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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.
PMCID: PMC2291066
3.  Screening of antimicrobial, antioxidant properties and bioactive compounds of some edible mushrooms cultivated in Bangladesh 
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.
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.
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.
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.
PMCID: PMC4328533
4.  An investigation of drug-resistant Acinetobacter baumannii infections in a comprehensive hospital of East China 
To investigate the drug resistant gene profiles and molecular typing of Acinetobacter baumannii isolates collected from clinical specimens in a comprehensive hospital, Jiangsu province.
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.
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.
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.
PMCID: PMC4328433  PMID: 25643932
Acinetobacter baumannii; Drug-resistant gene; PCR; PFGE
5.  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.
PMCID: PMC4322816  PMID: 25637361
FISH; Invasive mycoses; CSF; Blood culture; rRNA; Hybridisation
6.  Antibiotic resistance and genotype of beta-lactamase producing Escherichia coli in nosocomial infections in Cotonou, Benin 
Beta lactams are the most commonly used group of antimicrobials worldwide.
The presence of extended-spectrum lactamases (ESBL) affects significantly the treatment of infections due to multidrug resistant strains of gram-negative bacilli. The aim of this study was to characterize the beta-lactamase resistance genes in Escherichia coli isolated from nosocomial infections in Cotonou, Benin.
Escherichia coli strains were isolated from various biological samples such as urine, pus, vaginal swab, sperm, blood, spinal fluid and catheter. Isolated bacteria were submitted to eleven usual antibiotics, using disc diffusion method according to NCCLS criteria, for resistance analysis. Beta-lactamase production was determined by an acidimetric method with benzylpenicillin. Microbiological characterization of ESBL enzymes was done by double disc synergy test and the resistance genes TEM and SHV were screened by specific PCR.
ESBL phenotype was detected in 29 isolates (35.5%). The most active antibiotic was imipenem (96.4% as susceptibility rate) followed by ceftriaxone (58.3%) and gentamicin (54.8%). High resistance rates were observed with amoxicillin (92.8%), ampicillin (94%) and trimethoprim/sulfamethoxazole (85.7%). The genotype TEM was predominant in ESBL and non ESBL isolates with respectively 72.4% and 80%. SHV-type beta-lactamase genes occurred in 24.1% ESBL strains and in 18.1% of non ESBL isolates.
This study revealed the presence of ESBL producing Eschericiha coli in Cotonou. It demonstrated also high resistance rate to antibiotics commonly used for infections treatment. Continuous monitoring and judicious antibiotic usage are required.
PMCID: PMC4304606  PMID: 25595314
Escherichia coli; ESBL; Resistance gene
7.  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.
PMCID: PMC4299796  PMID: 25591623
Leptospirosis; Vaccine; Biomarkers; Diagnosis
8.  High dose intravenous colistin methanesulfonate therapy is associated with high rates of nephrotoxicity; a prospective cohort study from Saudi Arabia 
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.
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.
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.
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.
PMCID: PMC4301664  PMID: 25591721
Colistin; Colistin methanesulfonate; CMS; Nephrotoxicity; Acute kidney injury; Saudi Arabia
9.  Epidemiology of CTX-M-type extended-spectrum beta-lactamase (ESBL)-producing nosocomial -Escherichia coli infection in China 
Escherichia coli is one of the most common clinical pathogens causing nosocomial infection. The widespread cefotaxime-beta lactamases (CTX) has increased the multidrug resistance (MDR) of E. coli and has brought great trouble to the doctor treating the infection.
ESBL-positive E. coli isolates were collected from different hospitals in different areas and the minimal inhibitory concentration (MIC) was analyzed by the agar dilution method. The resistance gene types were detected using polymerase chain reaction (PCR) and the sequence types were determined by multilocus sequence typing (MLST).
We found that the blaCTX-M-1 group and the blaCTX-M-9 group were the main CTX-M gene types, with many kinds of MLST gene types. Except for TEM with high isolate, SHV, OXA and VEB were relatively rare, while no PER and GES was detected. Most strains may have other resistance mechanisms, and the ESBL positive strains have high resistance not only to cephalosporins but also to other kinds of antibiotics.
The study provides wide epidemiological data and enables more effective infection control and treatment plans.
PMCID: PMC4299296  PMID: 25591816
Escherichia coli; Epidemiology; Extended-spectrum beta-lactamase; Multilocus sequence typing; Nosocomial infection
10.  Molecular identification of non-tuberculous mycobacteria isolated from clinical specimens in Zambia 
The emergence of Acquired Immunodeficiency Syndrome has highlighted the increased incidence and importance of the disease caused by Non-tuberculous Mycobacteria (NTM). While disease due to M. avium-intracellulare complex is apparently common throughout the world, other Non-tuberculous mycobacterial species have been isolated from both immunocompromised and immunocompetent individuals. The increasing number of infections caused by these organisms has made it clinically important to quickly identify mycobacterial species. The diagnosis of a pathogenic versus a non-pathogenic species not only has epidemiological implications but is also relevant to the demands of patient management. Since antibiotic treatment varies according to the species encountered, species identification would reduce the burden of some of these emerging opportunistic pathogens especially in immunocompromised patients and improve their quality of life.
A total of 91 NTM suspected isolates from four regions of Zambia were included in the study. These isolates were identified using the sequence analysis of the 16S-23S rRNA intergenic transcribed spacer (ITS) region of Mycobacteria.
Fifty-four of the 91 (59%) isolates were identified as NTM and these included M. intracellulare (27.8%), M. lentiflavum (16.7%), M. avium (14.8%), M. fortuitum (7.4%), M. gordonae (7.4%), M. kumamotonense (3.7%), M. indicus pranii (3.7%), M. peregrinum (3.7%), M. elephantis (1.85%), M. flavescens (1.85%), M. asiaticum (1.85%), M. bouchedurhonense (1.85%), M. chimaera (1.85%), M. europaeum (1.85%), M. neourum (1.85%), M. nonchromogenicum (1.5%).
The study has shown that DNA sequencing of the ITS region may be useful in the preliminary identification of NTM species. All species identified in this study were potentially pathogenic.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-014-0059-8) contains supplementary material, which is available to authorized users.
PMCID: PMC4302154  PMID: 25592857
Non-tuberculous mycobacteria; Identification; Zambia
11.  Studies on the antimicrobial potential and structural characterization of fatty acids extracted from Sydney rock oyster Saccostrea glomerata 
The marine environment having vast resources of natural products with potential bioactivities. Among the marine natural products, fatty acids obtained from marine mollusks have broad range of biological activities including antimicrobial and antitumor activities. The present study aims to characterize the fatty acid derivatives from the Sydney rock oyster Saccostrea glomerata and its pharmacological activities.
S. glomerata fleshes were serially extracted with hexane, ethyl acetate and methanol and studied the antimicrobial activities against pathogenic bacteria, fungi and virus. Based on the better result, the ethyl acetate extract was selected and purified through silica column chromatography and screened the fractions for antimicrobial and antitumor activities. Also the best active fraction (FV) was functionally and structurally characterized.
The ethyl acetate extract of S. glomerata effectively controlled the bacterial pathogens and formed of more than 15 mm of zone of inhibition and also effectively suppressed the fungal growth and inhibit the shrimp white spot syndrome virus (WSSV). The secondary screening results revealed that, the fraction (FV) had potential antimicrobial and antitumor activities. The FV concentration (100 μg/ml) effectively suppressed the tumor mammary epithelial carcinoma cell of 14.45%. The GC–MS analysis revealed that, eleven compounds including N-hexadecanoic acid, L-(+)-ascorbic acid 2,6-dihexadecanoate and 6-Octadecenoic acid were characterized.
The fatty acid derivatives isolated and characterized from S. glomerata extracts had the potent antimicrobial and antitumor activities. This basic research can help to develop the antimicrobial and anticancer drugs from the nutraceuticals in future.
PMCID: PMC4298963  PMID: 25551394
Antimicrobial factors; Antitumor; Fatty acids; Saccostrea glomerata
12.  Infection and colonization by Stenotrophomonas maltophilia: antimicrobial susceptibility and clinical background of strains isolated at a tertiary care centre in Hungary 
Stenotrophomonas maltophilia is an important opportunistic, mainly nosocomial pathogen that emerged in the last decades worldwide. Due to its inherent extended antibiotic resistance, therapeutic options are strongly limited. New resistance mechanisms in S. maltophilia make antibiotic therapy even more difficult. The aim of our study was to investigate the antimicrobial resistance of S. maltophilia isolates collected in our laboratory and to reveal related clinical background.
Consecutive non-duplicate S. maltophilia isolates (n = 160) were collected in a three-year period. Conventional methods, automated identification system and MALDI-TOF MS was used for identification, ERIC-PCR for genetic relationship analysis and broth microdilution method to determine the susceptibility for trimethoprim/sulfamethoxazole (SXT), ciprofloxacin, levofloxacin, moxifloxacin, colistin, doxycycline and tigecycline. Clinical final reports were used retrospectively to collect clinical information.
ERIC-PCR revealed large heterogeneity. Trimethoprim/sulfamethoxazole, moxifloxacin and levofloxacin were found to be the most effective agents with MIC50/MIC90 0.5/1, 0.25/1, 1/2 mg/l, respectively. Seventy percent of patients with S. maltophilia infection were treated in intensive care units. All-cause mortality rate was 45%. Nearly 70% of the isolates were collected from polymicrobial infections/colonizations.
Trimethoprim/sulfamethoxazole is the most potent antibiotic agent against S. maltophilia. In case of SXT hypersensitivity, intolerance or resistance, fluoroquinolones are alternative therapeutic options. Missing clinical breakpoints, consensus antibiotic susceptibility testing guidelines and clinical trials make the interpretation of antibiotic susceptibility testing results difficult. The indirect pathogenicity of S. maltophilia in polymicrobial infections or colonizations has to be taken into consideration.
PMCID: PMC4307884  PMID: 25551459
Stenotrophomonas maltophilia; Antibiotic susceptibility
13.  Prevalence of methicillin-resistant Staphylococcus haemolyticus in companion animals: a cross-sectional study 
Among coagulase-negative staphylococci, Staphylococcus haemolyticus is the second most frequently isolated species from human blood cultures and has the highest level of antimicrobial resistance. This species has zoonotic character and is prevalent both in humans and animals. Recent studies have indicated that methicillin-resistant S. haemolyticus (MRSH) is one of the most frequent isolated Staphylococcus species among neonates in intensive care units. The aim of this study was to determine the presence of MRSH in different groups of companion animals and to characterize isolates according their antimicrobial resistance.
Samples (n = 754) were collected from healthy and diseased dogs and cats, female dogs in pure-breed kennels, healthy horses, and kennel owners. Classical microbiological tests along with molecular testing including PCR and 16S rRNA sequencing were performed to identify MRSH. Clonality of the isolates was assessed by Pulsed Field Gel Electrophoresis using the SmaI restriction enzyme. Antimicrobial susceptibility testing was performed using the broth micro-dilution method. Detection of genes encoding antimicrobial resistance was performed by PCR. Statistical analysis was performed using the R Project of Statistical Computing, “R 1.8.1” package.
From a total of 754 samples tested, 12 MRSH isolates were obtained. No MRSH were found in horses and cats. Eleven isolates were obtained from dogs and one from a kennel owner. Ten of the dog isolates were detected in pure-breed kennels. The isolates demonstrated the same clonality only within separate kennels.
The most frequent resistances of MRSH isolates was demonstrated to benzylpenicillin (91.7%), erythromycin (91.7%), gentamicin (75.0%), tetracycline (66.7%), fluoroquinolones (41.7%) and co-trimoxazole (41.7%). One isolate was resistant to streptogramins. All isolates were susceptible to daptomycin, rifampin, linezolid and vancomycin. The clone isolated from the kennel owner and one of the dogs was resistant to beta-lactams, macrolides, gentamicin and tetracycline.
Pure-breed kennels keeping 6 or more females were determined to be a risk factor for the presence of MRSH strains. MRSH isolated from companion animals were frequently resistant to some classes of critically important antimicrobials, although they remain susceptible to antibiotics used exclusively in human medicine.
PMCID: PMC4247881  PMID: 25431281
Staphylococcus haemolyticus; Methicillin-resistance; Kennels; Antimicrobial resistance; Companion animals
14.  Expression of enterotoxin-coding genes in methicillin-resistant Staphylococcus aureus strains isolated from Mexican haemodialysis patients 
Methicillin-resistant Staphylococcus aureus (MRSA) causes severe catheter-related infections in haemodialysis patients ranging from local-site infections and septic thrombophlebitis to bacteraemia but the associated virulence factors and exotoxins remain unclear.
We employed an in vitro infection model using reconstituted human epithelium (RHE) to analyse the expression profiles of 4 virulence genes and 12 exotoxin-coding virulence genes in 21 MRSA strains isolated from catheter-related infections in 21 Mexican patients undergoing haemodialysis.
All 21 strains (100%) expressed the seg, seh, sei, eta, etb, or hla genes coding staphylococcal toxins. Eleven MRSA strains (52.3%) expressed the sea gene coding staphylococcal enterotoxin A, and two strains (9.5%) expressed the v8 gene coding serine protease. The tst, chp, and arcA genes coding toxic shock syndrome toxin 1, chemotaxis inhibitory protein, and arginine deiminase, respectively, were expressed in separate single strains (4.7%). The most frequent expression profile (42.8% of the strains) comprised seg, seh, sei, eta, etb, and hla.
It is likely that the SEG, SEH, SEI, ETA, ETB, and Hla toxins may play a role in MRSA catheter-related infections. Consideration of these toxins in the development of a vaccine or as targets for monoclonal antibody therapy could provide an improved therapeutic strategy for the treatment of catheter-related infections in haemodialysis patients.
PMCID: PMC4245768  PMID: 25421262
MRSA, Haemodialysis catheter; Enterotoxins
15.  Antimicrobial activity of natural products against Helicobacter pylori: a review 
Throughout the genetic and physiological evolution of microorganisms, the microbiological sciences have been expanding the introduction of new therapeutic trials against microbial diseases. Special attention has been paid to the bacterium Helicobacter pylori, which induces gastric infections capable of causing damage, ranging from acute and chronic gastritis to the development of gastric cancer and death. The use of compounds with natural origins has gained popularity in scientific research focused on drug innovation against H. pylori because of their broad flexibility and low toxicity. The aim of this study was to describe the use of natural products against H. pylori in order to clarify important parameters for related fields. The study demonstrated the vast therapeutic possibilities for compounds originating from natural sources and revealed the need for innovations from future investigations to expand the therapeutic arsenal in the fight against H. pylori infection.
PMCID: PMC4243293  PMID: 25406585
Helicobacter pylori; Natural products; Antimicrobial activity; Helicobacter pylori; Produtos naturais; Atividade antimicrobiana
16.  International Nosocomial Infection Control Consortium (INICC) national report on device-associated infection rates in 19 cities of Turkey, data summary for 2003–2012 
Device-associated healthcare-acquired infections (DA-HAI) pose a threat to patient safety, particularly in the intensive care unit (ICU). We report the results of the International Infection Control Consortium (INICC) study conducted in Turkey from August 2003 through October 2012.
A DA-HAI surveillance study in 63 adult, paediatric ICUs and neonatal ICUs (NICUs) from 29 hospitals, in 19 cities using the methods and definitions of the U.S. NHSN and INICC methods.
We collected prospective data from 94,498 ICU patients for 647,316 bed days. Pooled DA-HAI rates for adult and paediatric ICUs were 11.1 central line-associated bloodstream infections (CLABSIs) per 1000 central line (CL)-days, 21.4 ventilator-associated pneumonias (VAPs) per 1000 mechanical ventilator (MV)-days and 7.5 catheter-associated urinary tract infections (CAUTIs) per 1000 urinary catheter-days. Pooled DA-HAI rates for NICUs were 30 CLABSIs per 1000 CL-days, and 15.8 VAPs per 1000 MV-days. Extra length of stay (LOS) in adult and paediatric ICUs was 19.4 for CLABSI, 8.7 for VAP and 10.1 for CAUTI. Extra LOS in NICUs was 13.1 for patients with CLABSI and 16.2 for patients with VAP. Extra crude mortality was 12% for CLABSI, 19.4% for VAP and 10.5% for CAUTI in ICUs, and 15.4% for CLABSI and 10.5% for VAP in NICUs. Pooled device use (DU) ratios for adult and paediatric ICUs were 0.54 for MV, 0.65 for CL and 0.88 for UC, and 0.12 for MV, and 0.09 for CL in NICUs. The CLABSI rate was 8.5 per 1,000 CL days in the Medical Surgical ICUs included in this study, which is higher than the INICC report rate of 4.9, and more than eight times higher than the NHSN rate of 0.9. Similarly, the VAP and CAUTI rates were higher compared with U.S. NHSN (22.3 vs. 1.1 for VAP; 7.9 vs. 1.2 for CAUTI) and with the INICC report (22.3 vs. 16.5 in VAP; 7.9 vs. 5.3 in CAUTI).
DA-HAI rates and DU ratios in our ICUs were higher than those reported in the INICC global report and in the US NHSN report.
PMCID: PMC4255447  PMID: 25403704
Hospital infection; Nosocomial infection; Healthcare-associated infection; INICC; International Nosocomial Infection Consortium; Turkey; Device-associated infection; Antibiotic resistance; Ventilator-associated pneumonia; Catheter-associated urinary tract infection; Central line-associated bloodstream infections; Bloodstream infection; Urinary tract infection; Network
17.  Determination of vancomycin minimum inhibitory concentration for ceftazidime resistant Streptococcus pneumoniae in Iran 
In the context of growing health concerns over antibiotic resistance, the evaluation of the minimum inhibitory concentration (MIC) of vancomycin for Streptococcus pneumoniae (S. pneumoniae) strains resistant to ceftazidime becomes important for guiding health policy makers. The aim of this study was to determine vancomycin MIC of ceftazidime resistant S. pneumoniae strains.
Fifty identified serotypes of ceftazidime resistant S. pneumoniae strains were included in the study. The vancomycin MIC of the above mentioned bacteria was determined based on the 0.5 McFarland standards, by using a microdilution broth and the Etest method.
The results showed that out of 50 ceftazidime resistant strains of S. pneumoniae, 46 strains (92%) have shown a vancomycin MIC ≤0.19 − 0.1.5 μg/ml and only four strains (8%) have shown a vancomycin MIC equal to 1.5 μg/ml and the related maximum zone of inhibition was of 10 millimeter diameters.
The results of this investigation point out the emergence of S. pneumoniae strains with a vancomycin MIC ≥1.5 μg/ml, which were resistant to ceftazidime. This finding uncovers a major health concern: a vancomycin MIC higher than 1.5 μg/ml and maximum zone of inhibition of only 10 millimeter. These findings represent an important warning for health authorities globally, concerning the treatment of patients, as the occurrence of S. pneumoniae strains with decreased vancomycin susceptibility has been demonstrated.
PMCID: PMC4261561  PMID: 25384528
Ceftazimdime resistance; Etest; Streptococcus pneumoniae; Vancomycin; Minimum inhibitory concentration; Maximum zone of inhibition
18.  Characterization of the clonal profile of MRSA isolated in neonatal and pediatric intensive care units of a University Hospital 
Methicillin-resistant Staphylococcus aureus (MRSA) are important pathogens in neonatal and pediatric intensive care units, which can cause severe infections in hospitalized children. Detection of the mecA gene and classification of the staphylococcal cassette chromosome mec (SCCmec) permit the characterization of MRSA strains isolated from infections caused by these microorganisms. In contrast, pulsed-field gel electrophoresis (PFGE) is used to type MRSA clones. This method is commonly used to analyze the epidemiology of bacteria causing nosocomial infections. The objective of this study was to detect and characterize MRSA isolated from clinical specimens of children hospitalized in the neonatal and pediatric intensive care units of the University Hospital of the Botucatu Medical School.
A total of 119 S. aureus strains were isolated from clinical specimens and the mecA gene was detected by PCR. SCCmec was detected by multiplex PCR and the clonal profile was analyzed by PFGE.
The mecA gene was detected in 17.6% (21/119) of the isolates; 42.9% (9/21) of MRSA were characterized as SCCmec type III and 57.1% (12/21) as type IV. Analysis of the clonal profile of these strains revealed three distinct clones, with SCCmec type III being related to the Brazilian endemic clone and type IV to clones JCSC4469 and USA800.
Replacement of clonal groups occurred in the neonatal and pediatric units over the period studied, a fact highlighting the importance of improving hygiene practices and control measures of nosocomial infections in these units.
PMCID: PMC4228086  PMID: 25376654
Nosocomial infections; NICU; PICU; MRSA
19.  Regional and global antimicrobial susceptibility among isolates of Streptococcus pneumoniae and Haemophilus influenzae collected as part of the Tigecycline Evaluation and Surveillance Trial (T.E.S.T.) from 2009 to 2012 and comparison with previous years of T.E.S.T. (2004-2008) 
We report here on 14438 Streptococcus pneumoniae and 14770 Haemophilus influenzae isolates collected from 560 centres globally between 2004 and 2012 as a part of the Tigecycline Evaluation and Surveillance Trial (T.E.S.T.).
MIC testing was performed using broth microdilution methods as described by the Clinical and Laboratory Standards Institute (CLSI) using CLSI-approved breakpoints; US Food and Drug Administration breakpoints were used for tigecycline as CLSI breakpoints are not available.
At least 99% of S. pneumoniae isolates globally were susceptible to levofloxacin, linezolid, tigecycline or vancomycin. Penicillin resistance was observed among 14.8% of S. pneumoniae and was highest in Asia/Pacific Rim (30.1%) and Africa (27.6%); 23.4% of S. pneumoniae isolates were penicillin-intermediate, which were most common in Africa (37.6%). Minocycline susceptibility among S. pneumoniae decreased by 20% between 2004-2008 and 2009-2012. High (>98.5%) susceptibility was reported among H. influenzae to all antimicrobial agents on the T.E.S.T. panel excluding ampicillin, to which only 78.3% were susceptible. β-lactamase production was observed among 20.2% of H. influenzae isolates; 1.5% of isolates were β-lactamase negative, ampicillin-resistant.
S. pneumoniae remained highly susceptible to levofloxacin, linezolid, tigecycline and vancomycin while H. influenzae was susceptible to most antimicrobial agents in the testing panel (excluding ampicillin).
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-014-0052-2) contains supplementary material, which is available to authorized users.
PMCID: PMC4239395  PMID: 25376749
Antimicrobial susceptibility; Streptococcus pneumoniae; Haemophilus influenzae; Tigecycline
20.  In-vitro antimicrobial, antibiofilm, cytotoxic, antifeedant and larvicidal properties of novel quinone isolated from Aegle marmelos (Linn.) Correa 
Plant metabolites have wide applications and have the potential to cure different diseases caused by microorganisms. The aim of the study was to evaluate the antimicrobial, antibiofilm, cytotoxic, antifeedant and larvicidal properties of novel quinine isolated from Aegle marmelos (Linn.) Correa.
A compound was obtained by eluting the crude extract, using varying concentrations of the solvents by the chromatographic purification. Broth micro dilution method was used to assess the antimicrobial activity and anticancer study was evaluated using MTT assay. Larvicidal activity was studied using leaf disc no-choice method.
Based on the IR, 13C NMR and 1H NMR spectral data, the compounds were identified as quinone related antibiotic. It exhibited significant activity against Gram positive and Gram negative bacteria. The lowest Minimum Inhibitory Concentration (MIC) of the compound against Bacillus subtilis and Staphylococcus aureus was 100 and 75 μg mL−1 respectively. Against Escherichia coli and Pseudomonas aeruginosa it exhibited MIC value of 25 μg mL−1. The MIC of the compound against Aspergillus niger, A. clavatus, Penicillium roqueforti was 20 μg mL−1 and that against Fusarium oxysporum (20 μg mL−1), A. oryzae (40 μg mL−1), and Candida albicans (60 μg mL−1), respectively. It showed effective antibiofilm activity against E. coli, S. typhii and P. aeroginosa at 8 μg mL−1 and did not exhibit considerable cytotoxic activity against Vero and HEP2 cell lines. Additionally, the compound documented significant antifeedant and larvicidal activities against Helicoverpa armigera and Spodoptera litura at 125, 250, 500 and 1000 ppm concentrations.
The results concluded that the compound can be evaluated further in industrial applications and also an agent to prepare botanical new pesticide formulations.
PMCID: PMC4216832  PMID: 25359605
Phenanthrenequinone; Antibacterial; Antifungal; Antibiofilm; Cytotoxic; Antifeedant
21.  Rifaximin for small intestinal bacterial overgrowth in patients without irritable bowel syndrome 
Rifaximin is a minimally absorbed antibiotic with high luminal activity, used to treat various gastrointestinal diseases. Although rifaximin has been proposed as first line treatment for small intestinal bacterial overgrowth (SIBO), few data are available regarding its efficacy in non-IBS subjects. We aimed to assess the ability of rifaximin to normalize lactulose-H2 breath tests in non-IBS subjects with symptoms suggestive of SIBO.
Materials and methods
Consecutive non-IBS patients presenting with bloating and flatulence were prospectively recruited and submitted to lactulose-H2 breath testing (LBT). Patients who had a positive result were offered rifaximin 1200 mg daily for 10 days. Breath testing was repeated two weeks after treatment completion in all patients in order to assess for response.
A total of 19 patients with a positive result received rifaximin and repeated the breath test (7 (36.8%) males, age 56.5 ± 17.6 years). The mean peak hydrogen excretion was 13.7 ± 2.8 and 10.3 ± 7.3 ppm at baseline and following rifaximin treatment, respectively (t = 1.98, p = 0.06). LBT normalized in 8/19 (42.1%) subjects. No patients reported symptom resolution. No adverse events were reported.
Strengths include the study's prospective design. Limitations include the small sample size and open label design.
Rifaximin was not effective in normalizing LBT in our cohort of non-IBS subjects with symptoms suggestive of SIBO.
PMCID: PMC4201689  PMID: 25319626
22.  Characterization of carbapenem-resistant Pseudomonas aeruginosa clinical isolates, carrying multiple genes coding for this antibiotic resistance 
Carbapenemase genes are one of the most frequent mechanisms reported in carbapenem-resistant P. aeruginosa; however, description of P. aeruginosa co-harbouring two or more carbapenemases is unusual.
In this study we evaluated the presence of carbapenemase genes and the clonality of P. aeruginosa isolates obtained from a hospital over a 12-year period. A total of 127 isolates of carbapenem-resistant P. aeruginosa recovered from 109 patients feces (four samples), rectal swab (three samples), nasal swab (one sample) and anal abscess (one sample), were evaluated. Minimum inhibitory concentrations of the following antibiotics imipenem, meropenem and polymyxin E were determined by broth microdilution. The molecular profile of isolates was evaluated by pulsed field gel electrophoresis (PFGE). PCR for the following carbapenemase genes blaIMP;blaSPM;blaVIM;blaSIM;blaNDM;blaKPC;blaGES and nucleotide sequencing to confirm the enzyme gene types were performed and compared with the database available on the Internet (BLAST-
All isolates were carbapenem-resistant, their MIC50 and MIC90 were respectively 64 μg/mL and 256 μg/mL to imipenem and 32 μg/mL and 256 μg/mL to meropenem, all isolates except one (MIC = 8 mg/L) were susceptible to polymyxin E. The most frequent carbapenemase genes identified were blaSPM identified in 41 isolates (32%), followed by 10 with blakpc and 5 with blaVIM (3.9%). All belonged to the class SPM-1 and VIM-2. In 2011, one isolate harbouring three carbapenemase genes (SPM-1, VIM-2 and KPC-2) that belonged to a new clone was identified in a hematopoietic stem cell transplanted patient. Then, 19 carbapenem-resistant P. aeruginosa were identified in an outbreak that occurred in the bone marrow transplant unit, all positive for SPM-1 gene, and 9 (47.3%) harbored both SPM-1 and KPC.
Our findings showed that PCR for KPC gene should be performed to evaluate carbapenem resistance in P. aeruginosa and that this agent can harbor more than one carbapenemase gene. Attention should be focused on the possible rapid spread of KPC in P. aeruginosa isolates and for the fact that P. aeruginosa may become a reservoir of this transmissible resistance mechanism.
PMCID: PMC4282171  PMID: 25179208
Pseudomonas; Carbapenemases; KPC; VIM; SPM
23.  Antimicrobial activity of alexidine, chlorhexidine and cetrimide against Streptococcus mutans biofilm 
The use of antimicrobial solutions has been recommended to disinfect demineralized dentin prior to placing the filling material. The aim of this study was to evaluate the ability of several antimicrobials in controlling Streptococcus mutans (SM) biofilm formed in dentin.
Antimicrobial activity of 0.2% and 2% chlorhexidine (CHX), 0.2% cetrimide (CTR) and 0.2%, 0.5%, 1% and 2% alexidine (ALX) was assayed on 1-week SM biofilm formed on standardized coronal dentin blocks. Results of SM biofilm antimicrobial activity by different protocols were expressed as the kill percentage of biofilm and the term “eradication” was used to denote the kill of 100% of the bacterial population. To compare the efficacies of the different protocols the Student t test was used, previously subjecting data to the Anscombe transformation.
All ALX concentrations tested and 0.2% CTR achieved a kill percentage higher than 99%, followed by 2% CHX with percentages above 96% (no statistically significant difference among them). Whereas 2% ALX and 0.2% CTR respectively showed eradication in 10 and 9 of the twelve specimens, 0.2% CHX did not produce eradication in any case.
The present study shows that, when used for one minute, 2% and 1% alexidine, and 0.2% cetrimide, achieve eradication of Streptococcus mutans biofilm in most specimens when applied to a dentin-volumetric model.
PMCID: PMC4236523  PMID: 25139679
Alexidine; Biofilm; Cetrimide; Chlorhexidine; Streptococcus mutans
24.  Ethnomedicinal and phytochemical review of Pakistani medicinal plants used as antibacterial agents against Escherichia coli 
Medicinal plants have always been part of human culture and have the potential to cure different diseases caused by microorganisms. In Pakistan, biologists are mainly focusing on plants’ antimicrobial activities against Escherichia coli due to its increasing resistance to antibiotics. In total, extracts from 34 ethnomedicinally valuable Pakistani plants were reported for in-vitro anti-E. coli activities. Mostly methanolic extracts of medicinal plants were used in different studies, which have shown comparatively higher inhibitory activities against E. coli than n-hexane and aqueous extracts. It has been found that increasing concentration (mg/ml) of methanolic extract can significantly increase (p < 0.01) anti-E. coli activities. Not all medicinal plants are extracted in solvents others than above, which should also be tested against E. coli. Moreover, medicinal plant species must be fully explored phytochemically, which may lead to the development of new drugs.
PMCID: PMC4236513  PMID: 25135359
Medicinal plants; Biological screening; Ethnomedicines; Phytochemistry; Bacteria
25.  Prevalence and drug resistance of mycobacteria in Turkish cystic fibrosis patients 
Isolation of mycobacteria in cystic fibrosis (CF) patients is increasingly being reported. Because of having long term antimicrobial treatment, CF patients are at risk of pulmonary infection with especially resistant nontuberculous mycobacteria (NTM) strains. The aim of the present study is to determine the prevalence of mycobacterium spp. and antimicrobial susceptibility in Turkish CF patients.
During a 5.5 year study period, 376 sputa from 130 CF patients were analyzed. Antimycobacterial susceptibility testing was performed by the Bactec 460 TB System and the E test method.
Totaly 28 (7.44%) Mycobacterium spp. were isolated from eight (6.15%) CF patients. Five isolates (17.9%) were identified as Mycobacterium tuberculosis complex (MTBC), 14 (50%) as Mycobacterium abscessus and nine (32.1%) as Mycobacterium lentiflavum. All MTBC isolates were found to be susceptible to streptomycin, isoniazid, rifampicin, and ethambutol. Resistance to some antibiotics was detected in some NTM strains. These are the first data about the prevalence of mycobacteria in CF patients from Turkey.
In pediatric CF patients, specific mycobacterial analysis of sputum specimens and susceptibility testing should be performed for allowing early detection, identification and the possibility of eradication of these bacteria.
PMCID: PMC4236507  PMID: 25123237
Mycobacteria; Nontuberculous mycobacteria; Mycobacterium tuberculosis complex; Cystic fibrosis; Drug resistance

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