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1.  Study of the frequency of Clostridium difficile tcdA, tcdB, cdtA and cdtB genes in feces of Calves in south west of Iran 
Background
Clostridium difficile (C. difficile) is a gram-positive, toxin-producing bacillus which is an intestinal pathogen in both humans and animals and causes a range of digestive disorders including inflammation of the bowel, abdominal pain, fever and diarrhea. C. difficile toxins include enterotoxin (Toxin A), cytotoxin (Toxin B) and a binary toxin. Two large protein toxins A and B are encoded by separate genes, tcdA and tcdB. Clostridium difficile infection (CDI) mainly caused by the activity of the genes tcdA and tcdB. The binary toxin is encoded by the genes cdtA and cdtB. The binary toxin caused increased adherence of bacteria to intestinal epithelium. The aim of the present study was isolation of C. difficile from feces of calves, and study of the frequency of C. difficile virulence genes.
Methods
150 samples of fresh feces from calves were collected and C. difficile was isolated from feces of calves using bacterial culture methods. DNA was extracted by a genomic DNA purification kit. Then PCR method was used for definitive diagnosis of C. difficile. Multiplex PCR method performed for identification of tcdA, tcdB, cdtA and cdtB genes. In the final stage antimicrobial resistance determining was carried out by standard Bauer-Kirby disk diffusion method.
Results
C. difficile was isolated from 90 samples (60%). The tcdA was observed in 8 isolates (8.8%), tcdB in 16 isolates (17.7%), cdtA in 8 isolates (8.8%) and cdtB in 14 isolates (15.5%). Only 1 isolated (1.1%) was containing all four genes tcdA, tcdB, cdtA and cdtB, 2 isolates (2.2%) only had both tcdA and tcdB genes, and there was no sample positive only for both cdtA and cdtB. The highest rate of drug resistance was against clindamycin (100%) and the highest rate of drug sensitivity was against ciprofloxacin (50%).
Conclusion
The results showed high incidence of C. difficile and also high antibiotic resistance of this bacterium, but frequency of strains containing virulence genes (tcdA, tcdB, cdtA and cdtB) was low.
doi:10.1186/1476-0711-13-21
PMCID: PMC4060091  PMID: 24903619
Clostridium difficile; Calves; Toxin A; Toxin B; Binary toxin
2.  Manuka honey treatment of biofilms of Pseudomonas aeruginosa results in the emergence of isolates with increased honey resistance 
Background
Medical grade manuka honeys are well known to be efficacious against Pseudomonas aeruginosa being bactericidal and inhibiting the development of biofilms; moreover manuka honey effectively kills P. aeruginosa embedded within an established biofilm. Sustained honey resistance has not been previously documented for planktonic or biofilm P. aeruginosa.
Methods
Minimum inhibitory concentrations for manuka honey and antibiotics were determined using broth micro-dilution methods. Minimum biofilm eliminating concentrations (MBEC) and biofilm biomass were determined using the crystal violet method. Sub-culture used non-selective media and the grid-plate method.
Results
When honey treated biofilm biomass of two strains of P. aeruginosa (reference strain ATCC 9027 and the clinical isolate 867) were sub-cultured onto non-selective media isolates emerged that exhibited reduced susceptibility to manuka honey. Significantly, this characteristic was sustained with repeated sub-culture onto non-selective media resulting in increased minimum inhibitory concentrations (MIC) of between 5-7% (w/v) and increased minimum biofilm eliminating concentrations (MBEC) of up to 15% (w/v). Interestingly the resistant isolates showed reduced susceptibility to antibiotic treatment with rifampicin and imipenem as well as being more prolific biofilm-formers than the progenitor strains.
Conclusions
P. aeruginosa biofilms treated with manuka honey equivalent to the MBEC harbour slow growing, viable persistor organisms that exhibit sustained, increased resistance to manuka honey and antibiotic treatment, suggesting a shared mechanism of resistance. This sheds new light on the propensity for biofilm embedded organisms to resist honey treatment and become persistor organisms that are tolerant to other antimicrobial therapies.
doi:10.1186/1476-0711-13-19
PMCID: PMC4023514  PMID: 24884949
Antimicrobial; Small colony variant
3.  Molecular characterization of clinical multidrug-resistant Klebsiella pneumoniae isolates 
Background
Klebsiella pneumoniae is a frequent nosocomial pathogen, with the multidrug-resistant (MDR) K. pneumoniae being a major public health concern, frequently causing difficult-to-treat infections worldwide. The aim of this study was to investigate the molecular characterization of clinical MDR Klebsiella pneumoniae isolates.
Methods
A total of 27 non-duplicate MDR K. pneumoniae isolates with a CTX-CIP-AK resistance pattern were investigated for the prevalence of antimicrobial resistance genes including extended spectrum β-lactamase genes (ESBLs), plasmid-mediated quinolone resistance (PMQR) genes, 16S rRNA methylase (16S-RMTase) genes, and integrons by polymerase chain reaction (PCR) amplification and DNA sequencing. Plasmid replicons were typed by PCR-based replicon typing (PBRT). Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were carried out to characterize the strain relatedness.
Results
All the isolates co-harbored 3 or more resistance determinants. OqxAB, CTX-M-type ESBLs and RmtB were the most frequent determinants, distributed among19 (70.4%),18 (66.7%) and 8 (29.6%) strains. Fourteen isolates harbored class 1 integrons, with orfD-aacA4 being the most frequent gene cassette array. Class 3 integrons were less frequently identified and contained the gene cassette array of blaGES-1-blaOXA-10-aac(6′)-Ib. IncFII replicon was most commonly found in this collection. One cluster was observed with ≥80% similarity among profiles obtained by PFGE, and one sequence type (ST) by MLST, namely ST11, was observed in the cluster.
Conclusion
K. pneumoniae carbapenemase (KPC)–producing ST11 was the main clone detected. Of particular concern was the high prevalence of multiple resistance determinants, classs I integrons and IncFII plasmid replicon among these MDR strains, which provide advantages for the rapid development of MDR strains.
doi:10.1186/1476-0711-13-16
PMCID: PMC4030571  PMID: 24884610
Multidrug resistance; Resistance determinants; Multi-locus sequence typing; Pulsed-field gel electrophoresis; Plasmid replicons
4.  Prescription antibiotics for outpatients in Bangladesh: a cross-sectional health survey conducted in three cities 
Background
Antibiotics prescribing by physicians have gained due importance across the globe, mainly because of an increase in antibiotic usage, prevalence of infections and drug resistances. The present study is aimed to evaluate the physicians prescribing pattern of antibiotics, their usages by outpatients and disease conditions for which the antibiotics are prescribed in three cities of Bangladesh.
Methods
This cross sectional health survey was carried out with a self designed standard questionnaire by manual data collection over a three months period (20.03.2013 to 20.06.2013) at three adjacent cities Jessore Sadar, Monirampur and Keshabpur upazila respectively. The data were collected from the patient’s prescription and by directly interviewing the patients who were prescribed at least one antibiotic during the study period. WHO Anatomical Therapeutic Chemical (ATC) classifications for antibiotics was used and descriptive statistics were applied to the collected data and analyzed using Microsoft Excel software. Modified Wald method was applied to calculate 95% CI.
Results
A total of 900 prescriptions were analyzed during the study period. It was found that the prescriber prescribed antibiotics to the patients who were suffering mainly from cold and fever, infections, diarrhea and gonorrhea. The highest prescribed antibiotic groups were cephalosporins (31.78%), macrolides (27.33%), quinolones (16.33%), penicillins (7.11%), and metronidazoles (6.78%) respectively. Two or more antibiotics were prescribed in 25.44% of prescriptions. A total of 66.89% prescriptions had complete information on dosage form, 57% had complete direction for antibiotics use and 64.22% patients completed full course of antibiotics. Although 83% prescriptions have no clinical test for using antibiotics, even though the percentages of patients’ disease recovery were 61.78% and incompliance were 38.22%.
Conclusion
From this research, it is observed that physicians prescribed antibiotics rationally in some cases but needs to ensure in all cases of prescription. Because irrational use leads to the spread of bacterial resistance to antibiotics and related health problems, our findings have important implications for public education and the enforcement of regulations regarding the prescription of antibiotics in Bangladesh.
doi:10.1186/1476-0711-13-15
PMCID: PMC4004450  PMID: 24755269
Antibiotics; Prescription patterns; Antibiotic resistance; Bangladesh
5.  Antimicrobial susceptibility pattern of bacterial isolates from wound infection and their sensitivity to alternative topical agents at Jimma University Specialized Hospital, South-West Ethiopia 
Background
Wound infection is one of the health problems that are caused and aggravated by the invasion of pathogenic organisms. Information on local pathogens and sensitivity to antimicrobial agents, and topical agents like acetic acid is crucial for successful treatment of wounds.
Objectives
To determine antimicrobial susceptibility pattern of bacterial isolates from wound infection and their sensitivity to alternative topical agents at Jimma University Specialized Hospital.
Methods
A cross sectional study was conducted among patients with wound infection visiting Jimma University Specialized Hospital, from May to September 2013. Wound swab was collected using sterile cotton swabs and processed for bacterial isolation and susceptibility testing to antimicrobial agents, acetic acid, hydrogen peroxide and dabkin solution following standard bacteriological techniques. Biochemical tests were done to identify the species of the organisms. Sensitivity testing was done using Kirby- Baur disk diffusion method. Minimum inhibitory and bactericidal concentration was done using tube dilution method.
Results
In this study 145 bacterial isolates were recovered from 150 specimens showing an isolation rate of 87.3%. The predominant bacteria isolated from the infected wounds were Staphylococcus aureus 47 (32.4%) followed by Escherichia coli 29 (20%), Proteus species 23 (16%), Coagulase negative Staphylococci 21 (14.5%), Klebsiella pneumoniae 14 (10%) and Pseudomonas aeruginosa 11 (8%). All isolates showed high frequency of resistance to ampicillin, penicillin, cephalothin and tetracycline. The overall multiple drug resistance patterns were found to be 85%. Acetic acid (0.5%), Dabkin solution (1%) and 3% hydrogen peroxide were bactericidal to all isolated bacteria and lethal effect observed when applied for 10 minutes.
Conclusions
On in vitro sensitivity testing, ampicillin, penicillin, cephalothin and tetracycline were the least effective. Gentamicin, norfloxacin, ciprofloxacin, vancomycin and amikacin were the most effective antibiotics. Acetic acid (0.5%), dabkin solution (1%) and H2O2 (3%) were bactericidal to all isolates.
doi:10.1186/1476-0711-13-14
PMCID: PMC4017222  PMID: 24731394
Bacterial pathogens; Drug resistance; Wound infection; Jimma; Ethiopia
6.  Asymmetric dimethylarginine levels in patients with cutaneous anthrax: a laboratory analysis 
Background
Asymmetric dimethylarginine (ADMA), the main endogenous inhibitor of nitric oxide synthase, is considered to be associated with endothelial dysfunction. High ADMA levels have been shown to be related with disorders causing vascular inflammation such as hypertension, hypercholesterolemia, atherosclerosis, chronic heart failure, stroke and sepsis. Cutaneous anthrax (CA) is a serious infectious disease which may cause vasculitis. The aim of the study was to investigate the serum ADMA levels in patients with CA.
Methods
A total of 35 serum samples of the patients with CA and 18 control sera were tested for ADMA levels using ADMA ELISA kit (Immunodiagnostik AG, Bensheim, Germany).
Results
ADMA levels were found to be significantly higher in the patients group than the controls (p < 0.001). In addition, ADMA levels were found to be positively associated with sedimentation rates (R = 0.413; p = 0.026), and inversely associated with international normalized ratio (INR) levels (R = -0.46; p = 0.011). A cut-off value of 0.475 of ADMA had a sensitivity of 74.3%, specificity of 77.8%, and accuracy of 75.5% in the diagnosis of CA.
Conclusion
Although the exact mechanism still remains unclear, ADMA levels could be related to immune activation in CA. In addition, these data might suggest the higher ADMA levels in patients could be due to the perivascular inflammation and vasculitis in CA.
doi:10.1186/1476-0711-13-12
PMCID: PMC3986940  PMID: 24669818
Dimethylarginine; Infection; Anthrax; Vasculitis
7.  Factors predicting prolonged empirical antifungal treatment in critically ill patients 
Objective
To determine the incidence, risk factors, and impact on outcome of prolonged empirical antifungal treatment in ICU patients.
Methods
Retrospective observational study performed during a one-year period. Patients who stayed in the ICU >48 h, and received empirical antifungal treatment were included. Patients with confirmed invasive fungal disease were excluded. Prolonged antifungal treatment was defined as percentage of days in the ICU with antifungals > median percentage in the whole cohort of patients.
Results
Among the 560 patients hospitalized for >48 h, 153 (27%) patients received empirical antifungal treatment and were included in this study. Fluconazole was the most frequently used antifungal (46% of study patients). Median length of ICU stay was 19 days (IQR 8, 34), median duration of antifungal treatment was 8 days (IQR 3, 16), and median percentage of days in the ICU with antifungals was 48% (IQR 25, 80). Seventy-seven patients (50%) received prolonged empirical antifungal treatment. Chemotherapy (OR [95% CI] 2.6 [1.07-6.69], p = 0.034), and suspected infection at ICU admission (3.1 [1.05-9.48], p = 0.041) were independently associated with prolonged empirical antifungal treatment.
Duration of mechanical ventilation and ICU stay were significantly shorter in patients with prolonged empirical antifungal treatment compared with those with no prolonged empirical antifungal treatment. However, ICU mortality was similar in the two groups (46 versus 52%, p = 0.62).
Conclusion
Empirical antifungal treatment was prescribed in a large proportion of study patients. Chemotherapy, and suspicion of infection at ICU admission are independently associated with prolonged empirical antifungal treatment.
doi:10.1186/1476-0711-13-11
PMCID: PMC3984712  PMID: 24621182
Antifungal treatment; Empirical treatment; Fungal infection; Invasive fungal disease; De-escalation
8.  Reviewer acknowledgement 2013 
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 2013.
doi:10.1186/1476-0711-13-8
PMCID: PMC3931273
9.  Prevalence of intestinal parasite, Shigella and Salmonella species among diarrheal children in Jimma health center, Jimma southwest Ethiopia: a cross sectional study 
Background
Diarrheal disease continues to be an important cause of morbidity and mortality among young children in developing countries including Ethiopia. Globally, intestinal parasite, Shigella and Salmonella species remain major contributors to acute enteric infections. The study was aimed at determining the frequency of intestinal parasite, Shigella and Salmonella species identified from diarrheic children at Jimma Health Centre, Jimma south west Ethiopia.
Methods
A health institution based cross sectional study was conducted from March to November 2012. A structured questionnaire was used for collection of data on socio- demographic characteristics. Parasite and bacteria identification as well as susceptibility testing was done using standard parasitological and bacteriological procedures.
Results
A total of 260 diarrheal children were included in the study. A total of 129 (49.6%) samples were positive for intestinal parasite, Shigella and Salmonella species. Of these, 107 (41.1%), 6 (2.3%) and 16 (6.2%) samples were positive for intestinal parasite, Shigella and Salmonella species respectively. The dominant isolated parasite was G. lamblia with prevalence of 13.5% followed by A. lumbricoides (11.5%). The least identified parasites were Schistosoma mansoni and Taenia species accounting 0.4% each. Multiple parasitic infections were observed in 19 (7.3%) patients. Shigella species showed hundred percent resistances to ampicillin, amoxacillin, and cotrimoxazole. All Salmonella isolates were resistant against amoxicillin. All Shigella and Salmonella species were susceptible to ceftriaxone, ciprofloxacin and gentamycin.
Conclusion
The presence of reasonably high amount of intestinal parasite and Salmonella and Shigella species that are drug resistance to the commonly prescribed drugs is a treat to the children and community at large. Therefore, measures including health education, improvement of safe water supply, sanitation facilities and continuous monitoring of microbiological and antimicrobial surveillance is crucial.
doi:10.1186/1476-0711-13-10
PMCID: PMC3922032  PMID: 24499189
Intestinal parasite; Shigella; Salmonella; Susceptibility test; Jimma; Ethiopia
10.  Effects of Carbapenem consumption on the prevalence of Acinetobacter infection in intensive care unit patients 
Background
The consumption of carbapenems has increased worldwide, together with the increase in resistant gram negative bacilli. Subsequently, the prevalence of carbapenem-resistant Acinetobacter infections has increased rapidly and become a significant problem particularly in intensive care unit patients. The aim of the present study was to evaluate the changes in the prevalence of Acinetobacter infection by restricting the consumption of carbapenems in intensive care unit patients.
Methods
This study was conducted between May 1, 2011 and February 28, 2013. The amount of carbapenem consumption and the number of patients with multi-drug resistant Acinetobacter baumannii (MDRAB) isolates during the study period were retrospectively obtained from the records of the patients, who were hospitalized in the intensive care unit. The study period was divided into two periods named as: Carbapenem non-restricted period (CNRP) and carbapenem-restricted period (CRP). During CNRP, no restrictions were made on the use of carbapenems. During CRP, the use of carbapenems was not allowed if there was an alternative to carbapenems. Primary Endpoint: MDRAB infection after ICU admission. The definition of nosocomial infections related to Acinetobacter spp. was based on the criteria of the Center for Disease Control (CDC). The correlation between the amount of carbapenem consumption and the number of infections with MDRAB strains between the two periods were evaluated.
Results
During the study period, a total of 1822 patients’ (1053 patients in CNRP and 769 patients in CRP) records were evaluated retrospectively. A total of 10.82 defined daily dose (DDD/100 ICU days) of anti-pseudomonal carbapenem were used in CNRP, and this figure decreased to 6.95 DDD/100 ICU days in CRP. In the 8-month CNRP, 42 (3.98%) MDRAB-related nosocomial infections were detected, and 14 (1.82%) infections were detected in CRP (p = 0.012).
Conclusion
The prevalence of MDRAB strains isolated in the CNRP was 2.24-fold higher than the prevalence in the CRP. The prevalence of Acinetobacter infections can be reduced by taking strict isolation measures as well as by implementing good antibiotics usage policy.
doi:10.1186/1476-0711-13-7
PMCID: PMC3898784  PMID: 24405720
Carbapenem; Acinetobacter infection; Carbapenem consumption
11.  Implementation of a novel in vitro model of infection of reconstituted human epithelium for expression of virulence genes in methicillin-resistant Staphylococcus aureus strains isolated from catheter-related infections in Mexico 
Background
Methicillin-resistant Staphylococcus aureus (MRSA) are clinically relevant pathogens that cause severe catheter-related nosocomial infections driven by several virulence factors.
Methods
We implemented a novel model of infection in vitro of reconstituted human epithelium (RHE) to analyze the expression patterns of virulence genes in 21 MRSA strains isolated from catheter-related infections in Mexican patients undergoing haemodialysis. We also determined the phenotypic and genotypic co-occurrence of antibiotic- and disinfectant-resistance traits in the S. aureus strains, which were also analysed by pulsed-field-gel electrophoresis (PFGE).
Results
In this study, MRSA strains isolated from haemodialysis catheter-related infections expressed virulence markers that mediate adhesion to, and invasion of, RHE. The most frequent pattern of expression (present in 47.6% of the strains) was as follows: fnbA, fnbB, spa, clfA, clfB, cna, bbp, ebps, eap, sdrC, sdrD, sdrE, efb, icaA, and agr. Seventy-one percent of the strains harboured the antibiotic- and disinfectant-resistance genes ermA, ermB, tet(M), tet(K), blaZ, qacA, qacB, and qacC. PFGE of the isolated MRSA revealed three identical strains and two pairs of identical strains. The strains with identical PFGE patterns showed the same phenotypes and genotypes, including the same spa type (t895), suggesting hospital personnel manipulating the haemodialysis equipment could be the source of catheter contamination.
Conclusion
These findings help define the prevalence of MRSA virulence factors in catheter-related infections. Some of the products of the expressed genes that we detected in this work may serve as potential antigens for inclusion in a vaccine for the prevention of MRSA-catheter-related infections.
doi:10.1186/1476-0711-13-6
PMCID: PMC3905915  PMID: 24405688
MRSA; Haemodialysis catheter; Virulence factors
12.  The interrelations of radiologic findings and mechanical ventilation in community acquired pneumonia patients admitted to the intensive care unit: a multicentre retrospective study 
Background
We evaluated patients admitted to the intensive care units with the diagnosis of community acquired pneumonia (CAP) regarding initial radiographic findings.
Methods
A multicenter retrospective study was held. Chest x ray (CXR) and computerized tomography (CT) findings and also their associations with the need of ventilator support were evaluated.
Results
A total of 388 patients were enrolled. Consolidation was the main finding on CXR (89%) and CT (80%) examinations. Of all, 45% had multi-lobar involvement. Bilateral involvement was found in 40% and 44% on CXR and CT respectively. Abscesses and cavitations were rarely found. The highest correlation between CT and CXR findings was observed for interstitial involvement. More than 80% of patients needed ventilator support. Noninvasive mechanical ventilation (NIV) requirement was seen to be more common in those with multi-lobar involvement on CXR as 2.4-fold and consolidation on CT as 47-fold compared with those who do not have these findings. Invasive mechanical ventilation (IMV) need increased 8-fold in patients with multi-lobar involvement on CT.
Conclusion
CXR and CT findings correlate up to a limit in terms of interstitial involvement but not in high percentages in other findings. CAP patients who are admitted to the ICU are severe cases frequently requiring ventilator support. Initial CT and CXR findings may indicate the need for ventilator support, but the assumed ongoing real practice is important and the value of radiologic evaluation beyond clinical findings to predict the mechanical ventilation need is subject for further evaluation with large patient series.
doi:10.1186/1476-0711-13-5
PMCID: PMC3898785  PMID: 24400646
Radiography; Thoracic; Pneumoniae; Imaging; Critical care
13.  Molecular characteristics of extended-spectrum β-lactamase-producing Escherichia coli in Riyadh: emergence of CTX-M-15-producing E. coli ST131 
Background
The prevalence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) has increased recently. The aim of this study was to further characterise and to assess the occurrence of ESBL-EC in Riyadh, to use pulsed field gel electrophoresis (PFGE) typing to investigate the epidemiology of ESBL-EC and to determine the prevalence of ST131 in ESBL-EC.
Methods
A total of 152 E. coli isolates were collected at a tertiary hospital in Riyadh from September 2010 to June 2011. Genotypic and phenotypic methods were used to characterise ESBLs. PFGE was used to determine genetic relatedness. Detection of ST131 and CTX-M-like ESBLs was performed using real-time PCR.
Results
Of 152 strains, 31 were positive for ESBLs by phenotypic methods. The blaCTX-M-15 gene was highly prevalent (30/31 strains, 96.77%) among the 31 ESBL-positive E. coli strains. The blaCTX-M-27 gene was detected in one strain. Twenty (64.5%) out of 31 of ESBL-EC were ST131. PFGE revealed 29 different pulsotypes.
Conclusions
Our study documented the high prevalence of ESBLs in E. coli isolates, with CTX-M-15 as the predominant ESBL gene. ST131 clone producing CTX-M-15 has a major presence in our hospital. The high prevalence of CTX-M producers was not due to the spread of a single clone. To the best of our knowledge, this study represents the first report of CTX-M-15 and CTX-M-27 β-lactamases and the detection of the ST131 clone in Saudi E. coli isolates.
doi:10.1186/1476-0711-13-4
PMCID: PMC3898780  PMID: 24397567
β-lactam resistance; Class A β-lactamases; PFGE; ST131; Saudi Arabia
14.  Real-time PCR TaqMan assay for rapid screening of bloodstream infection 
Background
Sepsis is one of the main causes of mortality and morbidity. The rapid detection of pathogens in blood of septic patients is essential for adequate antimicrobial therapy and better prognosis. This study aimed to accelerate the detection and discrimination of Gram-positive (GP) and Gram-negative (GN) bacteria and Candida species in blood culture samples by molecular methods.
Methods
The Real-GP®, -GN®, and -CAN® real-time PCR kit (M&D, Wonju, Republic of Korea) assays use the TaqMan probes for detecting pan-GP, pan-GN, and pan-Candida species, respectively. The diagnostic performances of the real-time PCR kits were evaluated with 115 clinical isolates, 256 positive and 200 negative blood culture bottle samples, and the data were compared to results obtained from conventional blood culture.
Results
Eighty-seven reference strains and 115 clinical isolates were correctly identified with specific probes corresponding to GP-bacteria, GN-bacteria and Candida, respectively. The overall sensitivity and specificity of the real-time PCR kit with blood culture samples were 99.6% and 89.5%, respectively.
Conclusions
The Real-GP®, -GN®, and -CAN® real-time PCR kits could be useful tools for the rapid and accurate screening of bloodstream infections (BSIs).
doi:10.1186/1476-0711-13-3
PMCID: PMC3898783  PMID: 24393579
Real-time polymerase chain reaction; Blood culture; Gram-positive bacteria; Gram-negative bacteria; Candida
15.  Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2 
Background
Clinical microbiology laboratories have to accurately identify clinical microbes. However, some isolates are difficult to identify by the automated biochemical text platforms, which are called “difficult-to-identify” microbes in this study. Therefore, the ability of 16S ribosomal DNA (16S rDNA) and internal transcribed spacer 2 (ITS2) sequencing to identify these “difficult-to-identify” bacteria and fungi was assessed in this study.
Methods
Samples obtained from a teaching hospital over the past three years were examined. The 16S rDNA of four standard strains, 18 clinical common isolates, and 47 “difficult-to-identify” clinical bacteria were amplified by PCR and sequenced. The ITS2 of eight standard strains and 31 “difficult-to-identify” clinical fungi were also amplified by PCR and sequenced. The sequences of 16S rDNA and ITS2 were compared to reference data available in GenBank by using the BLASTN program. These microbes were identified according to the percentage of similarity to reference sequences of strains in GenBank.
Results
The results from molecular sequencing methods correlated well with automated microbiological identification systems for common clinical isolates. Sequencing results of the standard strains were consistent with their known phenotype. Overall, 47 “difficult-to-identify” clinical bacteria were identified as 35 genera or species by sequence analysis (with 10 of these identified isolates first reported in clinical specimens in China and two first identified in the international literature). 31 “difficult-to-identify” clinical fungi tested could be identified as 15 genera or species by sequence analysis (with two of these first reported in China).
Conclusions
Our results show the importance of 16S rDNA and internal ITS2 sequencing for the molecular identification of “difficult-to-identify” bacteria and fungi. The development of this method with advantages of convenience, availability, and cost-effectiveness will make it worth extending into clinical practice in developing countries.
doi:10.1186/1476-0711-13-1
PMCID: PMC3905965  PMID: 24383440
Bacteria; Fungi; 16S rDNA; Internal transcribed spacer 2
16.  Prevalence of antibiotic resistance in multi-drug resistant coagulase-negative staphylococci isolated from invasive infection in very low birth weight neonates in two Polish NICUs 
Background
Multi-drug resistant coagulaso-negative staphylococci (CNS) have become an increasing problem in nosocomial infections connected with the presence of medical devices. The paper aimed to analyze the prevalence of antibiotic resistance in CNS isolated from invasive infection in very low birth weight (VLBW) neonates.
Methods
Continuous prospective target surveillance of infections was conducted in 2009 at two Polish NICUs that participated in the Polish Neonatology Surveillance Network (PNSN). The study covered 386 neonates with VLBW (≤1500 g), among which 262 cases of invasive infection were detected with predominance of CNS (123; 47%). Altogether, 100 CNS strains were analyzed. The resistance phenotypes were determined according to EUCAST. Resistance genes: mecA, ermA, ermB, ermC, msrA, aac(6')/aph(2''), ant(4')-Ia and aph(3')-IIIa were detected using multiplex PCR.
Results
The most common species was S. epidermidis (63%), then S. haemolyticus (28%) and other CNS (9%). Among S. epidermidis, 98% of isolates were resistant to methicillin, 90% to erythromycin, 39% to clindamycin, 95% to gentamicin, 60% to amikacin, 36% to ofloxacin, 2% to tigecycline, 3% to linezolid and 13% to teicoplanin. Among S. haemolyticus isolates, 100% were resistant to methicillin, erythromycin and gentamicin, 18% to clindamycin, 50% to amikacin, 86% to ofloxacin, 14% to tigecycline and 4% to teicoplanin. No resistance to linezolid was detected for S. haemolyticus isolates. Moreover, all isolates of S. epidermidis and S. haemolyticus were susceptible to vancomycin. The mecA gene was detected in 98% of S. epidermidis isolates and all of S. haemolyticus ones. Among macrolide resistance isolates, the ermC was most common in S. epidermidis (60%) while msrA was prevalent in S. haemolyticus (93%). The ermC gene was indicated in all isolates with cMLSB, whereas mrsA was found in isolates with MSB phenotype. Of the aminoglycoside resistance genes, aac(6')/aph(2'') were present alone in 83% of S. epidermidis, whereas aac(6')/aph(2'') with aph(3')-IIIa were predominant in 84% of S. haemolyticus.
Conclusions
Knowing the epidemiology and antibiotic resistance of CNS isolated from invasive infection in VLBW neonates is a key step in developing targeted prevention strategies and reducing antibiotic consumption.
doi:10.1186/1476-0711-12-41
PMCID: PMC3898809  PMID: 24359473
Multi-drug resistant coagulase-negative staphylococci; Resistance genes; Very-low-birth-weight neonates; Nosocomial infections
17.  Bacterial contamination, bacterial profile and antimicrobial susceptibility pattern of isolates from stethoscopes at Jimma University Specialized Hospital 
Introduction
Hospital acquired infections are recognized as critical public health problems. Infections are frequently caused by organisms residing in healthcare environment, including contaminated medical equipment like Stethoscopes.
Objective
To determine bacterial contamination, bacterial profile and anti-microbial susceptibility pattern of the isolates from stethoscopes at Jimma University Specialized Hospital.
Methodology
Cross-sectional study conducted from May to September 2011 at Jimma University Specialized Hospital. One hundred seventy-six stethoscopes owned by Health Care Workers (HCWs) and Medical students were randomly selected and studied. Self-administered structured questionnaire was used to collect socio-demographic data. Specimen was collected using moisten sterile cotton swab and 1 ml normal saline was used to transport the specimen, all laboratory investigations were done following standard microbiological techniques, at Microbiology Laboratory, Jimma University. SPSS windows version 16 used for data analysis and P <0.05 was considered statistically significant. Result: A total, of 151 (85.8%) stethoscopes were contaminated. A total of 256 bacterial strains and a mean of 1.44×104 CFUs/diaphragm of stethoscopes was isolated. Of the 256 isolates, 133 (52%) were potential pathogens like S. aureus, Klebsiella spp., Citrobacter spp., Salmonella spp., Proteus spp., Enterobacter spp., P. aeruginosa and E. coli. All strains were resistant to multiple classes of antibiotics (two to eight classes of antibiotics). Disinfection practice was poor. Disinfection practice was found to be associated with bacterial contamination of stethoscopes (P < 0.05). High contamination rate 100 (90.9%) was observed among stethoscopes that had never been disinfected; while the least contamination 29 (72.2%) was found on those disinfected a week or less before the survey.
Conclusion
Bacterial contamination of the stethoscope was significant. The isolates were potential pathogens and resistant to multiple classes of antibiotics. Stethoscope is potential vehicle in the transmission of infections between patients and Healthcare Workers. Stethoscope diaphragm should be disinfected before and after each patient contact.
doi:10.1186/1476-0711-12-39
PMCID: PMC3880102  PMID: 24330702
18.  A multicentre clinical study on the injection of ceftriaxone/sulbactam compared with cefoperazone/sulbactam in the treatment of respiratory and urinary tract infections 
Objective
This clinical study was designed to evaluate the efficacy and safety of this therapy in the treatment of respiratory and urinary infections caused by ceftriaxone-resistant bacteria in comparison with the effect of cefoperazone/sulbactam on cefoperazone-resistant bacteria.
Methods
A total of 285 patients aged from 18 to 65 years old, with a respiratory or urinary tract bacterial infection, were enrolled into this multicentre, open-label, controlled clinical study, and bacteria that were either ceftriaxone-resistant or cefoperazone-resistant were isolated from the patients, whose condition had not improved after three days of treatment with ceftriaxone or cefoperazone. To be selected for the study, bacterial cultures obtained from the patients had to be positive before enrolment, and all of the isolates were required to be β-lactamase-positive. Of these patients, 253 completed the trial, and 263 were enrolled into the intention-to-treat (ITT) analysis. All of the 285 patients were included in the safety analysis.
Results
The cure and effective rates were 39.55% and 85.07% in the ceftriaxone/sulbactam group and 36.43% and 79.84% in the cefoperazone/sulbactam group; the bacterial eradication rates were 83.58% and 83.72%; and the adverse-event rates were 7.48% and 7.80%, respectively. There were no significant differences between the two groups (p > 0.05).
Conclusion
Ceftriaxone/sulbactam is as effective and well-tolerated as cefoperazone/sulbactam for the treatment of intermediate and severe bacterial infections caused by resistant strains.
doi:10.1186/1476-0711-12-38
PMCID: PMC4029302  PMID: 24321187
Resistant bacterial infection; Ceftriaxone/sulbactam; Multicentre clinical study
19.  In vitro antifungal activity of farnesyltransferase inhibitors against clinical isolates of Aspergillus and Candida 
Background
Protein farnesylation is an important tosttranslational modification in fungi. We evaluated the antifungal activity of two farnesyltransferase inhibitors against clinical isolates of Aspergillus and Candida.
Methods
Disk diffusion assay and broth microdilution assay were used to determine the antifungal susceptibility of two farnesyltransferase inhibitors (manumycin A and tipifarnib) against clinical isolates of Aspergillus and Candida.
Results
Disk diffusion assay demonstrated both agents had activity against Aspergillus and Candida. The minimal inhibitory concentration (MIC) ranges for manumycin A against Aspergillus and Candida were 200 to 400 μM and 13 to >25 μM, respectively. Unfortunately, the MIC were vastly higher than the concentrations that inhibit the proliferation and viability of mammalian cells. The MICs of tipifarnib against Aspergillus and Candida were >1600 μM.
Conclusion
The outcome of present study showed that farnesyltransferase inhibitors have activity against Aspergillus and Candida. This suggests that farnesyltransferase may be used as anifungal target in designing and developing new drugs.
doi:10.1186/1476-0711-12-37
PMCID: PMC4029545  PMID: 24314136
Aspergillus; Candida; Farnesyltransferase inhibitors; Antifungal susceptibility testing
20.  Colistin use in pediatric intensive care unit for severe nosocomial infections: experience of an university hospital 
Background
The aim of this study was to investigate the efficacy and safety of colistin therapy in pediatric patients with severe nosocomial infections in pediatric intensive care unit.
Methods
The medical records of patients treated with colistin at a 200-bed university children hospital were reviewed.
Result
Thirty-one patients (male/female = 22/9; median age, 3 years; range, 3 months-17 years) received forty-one courses of colistin. The average dose of colistin was 4.9 ± 0.5 mg/kg/day and average treatment duration was 19.8 ± 10.3 days. Three patients who received concomitant nephrotoxic agent with colistin developed nephrotoxicity. Colistin treatment was well tolerated in other patients, and neurotoxicity was not seen in any patient. Favourable outcome was achieved in 28 (68.3%) episodes. Twelve patients died during the colistin therapy. Six of these patients died because of primary underlying disease. The infection-related mortality rate was found 14.6% in this study.
Conclusion
In our study, colistin therapy was found to be acceptable treatment option for the severe pediatric nosocomial infections caused by multi-drug resistant bacteria. However, the use of concomitant nephrotoxic drugs with colistin must be avoided and renal function test should be closely monitored.
doi:10.1186/1476-0711-12-32
PMCID: PMC3827824  PMID: 24199612
Colistin; Child; Multi-drug resistant bacteria; Nosocomial infection; Nephrotoxicity
21.  The establishment of a duplex real-time PCR assay for rapid and simultaneous detection of blaNDM and blaKPC genes in bacteria 
The latest threat of multidrug-resistant Gram-negative bacteria corresponds to the emergence of carbapenemase New Delhi metallo-β-lactamase (NDM) and Klebsiella pneumoniae carbapenemase (KPC) producers. Rapid molecular detection is essential to limit their spread. In this study, a duplex real-time polymerase chain reaction (PCR) that was specific for the detection of blaNDM and blaKPC with the same limit of detection of ten plasmid copies was developed. The assay was linear over eight log dilutions for blaNDM (R2 = 0.971; slope, -3.273) and blaKPC (R2 = 0.992; slope, -2.997) with efficiencies of 102% and 115%, respectively. The assay was validated with 157 clinical isolates and showed 100% concordance with conventional PCR. The excellent performance of the duplex PCR assay makes it a powerful tool for surveillance of the carbapenemases NDM and KPC.
doi:10.1186/1476-0711-12-30
PMCID: PMC3816589  PMID: 24143953
Duplex; Real-time PCR; Infection control; Carbapenemase
22.  Analysis of integrons and associated gene cassettes in clinical isolates of multidrug resistant Pseudomonas aeruginosa from Southwest Nigeria 
Background
Multidrug resistant Pseudomonas aeruginosa harbours integrons and other mobile genetic elements such as plasmids and transposons, which easily disseminate antibiotic resistance genes among clinical strains of P. aeruginosa.
Methodology
Plasmid extraction of 54 clinical isolates of P. aeruginosa was carried out by alkaline lysis method; and plasmid size estimation was done by using E. coli V517 standard plasmid marker. Fifty-four clinical strains of P. aeruginosa were isolated from 5 hospitals in 3 Southwestern states of Nigeria between March and September 2010. Plasmid extraction of isolates was carried out by alkaline lysis method; and plasmid size estimation was done by using E. coli V517 standard plasmid marker. PCR amplification for the 3 classes of resistance integrons, and gene cassette characterization were carried out using specific primers and by sequencing of PCR products. Conjugal mating of the integron positive P. aeruginosa strains with E. coli DH5α was performed to demonstrate transferability of integrons and gene cassettes.
Result
Agarose gel electrophoresis of plasmid DNA revealed that all the 54 P. aeruginosa harboured 1–4 plasmids with sizes ranging from 2.2 – >58 kb. Class 1 integron was identified in 31 (57%) strains; but none of them carried class 2 and class 3 integrons. High prevalence of aadA gene conferring resistance to streptomycin/spectinomycin was detected in the strains positive for class 1 integron. Sequencing of the 1.6 kb and 1.2 kb amplified band of gene cassettes revealed the presence of aadA6-orfD and aadA13 respectively.
Conclusion
This study demonstrates the presence of plasmids and integrons harbouring resistance gene cassettes, which may collectively constitute an efficient system for dissemination of resistance genes in P. aeruginosa. Disturbingly, the rapid and unabated spread of class 1 integron-associated multidrug resistant P. aeruginosa in Southwest Nigeria may greatly hamper successful treatment of infections caused by such strains. This necessitates the establishment of functional antimicrobial resistance surveillance programmes in Nigeria.
doi:10.1186/1476-0711-12-29
PMCID: PMC3842740  PMID: 24143920
Pseudomonas aeruginosa; Antibiotic resistance; Plasmids; Integrons; Gene cassettes
23.  Antibacterial activity of Nymphaea nouchali (Burm. f) flower 
Background
The present work aimed to find out the antibacterial activity of Nymphaea nouchali flower on human and plant pathogenic bacteria.
Methods
Antibacterial potency of methanol, acetone, ethyl acetate and petroleum spirit extracts of Nymphaea nouchali flower has been tested against four human pathogenic bacteria Bacillus subtilis (FO 3026) Escherichia coli (IFO 3007), Klebsiella pneumonia (ATTC 10031) and Sarcina lutea (IFO 3232) and one plant pathogenic bacterium Xanthomonas campestris (IAM 1671) by disc diffusion assay. Zone of inhibition produced by different extracts against the test bacteria was measured and compared with standard antibiotic disc.
Results
Methanol extract possessed better antibacterial activity against two pathogenic bacteria, B. subtilis (FO 3026) and S. lutea (IFO 3232) than commercial antibiotic nalidixic acid. Acetone extract showed moderate sensitivity whereas B. subtilis (FO 3026), S. lutea (IFO 3232) and X. campestris (IAM 1671) showed resistance to ethyl acetate and petroleum spirit extracts. The minimum inhibitory concentrations of various extracts were ranged between 128–2048 μgml-1.
Conclusions
Nymphaea nouchali flower could be a potential candidate for future development of novel broad spectrum antibacterial herbal formulation.
doi:10.1186/1476-0711-12-27
PMCID: PMC3852100  PMID: 24099586
Nymphaea nouchali flower; Antibacterial activity; Disc diffusion assay; Nalidixic acid
24.  In vitro antibacterial activity of Tabernaemontana alternifolia (Roxb) stem bark aqueous extracts against clinical isolates of methicillin resistant Staphylococcus aureus 
Background
The rise of antibiotic resistance among methicillin resistant Staphylococcus aureus (MRSA), have caused concerns for the treatment of MRSA infections. Hence, search for an alternative therapy for these infections is inevitable. Folk Indian medicine refers to the use of leaf and stem bark powder of Tabernaemontana alternifolia (Roxb) in treatment of skin infections, but no scientific report establishes its antibacterial activity.
Methods
Direct aqueous extracts and sequential aqueous extracts of the stem bark of T. alternifolia (using petroleum ether and ethyl acetate as other solvents) were prepared by soxhlet extraction. The antibiotic sensitivity profiles of the clinical isolates were determined against 18 antibiotics using disc diffusion method. The isolates were identified by 16S rRNA gene sequencing. The methicillin resistance among S. aureus (MRSA) was confirmed by PCR amplification of mecA gene. The disc diffusion method was used to determine the antibacterial activity of the extracts. The micro-dilution method was used to determine the minimum inhibitory concentration (MIC) of the extract against the test organism. To further evaluate the therapeutic potential of the extract, cell cytotoxicity was checked on Vero cells by MTT assay. Chemical profiling of the extract was done by HPTLC method.
Results
The aqueous extracts of T. alternifolia stem bark exhibited antibacterial activity against Gram-positive microorganisms, particularly against clinical isolates of MRSA and vancomycin resistant S. aureus (VRSA). The minimum inhibitory concentration (MIC) of extract against the isolates ranged from 600–800 μg/ml. The extract did not exhibit cytotoxic activity against Vero cells even at the concentration of 4 mg/ml. The chemical profiling revealed presence of alkaloids, flavonoids, coumarins, saponins and steroids. Petroleum ether and ethyl acetate extracts did not exhibit antibacterial activity.
Conclusion
Our results offer a scientific basis for the traditional use of T. alternifolia in the treatment of skin infections, showing that the plant extract has an enormous potential as a prospective alternative therapy against MRSA skin infections. The present study lays the basis for future studies, to validate the possible use of T. alternifolia as a candidate in the treatment of MRSA infections.
doi:10.1186/1476-0711-12-26
PMCID: PMC3851168  PMID: 24066905
Tabernaemontana alternifolia (Roxb); Anti-MRSA; Cytotoxicity; Plant extract; Antimicrobial
25.  Increased serum procalcitonin levels in pregnant patients with asymptomatic bacteriuria 
Background
Among the pregnancy urinary tract infections, asymptomatic bacteriuria (ASB) is the most common one. Untreated ASB can progress to pyelonephritis in 30-50% of the patients and can also result in prematurity in 27% of the pregnancy so it needs immediate diagnosis and treatment. In this study, we wanted to evaluate procalcitonin levels, compared to other inflammatory in pregnant women with ASB.
Methods
The study was designed between the period of January 2012 and February 2013 at Sakarya University School of Medicine, Department of Gynecology and Obstetrics. The study population included 30 pregnant patients with asymptomatic bacteriuria and 39 healthy pregnant controls.
Results
Mean age was 28 (SD, 5.5) of the study population; mean maternal weight was 70 (SD, 8) kilogram. There were no statically significant differences between the groups according to the routine biochemical parameters, but gestational age was significantly lower in the ASB group compared to the controls (20.4 vs 28.6, respectively; p < 0.001). Serum procalcitonin levels were negative in all of the controls. In ASB group, 9 (30%) patients had procalcitonin levels greater than >0.05 ng/ml and 21(70%) patients had negative procalcitonin levels (Chi-squrae, p < 0.001). The sensitivity and specificity of procalcitonin assay for ASB was calculated as 30% and 100%, respectively. The positive predictive value was 100% and the negative predictive value was 65%. The most frequent microorganisms in the urine culture were Escherichia coli (26 patients, 87%), Proteus mirabilis (3 patients, 10%) and Klebsiella (1 patient, 3%) in the ASB group. We experienced four (44%) recurrences among nine positive procalcitonin in ASB patients after completion of treatment of the first ASB diagnosis.
Discussion
Procalcitonin levels were significantly higher in ASB group than the control group and serum procalcitonin levels were higher in pregnant women with recurrent ASB. This finding is an important result revealed that high procalcitonin level can predict the further urinary tract infection risk. Finally, serum procalcitonin levels were normal in healthy pregnant women while other inflammatory markers such as WBC, ESR and CRP levels were higher.
doi:10.1186/1476-0711-12-25
PMCID: PMC3846744  PMID: 24006912
Asymptomatic bacteriuria; Procalcitonin; Pregnant women; Inflammatory markers

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