Modulation of the bacterial virulence and resistance by well-known European medicinal herbs

ETHNOPHARMACOLOGICAL RELEVANCE

Salvia officinalis L., Sambucus nigra L., Matricaria chamomilla L., Agrimonia eupatoria L., Fragaria vesca L. and Malva sylvestris L. are plants that have a long tradition in European folk medicine. To this day, they are part of medicinal teas or creams that help with the healing of skin wounds and the treatment of respiratory or intestinal infections. However, so far these plants have not been investigated more deeply than in their direct antibacterial effect.

AIM OF THE STUDY

Our research is focused on adjuvants that inhibit the mechanism of antibiotic resistance or modulate bacterial virulence. Based on a preliminary screening of 52 European herbs, which commonly appear as part of tea blends or poultice. Six of them were selected for their ability to revert the resistant phenotype of nosocomial bacterial strains.

METHODS

Herbs selected for this study were obtained from commercially available sources. For the extraction of active compounds ethanol was used. Modulation of virulence was observed as an ability to inhibit bacterial cell-to-cell communication using two mutant sensor strains of Vibrio campbellii. Biofilm formation, and planktonic cell adhesion was measured using a static antibiofilm test. Ethidium bromide assay was used to checked the potential of inhibition bacterial efflux pumps. The antibacterial activities of the herbs were evaluated against resistant bacterial strains using macro dilution methods.

RESULTS

Alcohol extracts had antibacterial properties mainly against Gram-positive bacteria. Of all of them, the highest antimicrobial activity demonstrated Malva sylvestris, killing both antibiotic resistant bacteria; Staphylococcus aureus with MIC of 0.8 g/L and Pseudomonas aeruginosa 0.7 g/L, respectively. Fragaria vesca extract (0.08 g/L) demonstrated strong synergism with colistin (4 mg/L) in modulating the resistant phenotype to colistin of Pseudomonas aeruginosa. Similarly, the extract of S. officinalis (0.21 g/L) reverted resistance to gentamicin (1 mg/L) in S. aureus. However, Sambucus nigra and Matricaria chamomilla seem to be a very promising source of bacterial efflux pump inhibitors.

CONCLUSION

The extract of F. vesca was the most active. It was able to reduce biofilm formation probably due to the ability to decrease bacterial quorum sensing. On the other hand, the activity of S. nigra or M. chamomilla in reducing bacterial virulence may be explained by the ability to inhibit bacterial efflux systems. All these plants have potential as an adjuvant for the antibiotic treatment.

Swarming Magnetic Photoactive Microrobots for Dental Implant Biofilm Eradication

Titanium dental implants are a multibillion dollar market in the United States alone. The growth of a bacterial biofilm on a dental implant can cause gingivitis, implant loss, and expensive subsequent care. Herein, we demonstrate the efficient eradication of dental biofilm on titanium dental implants via swarming magnetic microrobots based on ferromagnetic (Fe₃O₄) and photoactive (BiVO₄) materials through polyethylenimine micelles. The ferromagnetic component serves as a propulsion force using a transversal rotating magnetic field while BiVO₄ is the photoactive generator of reactive oxygen species to eradicate the biofilm colonies. Such photoactive magnetically powered, precisely navigated microrobots are able to destroy biofilm colonies on titanium implants, demonstrating their use in precision medicine.

Flavonolignans from silymarin modulate antibiotic resistance and virulence in Staphylococcus aureus

Antibiotic resistance is currently a serious health problem. Since the discovery of new antibiotics no longer seems to be a sufficient tool in the fight against multidrug-resistant infections, adjuvant (combination) therapy is gaining in importance as well as reducing bacterial virulence. Silymarin is a complex of flavonoids and flavonolignans known for its broad spectrum of biological activities, including its ability to modulate drug resistance in cancer. This work aimed to test eleven, optically pure silymarin flavonolignans for their ability to reverse the multidrug resistance phenotype of Staphylococcus aureus and reduce its virulence. Silybin A, 2,3-dehydrosilybin B, and 2,3-dehydrosilybin AB completely reversed antibiotic resistance at concentrations of 20 µM or less. Both 2,3-dehydrosilybin B and AB decreased the antibiotic-induced gene expression of representative efflux pumps belonging to the major facilitator (MFS), multidrug and toxic compound extrusion (MATE), and ATP-binding cassette (ABC) families. 2,3-Dehydrosilybin B also inhibited ethidium bromide accumulation and efflux in a clinical isolate whose NorA and MdeA overproduction was induced by antibiotics. Most of the tested flavonolignans reduced cell-to-cell communication on a tetrahydrofuran-borate (autoinducer-2) basis, with isosilychristin leading the way followed by 2,3-dehydrosilybin A and AB, which halved communication at 10 µM. Anhydrosilychristin was the only compound that reduced communication based on acyl-homoserine lactone (autoinducer 1), with an IC₅₀ of 4.8 µM. Except for isosilychristin and anhydrosilychristin, all of the flavonolignans inhibited S. aureus surface colonization, with 2,3-dehydrosilybin A being the most active (IC₅₀ 10.6 µM). In conclusion, the selected flavonolignans, particularly derivatives of 2,3-dehydrosilybin B, 2,3-dehydrosilybin AB, and silybin A are non-toxic modulators of S. aureus multidrug resistance and can decrease the virulence of the bacterium, which deserves further detailed research.

The characteristics of coalbed water and coal in a coal seam situated in the Red River Basin, Vietnam

An in-depth understanding of the hydrogeochemical characteristics of coal mines is helpful in establishing an effective and successful exploration program of coalbed methane (CBM). This study provides a comprehensive analysis of hydrogeological characteristics, characteristics of coalbed water, and characteristics of the coal sample from a coal seam located in the Red River Basin (RRB). These physicochemical characteristics along with the microbial composition of coalbed water were critically analyzed. A high concentration of chloride and sodium was found in the coalbed water, presumably due to the coal mine's stratigraphic association with marine or marine-transitional beds. A correlation between the occurrence of microbes and the chemical components in the coalbed water was established. The characteristics of the coal were systematically analyzed, including proximate, ultimate, and petrographic analyses. Based on the coal macerals, coal rank is classified as low-rank (sub-bituminous) with a vitrinite reflectance (R_{o, max}) of 0.36%, suggesting that this type of low-rank coal is favorable for biogenic methane generation. Pore structures and pore types were characterized using different methods, including low-temperature nitrogen adsorption/desorption (LTNA), mercury intrusion porosimetry (MIP), and scanning electron microscopy (SEM). Coal from the study area has microporous and macroporous features. Pore types of the coal were also characterized using SEM. The primary genetic pore types of the Red River coal include plant tissue holes and blowholes.

Multiplex real-time PCR assays for the prediction of cephalosporin, ciprofloxacin and azithromycin antimicrobial susceptibility of positive Neisseria gonorrhoeae nucleic acid amplification test samples

BACKGROUND

The incidence of antimicrobial-resistant Neisseria gonorrhoeae (GC) is rising in Canada; however, antimicrobial resistance (AMR) surveillance data are unavailable for infections diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs), representing over 80% of diagnoses. We developed a set of 10 improved molecular assays for surveillance of GC-AMR and prediction of susceptibilities in NAAT specimens.

METHODS

Multiplex real-time PCR (RT-PCR) assays were developed to detect SNPs associated with cephalosporin (ponA, porB, mtrR -35delA, penA A311V, penA A501, N513Y, G545S), ciprofloxacin (gyrA S91, parC D86/S87/S88) and azithromycin [23S (A2059G, C2611T), mtrR meningitidis-like promoter] resistance. The assays were validated on 127 gonococcal isolates, 51 non-gonococcal isolates and 50 NAATs with matched culture isolates. SNPs determined from the assay were compared with SNPs determined from in silico analysis of WGS data. MICs were determined for culture isolates using the agar dilution method.

RESULTS

SNP analysis of the 50 NAAT specimens had 96% agreement with the matched culture RT-PCR analysis. When compared with MICs, presence of penA A311V or penA A501 and two or more other SNPs correlated with decreased susceptibility and presence of three or more other SNPs correlated with intermediate susceptibility to cephalosporins; presence of any associated SNP correlated with ciprofloxacin or azithromycin resistance. NAAT-AMR predictions correlated with matched-culture cephalosporin, ciprofloxacin and azithromycin MICs at 94%, 100% and 98%, respectively.

CONCLUSIONS

We expanded molecular tests for N. gonorrhoeae AMR prediction by adding new loci and multiplexing reactions to improve surveillance where culture isolates are unavailable.

Antimicrobial Activity of Extracts of Two Native Fruits of Chile: Arrayan (Luma apiculata) and Peumo (Cryptocarya alba)

Arrayan and peumo fruits are commonly used in the traditional medicine of Chile. In this study, the concentration of the extracts halving the bacterial viability and biofilms formation and disruption of the drug-sensitive and drug-resistant strains of Staphylococcus aureus and Pseudomonas aeruginosa was determined. The chemical composition of extracts was analyzed by high-resolution liquid chromatography coupled with mass spectrometry (U-HPLC/MS). The arrayan extract (Inhibitory concentration IC₅₀ 0.35 ± 0.01 mg/mL) was more effective than peumo extract (IC₅₀ 0.53 ± 0.02 mg/mL) in the inhibition of S. aureus planktonic cells. Similarly, the arrayan extract was more effective in inhibiting the adhesion (S. aureus IC₅₀ 0.23 ± 0.02 mg/mL, P. aeruginosa IC₅₀ 0.29 ± 0.02 mg/mL) than peumo extracts (S. aureus IC₅₀ 0.47 ± 0.03 mg/mL, P. aeruginosa IC₅₀ 0.35 ± 0.01 mg/mL). Both extracts inhibited quorum sensing in a concentration-dependent manner, and the most significant was the autoinducer-2 type communication inhibition by arrayan extract. Both extracts also disrupted preformed biofilm of P. aeruginosa (arrayan IC₅₀ 0.56 ± 0.04 mg/mL, peumo IC₅₀ 0.59 ± 0.04 mg/mL). However, neither arrayan nor peumo extracts disrupted S. aureus mature biofilm. U-HPLC/MS showed that both fruit extracts mainly possessed quercetin compounds; the peumo fruit extract also contained phenolic acids and phenylpropanoids. Our results suggested that both extracts could be used as natural antimicrobials for some skin and nosocomial infections.

Occurrence and risk assessment of multiple classes of antibiotics in urban canals and lakes in Hanoi, Vietnam

Very little information on the occurrence and risk assessment of antibiotics in the aquatic environment is reported for Vietnam, where antibiotics are assumed to be omnipresent in urban canals and lakes at high concentrations due to the easy accessibility of antibiotics without doctor prescription. This study provides comprehensive analysis of the occurrence of 23 antibiotics in urban canals (To Lich and Kim Nguu) and lakes (West Lake, Hoan Kiem, and Yen So) in Hanoi, Vietnam. Of these 23 antibiotics, 18 were detected in urban canals at above 67.9% detection frequency (DF). The concentrations of detected antibiotics were in the range from below quantification limit (MQL) to almost 50,000 ng/L, depending on the compound and sampling site. In urban canals, median concentration of amoxicillin, erythromycin, and sulfamethoxazole was >1000 ng/L while other antibiotics such as ampicillin, chloramphenicol, clindamycin, sulfamethazine, tetracycline, tylosin and vancomycin were detected at median concentrations of <100 ng/L. Similarly, 16 target antibiotics were also detected in urban lakes. Macrolides (azithromycin, clarithromycin, and erythromycin-H₂O), fluoroquinolones (enrofloxacin and ofloxacin), lincosamides (clindamycin and lincomycin), and trimethoprim were ubiquitously detected in urban lakes (DF = 100%). In this study, potential risks of antibiotics in the investigated urban canals and lakes were assessed based on the predicted no-effect concentration (PNEC) from the existing literature for antibiotic resistance selection (PNEC_ARM) and ecological toxicity to aquatic organisms (PNEC_Ecotox). Ampicillin, amoxicillin, azithromycin, ciprofloxacin, clarithromycin, enrofloxacin, erythromycin, ofloxacin, tetracycline, and trimethoprim were found in the investigated urban canals at concentrations exceeding their PNEC_ARM and PNEC_Ecotox. Similarly, most of the target antibiotics (i.e. amoxicillin, ciprofloxacin, clarithromycin, clindamycin, enrofloxacin, erythromycin, lincomycin, ofloxacin, sulfamethoxazole, tetracycline, trimethoprim and tylosin) were detected in the investigated urban lakes at concentrations close to or exceeding PNEC_Ecotox for aquatic organisms. Further investigations on the occurrence and fate of antibiotic residues and antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in surface waters are recommended.

Increase in ST-11 serogroup W Neisseria meningitidis invasive meningococcal disease in Canada, 2016-2018

BACKGROUND

Many countries have experienced increases in invasive meningococcal disease (IMD) due to a serogroup W Neisseria meningitidis (MenW) strain of the multilocus sequence type (ST)-11 clonal complex (CC). MenW ST-11 was first reported in Ontario, Canada, in 2014. By 2016, this strain caused IMD in five provinces and was responsible for 18.8% of the IMD cases in Canada.

OBJECTIVE

To provide an update on invasive MenW disease in Canada including the strain characteristics, specimen source of isolates, age, sex and geographic distribution of cases.

METHODS

N. meningitidis from culture-positive IMD cases are routinely submitted to the National Microbiology Laboratory (NML) for serogroup, serotype, serosubtype and sequence type analysis. The data from January 1, 2016 to December 31, 2018 were analyzed by calculating the proportion of IMD cases caused by MenW compared with other serogroups. In addition, trends based on age, sex and geographic distribution of cases and specimen source of isolates were analyzed based on information on specimen requisition forms.

RESULTS

Over the 3-year period, 292 individual IMD case isolates were analyzed. The percentage of IMD case isolates typed as MenW more than doubled from 19% (n=15) to 44% (n=51) in 2018 when MenW became the most common serogroup, exceeded the number of MenB, MenC or MenY. In total, 93 MenW case isolates were identified, 91% (n=85) belonged to the ST-11 CC. The increase in MenW affected all age groups (but was most common in those older than 60) and both sexes, and occurred across the country but most prevalent in western Canada. The most common specimen source was blood.

CONCLUSION

In 2018, MenW was the most common serogroup for isolates received by the NML from culture-positive IMD cases in Canada. Over 90% of the MenW serogroup isolates belonged to the ST-11 CC. The quadrivalent ACWY meningococcal conjugate vaccine protects against IMD caused by strains in the A, C, W or Y serogroups and therefore may protect against IMD caused by the new MenW ST-11 strain; however, more research is needed. The emergence of variant strains highlight the importance of strain characterization in IMD surveillance and research.

Stromal invasion pattern identifies patients at lowest risk of lymph node metastasis in HPV-associated endocervical adenocarcinomas, but is irrelevant in adenocarcinomas unassociated with HPV

OBJECTIVE

The Silva invasion pattern-based classification system stratifies endocervical adenocarcinomas (ECAs) into 3 categories corresponding to risk of metastasis and recurrence, but has only been evaluated for HPV-associated ECAs of usual type. We examined whether the Silva system is applicable to all endocervical adenocarcinomas, especially those not associated with HPV.

METHODS

Complete slide sets from 341 surgical specimens of ECA were collected from 7 institutions worldwide. All specimens were associated with clinical records covering at least 5 years of follow-up. Tumors were classified as HPV-associated (HPVA) or not (NHPVA) by both morphology and detection of HPV using in situ hybridization. Recurrence and survival were analyzed by multivariate Mantel-Haenszel methods.

RESULTS

Most specimens (292; 85.6%) were HPVA, while 49 (14.3%) were NHPVA. All NHPVAs were Silva pattern C, while 76.0% of HPVAs were pattern C, 14.7% pattern A, and 9.3% pattern B. Including both HPVAs and NHPVAs, lymphovascular invasion (LVI) was detected in 0% of pattern A, 18.5% of pattern B and 62.6% of pattern C cases (p < 0.001). None of the pattern A or B cases were associated with lymph node metastases (LNM), in contrast to pattern C cases (21.8%). Among patients with Silva pattern C ECA, those with HPVA tumors had a lower recurrence rate and better survival than those with NHPVA; however, when adjusted for stage at diagnosis, the difference in recurrence and mortality was small and not statistically significant.

CONCLUSIONS

Application of the Silva system is only relevant in HPVA cervical adenocarcinoma.

Cytogenetic Findings on 11,451 Cases of Amniocentesis in Hanoi, Vietnam

Since the 1960s, amniocentesis has become a routine procedure performed in prenatal diagnostic clinics. This study aims to depict the results of amniocentesis, the frequency of chromosomal abnormality and emphasize on amniocentesis indications. A retrospective study was conducted on 11,451 cases who were referred to the Prenatal Diagnosis Center, the National Hospital of Obstetrics and Gynecology, Hanoi, Vietnam from 2012 to 2016. The rate of chromosomal abnormality was 6.7%. The chromosomal aberration in the group with mother or father carrying balanced parental translocations accounted for the highest rate of 22.0%. Triploidy was 1.2%, autosomal chromosome aberration was 59.7%, sex chromosome was 8.3%, and structural rearrangements was 30.8%. Trisomy 21 was the most frequent disorder founded in abnormal ultrasound findings (47.4%), following by the advanced maternal age (44.1%). The large sample size of this study provided reliable evidence to support the development of prenatal counseling and pregnancy management programs.

Decline in Decreased Cephalosporin Susceptibility and Increase in Azithromycin Resistance in Neisseria gonorrhoeae, Canada

Antimicrobial resistance profiles were determined for Neisseria gonorrhoeae strains isolated in Canada during 2010–2014. The proportion of isolates with decreased susceptibility to cephalosporins declined significantly between 2011 and 2014, whereas azithromycin resistance increased significantly during that period. Continued surveillance of antimicrobial drug susceptibilities is imperative to inform treatment guidelines.

The MOSART database: linking the SART CORS clinical database to the population-based Massachusetts PELL reproductive public health data system

Although Assisted Reproductive Technology (ART) births make up 1.6 % of births in the US, the impact of ART on subsequent infant and maternal health is not well understood. Clinical ART treatment records linked to population data would be a powerful tool to study long term outcomes among those treated or not by ART. This paper describes the development of a database intended to accomplish this task. We constructed the Massachusetts Outcomes Study of Assisted Reproductive Technology (MOSART) database by linking the Society of Assisted Reproductive Technologies Clinical Outcomes Reporting System (SART CORS) and the Massachusetts (MA) Pregnancy to Early Life Longitudinal (PELL) data systems for children born to MA resident women at MA hospitals between July 2004 and December 2008. PELL data representing 282,971 individual women and their 334,152 deliveries and 342,035 total births were linked with 48,578 cycles of ART treatment in SART CORS delivered to MA residents or women receiving treatment in MA clinics, representing 18,439 eligible women of whom 9,326 had 10,138 deliveries in this time period. A deterministic five phase linkage algorithm methodology was employed. Linkage results, accuracy, and concordance analyses were examined. We linked 9,092 (89.7 %) SART CORS outcome records to PELL delivery records overall, including 95.0 % among known MA residents treated in MA clinics; 70.8 % with full exact matches. There were minimal differences between matched and unmatched delivery records, except for unknown residency and out-of-state ART site. There was very low concordance of reported use of ART treatment between SART CORS and PELL (birth certificate) data. A total of 3.4 % of MA children (11,729) were identified from ART assisted pregnancies (6,556 singletons; 5,173 multiples). The MOSART linked database provides a strong basis for further longitudinal ART outcomes studies and supports the continued development of potentially powerful linked clinical-public health databases.

Adverse pregnancy outcomes after in vitro fertilization: effect of number of embryos transferred and plurality at conception

OBJECTIVE

To evaluate risks for adverse pregnancy outcomes by number of embryos transferred (ET) and fetal heartbeats (FHB) in assisted reproductive technology-conceived singleton live births.

DESIGN

Longitudinal cohort using cycles reported to the Society for Assisted Reproductive Technology Clinic Outcomes Reporting System between 2004 and 2008 among women who were treated and gave birth in Massachusetts.

SETTING

Not applicable.

PATIENT(S)

Assisted reproductive technology data on 6,073 births between 2004 and 2008 were linked to vital records and hospital data. Likelihood of ET ≥3 vs. 1-2, FHB >1 vs. 1, and risks of preterm birth (PTB, <37 weeks' gestation), low birth weight (LBW, <2,500 g), and small-for-gestational-age birth weight (SGA, <10th percentile) with FHB >1 were modeled with binary logistic regression using a backward-stepping algorithm, and presented as adjusted odds ratios (95% confidence intervals).

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

ET ≥3, FHB >1, PTB, LBW, and SGA.

RESULT(S)

Higher ET was significantly more likely with older maternal age, intracytoplasmic sperm injection, assisted hatching, cleavage-stage embryos, and thawed embryos. The likelihood of FHB >1 with ≥3 ET vs. 1-2 ET was 2.04 (1.68-2.48). Risks of PTB and LBW with FHB >1 were 1.63 (1.27-2.09) and 1.81 (1.36-2.39), respectively; the risk of SGA was not significant. Nulliparity was associated with higher risks of PTB (1.34 [1.12-1.59]), LBW (1.48 [1.20-1.83]), and SGA (2.17 [1.69-2.78]).

CONCLUSION(S)

Number of embryos transferred was strongly associated with FHBs, with twice the risk of FHB >1 with ≥3 ET vs. 1-2 ET. Increasing FHBs were associated with significantly greater risks for PTB and LBW outcomes.

Perinatal outcomes associated with assisted reproductive technology: the Massachusetts Outcomes Study of Assisted Reproductive Technologies (MOSART)

OBJECTIVE

To compare on a population basis the birth outcomes of women treated with assisted reproductive technologies (ART), women with indicators of subfertility but without ART, and fertile women.

DESIGN

Longitudinal cohort study.

SETTING

Not applicable.

PARTICIPANT(S)

A total of 334,628 births and fetal deaths to Massachusetts mothers giving birth in a Massachusetts hospital from July 1, 2004, to December 31, 2008, subdivided into three subgroups for comparison: ART 11,271, subfertile 6,609, and fertile 316,748.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Four outcomes-preterm birth, low birth weight, small for gestational age, and perinatal death-were modeled separately for singletons and twins with the use of logistic regression for the primary comparison between ART births and those to the newly created population-based subgroup of births to women with indicators of subfertility but no ART.

RESULT(S)

For singletons, the risks for both preterm birth and low birth weight were higher for the ART group (adjusted odds ratios [AORs] 1.23 and 1.26, respectively) compared with the subfertile group, and risks in both the ART and the subfertile groups were higher than those among the fertile births group. For twins, the risk of perinatal death was significantly lower among ART births than fertile (AOR 0.55) or subfertile (AOR 0.15) births.

CONCLUSION(S)

The use of a population-based comparison group of subfertile births without ART demonstrated significantly higher rates of preterm birth and low birth weight in ART singleton births, but these differences are smaller than differences between ART and fertile births. Further refinement of the measurement of subfertile births and examination of the independent risks of subfertile births is warranted.

Differential susceptibility of invasive Haemophilus influenzae serotype a and serotype b to ampicillin and other commonly prescribed antibiotics

Haemophilus influenzae serotype a (Hia) has become an important pathogen in the post-H. influenzae serotype b (Hib) vaccine era. Antibiotic resistance in H. influenzae is a global phenomenon, but few studies have looked at antibiotic resistance profiles with regard to serotype. Invasive Hia (n = 157), noninvasive Hia (n = 2) and invasive Hib (n = 42) collected over the last two decades from three Canadian Provinces were examined for resistance to several commonly prescribed antibiotics, and sequence types (STs) were determined by MLST. Only 1·9% of Hia showed antibiotic resistance, while 31% of Hib were resistant to one or more antibiotic. Resistance to ampicillin, sulfamethoxazole-trimethoprim, chloramphenicol and tetracycline was observed, with β-lactamase-mediated ampicillin resistance being the most common. Nine STs were identified for Hia with 7 STs belonging to the same clonal complex. Ten STs were observed in Hib strains, and all of them belonged to a single clonal complex. A possible correlation between sequence type and ampicillin resistance was observed for Hib, while no correlations were observed for Hia.

SIGNIFICANCE AND IMPACT OF THE STUDY

Despite H. influenzae serotype b (Hib) vaccine programs, invasive disease due to Hib still exists in Canada and is either second or third most common behind nontypeable and/or serotype a (Hia). Many previous studies on antibiotic resistance have focussed on respiratory isolates, and few have looked at resistance with regard to serotype. This study analysed antibiotic resistance in invasive Hia and Hib collected over 20 years from three provinces, and results found that significantly more Hib showed resistance compared to Hia. This provides a small snapshot of H. influenzae disease in Canada and highlights the importance to continually monitor antibiotic resistance profiles.

Serratia marcescens harbouring SME-type class A carbapenemases in Canada and the presence of blaSME on a novel genomic island, SmarGI1-1

OBJECTIVES

An increasing prevalence since 2010 of Serratia marcescens harbouring the Ambler class A carbapenemase SME prompted us to further characterize these isolates.

METHODS

Isolates harbouring bla(SME) were identified by PCR and sequencing. Phenotypic analysis for carbapenemase activity was carried out by a modified Hodge test and a modified Carba NP test. Antimicrobial susceptibilities were determined by Etest and Vitek 2. Typing was by PFGE of macrorestriction digests. Whole-genome sequencing of three isolates was carried out to characterize the genomic region harbouring the bla(SME)-type genes.

RESULTS

All S. marcescens harbouring SME-type enzymes could be detected using a modified Carba NP test. Isolates harbouring bla(SME) were resistant to penicillins and carbapenems, but remained susceptible to third-generation cephalosporins, as well as fluoroquinolones and trimethoprim/sulfamethoxazole. Isolates exhibited diverse genetic backgrounds, though 57% of isolates were found in three clusters. Analysis of whole-genome sequence data from three isolates revealed that the bla(SME) gene occurred in a novel cryptic prophage genomic island, SmarGI1-1.

CONCLUSIONS

There has been an increasing occurrence of S. marcescens harbouring bla(SME) in Canada since 2010. The bla(SME) gene was found on a genomic island, SmarGI1-1, that can be excised and circularized, which probably contributes to its dissemination amongst S. marcescens.

S3-5: Next Generation Sequencing Reveals Co-Activating Events in the MAPK and P13K/AKT Pathways in Metastatic Triple Negative Breast Cancers

INTRODUCTION: The clinical application of next generation sequencing to comprehensively characterize groups of driving mutations in individual metastatic triple negative breast cancer (mTNBC) genomes has the potential to reveal therapeutically relevant pathway dependencies. Towards this end, we harvested tissue from 14 patients with mTNBC and are conducting deep whole genome and transcriptome sequencing for each case to identify mutations that can guide therapeutic targeting within available phase I/II clinical trials.

METHODS: Metastatic tumor tissue was harvested from 14 mTNBC patients, and 7 samples have undergone total genome and transcriptome sequencing with the others currently underway. We are utilizing the Life Technologies SOLiD® system to sequence germline and tumor DNA to sufficient depth to identify somatic genome alterations including point mutations, indels, and structural events including translocations. Furthermore, RNA-seq is being performed on these tumors, along with a series of age- and ethnicity-matched normal breast controls to perform deep differential expression analysis, isoform expression analysis, and fusion transcript detection. Our team of genome scientists and clinical oncologists are evaluating the sequencing findings and are prioritizing the investigational therapeutic options for each patient.

RESULTS: Our whole genome and transcriptome sequencing study has revealed numerous known and novel mutations in mTNBC. However, all patients’ cancers analyzed to date had alterations that would activate the MAPK pathway, but through various mechanisms in different patients. These include BRAF amplification and overexpression, NF1 homozygous deletion, and consistent IQGAP3 overexpression. Furthermore, all patients’ cancers also harbor mutations that would activate the PI3K/AKT pathway including PTEN homozygous deletion or down-regulation, consistent INPP4B down-regulation, FBXW7 homozygous deletion, and ERAS overexpression. Moreover, although we and others show ERBB4 down-regulation in breast tumors, we are the first to report unique somatic genomic events that significantly alter the ERBB4 locus leading to its loss in the majority (5/7) of our patients’ tumors. Importantly, we are beginning to use these insights to prioritize therapeutic targeting and have observed that one chemotherapy-refractory mTNBC patient, with a high-level BRAF amplification/overexpression along with down-regulation of PTEN and INPP4B, had a major response to combined mek plus akt inhibitors on a phase I study.

CONCLUSIONS: Comprehensive genomic and transcriptomic interrogation of mTNBCs has revealed events supporting co-activation of the MAPK and PI3K/AKT pathways in all the tumors albeit by different mutational mechanisms and supports potential effectiveness of combination therapy in the treatment of mTNBC. We plan to treat these patients with combined mek plus akt inhibitors on a new phase I study beginning in August 2011 to determine the effectiveness of co-inhibition of these pathways based on this frequent genomic context.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr S3-5.

[Severe cases of A(H1N1)v2009 infection in Réunion Island in 2009 and 2010]

Dans l’hémisphère sud, La Réunion est la sentinelle des infections survenant préférentiellement au cours de l’hiver austral, susceptibles de gagner quelques mois plus tard l’hémisphère nord, telle l’infection à A(H1N1)v2009. Nous rapportons les caractéristiques des patients admis en 2009 et 2010 dans notre service de réanimation principalement pour détresse respiratoire aiguë, à la suite d’une infection à A(H1N1)v2009. Les données démographiques, cliniques, biologiques, ainsi que les traitements et le devenir des patients admis pour infection virale à A(H1N1)v2009 exclusivement confirmée par RT-PCR ont été recueillis de façon prospective. Au cours des années 2009 et 2010, 25 patients ont répondu aux critères définis d’infection à A(H1N1)v2009. L’âge médian était de 40,4 (±17,4) ans. La plupart d’entre eux (22/25) présentaient des facteurs de comorbidité: pathologies chroniques, surpoids ou obésité, grossesse, trisomie. Les principaux motifs d’admission en réanimation ont été les pneumonies virales avec tableau de syndrome de détresse respiratoire aiguë. Le recours à la ventilation artificielle a été nécessaire chez 22 des 25 patients, avec recours à des méthodes sophistiquées et réservées à quelques centres au niveau national, telles que les techniques d’oxygénation extracorporelle (ECMO) ou ventilation à haute fréquence (HFO). Au cours des deux années, 12 décès (48 %) sont survenus essentiellement dans des tableaux de défaillance multiviscérale. Au cours des hivers et automnes australs 2009 et 2010 et pendant une période de plusieurs semaines, l’infection à A(H1N1) v2009 a entraîné une surcharge d’activité notable dans les services de réanimation de La Réunion. L’échec de la campagne de vaccination, notamment des personnes à risques, a eu pour conséquence la survenue de nouveaux cas graves en 2010, notamment parmi les personnes à risques. Le recueil de ces données peut aider à la planification et à l’anticipation de la prise en charge d’autres épidémies grippales.

The phenylalanine hydroxylase locus: a marker for the history of phenylketonuria and human genetic diversity. PAH Mutation Analysis Consortium

Disease-producing allelic variation describes one aspect of human genetic diversity. Phenylketonuria, the major type of hyperphenylalaninaemia and formerly a functional genetic lethal, has a 2% carrier frequency in temperate-zone populations. Newborn screening for hyperphenylalaninaemia (incidence of 1 in 10000) has made it one of the most widely ascertained human Mendelian traits; 99% of hyperphenylalaninaemia mutations map to the PAH (phenylalanine hydroxylase) gene on 12q24.1, and most cause phenylketonuria. The gene is well characterized. Analysis of 3986 mutant chromosomes by 81 investigators in 26 countries has identified 243 different mutations in 788 different associations (with polymorphic intragenic haplotypes [seven diallelic sites, one short tandem repeat, one variable number of tandem repeats], populations and regions). These data are compiled on a database accessible on the World-Wide Web or as a stand-alone software package. A few phenylketonuria alleles occur at high relative frequencies in particular populations on one or only a few haplotypes, suggesting positive selection in the past. Additional mechanisms (founder effect, drift and recurrent mutation) can explain frequencies and distributions of particular alleles. Allele stratification in Europeans and Orientals implies that mechanism(s) accounting for distribution and high frequencies of PAH alleles were acting before and during demic expansion in Europe and after the European and Oriental radiations.

Effects of Hippocampus and Medial Caudate Nucleus Lesions on Memory for Direction Information in Rats

A delayed matching-to-sample task was designed to assess memory for direction information in rats. During the study phase, rats traversed a maze arm oriented in 1 of 3 directions. After a delay period, a test phase was presented that required a choice between the study phase direction and a foil direction. Once rats reached a learning criterion, probe trials suggested that normal rats favor the use of direction, rather than turning response, information and use vestibular feedback. Rats were then given hippocampus, medial caudate nucleus (MCN), or cortical control lesions. Unlike control rats, those with hippocampus and MCN lesions exhibited marked impairments when retested. However, all rats were able to learn a direction discrimination task. These results suggest that the hippocampus and MCN support processes associated with short-term memory for direction information.

Water magnetic relaxation dispersion in biological systems: the contribution of proton exchange and implications for the noninvasive detection of cartilage degradation

Magnetic relaxation has been used extensively to study and characterize biological tissues. In particular, spin-lattice relaxation in the rotating frame (T(1rho)) of water in protein solutions has been demonstrated to be sensitive to macromolecular weight and composition. However, the nature of the contribution from low frequency processes to water relaxation remains unclear. We have examined this problem by studying the water T(1rho) dispersion in peptide solutions ((14)N- and (15)N-labeled), glycosaminoglycan solutions, and samples of bovine articular cartilage before and after proteoglycan degradation. We find in model systems and tissue that hydrogen exchange from NH and OH groups to water dominates the low frequency water T(1rho) dispersion, in the context of the model used to interpret the relaxation data. Further, low frequency dispersion changes are correlated with loss of proteoglycan from the extra-cellular matrix of articular cartilage. This finding has significance for the noninvasive detection of matrix degradation.

An amino acid code for protein folding

Direct structural information obtained for many proteins supports the following conclusions. The amino acid sequences of proteins can stabilize not only the final native state but also a small set of discrete partially folded native-like intermediates. Intermediates are formed in steps that use as units the cooperative secondary structural elements of the native protein. Earlier intermediates guide the addition of subsequent units in a process of sequential stabilization mediated by native-like tertiary interactions. The resulting stepwise self-assembly process automatically constructs a folding pathway, whether linear or branched. These conclusions are drawn mainly from hydrogen exchange-based methods, which can depict the structure of infinitesimally populated folding intermediates at equilibrium and kinetic intermediates with subsecond lifetimes. Other kinetic studies show that the polypeptide chain enters the folding pathway after an initial free-energy-uphill conformational search. The search culminates by finding a native-like topology that can support forward (native-like) folding in a free-energy-downhill manner. This condition automatically defines an initial transition state, the search for which sets the maximum possible (two-state) folding rate. It also extends the sequential stabilization strategy, which depends on a native-like context, to the first step in the folding process. Thus the native structure naturally generates its own folding pathway. The same amino acid code that translates into the final equilibrium native structure-by virtue of propensities, patterning, secondary structural cueing, and tertiary context-also produces its kinetic accessibility.

Evaluation of molecular techniques to biotype Giardia duodenalis collected during an outbreak

Twenty-seven Giardia duodenalis cyst-positive specimens (human, animal, or drinking water) were obtained from a waterborne outbreak in a community in British Columbia, western Canada. Parasite isolates were characterized using molecular techniques at 4 different steps of organism retrieval. None of the drinking water samples (n = 20) infected gerbils and none was successfully amplified using polymerase chain reaction (PCR). We were able to genotype 4 of 7 (human and animal) isolates by amplification of DNA from original specimens at the triosephosphate isomerase (tpi) gene locus using PCR followed by restriction fragment length polymorphism (RFLP) analysis. Five of the original specimens inoculated into Mongolian gerbils (Meriones unguiculatus) were infective and genotyped at the tpi locus using parasite material collected from the gerbil (cysts and trophozoites). Pulsed field gel electrophoresis (PFGE) was used to biotype trophozoites collected from the gerbils as well as trophozoites from the 4 isolates that adapted to culture. Four of these 5 isolates displayed the same (designated outbreak) biotype at all parasite retrieval steps with all molecular techniques including the originally amplified isolates. PCR-RFLP identified an additional biotype group. The 4 isolates that adapted to in vitro culture were also characterized by isoenzyme electrophoresis (IE). Biotype groups identified in these axenized isolates were all the same with each molecular technique (PCR-RFLP, PFGE, IE) tested. Results of this study demonstrate a need for more sensitive molecular methods to detect and characterize Giardia in original host and environmental samples. Results are also consistent with evidence of biotype changes that occur during the presently used process of isolate retrieval.

Bacterial endotoxin alters kinetics of BK channels in rat cerebrovascular smooth muscle cells

Patch-clamp recordings were used to study the effects of Escherichia coli bacterial endotoxin (lipopolysaccharide, LPS) on the properties of large-conductance, Ca2+-dependent K+ channels (BK channels) in the membrane of enzymatically dispersed rat cerebrovascular smooth muscle cells (CVSMCs). LPS had negligible effects on the kinetic and conductance properties of BK channels when applied to the extracellular domain of these channels. However, acute application of LPS (10-100 microg/ml) to inside-out patches of CVSMC membrane isolated in a cell-free environment rapidly and reversibly increased the open probability of BK channels, leaving the conductance of these channels unaltered. The magnitude of this effect decreased as the concentration of free Ca2+ at the cytoplasmic membrane face was lowered, but was little affected by changes in membrane potential. Kinetic analysis showed that LPS accelerated reopening of BK channels while having little effect on mean channel open time. Detoxified E. coli LPS, from which the fatty acid chains of Lipid A were partially removed, showed slightly reduced activity when compared to the parent endotoxin molecule. A purified E. coli Lipid A had negligible effects on BK channel function. These results indicate that LPS activates BK channels in cerebrovascular smooth muscle cells when present at the cytoplasmic membrane face. This novel mechanism may provide insights into the regulation of BK channels by intracellular, membrane-associated elements.

Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics

The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium thermoautotrophicum deltaH has been determined by a whole-genome shotgun sequencing approach. A total of 1,855 open reading frames (ORFs) have been identified that appear to encode polypeptides, 844 (46%) of which have been assigned putative functions based on their similarities to database sequences with assigned functions. A total of 514 (28%) of the ORF-encoded polypeptides are related to sequences with unknown functions, and 496 (27%) have little or no homology to sequences in public databases. Comparisons with Eucarya-, Bacteria-, and Archaea-specific databases reveal that 1,013 of the putative gene products (54%) are most similar to polypeptide sequences described previously for other organisms in the domain Archaea. Comparisons with the Methanococcus jannaschii genome data underline the extensive divergence that has occurred between these two methanogens; only 352 (19%) of M. thermoautotrophicum ORFs encode sequences that are >50% identical to M. jannaschii polypeptides, and there is little conservation in the relative locations of orthologous genes. When the M. thermoautotrophicum ORFs are compared to sequences from only the eucaryal and bacterial domains, 786 (42%) are more similar to bacterial sequences and 241 (13%) are more similar to eucaryal sequences. The bacterial domain-like gene products include the majority of those predicted to be involved in cofactor and small molecule biosyntheses, intermediary metabolism, transport, nitrogen fixation, regulatory functions, and interactions with the environment. Most proteins predicted to be involved in DNA metabolism, transcription, and translation are more similar to eucaryal sequences. Gene structure and organization have features that are typical of the Bacteria, including genes that encode polypeptides closely related to eucaryal proteins. There are 24 polypeptides that could form two-component sensor kinase-response regulator systems and homologs of the bacterial Hsp70-response proteins DnaK and DnaJ, which are notably absent in M. jannaschii. DNA replication initiation and chromosome packaging in M. thermoautotrophicum are predicted to have eucaryal features, based on the presence of two Cdc6 homologs and three histones; however, the presence of an ftsZ gene indicates a bacterial type of cell division initiation. The DNA polymerases include an X-family repair type and an unusual archaeal B type formed by two separate polypeptides. The DNA-dependent RNA polymerase (RNAP) subunits A', A", B', B" and H are encoded in a typical archaeal RNAP operon, although a second A' subunit-encoding gene is present at a remote location. There are two rRNA operons, and 39 tRNA genes are dispersed around the genome, although most of these occur in clusters. Three of the tRNA genes have introns, including the tRNAPro (GGG) gene, which contains a second intron at an unprecedented location. There is no selenocysteinyl-tRNA gene nor evidence for classically organized IS elements, prophages, or plasmids. The genome contains one intein and two extended repeats (3.6 and 8.6 kb) that are members of a family with 18 representatives in the M. jannaschii genome.

G protein alpha subunit multigene family in the Japanese puffer fish Fugu rubripes: PCR from a compact vertebrate genome

We compare the complexity and organization of the G protein alpha subunit multigene family in the vertebrate genomes of mammals and the Japanese puffer fish Fugu rubripes. Fourteen Fugu G alpha genes were identified of the 16 genes characterized previously in mammals, including Fugu genes from the four classes of alpha subunits Gs, Gi, Gq, and G12. Fugu and mammalian G alpha coding sequences are highly homologous, and the intron/exon structure of the fish and mammalian orthologs is identical throughout the coding regions. A novel G alpha gene, G alpha p1, was also identified in Fugu rubripes and two other species of puffer fish. The complete sequence of Gnaz and the tandemly duplicated genes Gnai2 and Gnat1 were obtained from a Fugu genomic cosmid library. Introns in the puffer fish G alpha genes lacked repeat DNA sequences, other than simple sequence length repeats, and most introns were significantly shorter in Fugu than in mammalian orthologs. The compact genome of puffer fish provides a unique vertebrate model for characterizing multigene families and identifying novel genes directly from genomic DNA by PCR amplification with degenerate primers. The fact that Fugu encodes most, if not all, of the G protein alpha subunits identified in mammals strongly supports Fugu as a model organism for vertebrate genome research.

PAH Mutation Analysis Consortium Database: a database for disease-producing and other allelic variation at the human PAH locus

The PAH Mutation Analysis Consortium (81 investigators, 26 countries) is engaged in mutation detection at the human PAH locus. Ascertainment of probands occurs largely through newborn screening for hyperphenylalaninemia. A relational database records allelic variation (disease-producing and polymorphic) at the locus. Information is distributed by Newsletter, diskette (WINPAHDB software stand-alone executable on IBM compatible hardware), and at a 'real' site on the Worldwide Web (http://www.mcgill.ca/pahdb). The database presently records (Sept. 27, 1995) 248 alleles in 798 different associations (with polymorphic haplotype, geographic region and population) along with additional information. The database, as a record of human genetic diversity, at a particular locus, contributes to the study of human evolution and demic expansion; it also has medical relevance.

ATP sulfurylase from Penicillium chrysogenum: measurements of the true specific activity of an enzyme subject to potent product inhibition and a reassessment of the kinetic mechanism

Homogeneous ATP sulfurylase from Penicillium chrysogenum has been reported to have an extremely low activity toward its physiological inorganic substrate, sulfate. This low activity is an artifact resulting from potent product inhibition by 5'-adenylylsulfate (APS) (Ki less than 0.25 microM). Assays based on 35S incorporation from 35SO4(2-) into charcoal-adsorbable [35S]APS are nonlinear with time, even in the presence of a large excess of inorganic pyrophosphatase. However, in the presence of excess APS kinase (along with excess pyrophosphatase), the ATP sulfurylase reaction is linear with time and the enzyme has a specific activity (Vmax) of 6 to 7 units mg protein-1 corresponding to an active site turnover number of at least 400 min-1. Monovalent oxyanions such as NO3-, ClO3-, ClO4-, and FSO3- are competitive with sulfate (or molybdate) and essentially uncompetitive with respect to MgATP. However, thiosulfate (SSO3(2-)), a true sulfate analog and dead-end inhibitor of the enzyme (competitive with sulfate or molybdate), exhibited clear noncompetitive inhibition against MgATP. Furthermore, APS was competitive with both MgATP and molybdate in the molybdolysis assay. These results suggest (a) that the mechanism of the normal forward reaction may be random rather than ordered and (b) that the monovalent oxyanions have a much greater affinity for the E X MgATP complex than for free E. In this respect, FSO3-, ClO4-, etc., are not true sulfate analogs although they might mimic an enzyme-bound species formed when MgATP is at the active site. The nonlinear ATP sulfurylase reaction progress curves (with APS accumulating in the presence of excess pyrophosphatase or PPi accumulating in the presence of excess APS kinase) were analyzed by means of "average velocity" plots based on an integrated rate equation. This new approach is useful for enzymes subject to potent product inhibition over a reaction time course in which the substrate concentrations do not change significantly. The analysis showed that ATP sulfurylase has an intrinsic specific activity of 6 to 7 units mg protein-1. Thus, the apparent stimulation of sulfurylase activity by APS kinase results from the continual removal of inhibitory APS rather than from an association of the two sulfate-activating enzymes to form a "3'-phospho-5'-adenylylsulfate synthetase" complex in which the sulfurylase has an increased catalytic activity. The progress curve analyses suggest that APS is competitive with both MgATP and sulfate, while MgPPi is a mixed-type inhibitor with respect to both substrates. The cumulative data point to a random sequence for the forward reaction with APS release being partially rate limiting.