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26.  Antibacterial activity of native California medicinal plant extracts isolated from Rhamnus californica and Umbellularia californica 
Background
Antimicrobial resistance (AMR) is a major threat to global public health. Medicinal plants have long been used as remedies for infectious diseases by native cultures around the world and have the potential for providing effective treatments for antibiotic-resistant infections. Rhamnus californica (Rhamnaceae) and Umbellularia californica (Lauraceae) are two indigenous California plant species historically used by Native Americans to treat skin, respiratory and gastrointestinal infections. This study aimed to assess the in vitro antimicrobial activity of methanolic extracts of leaves and bark of R. and U. californica against methicillin-resistant Staphylococcus aureus (MRSA) and other Gram-positive and Gram-negative bacteria.
Methods
Methanolic extracts of leaves and bark of R. and U. californica were prepared by soxhlet extraction and evaluated for their antimicrobial activity against Bacillus cereus, Streptococcus pyogenes, Mycobacterium smegmatis, Staphylococcus aureus, MRSA, Escherichia coli and Pseudomonas aeruginosa using disc diffusion and minimal inhibitory concentration (MIC) assays. Chemical profiling of the extracts was performed using standard methods.
Results
All extracts inhibited the growth of MRSA and other Gram-positive bacteria with MICs of 3.3-6.0 mg/ml. Gram-negative organisms were unaffected by these extracts. U. californica extracts (leaves and bark) had the lowest MIC values. Chemical profiling detected the presence of quinones, alkaloids, flavonoids, cardenolides, tannins and saponins in these extracts. Our study is the first to report the antimicrobial properties of R. and U. californica and illustrates their promising anti-MRSA potential.
Conclusions
Our results give scientific credence to the traditional medicinal uses of these plants by the indigenous peoples of California. Further investigation of the secondary metabolites responsible for the antimicrobial activity of these extracts against MRSA is warranted.
doi:10.1186/s12941-015-0086-0
PMCID: PMC4443625  PMID: 26001558
Methicillin-resistant S. aureus; Medicinal plants; Antimicrobial activity; Rhamnus californica; Umbellularia californica
27.  The large scale antibacterial, antifungal and anti-phage efficiency of Petamcin-A: new multicomponent preparation for skin diseases treatment 
Background
Human and animal skin diseases of bacterial, fungal and viral nature and their complications are widespread and globally cause a serious trouble. Their prevalence is increasing mainly due to drug resistance. Consequently, demand has increased for new effective antimicrobial drugs, which also should be less toxic, possess a wider spectrum of action and be economically more beneficial. The goal was to investigate antibacterial, antifungal and anti-phage activity of Petamcin-A-a new multicomponent preparation. It contains acetic acid and hexamethylenetetramine as main active antimicrobial components, as well as phosphatidylcholine, tocopheryl acetate and glycerol as excipients.
Methods
Bacteriostatic activity and minimal inhibitory concentrations of the preparation against various test-organisms were determined by agar well diffusion assay. Antifungal activity was tested by agar dilution assay. To explore anti-phage activity double agar overlay plaque assay was used. Nystatin, chlorhexidine and acetic acid were used as control agents for comparative analysis. Statistical analysis was done with GraphPad Prism 5.03 or R 3.1.0 software.
Results
The results showed a higher activity of Petamcin-A against all bacterial and fungal test strains compared with its components or control agents. The preparation was more effective against tested gram-positive bacteria than gram-negative ones. Petamcin-A expressed bactericidal activity against almost all test strains. In addition, the preparation demonstrated high activity against T4 phage of Escherichia coli C-T4 completely inhibiting its growth. 5-fold diluted Petamcin-A also exhibited considerable activity reducing phage concentration by 2.6 Log10.
Conclusions
Petamcin-A has a high antimicrobial activity against all tested strains of bacteria, yeasts and moulds. The preparation also exhibited high anti-phage activity. Moreover, taking into account that Petamcin-A has no observable toxicity on skin and its components are not expensive, it can be advantageous for management of various skin medical conditions.
doi:10.1186/s12941-015-0087-z
PMCID: PMC4437556  PMID: 25982441
Acetic acid; Petamcin-A; Antimicrobial activity; Anti-phage activity; Biologically active compounds; Skin infectious disease
28.  Global in vitro activity of tigecycline and comparator agents: Tigecycline Evaluation and Surveillance Trial 2004–2013 
Background
The Tigecycline Evaluation and Surveillance Trial (TEST) is a global antimicrobial susceptibility surveillance study which has been ongoing since 2004. This report examines the in vitro activity of tigecycline and comparators against clinically important pathogens collected globally between 2004 and 2013.
Methods
Antimicrobial susceptibility was determined using guidelines published by the Clinical and Laboratory Standards Institute. The Cochran Armitage Trend Test was used to identify statistically significant changes in susceptibility between 2004 and 2013.
Results
Among the Enterobacteriaceae susceptibility was highest to the carbapenems [imipenem 97.1% (24,655/25,381), meropenem 97.0% (90,714/93,518)], tigecycline (97.0%, 115,361/118,899) and amikacin (96.9%, 115,200/118,899). Against Acinetobacter baumannii the highest rates of susceptibility were for minocycline (84.5%, 14,178/16,778) and imipenem (80.0%, 3,037/3,795). The MIC90 for tigecycline was 2 mg/L. 40% (6,743/16,778) of A. baumannii isolates were multidrug-resistant. Enterococci were highly susceptible to tigecycline and linezolid (>99%); vancomycin resistance was observed among 2% of Enterococcus faecalis (325/14,615) and 35% of Enterococcus faecium (2,136/6,167) globally. 40% (14,647/36,448) of Staphylococcus aureus were methicillin-resistant while 15% (2,152/14,562) of Streptococcus pneumoniae were penicillin-resistant. Against S. aureus and S. pneumoniae susceptibility to linezolid, vancomycin, and tigecycline was ≥99.9%. Globally, 81% (331/410) of statistically significant susceptibility changes during the study period were decreases in susceptibility.
Conclusions
Amikacin, the carbapenems, and tigecycline were active against most gram-negative pathogens while linezolid, tigecycline, and vancomycin retained activity against most gram-positive pathogens collected in TEST during 2004–2013.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-015-0085-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-015-0085-1
PMCID: PMC4489028  PMID: 25958201
Antimicrobial drug resistance; Surveillance; Gram-positive bacteria; Gram-negative bacteria; Tigecycline
29.  Reviewer acknowledgement 2014 
Contributing reviewers
Annals of Clinical Microbiology and Antimicrobials would like to thank the following colleagues for their assistance with peer review of manuscripts for the journal in 2014.
doi:10.1186/s12941-015-0068-2
PMCID: PMC4404012
30.  Antibacterial, antibiofilm and cytotoxic activities of Terminalia fagifolia Mart. extract and fractions 
Background
The methicillin resistance of bacteria from the genus Staphylococcus and its ability to form biofilms are important factors in pathogenesis of these microorganisms. Thus, the search for new antimicrobials agents, especially from plants, has been intensified. In this context, Terminalia species have been the subject of research for many pharmacological activities. In this study we evaluated the antibacterial, antibiofilm and cytotoxic activities of the ethanol extract (EtE) from Terminalia fagifolia stem bark as well as that of three fractions of the extract (AqF, HaF and WSF).
Methods
We determined the minimum inhibitory concentration (MIC) by microdilution in 96-well plates, where the strains were exposed to serial dilutions of the ethanol extract and fractions, ranging from 12.5 to 400 μg/mL. We then determined the minimum bactericidal concentration (MBC), seeding the inoculum (10 μL) with concentrations equal to or greater than the MIC in Mueller-Hinton agar. To test the antibiofilm activity biofilm formation was induced in the presence of concentrations equivalent to 1/2, 1/4 and 1/8 of the MIC extract or fraction tested. In addition, the effect of the EtE and the fractions on cell viability was tested by the MTT assay on human MCF-7 breast cancer and mouse fibroblast NIH/3T3. To obtain high-resolution images of the effect of the aqueous fraction on the bacterial morphology, atomic force microscopy (AFM) imaging of treated S. aureus cells was performed.
Results
We observed antibacterial activity of EtE and fractions with MICs ranging from 25–200 μg/mL and MBCs ranging from 200–400 μg/mL. Regarding antibiofilm activity, both the EtE as the AqF, HaF and WSF fractions showed significant inhibition of the biofilm formation, with inhibition of biofilms formation of over 80% for some strains. The EtE and fractions showed a moderate cytotoxicity in cell line NIH/3T3 viability and potential antitumoral activity on human breast cancer cell line MCF-7. The microscopic images obtained revealed morphological changes to the S. aureus ATCC 29213 surface caused by AqF, as well as significant size alterations.
Conclusions
The results show potential antibacterial, antibiofilm and antitumoral activities of the ethanol extract and fractions of T. fagifolia.
doi:10.1186/s12941-015-0084-2
PMCID: PMC4406121  PMID: 25902872
Terminalia; Staphylococcus; Antibacterial; Antibiofilm; Cytotoxicity
31.  Simple multiplex PCR assays to detect common pathogens and associated genes encoding for acquired extended spectrum betalactamases (ESBL) or carbapenemases from surgical site specimens in Vietnam 
Abstract
Surgical site infection (SSI) is common in Vietnamese post-operative patients. It contributes to increased morbidity, mortality, hospitalization time and health care expenditure. Bacterial culture is considered the gold standard procedure to identify SSI pathogens and antibiotic resistant properties; however, it can detect microbes that can readily grow and is time-consuming. We propose optimized multiplex PCR assays to diagnose the most relevant microbes and associated genes encoding for acquired extended spectrum betalactamases (ESBL) or carbapenemases from Vietnamese patients with SSI in a hospital setting in Hanoi.
Methods
Ninety-one patients (n = 91) were collected in order to identify microbial pathogens and associated genes encoding for acquired extended spectrum betalactamases (ESBL) or carbapenemases by both conventional bacterial culture and in-house multiplex PCR assays.
Result and conclusion
The novel in-house multiplex PCR assays are comparable to the bacterial culture approach in screening for common pathogens causing SSI and for relevant genotypes conferring betalactam/carbapenem resistance for bacteria. This is the first report of Turkey-specific ESBL gene (PER-1) and two Oxacilinase families (Oxa23 and Oxa 58) in Vietnam.
doi:10.1186/s12941-015-0079-z
PMCID: PMC4399146  PMID: 25890291
Surgical site infection; Betalactam/carbapenem resistance; Vietnam
32.  Evaluation of regional antibiograms to monitor antimicrobial resistance in hampton roads, Virginia 
We studied recent antibiograms (2010 to 2011) from 12 hospitals in the Hampton Roads area, Virginia, that refer patients to a tertiary-care facility affiliated with Eastern Virginia Medical School. The data was compiled into a regional antibiogram, and sensitivity rates of common isolates from the tertiary-care facility (central) were compared to those of referring hospitals grouped by locale. Staphylococcus aureus was the most common Gram- positive and E. coli the most common Gram- negative organism grown from clinical samples in the area. Overall 53% of S.aureus isolates were resistant to oxacillin. There was a broad scatter of MIC (minimum inhibitory concentration) for vancomycin within the susceptibility range, and MIC of 4 μg/mL was reported in 2012. Penicillin resistance was seen in 50% and erythromycin resistance in 45% of Streptococcus pneumoniae. Vancomycin resistance was seen in 75% of Enterococcus faecium and 2% of Enterococcus faecalis respectively. Acinetobacter baumannii was the most resistant Gram negative organism in the data compiled. Among the Escherichia coli, 26%, 44% and 52%were resistant to Trimethoprim/Sulfamethoxazole ( SXT) ampicillin- sulbactam and ampicillin respectively. We found significant differences in methodology, interpretation and antibiotic panels used by area laboratories. Based on these findings, we are now prospectively following resistance patterns in the tertiary-care facility, sharing data, and creating a consistent approach to antimicrobial susceptibility testing in the region.
doi:10.1186/s12941-015-0080-6
PMCID: PMC4397712  PMID: 25890362
Antibacterial susceptibility; Antibiogram; Antibiotic resistance; Antibiotic utilization; Antimicrobial stewardship; Antimicrobial susceptibility; Surveillance
33.  Antifungal activity of amphotericin B and voriconazole against the biofilms and biofilm-dispersed cells of Candida albicans employing a newly developed in vitro pharmacokinetic model 
Background
Candida albicans is a common cause of a variety of superficial and invasive disseminated infections the majority of which are associated with biofilm growth on implanted devices. The aim of the study is to evaluate the activity of amphotericin B and voriconazole against the biofilm and the biofilm-dispersed cells of Candida albicans using a newly developed in vitro pharmacokinetic model which simulates the clinical situation when the antifungal agents are administered intermittently.
Methods
RPMI medium containing 1–5 X 106 CFU/ml of C. albicans was continuously delivered to the device at 30 ml/h for 2 hours. The planktonic cells were removed and biofilms on the catheter were kept under continuous flow of RPMI medium at 10 ml/h. Five doses of amphotericin B or voriconazole were delivered to 2, 5 and 10 day-old biofilms at initial concentrations (2 and 3 μg/ml respectively) that were exponentially diluted. Dispersed cells in effluents from the device were counted and the adherent cells on the catheter were evaluated after 48 h of the last dose.
Results
The minimum inhibitory concentration of voriconazole and amphotericin B against the tested isolate was 0.0325 and 0.25 μg/ml respectively. Amphotericin B significantly reduced the dispersion of C. albicans cells from the biofilm. The log10 reduction in the dispersed cells was 2.54-3.54, 2.30-3.55, and 1.94-2.50 following addition of 5 doses of amphotericin B to 2-, 5- and 10-day old biofilms respectively. The number of the viable cells within the biofilm was reduced by 18 (±7.63), 5 and 4% following addition of the 5 doses of amphotericin B to the biofilms respectively. Voriconazole showed no significant effect on the viability of C. albicans within the biofilm.
Conclusion
Both antifungal agents failed to eradicate C. albicans biofilm or stop cell dispersion from them and the resistance progressed with maturation of the biofilm. These findings go along with the need for removal of devices in spite of antifungal therapy in patients with device-related infection. This is the first study which investigates the effects of antifungal agents on the biofilm and biofilm-dispersion of C. albicans in an in vitro pharmacokinetic biofilm model.
doi:10.1186/s12941-015-0083-3
PMCID: PMC4389768  PMID: 25885806
Candida albicans; Biofilm; Amphotericin B; Voriconazole; Pharmacokinetic biofilm model
34.  Use of vancomycin as a surrogate for dalbavancin in vitro susceptibility testing: results from the DISCOVER studies 
Background
Dalbavancin is a lipoglycopepetide antibiotic with activity against gram positive pathogens recently approved for treatment of acute bacterial skin and skin structure infections. Pending the introduction of antimicrobial susceptibility tests, we examined the utility of vancomycin inhibitory concentrations to predict dalbavancin susceptibility in a panel of isolates obtained from phase 3 registration studies.
Findings
99.6% of Staphylococcus aureus and 99.0% of beta-hemolytic streptococci which are susceptible to vancomycin will have an MIC at or below the US FDA susceptibility breakpoint for dalbavancin.
Conclusion
Vancomycin should be considered as a surrogate for in vitro dalbavancin susceptibility testing.
doi:10.1186/s12941-015-0081-5
PMCID: PMC4389583  PMID: 25885674
Susceptibility testing; Vancomycin; Dalbavancin; Antimicrobial agents; Acute bacterial skin and skin structure infections
35.  Foaming Betadine Spray as a potential agent for non-labor-intensive preoperative surgical site preparation 
Background
The Centers for Disease Control and Prevention’s (CDC) National Healthcare Safety Network (NHSN) report published in 2009 shows that there were about 16,000 cases of surgical site infection (SSI) following ~ 850,000 operative procedures making SSI one of the most predominant infection amongst nosocomial infections. Preoperative skin preparation is a standard procedure utilized to prevent SSIs thereby improving patient outcomes and controlling associated healthcare costs. Multiple techniques/ products have been used for pre-operative skin preparation, like 2 step scrubbing and painting, 2 step scrubbing and drying, and 1 step painting with a drying time. However, currently used products require strict, time consuming and labor-intensive protocols that involve repeated mechanical scrubbing. It can be speculated that a product requiring a more facile protocol will increase compliance, thus promoting a reduction in SSIs. Hence, the antimicrobial efficacy of a spray-on foaming formulation containing Betadine (povidone-iodine aerosol foam) that can be administered with minimum effort is compared to that of an existing formulation/technique (Wet Skin Scrub).
Methods
In vitro antimicrobial activities of (a) 5% Betadine delivered in aerosolized foam, (b) Wet Skin Scrub Prep Tray and (c) liquid Betadine are tested against three clinically representative microorganisms (S. aureus, S. epidermidis and P. aeruginosa,) on two surfaces (agar-gel on petri-dish and porcine skin). The log reduction/growth of the bacteria in each case is noted and ANOVA statistical analysis is used to establish the effectiveness of the antimicrobial agents, and compare their relative efficacies.
Results
With agar gel as the substrate, no growth of bacteria is observed for all the three formulations. With porcine skin as the substrate, the spray-on foam’s performance was not statistically different from that of the Wet Skin Scrub Prep technique for the microorganisms tested.
Conclusions
The povidone-iodine aerosolized foam could potentially serve as a non-labor intensive antimicrobial agent for surgical site preparation.
doi:10.1186/s12941-015-0076-2
PMCID: PMC4392728  PMID: 25880072
Surgical site preparation; Povidone-iodine aerosol foam; Wet skin scrub Prep; Betadine; Foaming Betadine Spray
36.  Some biological activities of Epaltes divaricata L. - an in vitro study 
Background
Novel chemical molecules recovered from endangered medicinal plants have wide applications and have the potential to cure different diseases caused by microorganisms. The aim of this study was to investigate In vitro antimicrobial, α-glucosidase inhibition and antioxidant activity of different solvent extracts of Epaltes divaricata L.
Methods
Antimicrobial activity of hexane, ethyl acetate and methanol extract of Epaltes divaricata was determined against bacteria and fungi using disc diffusion and microdilution method respectively. α-glucosidase inhibition, Total phenolic content (TPC), Reducing power activity, DPPH radical scavenging assay, hydroxyl radical scavenging activity, nitric oxide scavenging activity, superoxide scavenging activity and lipid peroxidation assay of plant extracts were performed according to standard protocol. Compound detection from the potential solvent extract was done through GC-MS analysis.
Results
Epaltes divaricata ethyl acetate extracts (EDEa) (1.25 mg/disc) showed significant inhibition for E. lentum (23 mm), E. aerogenes (18 mm), P. fluorescence (15 mm) and A. baumanii (15 mm). Minimum inhibitory concentration (MIC) of EDEa was found to be 31.25 μg/ml, 62.5 μg/ml and 62.5 μg/ml against A. flavus, A. niger and T. rubrum respectively. EDEa showed more α-glucosidase inhibition and antioxidant activity compared to hexane and methanol. EDEa showed 50% α-glucosidase inhibition at the concentration of 525.20 ± 2.37 μg/ml. The TPC of EDEa was 412.0 ± 2.21 mg of catechol equivalents/g extract. EDEa showed great scavenging activity on 2,2-diphenyl-picrylhydrazyl (DPPH) (IC50 560 ± 2.02 μg/ml), hydroxyl (IC50 314.75 ± 2.56 μg/ml), nitric oxide (IC50 648.20 ± 2.09 μg/ml) and superoxide (IC50 361.14 ± 1.45 μg/ml) radicals, as well as high reducing power. EDEa also showed a more suppressive effect on lipid peroxidation. Using Antioxidant β-carotene linoleate method, the scavenging values of EDEa was significantly lower than BHT. GC-MS analysis of EDEa showed maximum amount of 2-butenamide, N-(4-fluorophenyl)-3-methyl trans-cinnamyl tiglate silane and trichlorocyclohexyl silane (36.86%).
Conclusion
The results obtained in this study clearly indicate that EDEa can be used as a natural antimicrobial, α-glucosidase inhibition and antioxidant agent.
doi:10.1186/s12941-015-0074-4
PMCID: PMC4419414  PMID: 25879935
Antimicrobial activity; α-glucosidase inhibition; Antioxidants activity; Epaltes divaricata; GC-MS analysis
37.  The combination of decoy receptor 3 and soluble triggering receptor expressed on myeloid cells-1 for the diagnosis of nosocomial bacterial meningitis 
Background
Early diagnosis and appropriate antibiotic treatment can significantly reduce mortality of nosocomial bacterial meningitis. However, it is a challenge for clinicians to make an accurate and rapid diagnosis of bacterial meningitis. This study aimed at determining whether combined biomarkers can provide a useful tool for the diagnosis of bacterial meningitis.
Methods
A retrospective study was carried out. Cerebrospinal fluid (CSF) levels of decoy receptor 3 (DcR3) and soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) were detected by enzyme-linked immunosorbent assay (ELISA).
Results
The patients with bacterial meningitis had significantly elevated levels of the above mentioned biomarkers. The two biomarkers were all risk factors with bacterial meningitis. The biomarkers were constructed into a “bioscore”. The discriminative performance of the bioscore was better than that of each biomarker, with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.842 (95% confidence intervals (CI) 0.770–0.914; p< 0.001).
Conclusions
Combined measurement of CSF DcR3 and sTREM-1 concentrations improved the prediction of nosocomial bacterial meningitis. The combined strategy is of interest and the validation of that improvement needs further studies.
doi:10.1186/s12941-015-0078-0
PMCID: PMC4373519  PMID: 25857356
Bacterial meningitis; Diagnosis; DcR3; sTREM-1; Nosocomial infection
38.  In vitro evaluation of six chemical agents on smooth Brucella melitensis strain 
Brucellosis is a zoonosis that disseminated by a variety of ways between animals and humans. The effective disinfection of contaminated environments, soil, feces, and animal bodies plays an irreplaceable role in the prevention and control of brucellosis. To kill Brucella effectively, the bactericidal effects of frequently used disinfectants (including aldehydes, halogens, quaternary ammonium compound, phenolics, and alkalines) and the potential factors that influence disinfection effects were determined in the present study. The results revealed that the minimum bactericidal concentrations (MBCs) of the six disinfectants were all significantly lower than the routinely used concentrations, and all the tested disinfectants were effective against B. melitensis NI. The results of quantitative determination showed that the bactericidal effects of the disinfectants were influenced by their concentration, exposure time, dirty condition and the temperature. Under dirty conditions and a low temperatures, sodium hypochlorite and sodium hydroxide showed better bactericidal effect, while benzalkonium chloride was almost without bactericidal ability. In addition, increasing the disinfectant concentration at low temperatures can improve the bactericidal effect. The present study suggested that Brucella is sensitive to commonly used disinfectants. However, the bactericidal effect is vulnerable to dirty conditions and low temperatures. Thus, it is necessary to test the in vitro sensitivity of disinfectants that are commonly used on farms or the new disinfectant formulations periodically, with the aim of improving the efficacy of animal and human brucellosis prevention programs.
doi:10.1186/s12941-015-0077-1
PMCID: PMC4376339  PMID: 25857255
Brucella; Bactericidal effect; Disinfectants; Zoonosis
39.  In vitro antibacterial activities of compounds isolated from roots of Caylusea abyssinica 
Background
Caylusea absyssinica, a plant used as vegetable and for medicinal purposes was selected for in vitro antibacterial evaluation in this study. The main aim of this study was to isolate compounds from the plant roots and evaluate their antibacterial activities on clinical bacterial test strains.
Methods
Compounds from roots of Caylusea absyssinica (fresen) were identified based on observed spectral (1H-NMR, 13C-NMR and IR) data and physical properties (melting point) as well as reported literature. Disk diffusion method was employed to evaluate the antibacterial activities of the isolated compounds on four test bacterial strains namely, Staphylococcus aureus (ATCC25903), Escherichia coli (ATCC25722), Pseudomonas aeruginosa (DSMZ1117) and Salmonella thyphimurium (ATCC13311).
Results
Two compounds, CA1 and CA2 were isolated from the methanol crude extract of the roots of Caylusea absyssinica (fresen). The compounds were identified as β-sitosterol and stigmasterol, respectively. Evaluation of antibacterial activities revealed that the compounds are active against all the bacterial strains in the experiment, showing inhibition zones ranging from 12 mm-15 mm by CA1 and 11 mm-18 mm by CA2 against the different test strains. However, the compounds were less active than the reference drug (Gentamycine), which showed minimum inhibition zone of 21 mm (Pseudomonas aeruginosa) and maximum of 28 mm (Escherichia coli) inhibition zone.
Discussion and conclusion
The isolation of the compounds is the first report from roots of Caylusea abyssinica and could be potential candidates for future antibacterial drug development programs.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-015-0072-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-015-0072-6
PMCID: PMC4379615  PMID: 25858449
Disk diffusion method; β-sitosterol; Secondary metabolite; Stigmasterol
40.  Clonality and antimicrobial susceptibility of methicillin-resistant Staphylococcus aureus at the University Hospital Zurich, Switzerland between 2012 and 2014 
Background
Methicillin-resistant Staphylococcus aureus (MRSA) is a global epidemic threat. The aim of this study was to determine which globally known MRSA lineages are currently present at our tertiary care hospital in Switzerland, a hospital with low MRSA prevalence. In light of the increasing prevalence of multi drug resistance including vancomycin resistance we also assessed antibiotic susceptibilities.
Methods
The 146 MRSA strains collected over two years (March 2012 until February 2014) at the University Hospital Zurich, Switzerland, were analyzed by PFGE analysis of SmaI digests in combination with spa-typing. In addition, representative isolates were analyzed by multi locus sequence typing (MLST). Susceptibilities to eight antibiotics were assessed using the Kirby-Bauer disc diffusion method.
Results
Isolates showed resistance to erythromycin (48%), ciprofloxacin (43%), clindamycin (31%), tetracycline (22%), and gentamicin (16%). All isolates were susceptible to vancomycin, 95% were susceptible to sulfamethoxazole/trimethoprim and rifampicin, respectively. PFGE analysis revealed 22 different patterns, with four major patterns that accounted for 53.4% of all MRSA isolates, and seven sporadic patterns. Spa typing revealed 50 different spa types with the predominant types being t008 (14%), t002 (10%), and t127 (9%). 82% of the MRSA isolates could be assigned to six clonal complexes (CCs) namely CC1 (10%), CC5 (23%), CC8 (18%), CC22 (17%), CC30 (11%), and CC45 (3%) based on spa-types, PFGE patterns, and MLST. Two isolates could not be typed by either PFGE analysis or spa-typing and three isolates had spa-types that have not yet been described.
Conclusions
The combination of the two typing methods was more discriminatory as compared to the use of a single method. Several of the lineages that are predominant in Europe are present in our hospital. Resistances to antibiotics have decreased in comparison to a study conducted between 2004 and 2006.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-015-0075-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-015-0075-3
PMCID: PMC4369350  PMID: 25858549
MRSA; Epidemiology; Antibiotic susceptibility; Molecular typing
41.  Bed capacities and disinfection practices in hospitals in Istanbul are correlated 
Background
Disinfection, antisepsis and sterilization (DAS) practices are of critical importance in hospital practice. This study aims to investigate the daily DAS practices of private hospitals in Istanbul, Turkey.
Methods
The DAS practices of 155 private hospitals in Istanbul province were investigated using a questionnaire including 26 questions. The questionnaire forms were faxed to all private hospitals located in Istanbul. A p value < 0.05 accepted as significant.
Results
The 75 [48%] hospitals out of 155 hospitals responded. The quality of DAS practice was correlated with hospital bed capacity. In these hospitals, glutaraldehyde (27%) was the most common chemical used to disinfect endoscopy instruments. The rate of availability of air gun in endoscopy units in these hospitals was significantly associated with hospital bed capacity (p <0.001). Sticky mats placed at doors of risky areas were not reported to be used in the large bed capacity (LBC) hospitals unlike the small bed capacity (SBC) hospitals where 50% of these hospitals reported to use the sticky door mats (p =0.0144).
Conclusions
Private hospitals in Istanbul need in-service training towards sterilization and disinfection issues. It is concluded that private hospitals need policies and educational activities for DAS practices.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-015-0073-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-015-0073-5
PMCID: PMC4458342  PMID: 25885540
Sterilization; Disinfection; Antisepsis; Disinfection error; Private hospital
42.  Two novel CMY-2-type β-lactamases encountered in clinical Escherichia coli isolates 
Background
Chromosomally encoded AmpC β-lactamases may be acquired by transmissible plasmids which consequently can disseminate into bacteria lacking or poorly expressing a chromosomal blaAmpC gene. Nowadays, these plasmid-mediated AmpC β-lactamases are found in different bacterial species, namely Enterobacteriaceae, which typically do not express these types of β-lactamase such as Klebsiella spp. or Escherichia coli. This study was performed to characterize two E. coli isolates collected in two different Portuguese hospitals, both carrying a novel CMY-2-type β-lactamase-encoding gene.
Findings
Both isolates, INSRA1169 and INSRA3413, and their respective transformants, were non-susceptible to amoxicillin, amoxicillin plus clavulanic acid, cephalothin, cefoxitin, ceftazidime and cefotaxime, but susceptible to cefepime and imipenem, and presented evidence of synergy between cloxacilin and cefoxitin and/or ceftazidime. The genetic characterization of both isolates revealed the presence of blaCMY-46 and blaCMY-50 genes, respectively, and the following three resistance-encoding regions: a Citrobacter freundii chromosome-type structure encompassing a blc-sugE-blaCMY-2-type-ampR platform; a sul1-type class 1 integron with two antibiotic resistance gene cassettes (dfrA1 and aadA1); and a truncated mercury resistance operon.
Conclusions
This study describes two new blaCMY-2-type genes in E. coli isolates, located within a C. freundii-derived fragment, which may suggest their mobilization through mobile genetic elements. The presence of the three different resistance regions in these isolates, with diverse genetic determinants of resistance and mobile elements, may further contribute to the emergence and spread of these genes, both at a chromosomal or/and plasmid level.
doi:10.1186/s12941-015-0070-8
PMCID: PMC4399151  PMID: 25885413
β-lactamase; Resistance regions; Genetic environment; Escherichia coli
43.  Extremely high prevalence of antiseptic resistant Quaternary Ammonium Compound E gene among clinical isolates of multiple drug resistant Acinetobacter baumannii in Malaysia 
Background
Antiseptics are commonly used for the management of MDR (multiple drug resistance) pathogens in hospitals. They play crucial roles in the infection control practices. Antiseptics are often used for skin antisepsis, gauze dressing, preparation of anatomical sites for surgical procedure, hand sterilization before in contact with an infected person, before an invasive procedure and as surgical scrub.
Methods
We screened 122 multiple drug resistant Acinetobacter baumannii (MDRAB) isolated from admitted patients in one of the tertiary care hospital in Malaysia for the presence of antiseptic resistant genes qacA and qacE (Quaternary Ammonium Compound) and susceptibility towards chlorhexidine (CLX), benzalkonium (BZK) and benzethonium (BZT).
Results
Eighty-nine (73%) isolates harboured qacE gene, while none were positive for qacA. The MIC ranged from 0.2 to 0.6 for CLX, 0.02 to 0.2 for BZK and 0.04 to 0.2 μg/mL for BZT. The highest number of qacE positive isolates were obtained from surgery (n = 24; 27%; p < 0.05), followed by medical ward (n = 23; 25.8%) and ICU (n = 21; 23.6%). Majority of the isolates from wound swabs (n = 33; 37%), T/aspirate (n = 16; 18%) and tissue (n = 10; 11.2%) harboured the qacE genes.
Conclusion
The present investigation showed high prevalence of qacE gene among the studied isolates. Antiseptics are important components of infection control, continuous monitoring of antiseptics use in the hospital is cautioned.
doi:10.1186/s12941-015-0071-7
PMCID: PMC4363066  PMID: 25858356
Antiseptic; Acinetobacter baumannii; Multiple drug resistance
44.  The prevalence of malaria among HIV seropositive individuals and the impact of the co- infection on their hemoglobin levels 
Background
Malaria and HIV/AIDS are the two most common infections in sub-Sahara Africa. There are hypotheses and study reports on the possible association between these two infections, hence the prevalence and outcome of their co-infection in an endemic population will be important in defining healthcare strategies. A cross sectional study was carried out at the Holy Family Hospital in Techiman, Ghana, between November 2011 and January 2012, to determine the prevalence of malaria among HIV sero-positive patients and its impact on hemoglobin levels.
Method
A total of 400 HIV sero-positive participants (292 females and 108 males) aged between 1 and 73 years were randomly sampled for the study. A questionnaire was administered and 2 ml of venous blood samples were drawn for malaria parasites detection, CD4 count and haemoglobin level estimations.
Results
Malaria parasites were detected in 47 (11.75%) of the participants. There was no statistically significant difference between the malaria prevalence rate of females (12.1%) and males (10.2%) P = 0.6047. An overall anaemia prevalence of 67% was observed. Among participants with malaria the anaemia prevalence was 93.6%. The CD4 cell count of all the participants ranged between 3 and 1604 cells/μl with a mean of 386.2 (±274.3) cells/μl. Participants with malaria had CD4 cell count ranged 3 and 512 Cells/μl with the mean being 186.33 (±133.49) Cells/μl. Out of 377 participants (all above 15 years) interviewed on knowledge of malaria transmission and prevention, 87.0% had knowledge on transmission but only 8.5% use in bed nets.
Conclusion
It was revealed that almost all the patients with malaria infection were anemic.
doi:10.1186/s12941-015-0064-6
PMCID: PMC4355357  PMID: 25857950
HIV/AIDS; CD4 cells; Malaria co-infection; Anaemia; Anti-retroviral
45.  In-vitro antibacterial, antifungal, antioxidant and functional properties of Bacillus amyloliquefaciens 
Background
Food born pathogenic bacteria and filamentous fungi are able to grow on most foods, including natural foods, processed foods, and fermented foods and create considerable economic loss. The aim of this study was to determine the antibacterial, antifungal, antioxidant and functional properties of Bacillus amyloliquefaciens recovered from silage.
Methods
Minimum Inhibitory Concentration (MIC) of the compounds was assessed by using broth micro dilution method. The 1,1-diphenyl–2-picrylhydrazyl (DPPH)-radical scavenging and hydroxyl radical-scavenging abilities were measured to evaluate antioxidant activity of the strain.
Results
Primary antimicrobial compound production screening revealed that B. amyloliquefaciens exhibited significant activity against all the tested bacteria and fungi compared to other strains. The 16S rRNA and gyrase A gene sequence analysis determined using molecular biological tools confirmed that the strain was 99% similarity towards B. amyloliquefaciens. The Minimum Inhibitory Concentration (MIC) of ethyl acetate extract against Bacillus subtilis, Enterococcus cloacae and Staphylococcus aureus were 25.0 μg ml−1, and S, epidermidis were 12.5 μg ml−1, respectively. Filamentous fungi Aspergillus clavatus, A. fumigates, A. niger and Gibberella moniliformis showed 25 μg ml−1. VJ-1 was able to survive the gastrointestinal conditions simulating the stomach and duodenum passage with the highest percentage of hydrophobicity. In addition, its resistance to hydrogen peroxide and highest hydroxyl radical and 2, 2-diphenyl–1-picrylhydrazyl (DPPH) scavenging activities, with inhibition rates of 56.84% and 67.12% respectively, were its advantage. An antimicrobial susceptibility pattern was an intrinsic feature of this strain, and thus, consumption does not represent a health risk to humans.
Conclusion
Bacillus amyloliquefaciens might be a promising candidate for new pharmaceutical agents and probiotics.
doi:10.1186/s12941-015-0069-1
PMCID: PMC4342198  PMID: 25858278
Bacillus amyloliquefaciens; Antimicrobial activity; Probiotics; Antioxidant activities
46.  Screening of antimicrobial, antioxidant properties and bioactive compounds of some edible mushrooms cultivated in Bangladesh 
Background
For a long time mushrooms have been playing an important role in several aspects of the human activity. Recently edible mushrooms are used extensively in cooking and make part of new food in Bangladesh for their beneficial properties. The aim of this study is to screen some values of mushrooms used in Bangladesh.
Methods
Methanolic extracts of 3 edible mushrooms (Pleurotus ostreatus, Lentinula edodes, Hypsizigus tessulatus) isolated from Chittagong, Bangladesh were used in this study. Phenolic compounds in the mushroom methanolic extracts were estimated by a colorimetric assay. The antioxidant activity was determined by radical 1, 1-diphenyl;-2-picrylhydrazyl (DPPH) radical scavenging assay. Eight microbial isolates were used for antimicrobial activity of methanolic extract of mushrooms by the agar well diffusion method with slight modification.
Results
Determination of antimicrobial activity indicated considerable activity against all bacteria and fungi reveling zone of inhibition ranged from 7 ± 0.2 to 20 ± 0.1 mm. Minimum inhibitory concentration values of the extracts showed that they are also active even in least concentrations ranged from 1 mg/ml to 9 mg/ml. Lentinula edodes showed the best antimicrobial activity than others. Pseudomonas aeruginosa was quite resistant and Saccharomyces cerevisiae was more sensitive than others microbial isolates. Antioxidant efficiency by inhibitory concentration on 1,1-Diphenly-2-picrylhydrazyl (DPPH) was found significant when compared to standard antioxidant like ascorbic Acid . The concentration (IC50) ranged from 100 ± 1.20 to 110 ± 1.24 μg/ml. Total phenols are the major bioactive component found in extracts of isolates expressed as mg of GAE per gram of fruit body, which ranged from 3.20 ± 0.05 to 10.66 ± 0.52 mg/ml. Average concentration of flavonoid ranged from 2.50 ± 0.008 mg/ml to 4.76 ± 0.11 mg/ml; followed by very small concentration of ascorbic acid (range, 0.06 ± 0.00 mg/ml to 0.21 ± 0.01 mg/ml) in all the isolates. All the isolates showed high phenol and flavonoid content (except Pleurotus ostreatus), but ascorbic acid content was found in traces.
Conclusion
This study has revealed that selected edible mushrooms have not only nutritional values but also some therapeutic values. Proper and more investigations can lead us to use these as strong medicine in future.
doi:10.1186/s12941-015-0067-3
PMCID: PMC4328533  PMID: 25858107
47.  An investigation of drug-resistant Acinetobacter baumannii infections in a comprehensive hospital of East China 
Background
To investigate the drug resistant gene profiles and molecular typing of Acinetobacter baumannii isolates collected from clinical specimens in a comprehensive hospital, Jiangsu province.
Methods
This study included 120 patients in a comprehensive hospital with drug-resistant A. baumannii infections on clinical specimens from October 2011 to December 2013. Antibiotic susceptibility test was determined by Vitek 2 Compact system. OXA-51, OXA-23, OXA-24, OXA-58, VIM, IMP, SHV, GES, TEM, AmpC, qacEΔ1-sul1, intI l, CarO, aac(6′)-Ib, and aac(6′)-II were analyzed by PCR. The analysis of molecular typing for 50 multidrug resistant A. baumannii isolates was performed by PFGE.
Results
A total of 64(53%) isolates were multidrug-resistant A.baumannii. The antibiotic susceptibility tests showed that the resistant rates to common antibiotics of mutidrug-resistant A. baumannii were extremely high, most of which over 60%. One hundred and ten isolates harbored OXA-51 (91.7%), 100 for OXA-23(83.3%), 103 for VIM-1(85.8%), 90 for AmpC(75.00%), 50 for aac(6′)-Ib(41.7%), 77 for the loss of CarO (64.2%), 85 for intl1(70.8%), and 64 for qacEΔ1-sul1(53.33%), while OXA-24 was undetected. Fifty multidrug-resistant A. baumannii isolates belong to 14 clones according to the PFGE DNA patterns. Main clone A includes 24 isolates, while clone B and clone C includes 6 and 9 isolates, respectively and others with no common source identified.
Conclusion
There is high morbidity of A. baumannii infections in the hospital, especially in ICU and sputum is the most common sample type.The mainly drug-resistant genes of A. baumannii are OXA-51, OXA-23, and VIM-1 in the hospital. Clonal dissemination provides evidence for the prevalence of multidrug-resistant A. baumannii among clinical isolates. It is suggested that there is an urgent need for effective control and prevention measures.
doi:10.1186/s12941-015-0066-4
PMCID: PMC4328433  PMID: 25643932
Acinetobacter baumannii; Drug-resistant gene; PCR; PFGE
48.  Evaluation of fluorescence in situ hybridisation (FISH) for the detection of fungi directly from blood cultures and cerebrospinal fluid from patients with suspected invasive mycoses 
The aim of this study was to evaluate the diagnostic performance of in-house FISH (fluorescence in situ hybridisation) procedures for the direct identification of invasive fungal infections in blood cultures and cerebrospinal fluid (CSF) samples and to compare these FISH results with those obtained using traditional microbiological techniques and PCR targeting of the ITS1 region of the rRNA gene. In total, 112 CSF samples and 30 positive blood cultures were investigated by microscopic examination, culture, PCR-RFLP and FISH. The sensitivity of FISH for fungal infections in CSF proved to be slightly better than that of conventional microscopy (India ink) under the experimental conditions, detecting 48 (instead of 46) infections in 112 samples. The discriminatory powers of traditional microbiology, PCR-RFLP and FISH for fungal bloodstream infections were equivalent, with the detection of 14 fungal infections in 30 samples. However, the mean times to diagnosis after the detection of microbial growth by automated blood culture systems were 5 hours, 20 hours and 6 days for FISH, PCR-RFLP and traditional microbiology, respectively. The results demonstrate that FISH is a valuable tool for the identification of invasive mycoses that can be implemented in the diagnostic routine of hospital laboratories.
doi:10.1186/s12941-015-0065-5
PMCID: PMC4322816  PMID: 25637361
FISH; Invasive mycoses; CSF; Blood culture; rRNA; Hybridisation
49.  Current immunological and molecular tools for leptospirosis: diagnostics, vaccine design, and biomarkers for predicting severity 
Leptospirosis is a zoonotic spirochaetal illness that is endemic in many tropical countries. The research base on leptospirosis is not as strong as other tropical infections such as malaria. However, it is a lethal infection that can attack many vital organs in its severe form, leading to multi-organ dysfunction syndrome and death. There are many gaps in knowledge regarding the pathophysiology of leptospirosis and the role of host immunity in causing symptoms. This hinders essential steps in combating disease, such as developing a potential vaccine. Another major problem with leptospirosis is the lack of an easy to perform, accurate diagnostic tests. Many clinicians in resource limited settings resort to clinical judgment in diagnosing leptospirosis. This is unfortunate, as many other diseases such as dengue, hanta virus, rickettsial infections, and even severe bacterial sepsis, can mimic leptospirosis. Another interesting problem is the prediction of disease severity at the onset of the illness. The majority of patients recover from leptospirosis with only a mild febrile illness, while a few others have severe illness with multi-organ failure. Clinical features are poor predictors of potential severity of infection, and therefore the search is on for potential biomarkers that can serve as early warnings for severe disease. This review concentrates on these three important aspects of this neglected tropical disease: diagnostics, developing a vaccine, and potential biomarkers to predict disease severity.
doi:10.1186/s12941-014-0060-2
PMCID: PMC4299796  PMID: 25591623
Leptospirosis; Vaccine; Biomarkers; Diagnosis
50.  High dose intravenous colistin methanesulfonate therapy is associated with high rates of nephrotoxicity; a prospective cohort study from Saudi Arabia 
Background
Nephrotoxicity is an important adverse effect of colistin methanesulfonate (CMS) therapy. No data exist on rates and risk factors for colistin-related nephrotoxicity in Saudi Arabia (SA). We conducted a prospective cohort study to identify rates and risk factors for CMS nephrotoxicity in our patient population.
Methods
We prospectively included adult patients who received ≥48 hours of intravenous CMS therapy. Pregnant patients and those on renal replacement were excluded. Patients received 9 million units (mU) loading dose followed by 3 mU 8 hourly. In renal impairment, CMS dosing was adjusted according to calculated creatinine clearance (CrCl). Nephrotoxicity was defined as per RIFLE criteria (Risk, Injury, Failure, Loss and End-stage renal disease). Statistical analysis was performed using SPSS version 20.0 (IBM, Armonk, New York, USA). The study was approved by the institution’s Research Ethics Committee.
Results
A total of 67 patients were included in the study. Mean (±standard deviation) age was 57.5 (±24.0) years, Charlson Co-morbidity Score 2.88 (±2.39), CrCl 133.60 (±92.54) mL/min and serum albumin 28.65 (±4.45) g/L. Mean CMS dose was 0.11 (±0.04) mU/kg/day and mean total CMS dose received was 101.21 (±47.37) mU. Fifty-one (76.1%) patients developed RIFLE-defined nephrotoxicity. Mean total CMS dose and duration of therapy before onset of nephrotoxicity were 66.71 (±43.45) mU and 8.70 (±6.70) days, respectively. In bivariate analysis, patients with nephrotoxicity were significantly older (P 0.013) and had lower baseline serum albumin (P 0.008). Multivariate logistic regression identified serum albumin [odds ratio (OR) 0.72; 95% confidence interval (CI) 0.57–0.93; P 0.010] and intensive care admission (OR 16.38; 95% CI 1.37–195.55; P 0.027) as independent risk factors for CMS nephrotoxicity.
Conclusions
High dose intravenous CMS therapy is associated with high rates of nephrotoxicity in SA. Independent risk factors for colistin nephrotoxicity were baseline hypoalbuminemia and intensive care admission.
doi:10.1186/s12941-015-0062-8
PMCID: PMC4301664  PMID: 25591721
Colistin; Colistin methanesulfonate; CMS; Nephrotoxicity; Acute kidney injury; Saudi Arabia

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