeruginosa was performed at the Spedali Civili Hospital in Brescia, Italy, from 2007 to 2010. A total of 167 (0.52%) A. baumannii isolates and 2797 P. aeruginosa (8.7%) isolates were identified among 31,850 isolates. Amikacin and colistin were the most active agents against A. baumannii strains. Multidrug resistance (MDR) was observed in 57 isolates (54%). Most MDR isolates (42 out of 57, 73%) were resistant to four classes of antibiotics. P. aeruginosa was recovered more frequently from the respiratory tract, followed by the skin/soft tissue, urine and blood. Colistin, amikacin and piperacillin/tazobactam were active against 100%, 86% and 75% of P. aeruginosa isolates, respectively. A total of 20% (n=316) of P. aeruginosa isolates were MDR. In summary, A. baumannii was more rare than P. aeruginosa but was more commonly MDR. Epidemiological data will help to implement better infection control strategies, and developing a local antibiogram database will improve the knowledge of antimicrobial resistance patterns in our region.

Phenotypes, genotypes, serotypes and molecular epidemiology of erythromycin-resistant Streptococcus agalactiae in Italy.

The purpose of this investigation was to analyse Streptococcus agalactiae (group B Streptococcus, GBS) isolates collected in Italy from vaginal and urine samples in respect to their clonality, distribution of virulence factors and antimicrobial resistance determinants. Three hundred and eighty-eight GBS were recovered from clinical samples. They were analysed for antibiotic resistance profiling. Erythromycin-resistant strains were further characterised by multilocus sequence typing (MLST), serotyping and the detection of alp genes of the alpha-like protein (Alp) family. GBS isolates represented 40 different sequence types (STs), grouped in five clonal complexes (CCs) and belonged to seven serotypes. Most serotype V strains (81%) possessed alp2-3; serotype Ia carried mainly epsilon, while the serotype III mainly rib. All isolates were susceptible to penicillin, whereas resistance to erythromycin was detected in 15% of isolates. Most erythromycin-resistant GBS strains were of serotype V (56.8%) and belonged to the CC-1 group (50%). Macrolide resistance phenotypes were the cMLS(B) (46.5%) and the M phenotypes (46.5%) due to the presence of ermB and mefA/E genes, respectively. These results provide data which establish a baseline for monitoring erythromycin resistance in this region and also provide an insight into the correlation among clonal types, serotypes, surface protein and resistance genes. The increased prevalence of strains that displayed the M phenotype strengthens the importance of the epidemiological surveillance of macrolide resistance in GBS, which may also represent an important reservoir of resistance genes for other species.

Detection of Ureaplasma biovars and polymerase chain reaction-based subtyping of Ureaplasma parvum in women with or without symptoms of genital infections.

Ureaplasma parvum colonises human mucosal surfaces, primarily in the urogenital and respiratory tracts, causing a wide spectrum of diseases, from non-gonococcal urethritis to pneumonitis in immunocompromised hosts. Although the basis for these diverse clinical outcomes is not yet understood, it has been suggested that only certain strains of these micro-organisms are disease-associated. The aim of this study was to determine the distribution of Ureaplasma biovars and U. parvum serovars and to estimate their possible association with age, absence of lactobacilli, clinical symptoms and antibiotic resistance. DNA was extracted by endocervical, vaginal and urethral samples obtained from 158 women positive for U. urealyticum by culture and were biotyped by polymerase chain reaction (PCR) targeting the multiple-banded gene. Parvo biovar (biovar 1) was found in 136 (86%) and T960 biovar (biovar 2) in 22 (14%) patients. Among the different serovars of U. parvum, we found that serovar 3/14 was present maximally in the 21-25-year-old age group, while T960 biovar was distributed with quite similar frequency in women of 26-30 and >40 years of age. In this study, U. parvum serovar 3/14 and T960 biovar were found to be significantly associated with symptomatic patients and a loss of lactobacilli, while, on the contrary, U. parvum serovar 6 was significantly correlated with asymptomatic women and normal vaginal flora. The most active antibiotic for the majority of Ureaplasma isolates was tetracycline. These preliminary data show the possibility of distinguishing between the more or less virulent strains of Ureaplasma, with important consequences for therapeutic treatment.

Different sequence strains of Streptococcus agalactiae elicit various levels of cytokine production.

Group B streptococcus (GBS) is the most common cause of neonatal and obstetric sepsis and an increasingly important cause of septicemia in elderly subjects and immunocompromised patients. Our aim was to evaluate whether different genotypes of GBS may induce a different production of pro-inflammatory and anti-inflammatory cytokines. We used multilocus sequence typing to identify 71 clones isolated from asymptomatic healthy carriers and symptomatic individuals. All these clinical isolates were used to infect purified human monocytes. TNF-alpha, IL-6, IL-8 and IL-10 secretion was measured. Fifteen allelic sequence types (STs) were identified. The MLST (multilocus sequence typing) analysis grouped the bacteria into four different lineages (clonal cluster) and two of these were closely involved in the infection of symptomatic subjects: CC17 and CC19. Furthermore, CC17 and CC19 stimulated TNF-alpha, IL-6 and IL-8 production significantly more than the other lineages, while CC17 induced a decreased IL-10 production. These results suggest the existence of differences in immune response to infection with particular genotypes of GBS.

Phenotypic and genotypic characterization of Neisseria gonorrhoeae in parts of Italy: detection of a multiresistant cluster circulating in a heterosexual network.

Data concerning Neisseria gonorrhoeae infections in Italy are scarce, and there is little information on the phenotypic and genotypic characteristics of the circulating strains. In this study, 326 isolates collected from 397 patients, with or without concurrent human immunodeficiency virus (HIV) infection, were cultured and characterized by serovar and antimicrobial susceptibility to five antimicrobials. N. gonorrhoeae multi-antigen sequence typing (NG-MAST) was also performed for strain characterization and to identify a transmission network. Gonococcal infection was diagnosed in 364 males and 33 females, 296 of whom were Italian and 96 of whom were foreigners (nationality was unknown in five cases). Among the 364 males, 197 were heterosexual, and the median age was 31 years. Approximately 8.3% of all the investigated patients were HIV-1-positive. The isolates were assigned to three different serovars (IA, IB, IA/IB), IB being the most frequently encountered. A significant rate of resistant gonococci was also observed; 34%, 25.5% and 19.1% of ciprofloxacin-resistant, penicillin-resistant and tetracycline-resistant phenotypes, respectively, were detected, and 10.2% of strains were multidrug-resistant. Together with the presence of different sequence types (STs), identified by NG-MAST, a multidrug-resistant cluster, ST661, was detected in a heterosexual network in a precise geographical area of the country. In particular, all strains belonging to ST661 showed identical profiles according to pulsed-field gel electrophoresis (PFGE), all were serotype IB, and all were resistant to penicillin, ciprofloxacin and tetracycline.

Comparison of the AMPLICOR human papillomavirus test and the hybrid capture 2 assay for detection of high-risk human papillomavirus in women with abnormal PAP smear.

Infection with human papillomavirus (HPV) is a necessary step in the progression to cervical cancer. Many methods for HPV testing are currently available, mostly developed to detect pools of HPV types. Hybrid Capture 2 (HC2) is one of the most widely used. A new PCR-based assay, the Roche AMPLICOR HPV test, has been recently developed. Both assays recognize a group of 13 HR HPV types contemporaneously. This study evaluated the performance of both methods for detecting high-grade cervical lesions as a part of management for abnormal PAP smears. The study population was composed of 213 women, all referred to colposcopy and histologic diagnosis following an abnormal PAP test. Biopsy-confirmed high-grade cervical intraepithelial neoplasia was used as a gold standard. Overall agreement was 84.9% with a kappa value of 0.6. When comparing the ability to detect moderate cervical intraepithelial neoplasia (CIN2+) and high-grade cervical intraepithelial neoplasia (CIN3+/cancer), AMPLICOR proved slightly more sensitive than HC2, a finding that is important when HPV testing is used in a triage of borderline smear results. Genotyping of discordant results showed a prevalence of LR-HPV types in HC2 positive/AMPLICOR negative samples, and a similar prevalence of HR- and LR-HPV types in AMPLICOR positive/HC2 negative samples. In conclusion, the study shows that the AMPLICOR assay is more sensitive than HC2, which makes it a valid alternative for routine clinical use.

Prevalence and distribution of single and multiple HPV infections in cytologically abnormal cervical samples from Italian women.

The prevalence of single and multiple HPV infections was assessed over a cohort of 213 women with cytological abnormalities and its association with cervical neoplasia established. Roche linear array HPV genotyping test was used to identify HPV genotypes. The most prevalent HPV genotypes in cervical cancer samples were HPV16 (61.2%), HPV52 (16.1%), HPV18 (12.9%) and HPV 31 (9.6%). Multiple HR and LR HPV infections, comprising between two and 5+ HPV types, were identified in 49.7% of samples, with a significantly lower number in severe dysplasia and cervical cancer samples (p<0.05). These results seem to indicate that detection of multiple HPV infection with HR-HPV types is not significantly better as a predictor of cervical cancer than single HR-HPV infection, though further longitudinal studies are needed to better clarify the relevance of these infections to the progression of cervical neoplasia.

HIV p17 reverses the anti-inflammatory activity of IL-4 on IL-15 stimulated monocytes and modulates their ability to secrete MIP-1 alpha.

Monocytes play a central role in the immune system by producing and reacting to different soluble factors. Cytokine dysregulation is an hallmark in HIV-infected individuals and it is one of the most significant factors leading to impaired immunity in HIV/AIDS disease. This study investigates the possibility of modulation in the secretion of some inflammatory cytokines and chemokines induced by HIV p17 in monocytes. The results show that p17, while ineffective on resting monocytes, exerts an inflammatory action on IL-4 mediated inhibition of TNF-alpha and IFN-gamma production induced by IL-15 stimulation. In addition, p17 is able to reduce MIP-1alpha secretion, but unable to influence IL-6 production. The ability of HIV p17 to contribute to an altered pattern of secreted soluble factors might imply a key role for this viral protein in the development of AIDS pathogenesis.

Detection and genotyping of human papillomavirus in cervical samples from Italian patients.

Human papillomaviruses (HPVs) are etiological agents of cervical cancer. In order to assess the epidemiological incidence and frequency of different HPV types, we applied a polymerase chain reaction (PCR)-direct sequencing approach based on the use of MY09/MY11 primers as compared to Hybrid Capture assay. Cervical samples were taken from 1,500 women, both with normal and abnormal cytological smears, and we found an incidence of 6.6% of HPV infection in Brescia. Overall, 97 samples tested HPV-positive, yielding 18 HPV types. The four most frequent HPV types were: HPV 16, -31, -6, and -58. This approach could be used in ordinary laboratory settings for quick and reliable typing of known and novel HPVs from clinical specimens and it could also be applied to anti-cancer vaccine development.

Prevalence of drug resistance and newly recognised treatment-related substitutions in the HIV-1 reverse transcriptase and protease genes from HIV-positive patients naïve for anti-retrovirals.

The aim of this study was to assess the prevalence of genetic changes in either the HIV reverse transcriptase (RT) or protease (Pro) genes in a cohort of patients naïve for anti-retroviral therapy. Of 61 patients, 43 (70.5%) were infected with HIV strains harbouring at least one resistance-related mutation, with 41 (67.2%) harbouring newly recognised treatment-related mutations. Among the 61 patients, the prevalence of specific mutations in the RT gene was as follows: 39A, 1.6%; 43E, 1.6%; and 228H, 1.6%. The prevalence of specific mutations in the Pro gene was as follows: 11I, 1.6%; 13V, 26.2%; 35D, 19.6%; 45R, 1.6%; 58E, 1.6%; 62V, 31%; 72V, 11.4%; 72M, 6.5%; 72T, 3.2%; 75I, 1.6%; and 89M, 13%. A higher prevalence of newly recognised mutations was found in strains from patients infected through sexual practices (30/36 = 83.4% vs. 11/25 = 44%; p 0.0023; OR 10.91; 95% CI 3.14-40.39). These findings support the use of resistance testing in patients naïve for anti-retroviral therapy, and suggest that the possible impact of newly recognised treatment-related mutations on clinical outcome requires further investigation.

Polymorphism analysis of Epstein-Barr virus isolates of lymphoblastoid cell lines from patients with mycosis fungoides.

In order to determine whether there is an association between the presence of Epstein-Barr virus (EBV) and mycosis fungoides (MF) disease progression, PCR was performed to detect the EBV status of 20 MF patients; six EBV-positive patients were found. EBV variants may differ in their biological properties, such as their ability to transform cells; therefore, the ability of these variants to immortalize B cells in vitro was analysed. Six continuously growing cell lines were obtained from prolonged cultures of unstimulated peripheral blood mononuclear cells that were taken from the six EBV-positive patients with MF. In order to characterize the EBV strains, EBNA-2 and LMP-1/LMP-2 gene polymorphisms in the six cell lines were also analysed. All patients were followed up for 10 years and it was noticed that EBV-positive patients had a poor prognosis with rapid disease progression and high mortality rates, compared to EBV-negative patients. EBV may therefore constitute a co-factor that accelerates the progression of disease.

Lack of polarized type 1 or type 2 cytokine profile in asymptomatic HIV-1-infected patients during a two-year bimonthly follow-up.

The production of type 1 (interferon or IFN-gamma) and type 2 (interleukin or IL-4 and IL-10) cytokines by mitogen-stimulated peripheral blood mononuclear cells (PBMCs) obtained from asymptomatic human immunodeficiency virus-seropositive (HIV+) patients untreated with any antiviral, antibacterial or antimycotic drugs, and from healthy individuals, was evaluated by quantitative ELISA. Patients who were HIV+ were characterized by the absence of abnormal cytokine production. The level of each cytokine differed among individuals in the same group with intersubject variations greater for HIV+ patients than for healthy individuals. The longitudinal evaluation of IFN-gamma, IL-4 and IL-10 production showed intrasubject variations which were particularly marked in HIV+ patients. Accordingly, HIV+ patients and, to a lesser extent, healthy individuals were characterized by a wide spectrum of possible profiles, which were confined to type 0 phenotype. In HIV+ patients no correlation was found between each cytokine level and the number of CD4+ T cells, not even in those with a falling CD4+ T-cell count and clinical symptoms.

HIV p17 enhances lymphocyte proliferation and HIV-1 replication after binding to a human serum factor.

OBJECTIVE: To analyse the role of recombinant HIV-1 protein p17 in the modulation of cell activity. METHODS: Peripheral blood mononuclear cells (PBMC) obtained from healthy donors were cultured in the presence or absence of p17 with mitogens such as phytohaemagglutinin or interleukin-2 and their response assayed by cell proliferation. Cross-linking experiments were employed to investigate the presence of a binding between p17 and factor(s) present in human serum. An immunoenzymatic assay for p24 antigen detection was used to analyse the effect of the addition of exogenous p17 to cultures of PBMC infected with HIV-1 in vitro. RESULTS: Purified recombinant p17 protein at a concentration of 0.25 microg/ml significantly increased the proliferation of preactivated PBMC obtained from healthy donors. This effect was obtained by binding p17 to factor(s) present in human serum and observed on both CD4+ and CD8+ T cells. Recombinant p17 also induced an increased rate of HIV-1 replication, probably due to enhanced T-cell proliferation. The activity of p17 protein was inhibited by anti-p17 antibodies generated by injecting recombinant p17 in rabbits, but not by human antibodies generated during the natural course of HIV infection. CONCLUSION: Characterization of the human factor(s) and identification of the interacting p17 epitope(s) will improve our understanding of the mechanisms used by HIV to efficiently replicate in our organisms.