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1.  Correction: Helicobacter pylori and gastroduodenal pathology: New threats of the old friend 
Since publication of our article (Ahmed and Sechi: Ann Clin Microbiol Antimicrob 2005, 4:1), we have noticed several errors.
doi:10.1186/1476-0711-7-6
PMCID: PMC2291066
3.  Antimicrobial activity of polyhexamethylene guanidine phosphate in comparison to chlorhexidine using the quantitative suspension method 
Background
Polyhexamethylene guanidine phosphate (PHMG-P) belongs to the polymeric guanidine family of biocides and contains a phosphate group, which may confer better solubility, a detoxifying effect and may change the kinetics and dynamics of PHMG-P interactions with microorganisms. Limited data regarding PHMG-P activity against periodontopathogenic and cariogenic microorganisms necessitates studies in this area. Aim is to evaluate polyhexamethylene guanidine phosphate antimicrobial activity in comparison to chlorhexidine.
Methods
Quantitative suspension method was used enrolling Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli and Candida albicans, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Streptococcus mutans and Lactobacillus acidophilus.
Results
Both tested antiseptics at their clinically-used concentrations, of 0.2% (w/v) and 1% (w/v), correspondingly provided swift bactericidal effects against S. aureus, P. aeruginosa, E. coli andC. albicans, A. actinomycetemcomitans and P. gingivalis with reduction factors higher than 6.0. Diluted polyhexamethylene guanidine phosphate and chlorhexidine to 0.05% continued to display anti-bacterial activity and decreased titers of standard quality control, periopathogens to below 1.0 × 103 colony forming units/ml, albeit requiring prolonged exposure time. To achieve a bactericidal effect against S. mutans, both antiseptics at all concentrations required a longer exposure time. We found that a clinically-used 1% of polyhexamethylene guanidine phosphate concentration did not have activity against L. acidophilus.
Conclusion
High RF of polyhexamethylene guanidine phosphate and retention of bactericidal effects, even at 0.05%, support the use of polyhexamethylene guanidine phosphate as a biocide with sufficient anti-microbial activity against periopathogens. Polyhexamethylene guanidine phosphate displayed bactericidal activity against periopathogens and S. mutans and could potentially be applied in the management of oral diseases.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-015-0097-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-015-0097-x
PMCID: PMC4504446  PMID: 26182984
Periodontal disease; Chlorhexidine; Polyhexamethylene guanidine phosphate
4.  Prevalence of tetracycline resistance genes among multi-drug resistant bacteria from selected water distribution systems in southwestern Nigeria 
Background
Antibiotic resistance genes [ARGs] in aquatic systems have drawn increasing attention they could be transferred horizontally to pathogenic bacteria. Water treatment plants (WTPs) are intended to provide quality and widely available water to the local populace they serve. However, WTPs in developing countries may not be dependable for clean water and they could serve as points of dissemination for antibiotic resistant bacteria. Only a few studies have investigated the occurrence of ARGs among these bacteria including tetracycline resistance genes in water distribution systems in Nigeria.
Methodology
Multi-drug resistant (MDR) bacteria, including resistance to tetracycline, were isolated from treated and untreated water distribution systems in southwest Nigeria. MDR bacteria were resistant to >3 classes of antibiotics based on break-point assays. Isolates were characterized using partial 16S rDNA sequencing and PCR assays for six tetracycline-resistance genes. Plasmid conjugation was evaluated using E. coli strain DH5α as the recipient strain.
Results
Out of the 105 bacteria, 85 (81 %) and 20 (19 %) were Gram- negative or Gram- positive, respectively. Twenty-nine isolates carried at least one of the targeted tetracycline resistance genes including strains of Aeromonas, Alcaligenes, Bacillus, Klebsiella, Leucobacter, Morganella, Proteus and a sequence matching a previously uncultured bacteria. Tet(A) was the most prevalent (16/29) followed by tet(E) (4/29) and tet30 (2/29). Tet(O) was not detected in any of the isolates. Tet(A) was mostly found with Alcaligenes strains (9/10) and a combination of more than one resistance gene was observed only amongst Alcaligenes strains [tet(A) + tet30 (2/10), tet(A) + tet(E) (3/10), tet(E) + tet(M) (1/10), tet(E) + tet30 (1/10)]. Tet(A) was transferred by conjugation for five Alcaligenes and two E. coli isolates.
Conclusions
This study found a high prevalence of plasmid-encoded tet(A) among Alcaligenes isolates, raising the possibility that this strain could shuttle resistance plasmids to pathogenic bacteria.
doi:10.1186/s12941-015-0093-1
PMCID: PMC4481114  PMID: 26108344
Tetracycline resistance; Multidrug resistance; Water treatment; 16S rDNA library
5.  Comparative analysis of pulmonary and extrapulmonary tuberculosis of 411 cases 
Background
Tuberculosis is a disease that can involve every organ system. While pulmonary tuberculosis is the most common presentation, extrapulmonary tuberculosis (EPT) is also an important clinical problem. The current study aimed to outline and compare the demographic and clinical features of pulmonary and extrapulmonary tuberculosis cases in adults.
Methods
Medical records of 411 patients (190 women, 221 men) treated between January 2010 and July 2014 in provincial tuberculosis control dispensary was retrospectively reviewed. Demographic and clinical characteristics were compared for pulmonary and extrapulmonary tuberculosis cases.
Results
Of these 411 cases, 208 (50.6 %) had pulmonary tuberculosis (PTB) and 203 were diagnosed with extrapulmonary tuberculosis (EPTB) (49.4 %). The average ages for PTB and EPTB groups were 33.00-27.00 and 31.00-29.75, respectively (p = 0.513). Men were more frequently affected by PTB (59.6 %), while EPTB was more commonly detected in women (52.2 %) (p = 0.016). Main diagnostic modalities for PTB were sputum/smear analyses (72.7 %), clinical-radiological data (21.7 %) and biopsy (6.1 %); while biopsy (71.5 %), sputum/fluid analysis (18.8 %) and clinical-radiological data (4.9 %) were used for confirming EPTB (p < 0.0019). The most common sites of EPTB involvement were lymph nodes (39.4 %), followed by pleura (23.6 %), peritoneum (9.9 %) and bone (7.4 %).
Conclusıons
Extrapulmonary involvement of tuberculosis is common and females are more likely to be affected. Increased clinical awareness is important since atypical presentations of the disease may constitute diagnostic and therapeutic challenges.
doi:10.1186/s12941-015-0092-2
PMCID: PMC4504222  PMID: 26104066
Tuberculosis; Pulmonary; Extrapulmonary; Epidemiology
6.  Point-of-care multiplex PCR promises short turnaround times for microbial testing in hospital-acquired pneumonia – an observational pilot study in critical ill patients 
Background
The early beginning of an adequate antibiotic therapy is crucial in hospital-acquired pneumonia (HAP), but depends on the results of conventional microbiological diagnostics (cMD). It was the aim of this study to evaluate the performance and turnaround times of a new point-of-care multiplex polymerase chain reaction (mPCR) system for rapid identification of pathogens and antibiotic resistance markers. We assessed the applicability of the system under real-life conditions in critical ill patients with HAP.
Methods
We enrolled forty critical ill patients with clinical signs for HAP into an observational study. Two samples of respiratory secretions were collected during one course of aspiration and cMD and mPCR testing (Unyvero, Curetis AG, Holzgerlingen, Germany) were performed immediately. The mPCR device was operated as a point-of-care system at the intensive care unit. We compared turnaround times, results of pathogen identification and results of antibiotic resistance testing of both methods.
Results
Mean turnaround times (min-max) were 6.5 h (4.7–18.3 h) for multiplex PCR and 71 h (37.2–217.8 h) for conventional microbiology (final cMD results, incomplete results neglected). 60 % (n = 24) of the mPCR tests were completely valid. Complete test failure occurred in 10 % (n = 4) and partial test failure occurred in 30 % (n = 12). We found concordant results in 45 % (n = 18) and non-concordant results in 45 % (n = 18) of all patients. 55 % (n = 16) of the results were concordant in patients with a clinical pulmonary infection score (CPIS) > 5 (n = 29). Concordant results included three cases of multidrug resistant bacteria. MPCR frequently detected antibiotic resistance markers that were not found by cMD.
Conclusions
Unyvero allowed point-of-care microbial testing with short turnaround times. The performance of the system was poor. However, an improved system with a more reliable performance and an extended microbial panel could be a useful addition to cMD in intensive care medicine.
Trial registration
ClinicalTrials.gov NCT01858974 (registered 16 May 2013)
doi:10.1186/s12941-015-0091-3
PMCID: PMC4469099  PMID: 26071191
Pneumonia; Point-of-care systems; Microbiological techniques; Multiplex polymerase chain reaction; Molecular diagnostic techniques; Drug resistance
7.  Repurposing FDA approved drugs against the human fungal pathogen, Candida albicans 
Background
The high cost and prolonged timeline of new drug discovery and development are major roadblocks to creating therapies for infectious diseases. Candida albicans is an opportunistic fungal pathogen that is the most common cause of fatal fungal infections in humans and costs $2–4 billion dollars to treat in the US alone.
Methods
To accelerate drug discovery, we screened a library of 1581 existing FDA approved drugs, as well as drugs approved abroad, for inhibitors of C. albicans. The screen was done on YPD yeast growth media as well as on the serum plate assay developed in this study.
Results
We discovered that fifteen drugs, all which were originally approved for treating various infectious and non-infectious diseases, were able to kill Candida albicans. Additionally, one of those drugs, Octodrine, displays wide-spectrum anti-microbial activity. Compared to other selected anti-Candida drugs, Octodrine was shown to be one of the most effective drugs in killing serum-grown Candida albicans without significantly affecting the survival of host macrophages and skin cells.
Conclusions
This approach is useful for the discovery of economically viable new therapies against infectious diseases.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-015-0090-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-015-0090-4
PMCID: PMC4462072  PMID: 26054754
Antifungal; Drug-discovery; Off-label drug use; Small molecules
8.  Simple bedside score to optimize the time and the decision to initiate appropriate therapy for carbapenem-resistant Enterobacteriaceae 
Background
Epidemiological characteristics of patients with bloodstream infections (BSI) due to extended-spectrum β-lactamase producing (ESBL) and carbapenem-resistant (CRE) strains are often similar. Mortality rates for CRE BSI are 70 %, and mean time to initiation of appropriate therapy is ~5 days. A bedside score was developed to differentiate CRE-BSIs from ESBL-BSIs, in order to help decrease the time to initiation of appropriate therapy for CRE and mortality rates.
Findings
Score was developed based of data (2007–2010) abstracted from charts of adult patients from Assaf Harofeh Medical Center (AHMC, Zeriffin, Israel), and validated on a cohort of patients from Detroit Medical Center (DMC, MI, USA). A multivariate model for presence of CRE was generated. A clinical prediction score and ROC curve was derived. 451 patients with ESBL BSIs (285 from AHMC and 166 from DMC) and 74 patients with CRE BSIs (58 from AHMC and 16 from DMC) were included. The prediction score included chemotherapy in the past 3 months (19 points), presence of foreign invasive devices (10 points), no peripheral vascular disease (10 points), reduced consciousness or cognition at time of acute illness (9 points), time in hospital prior to BSI ≥ 3 days (7 points), and age younger than 65 years (6 points). A score of ≥32 to define “high CRE risk” had sensitivity of 59 %, specificity of 76 %, PPV of 34 % and NPV of 90 %.
Conclusions
The score’s 90 % NPV implies it could reduce un-necessary (and toxic) empiric use of anti-CRE therapeutics, but this should be studied prospectively and on broader populations in order to test its potential role in reducing mortality.
doi:10.1186/s12941-015-0088-y
PMCID: PMC4460756  PMID: 26041137
CRE; KPC; ESBL; Prediction score; Nosocomial infection; Multidrug resistant
9.  Ebola virus disease and the veterinary perspective 
Ebola virus disease (EVD) is a potentially fatal haemorrhagic disease of humans. The last and most serious outbreak of Ebola virus (EBOV) started in December 2013 in West Africa and also affected other continents. Animals such as fruit bats and non-human primates are potential sources of EBOV. This review highlights the clinical features of EVD in humans and animals and addresses the public health implications of EVD outbreaks from the veterinary perspective.
doi:10.1186/s12941-015-0089-x
PMCID: PMC4450609  PMID: 26018030
Ebolavirus; Ebolavirus disease; Prevention; Animals; Human and veterinary perspective
10.  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
11.  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
12.  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
13.  Urinary tract infections and antimicrobial sensitivity among diabetic patients at Khartoum, Sudan 
Background
Patients with diabetes mellitus (DM) are more susceptible to urinary tract infection (UTI) than non-diabetics. Due to the emergence of multidrug resistant (MDR) uropathogenic strains, the choice of antimicrobial agent is restricted. This study investigated the epidemiology of UTI, antimicrobial susceptibility, and resistance patterns of bacterial isolates from adult diabetic patients.
Methods
A cross-sectional study was conducted at Khartoum Hospital, Sudan during the period of March − September 2013. Consecutive patients (men and women) were approached to participate in the study, irrespective of UTI symptoms. Socio-demographic and clinical data were obtained from each participant using pre-tested questionnaires. Clean-catch, midstream urine samples were collected and cultured for UTI diagnosis and antimicrobial susceptibility. Symptomatic bacteriuria was defined as a positive urine culture (≥105 colony-forming units [CFU]/mL of a single bacterial species) from patients with symptoms associated with UTI; asymptomatic bacteriuria was defined as a positive urine culture from patients without symptoms associated with UTI.
Results
A total of 200 diabetic patients were enrolled, 121 (60.5%) men and 79 (39.5%) women; 193 (96.5%) had type II DM. The overall prevalence of UTI was 39 (19.5%). Among the total population, 17.1% and 20.9% had symptomatic and asymptomatic bacteriuria, respectively. According to multivariate logistic regression, none of the investigated factors (age, sex, type of DM and duration) were associated with UTI. The predominant isolates were Escherichia coli (22, [56.4%]), and Klebsiella pneumoniae, [9, (23%)]. Eight of 22 E. coli, four of nine K. pneumoniae and one of five Enterococcus faecalis isolates originated from symptomatic patients. Six, four, three, and two of 22 E. coli isolates showed resistance to ampicillin, co-trimoxazole, nitrofurantoin, and amoxicillin-clavulanic acid, respectively. Two, two, one and one of nine K. pneumoniae isolates were resistant to ampicillin, co-trimoxazole, cephalexin, and amoxicillin-clavulanic acid. All 22 E. coli isolates were sensitive (100%) to gentamicin and cephalexin. All nine K. pneumoniae were sensitive to gentamicin (100%) and 88.8% were sensitive to cephalexin.
Conclusion
In Sudan, about one-fifth of diabetic patients have UTI. E. coli is the most frequent isolate followed by K. pneumoniae.
doi:10.1186/s12941-015-0082-4
PMCID: PMC4406170  PMID: 25896611
Diabetes; Urinary tract infection; Bacteriuria; E. coli; K. pneumoniae; Sudan
14.  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
15.  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
16.  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
17.  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
18.  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
19.  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
20.  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
21.  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
22.  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
23.  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
24.  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
25.  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

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