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1.  Antifungal activity of synthetic naphthoquinones against dermatophytes and opportunistic fungi: preliminary mechanism-of-action tests 
This study evaluated the antifungal activities of synthetic naphthoquinones against opportunistic and dermatophytic fungi and their preliminary mechanisms of action. The minimum inhibitory concentrations (MICs) of four synthetic naphthoquinones for 89 microorganisms, including opportunistic yeast agents, dermatophytes and opportunistic filamentous fungi, were determined. The compound that exhibited the best activity was assessed for its action against the cell wall (sorbitol test), for interference associated with ergosterol interaction, for osmotic balance (K+ efflux) and for membrane leakage of substances that absorb at the wavelength of 260 nm. All tested naphthoquinones exhibited antifungal activity, and compound IVS320 (3a,10b-dihydro-1H-cyclopenta [b] naphtho [2,3-d] furan-5,10-dione)-dione) demonstrated the lowest MICs across the tested species. The MIC of IVS320 was particularly low for dermatophytes (values ranging from 5–28 μg/mL) and Cryptococcus spp. (3–5 μg/mL). In preliminary mechanism-of-action tests, IVS320 did not alter the fungal cell wall but did cause problems in terms of cell membrane permeability (efflux of K+ and leakage of substances that absorb at 260 nm). This last effect was unrelated to ergosterol interactions with the membrane.
doi:10.1186/1476-0711-13-26
PMCID: PMC4094904  PMID: 24998949
Naphthoquinones; Antifungal activity; Mechanism of action
2.  Nasopharyngeal carriage of Staphylococcus aureus among imprisoned males from Brazil without exposure to healthcare: risk factors and molecular characterization 
Background
Previous studies report high prevalence of Methicillin-resistant Staphylococcus aureus (MRSA) colonization among imprisoned populations. However, there are no data on that prevalence in Brazilian correctional institutions.
Findings
We tested 302 male prisoners for nasopharyngeal colonization with Staphylococcus aureus from February 2009 through April 2010. The overall isolation rate of S. aureus was 16.5% (50/302). Men who had sex with men, users of inhalatory drugs and those with previous lung or skin diseases were more likely to be colonized with S. aureus. MRSA was isolated from 0.7% of subjects (2/302). The two Community-associated (CA)-MRSA belonged to ST5 but were unrelated based on the PFGE results. Both harbored SCCmec IV, and did not possess the Panton-Valentine Leukocidin gene.
Conclusion
We found low prevalence of S. aureus and CA-MRSA among prisoners. MRSA isolates ST5 from two subjects harboured SCCmec IV and presented different PFGE patterns.
doi:10.1186/1476-0711-13-25
PMCID: PMC4099405  PMID: 24990470
Staphylococcus aureus; MRSA; Inmates
3.  Acute liver failure caused by severe acute hepatitis B: a case series from a multi-center investigation 
Background
Few data can be available regarding acute liver failure (ALF) caused by severe acute hepatitis B up to now. This study aims to report such cases from China.
Findings
We conducted a multi-center investigation on ALF from 7 tertiary hospitals in different areas of China. A total of 11 patients with ALF caused by severe acute hepatitis B were finally identified. In these patients, there were 10 male and 1 female patients. As a serious complication, apparent hemorrhage occurred in 9 patients. Eventually, in these 11 patients, 4 survived and 7 died. 4 died of heavy bleeding, 2 died of systemic inflammatory response syndrome and 1 died of irreversible coma. No patients received liver transplantation.
Conclusions
ALF caused by severe acute hepatitis B is worthy of formal studies based on its rarity and severity.
doi:10.1186/1476-0711-13-23
PMCID: PMC4077644  PMID: 24958233
Acute liver failure; Acute hepatitis B; Prognosis
4.  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
5.  Genetic characteristics and antimicrobial resistance of Staphylococcus epidermidis isolates from patients with catheter-related bloodstream infections and from colonized healthcare workers in a Belgian hospital 
Background
Staphylococcus epidermidis is a pathogen that is frequently encountered in the hospital environment. Healthcare workers (HCWs) can serve as a reservoir for the transmission of S. epidermidis to patients.
Methods
The aim of this study was to compare and identify differences between S. epidermidis isolated from 20 patients with catheter-related bloodstream infections (CRBSIs) and from the hands of 42 HCWs in the same hospital in terms of antimicrobial resistance, biofilm production, presence of the intercellular adhesion (ica) operon and genetic diversity (pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and staphylococcal cassette chromosome (SCC) mec typing).
Results
S. epidermidis isolates that caused CRBSI were resistant to significantly more non-betalactam drugs than were isolates collected from HCWs. Among the 43 mecA positive isolates (26 from HCWs), the most frequent SCCmec type was type IV (44%). The ica operon was significantly more prevalent in CRBSI isolates than in HCWs (P < 0.05). Weak in vitro biofilm production seemed to correlate with the absence of the ica operon regardless of the commensal or pathogenic origin of the isolate. The 62 isolates showed high diversity in their PFGE patterns divided into 37 different types: 19 harbored only by the CRBSI isolates and 6 shared by the clinical and HCW isolates. MLST revealed a total of ten different sequence types (ST). ST2 was limited to CRBSI-specific PFGE types while the “mixed” PFGE types were ST5, ST16, ST88 and ST153.
Conclusion
One third of CRBSI episodes were due to isolates belonging to PFGE types that were also found on the hands of HCWs, suggesting that HCW serve as a reservoir for oxacillin resistance and transmission to patients. However, S. epidermidis ST2, mecA-positive and icaA-positive isolates, which caused the majority of clinically severe CRBSI, were not recovered from the HCW’s hands.
doi:10.1186/1476-0711-13-20
PMCID: PMC4066695  PMID: 24899534
Staphylococcus epidermidis; Catheter-related bloodstream infection; Molecular epidemiology; PFGE; MLST
6.  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
7.  The polyene antifungals, amphotericin B and nystatin, cause cell death in Saccharomyces cerevisiae by a distinct mechanism to amphibian-derived antimicrobial peptides 
Background
There is a pressing need to identify novel antifungal drug targets to aid in the therapy of life-threatening mycoses and overcome increasing drug resistance. Identifying specific mechanisms of action of membrane-interacting antimicrobial drugs on the model fungus Saccharomyces cerevisiae is one avenue towards addressing this issue. The S. cerevisiae deletion mutants Δizh2, Δizh3, Δaif1 and Δstm1 were demonstrated to be resistant to amphibian-derived antimicrobial peptides (AMPs). The purpose of this study was to examine whether AMPs and polyene antifungals have a similar mode of action; this was done by comparing the relative tolerance of the mutants listed above to both classes of antifungal.
Findings
In support of previous findings on solid media it was shown that Δizh2 and Δizh3 mutants had increased resistance to both amphotericin B (1–2 μg ml−1) and nystatin (2.5 – 5 μg ml−1) in liquid culture, after acute exposure. However, Δaif1 and Δstm1 had wild-type levels of susceptibility to these polyenes. The generation of reactive oxygen species (ROS) after exposure to amphotericin B was also reduced in Δizh2 and Δizh3. These data indicated that polyene antifungal and AMPs may act via distinct mechanisms of inducing cell death in S. cerevisiae.
Conclusions
Further understanding of the mechanism(s) involved in causing cell death and the roles of IZH2 and IZH3 in drug susceptibility may help to inform improved drug design and treatment of fungal pathogens.
doi:10.1186/1476-0711-13-18
PMCID: PMC4036090  PMID: 24884795
Amphotericin B; Antifungal resistance; YOL002C; Antifungals
8.  Recurrent paratyphoid fever A co-infected with hepatitis A reactivated chronic hepatitis B 
We report here a case of recurrent paratyphoid fever A with hepatitis A co-infection in a patient with chronic hepatitis B. A 26-year-old male patient, who was a hepatitis B virus carrier, was co-infected with Salmonella enterica serovar Paratyphi A and hepatitis A virus. The recurrence of the paratyphoid fever may be ascribed to the coexistence of hepatitis B, a course of ceftriaxone plus levofloxacin that was too short and the insensitivity of paratyphoid fever A to levofloxacin. We find that an adequate course and dose of ceftriaxone is a better strategy for treating paratyphoid fever. Furthermore, the co-infection of paratyphoid fever with hepatitis A may stimulate cellular immunity and break immunotolerance. Thus, the administration of the anti-viral agent entecavir may greatly improve the prognosis of this patient with chronic hepatitis B, and the episodes of paratyphoid fever and hepatitis A infection prompt the use of timely antiviral therapy.
doi:10.1186/1476-0711-13-17
PMCID: PMC4055195  PMID: 24884719
Recurrent paratyphoid fever A; Hepatitis A; Chronic hepatitis B reactivation
9.  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
10.  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
11.  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
12.  Intracellular activity of tedizolid phosphate and ACH-702 versus Mycobacterium tuberculosis infected macrophages 
Background
Due to the emergency of multidrug-resistant strains of Mycobacterium tuberculosis, is necessary the evaluation of new compounds.
Findings
Tedizolid, a novel oxazolidinone, and ACH-702, a new isothiazoloquinolone, were tested against M. tuberculosis infected THP-1 macrophages. These two compounds significantly decreased the number of intracellular mycobacteria at 0.25X, 1X, 4X and 16X the MIC value. The drugs were tested either in nanoparticules or in free solution.
Conclusion
Tedizolid and ACH-702 have a good intracellular killing activity comparable to that of rifampin or moxifloxacin.
doi:10.1186/1476-0711-13-13
PMCID: PMC3986449  PMID: 24708819
ACH-702; Tuberculosis; Oxazolidinones
13.  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
14.  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
15.  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
16.  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
17.  Sacroiliitis secondary to catheter-related bacteremia due to Mycobacterium abscessus (sensu stricto) 
We describe a case of sacroiliitis secondary to catheter-related bacteremia due to Mycobacterium abscessus (sensu stricto). This case confirms that MultiLocus sequence typing and variable-number tandem-repeat methods are very robust techniques to identify the pathogen species and to validate molecular epidemiological links among complex M. abscessus isolates.
doi:10.1186/1476-0711-13-9
PMCID: PMC3943385  PMID: 24479655
Sacroiliitis; Catheter-related; Bacteremia; Mycobacterium abscessus complex; MultiLocus sequence typing method; Variable-number tandem-repeat method
18.  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
19.  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
20.  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
21.  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
22.  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
23.  Investigation of aminoglycoside resistance inducing conditions and a putative AmrAB-OprM efflux system in Burkholderia vietnamiensis 
Background
Burkholderia cepacia complex (BCC) bacteria are highly virulent, typically multidrug-resistant, opportunistic pathogens in cystic fibrosis (CF) patients and other immunocompromised individuals. B. vietnamiensis is more often susceptible to aminoglycosides than other BCC species, and strains acquire aminoglycoside resistance during chronic CF infection and under tobramycin and azithromycin exposure in vitro, apparently from gain of antimicrobial efflux as determined through pump inhibition. The aims of the present study were to determine if oxidative stress could also induce aminoglycoside resistance and provide further observations in support of a role for antimicrobial efflux in aminoglycoside resistance in B. vietnamiensis.
Findings
Here we identified hydrogen peroxide as an additional aminoglycoside resistance inducing agent in B. vietnamiensis. After antibiotic and hydrogen peroxide exposure, isolates accumulated significantly less [3H] gentamicin than the susceptible isolate from which they were derived. Strains that acquired aminoglycoside resistance during infection and after exposure to tobramycin or azithromycin overexpressed a putative resistance-nodulation-division (RND) transporter gene, amrB. Missense mutations in the repressor of amrB, amrR, were identified in isolates that acquired resistance during infection, and not in those generated in vitro.
Conclusions
These data identify oxidative stress as an inducer of aminoglycoside resistance in B. vietnamiensis and further suggest that active efflux via a RND efflux system impairs aminoglycoside accumulation in clinical B. vietnamiensis strains that have acquired aminoglycoside resistance, and in those exposed to tobramycin and azithromycin, but not hydrogen peroxide, in vitro. Furthermore, the repressor AmrR is likely just one regulator of the putative AmrAB-OprM efflux system in B. vietnamiensis.
doi:10.1186/1476-0711-13-2
PMCID: PMC4077030  PMID: 24393536
Burkholderia vietnamiensis; Aminoglycoside; Azithromycin; Hydrogen peroxide; Efflux; AmrB; AmrR
24.  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
25.  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

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