Phenotypic and genotypic characterisation of Neisseria gohorrhoeae isolates from New Zealand with reduced susceptibility to ceftriaxone : a thesis submitted to the College of Health in partial fulfilment of the requirements for the Master of Science in Microbiology at Massey University, New Zealand

Objectives Currently, ceftriaxone is the last remaining drug recommended for empirical treatment of gonorrhoea. Neisseria gonorrhoeae with reduced susceptibility to ceftriaxone have been isolated worldwide in countries such as Japan, France, Spain, Slovenia, Australia and Sweden. These have led to treatment failures and the emergence of ceftriaxone-resistant N. gonorrhoeae. Various mutations in penA (mosaic and nonmosaic), which encodes the penicillin-binding protein 2 (PBP2), have been reported to be the primary reason for reduced ceftriaxone susceptibility, but it can be reduced further by mutations in mtrR, porBIB and ponA. In this study, we aimed to determine the antimicrobial resistance patterns of New Zealand isolates of N. gonorrhoeae with reduced susceptibility to ceftriaxone and to characterise the penA, mtrR, porBIB and ponA in the isolates. Methods A total of 28 N. gonorrhoeae isolates with elevated ceftriaxone MIC (0.03 to 0.12 mg/L), collected from 2012 to 2015 and obtained from the Institute of Environmental Science and Research (ESR), were examined in this study. Samples came from laboratories in Auckland (26), Wellington (1) and Taranaki (1). The antimicrobial resistance of penicillin G, tetracycline, ciprofloxacin, azithromycin and ceftriaxone were determined through antimicrobial susceptibility test, using minimum inhibitory concentration (MIC) test strips. Polymerase chain reactions (PCRs) and sequencing to identify specific mutations in penA, mtrR, porBIB and ponA, that are associated with elevated minimum inhibitory concentrations (MICs) to ceftriaxone, were undertaken. The association between the phenotypic and genotypic results was investigated by comparing the presence of the number of mutated genes and the MIC level of ceftriaxone. Results Based on the AST results using MIC test strips and interpreted using The European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria, 23 out of 28 isolates (82%) showed reduced susceptibility to ceftriaxone, with MICs of 0.03 to 0.06 mg/L. All of the isolates were resistant to ciprofloxacin, while 36%, 25% and 7% were resistant to penicillin G, tetracycline and azithromycin, respectively. Two azithromycin-resistant N. gonorrhoeae isolates were observed, and isolate 264 (azithromycin MIC: 4mg/L) also exhibited reduced susceptibility to ceftriaxone (MIC: 0.03 mg/L). A total of 21% (6/28) of the isolates produced ß- lactamase. The 23 isolates that conveyed reduced ceftriaxone susceptibility were found to harbour three or four mutated genes (penA, mtrR and/or porBIB and ponA). Reduced susceptibility to ceftriaxone among N. gonorrhoeae isolates in this study was associated with mosaic PBP2 (encoded by penA) with G545S/A501V mutations, with nonmosaic PBP2 with an A501V mutation, plus the presence of mutation in mtrR promoter with G120 and A121 alterations in PorBIB. A total of 65% (15/23) of the N. gonorrhoeae isolates with reduced susceptibility to ceftriaxone harboured mosaic PBP2 XXXIV, a pattern found in N. gonorrhoeae associated with ceftriaxone treatment failures in Europe and Australia. The current study also revealed that the partial sequences of four mosaic PBP2 (M-2, M-3, M-4, M-5) were different from the common mosaic PBP2 sequences reported in various studies. Conclusion There is an association between the phenotypic and genotypic character of N. gonorrhoeae isolates expressing reduced susceptibility to ceftriaxone in this study population. Furthermore, the presence of important mosaic PBP2 that link to ceftriaxone treatment failure might be circulating among N. gonorrhoeae isolates in New Zealand . Keywords: Neisseria gonorrhoeae, ceftriaxone, reduced susceptibility, New Zealan

Clinical, Microbiological, and Genetic Characteristics of Heteroresistant Vancomycin-Intermediate Staphylococcus aureus Bacteremia in a Teaching Hospital

The emergence of vancomycin intermediate Staphylococcus aureus (VISA) and heterogeneous VISA (hVISA) is of major concern worldwide. Our objective was to investigate the prevalence, phenotypic and molecular features of hVISA strains isolated from bacteremic patients and to determine the clinical significance of the hVISA phenotype in patients with bacteremia. A total of 104 S. aureus blood isolates were collected from a teaching hospital of Argentina between August 2009 and November 2010. No VISA isolate was recovered, and 3 out of 92 patients (3.3%) were infected with hVISA, 2 of them methicillin-resistant S. aureus (MRSA) (4.5% of MRSA). Macro Etest and prediffusion method detected 3/3 and 2/3 hVISA respectively. Considering the type of bacteremia, the three cases were distributed as follows: two patients had suffered multiple episodes of bacteremia (both hVISA strains recovered in the second episode), while only one patient had suffered a single episode of bacteremia with hVISA infection. MRSA bloodstream isolates exhibiting the hVISA phenotype were related to HA-MRSA Cordobes clone (ST5-SCCmec I-spa t149) and MRSA Argentinean pediatric clone (ST100-SCCmec IVNV-spa t002), but not to CA-MRSA-ST30-SCCmec IV-spa t019 clone that was one of the most frequent in our country. Although still relatively infrequent in our hospital, hVISA strains weresignificantly associated with multiple episodes of bacteremia ( p = 0.037) and genetically unrelated.Fil: Di Gregorio, Sabrina Noelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: Perazzi, Beatriz Elizabeth. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: Martinez Ordoñez, Andrea. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Bioquímica Clínica; ArgentinaFil: de Gregorio, Stella. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Focoli, Mónica. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Lasala, María Beatriz. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Garcia, Susana. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: Vay, Carlos Alberto. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Famiglietti, Angela María Rosa. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Mollerach, Marta Eugenia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentin

Drug Resistant Streptococcus pneumoniae (DRSP) in the Maltese Islands

The DRSP prevalence rate for the Maltese Islands was investigated. Consecutive samples were obtained, both from adults and children, from September 2000 through April 2002. Penicillin-intermediately-resistant isolates amounted to 27%, erythromycin-resistant isolates 31%, and clindamycin-resistant isolates 19%. The oxacillin disk was found to be an effective screening method for the detection of penicillin resistance. An association was found in patients who had DRSP, as well as diabetes and/ or cardiovascular disease. Finally, an investigation of the local antibiotic consumptions over the period 1997-2000, for the National Health Service was conducted. The highest consumption rates were obtained with co-amoxiclav, amoxicillin, erythromycin, cephalexin and ciprofloxacin. The results obtained here call for more judicious use of antibiotics. In addition, the setting up of a local DRSP surveillance unit is mandatory. Moreover, the use of molecular techniques to investigate specific genes, such as ermAM and mefE associated with macrolide-resistance, should be introduced as part of investigational laboratory work.peer-reviewe

PHOTOS Monte Carlo: a precision tool for QED corrections in Z and W decays

We present a discussion of the precision for the PHOTOS Monte Carlo algorithm, with improved implementation of QED interference and multiple-photon radiation. The main application of PHOTOS is the generation of QED radiative corrections in decays of any resonances, simulated by a "host" Monte Carlo generator. By careful comparisons automated with the help of the MC-TESTER tool specially tailored for that purpose, we found that the precision of the current version of PHOTOS is of 0.1% in the case of Z and W decays. In the general case, the precision of PHOTOS was also improved, but this will not be quantified here.Comment: Version 2: -Figure 8a replaced by link to hep-ph/040600

CSNE : Conditional Signed Network Embedding

Signed networks are mathematical structures that encode positive and negative relations between entities such as friend/foe or trust/distrust. Recently, several papers studied the construction of useful low-dimensional representations (embeddings) of these networks for the prediction of missing relations or signs. Existing embedding methods for sign prediction generally enforce different notions of status or balance theories in their optimization function. These theories, however, are often inaccurate or incomplete, which negatively impacts method performance. In this context, we introduce conditional signed network embedding (CSNE). Our probabilistic approach models structural information about the signs in the network separately from fine-grained detail. Structural information is represented in the form of a prior, while the embedding itself is used for capturing fine-grained information. These components are then integrated in a rigorous manner. CSNE's accuracy depends on the existence of sufficiently powerful structural priors for modelling signed networks, currently unavailable in the literature. Thus, as a second main contribution, which we find to be highly valuable in its own right, we also introduce a novel approach to construct priors based on the Maximum Entropy (MaxEnt) principle. These priors can model the polarity of nodes (degree to which their links are positive) as well as signed triangle counts (a measure of the degree structural balance holds to in a network). Experiments on a variety of real-world networks confirm that CSNE outperforms the state-of-the-art on the task of sign prediction. Moreover, the MaxEnt priors on their own, while less accurate than full CSNE, achieve accuracies competitive with the state-of-the-art at very limited computational cost, thus providing an excellent runtime-accuracy trade-off in resource-constrained situations

Study of Molecular Mechanism of Antibiotic susceptibility against Polymicrobial Oral infection

Abstract

Introduction- Antibiotic to treat dental caries infection are routinely prescribed. Bacteria have increased resistance to the currently recommended antibiotics. The purpose of this investigation was to perform antibiotic susceptibility on a panel pathogenic strain of bacteria isolated step by step from dental caries infection. 
Materials and Methods-Bacteria were isolated from caries site of patients and cultivated identified at the species level. Each of 150 species of bacteria was tested for antibiotics susceptibility to a five antibiotics using Etest. Antibiotic used were Amoxicillin, Cloxocillin, Erythromycin, Tetracycline, Penicillin-V.
Results- The percentages of Resistance in treatment for each antibiotic in this study were penicillin V: 72/150 (48%), Tetracycline: 99/150 (66%), amoxicillin: 135/150 (90%), Cloxocillin: 117/150 (78%), and Erythromycin: 90/150 (60%) (Table 1). If combination antibiotic therapy had been used to treat the bacteria isolated from dental caries, the percentage of Resistance for the combination of penicillin V/Amoxicillin would have been 39/150 (26%), and the combination of amoxicillin/ Erythromycin would have been 45/150 (30%).
Conclusion- This study demonstrated the Molecular Mechanism of antibiotic resistance and susceptibility pattern, of bacteria causing dental caries. The comprehensive results data obtained will allow in investigating spatial distribution of pathogenic antibiotic resistant bacteria in patients of dental caries. In turn this will allow the development of novel diagnostic and treatment methods. 
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Effect of Rectal Hygiene on Sexually Transmitted Infections Among HIV-Negative Men Who Have Sex with Men (MSM)

Abstract Background Rectal gonorrhea (NG) and chlamydia (Connecticut) infections are common among men who have sex with men (MSM). Rectal douching/enema (RDE) is a common practice among MSM that can affect the rectal microbiome. It is unclear if this practice is associated with acquiring rectal infections (RI) with either NG or CT. Methods From 2013–2015, 398 adult HIV-negative MSM and transwomen were enrolled in a randomized controlled study on text messaging for adherence to pre-exposure prophylaxis (PrEP). Participants were surveyed on sexual behavior, frequency of RDE, drug use, and nutritional habits in conjunction with routine sexually transmitted infection testing. Pearson’s χ 2 and two sample t-tests were used to measure significance of RDE and other risk factors with RI. Multivariable logistic regression model was used to control for confounding and assess the association of RDE with RIs. Confounders (i.e., age, number anal receptive sex, number sex partners) were selected a priori for inclusion in the final model based on a causal model and statistical significance. Results Of 397 participants, 262 (67%) performed RDE and 132 (33%) had at least one NG or CT rectal infection over 48 weeks. Number of condomless anal receptive sex acts (mean = 19, P < 0.001), condom use for anal receptive sex (P = 0.017), number of male sex partners in past 3 months (mean = 14, P = 0.001), and the use of poppers (P < 0.001) were associated with RI. There was no significant association between nutritional habits, probiotic foods or supplements and RI, with the exception of energy bars (P = 0.029). Controlling for confounders, RI was associated with RDE less than weekly with OR = 1.02 (95% CI 0.52–1.99) while RDE weekly or more had OR = 2.08 (95% CI 1.03–4.17). Stratified by number of partners, MSMs with more than the median (>6) number of partners had OR = 4.96 (95% CI 1.29–19.03) if performing RDE less than weekly, and OR = 6.03 (95% CI 1.55–23.49) if weekly or more. Conclusion Rectal hygiene with douching/enemas is a common practice among MSMs on PrEP, which increases the odds of acquiring rectal NG and/or CT. This finding is suggestive for the use of rectal hygiene products/practices as potential targets for sexually transmitted infection prevention. Disclosures All authors: No reported disclosures

TAUOLA as tau Monte Carlo for future applications

The status of the Monte Carlo programs for the simulation of tau-lepton production and decay in high-energy accelerator experiments is reviewed. In particular, the status of the following packages is discussed: (i) TAUOLA for tau-lepton decay, (ii) PHOTOS for radiative corrections in decays, (iii) MC-TESTER packages for various types of semi-automatic tests, and (iv) universal interface of TAUOLA for the decay of tau leptons produced by `any' generator. Emphasis is put on recent developments for high-precision tests and extensions of PHOTOS. Some considerations for the software organization necessary in future applications for Belle and BaBar will be given; examples of TAUOLA universal interface use will only be listed at the end of the review.Comment: 7 pages, 2 figure, Presented at International workshop on Tau Lepton Physics, TAU04 Nara, Japan September 14-17,200

Frame me if you must: PrEP framing and the impact on adherence to HIV Pre-exposure Prophylaxis

Abstract Background “PrEP whore” has been used both as a pejorative by PrEP opponents in the gay community and, reactively, by PrEP advocates as a method to reclaim the label from stigmatization and “slut-shaming.” The actual prevalence and impact of such PrEP-directed stigma on adherence have been insufficiently studied. Methods CCTG 595 was a randomized controlled PrEP demonstration project in 398 HIV-uninfected MSM and transwomen. Intracellular tenofovir-diphosphate (TFV-DP) levels at weeks 12 and 48 were used as a continuous measure of adherence. At study visits, participants were asked to describe how they perceived others’ reactions to them being on PrEP. These perceptions were categorized a priori as either “positively framed,” “negatively framed,” or both. We used Wilcoxon rank-sum to determine the association between positive and negative framing and TFV-DP levels at weeks 12 and 48. Results By week 4, 29% of participants reported perceiving positive reactions from members of their social groups, 5% negative, and 6% both. Reporting decreased over 48 weeks, but positive reactions were consistently reported more than negative. At week 12, no differences in mean TFV-DP levels were observed in participants with positively-framed reactions compared with those reporting no outcome or only negatively-framed (1338 [IQR, 1036-1609] vs. 1281 [946-1489] fmol/punch, P = 0.17). Additionally, no differences were observed in those with negative reactions vs. those without (1209 [977–1427] vs. 1303 [964–1545], P = 0.58). At week 48, mean TFV-DP levels trended toward being higher among those that report any reaction, regardless if positive (1335 [909–1665] vs. 1179 [841–1455], P = 0.09) or negative (1377 [1054–1603] vs. 1192 [838–1486], P = 0.10) than those reporting no reaction. At week 48, 46% of participants reported experiencing some form of PrEP-directed judgment, 23% reported being called “PrEP whore,” and 21% avoiding disclosing PrEP use. Conclusion Over 48 weeks, nearly half of participants reported some form of judgment or stigmatization as a consequence of PrEP use. However, individuals more frequently perceived positively framed reactions to being on PrEP than negative. Importantly, long-term PrEP adherence does not appear to suffer as a result of negative PrEP framing. Disclosures All authors: No reported disclosures