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1.  Correction: Helicobacter pylori and gastroduodenal pathology: New threats of the old friend 
Since publication of our article (Ahmed and Sechi: Ann Clin Microbiol Antimicrob 2005, 4:1), we have noticed several errors.
doi:10.1186/1476-0711-7-6
PMCID: PMC2291066
2.  Antibiotic resistance and genotype of beta-lactamase producing Escherichia coli in nosocomial infections in Cotonou, Benin 
Background
Beta lactams are the most commonly used group of antimicrobials worldwide.
The presence of extended-spectrum lactamases (ESBL) affects significantly the treatment of infections due to multidrug resistant strains of gram-negative bacilli. The aim of this study was to characterize the beta-lactamase resistance genes in Escherichia coli isolated from nosocomial infections in Cotonou, Benin.
Methods
Escherichia coli strains were isolated from various biological samples such as urine, pus, vaginal swab, sperm, blood, spinal fluid and catheter. Isolated bacteria were submitted to eleven usual antibiotics, using disc diffusion method according to NCCLS criteria, for resistance analysis. Beta-lactamase production was determined by an acidimetric method with benzylpenicillin. Microbiological characterization of ESBL enzymes was done by double disc synergy test and the resistance genes TEM and SHV were screened by specific PCR.
Results
ESBL phenotype was detected in 29 isolates (35.5%). The most active antibiotic was imipenem (96.4% as susceptibility rate) followed by ceftriaxone (58.3%) and gentamicin (54.8%). High resistance rates were observed with amoxicillin (92.8%), ampicillin (94%) and trimethoprim/sulfamethoxazole (85.7%). The genotype TEM was predominant in ESBL and non ESBL isolates with respectively 72.4% and 80%. SHV-type beta-lactamase genes occurred in 24.1% ESBL strains and in 18.1% of non ESBL isolates.
Conclusion
This study revealed the presence of ESBL producing Eschericiha coli in Cotonou. It demonstrated also high resistance rate to antibiotics commonly used for infections treatment. Continuous monitoring and judicious antibiotic usage are required.
doi:10.1186/s12941-014-0061-1
PMCID: PMC4304606  PMID: 25595314
Escherichia coli; ESBL; Resistance gene
3.  Epidemiology of CTX-M-type extended-spectrum beta-lactamase (ESBL)-producing nosocomial -Escherichia coli infection in China 
Background
Escherichia coli is one of the most common clinical pathogens causing nosocomial infection. The widespread cefotaxime-beta lactamases (CTX) has increased the multidrug resistance (MDR) of E. coli and has brought great trouble to the doctor treating the infection.
Methods
ESBL-positive E. coli isolates were collected from different hospitals in different areas and the minimal inhibitory concentration (MIC) was analyzed by the agar dilution method. The resistance gene types were detected using polymerase chain reaction (PCR) and the sequence types were determined by multilocus sequence typing (MLST).
Results
We found that the blaCTX-M-1 group and the blaCTX-M-9 group were the main CTX-M gene types, with many kinds of MLST gene types. Except for TEM with high isolate, SHV, OXA and VEB were relatively rare, while no PER and GES was detected. Most strains may have other resistance mechanisms, and the ESBL positive strains have high resistance not only to cephalosporins but also to other kinds of antibiotics.
Conclusion
The study provides wide epidemiological data and enables more effective infection control and treatment plans.
doi:10.1186/s12941-015-0063-7
PMCID: PMC4299296  PMID: 25591816
Escherichia coli; Epidemiology; Extended-spectrum beta-lactamase; Multilocus sequence typing; Nosocomial infection
4.  Molecular identification of non-tuberculous mycobacteria isolated from clinical specimens in Zambia 
Background
The emergence of Acquired Immunodeficiency Syndrome has highlighted the increased incidence and importance of the disease caused by Non-tuberculous Mycobacteria (NTM). While disease due to M. avium-intracellulare complex is apparently common throughout the world, other Non-tuberculous mycobacterial species have been isolated from both immunocompromised and immunocompetent individuals. The increasing number of infections caused by these organisms has made it clinically important to quickly identify mycobacterial species. The diagnosis of a pathogenic versus a non-pathogenic species not only has epidemiological implications but is also relevant to the demands of patient management. Since antibiotic treatment varies according to the species encountered, species identification would reduce the burden of some of these emerging opportunistic pathogens especially in immunocompromised patients and improve their quality of life.
Findings
A total of 91 NTM suspected isolates from four regions of Zambia were included in the study. These isolates were identified using the sequence analysis of the 16S-23S rRNA intergenic transcribed spacer (ITS) region of Mycobacteria.
Fifty-four of the 91 (59%) isolates were identified as NTM and these included M. intracellulare (27.8%), M. lentiflavum (16.7%), M. avium (14.8%), M. fortuitum (7.4%), M. gordonae (7.4%), M. kumamotonense (3.7%), M. indicus pranii (3.7%), M. peregrinum (3.7%), M. elephantis (1.85%), M. flavescens (1.85%), M. asiaticum (1.85%), M. bouchedurhonense (1.85%), M. chimaera (1.85%), M. europaeum (1.85%), M. neourum (1.85%), M. nonchromogenicum (1.5%).
Conclusion
The study has shown that DNA sequencing of the ITS region may be useful in the preliminary identification of NTM species. All species identified in this study were potentially pathogenic.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-014-0059-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-014-0059-8
PMCID: PMC4302154  PMID: 25592857
Non-tuberculous mycobacteria; Identification; Zambia
5.  Prevalence of class 1 and 2 integrons in multi-drug resistant Escherichia coli isolated from aquaculture water in Chaharmahal Va Bakhtiari province, Iran 
Background
Integrons play important role in the spread and maintenance of antimicrobial resistance among strains of Escherichia coli (E. coli) and other species of Enterobacteriaceae. This study investigated the prevalence of class 1 and 2 integrons among E. coli strains isolated from aquaculture water of fish fields in Iran.
Methods
One hundred and fifty water samples from different geographical regions in Chaharmahal Va Bakhtiari province were examined over a 2 months period. Isolation was through culture and biochemical tests. Integrons were identified through polymerase chain reaction (PCR) using oligonucleotide primers specific for class 1 and 2 integrons. Antimicrobial susceptibility testing was carried out using disc diffusion methods.
Results
Eighteen percent of the water samples were positive for E. coli. All the strains were multi-drug resistant; 100% to ciprofloxacin, chloramphenicol, gentamycin, ampicillin and tetracycline and least resistant to imipenem (7.2%). Ten (50%) of the most resistant strains were positive for class 1 (40%) and class 2 (10%).
Conclusions
Escherichia coli in aquaculture in Iran carried integrons class 1 and 2 which could be of public health concern since they could play a role in the spread and maintenance of antimicrobial resistance among bacterial population in the region and should be constantly monitored.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-015-0096-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-015-0096-y
PMCID: PMC4521343  PMID: 26227260
Antimicrobial resistance; Aquaculture; E. coli; Integrons; Iran
6.  Urinary tract infections and antimicrobial sensitivity among diabetic patients at Khartoum, Sudan 
Background
Patients with diabetes mellitus (DM) are more susceptible to urinary tract infection (UTI) than non-diabetics. Due to the emergence of multidrug resistant (MDR) uropathogenic strains, the choice of antimicrobial agent is restricted. This study investigated the epidemiology of UTI, antimicrobial susceptibility, and resistance patterns of bacterial isolates from adult diabetic patients.
Methods
A cross-sectional study was conducted at Khartoum Hospital, Sudan during the period of March − September 2013. Consecutive patients (men and women) were approached to participate in the study, irrespective of UTI symptoms. Socio-demographic and clinical data were obtained from each participant using pre-tested questionnaires. Clean-catch, midstream urine samples were collected and cultured for UTI diagnosis and antimicrobial susceptibility. Symptomatic bacteriuria was defined as a positive urine culture (≥105 colony-forming units [CFU]/mL of a single bacterial species) from patients with symptoms associated with UTI; asymptomatic bacteriuria was defined as a positive urine culture from patients without symptoms associated with UTI.
Results
A total of 200 diabetic patients were enrolled, 121 (60.5%) men and 79 (39.5%) women; 193 (96.5%) had type II DM. The overall prevalence of UTI was 39 (19.5%). Among the total population, 17.1% and 20.9% had symptomatic and asymptomatic bacteriuria, respectively. According to multivariate logistic regression, none of the investigated factors (age, sex, type of DM and duration) were associated with UTI. The predominant isolates were Escherichia coli (22, [56.4%]), and Klebsiella pneumoniae, [9, (23%)]. Eight of 22 E. coli, four of nine K. pneumoniae and one of five Enterococcus faecalis isolates originated from symptomatic patients. Six, four, three, and two of 22 E. coli isolates showed resistance to ampicillin, co-trimoxazole, nitrofurantoin, and amoxicillin-clavulanic acid, respectively. Two, two, one and one of nine K. pneumoniae isolates were resistant to ampicillin, co-trimoxazole, cephalexin, and amoxicillin-clavulanic acid. All 22 E. coli isolates were sensitive (100%) to gentamicin and cephalexin. All nine K. pneumoniae were sensitive to gentamicin (100%) and 88.8% were sensitive to cephalexin.
Conclusion
In Sudan, about one-fifth of diabetic patients have UTI. E. coli is the most frequent isolate followed by K. pneumoniae.
doi:10.1186/s12941-015-0082-4
PMCID: PMC4406170  PMID: 25896611
Diabetes; Urinary tract infection; Bacteriuria; E. coli; K. pneumoniae; Sudan
7.  Prevalence of methicillin-resistant Staphylococcus haemolyticus in companion animals: a cross-sectional study 
Background
Among coagulase-negative staphylococci, Staphylococcus haemolyticus is the second most frequently isolated species from human blood cultures and has the highest level of antimicrobial resistance. This species has zoonotic character and is prevalent both in humans and animals. Recent studies have indicated that methicillin-resistant S. haemolyticus (MRSH) is one of the most frequent isolated Staphylococcus species among neonates in intensive care units. The aim of this study was to determine the presence of MRSH in different groups of companion animals and to characterize isolates according their antimicrobial resistance.
Methods
Samples (n = 754) were collected from healthy and diseased dogs and cats, female dogs in pure-breed kennels, healthy horses, and kennel owners. Classical microbiological tests along with molecular testing including PCR and 16S rRNA sequencing were performed to identify MRSH. Clonality of the isolates was assessed by Pulsed Field Gel Electrophoresis using the SmaI restriction enzyme. Antimicrobial susceptibility testing was performed using the broth micro-dilution method. Detection of genes encoding antimicrobial resistance was performed by PCR. Statistical analysis was performed using the R Project of Statistical Computing, “R 1.8.1” package.
Results
From a total of 754 samples tested, 12 MRSH isolates were obtained. No MRSH were found in horses and cats. Eleven isolates were obtained from dogs and one from a kennel owner. Ten of the dog isolates were detected in pure-breed kennels. The isolates demonstrated the same clonality only within separate kennels.
The most frequent resistances of MRSH isolates was demonstrated to benzylpenicillin (91.7%), erythromycin (91.7%), gentamicin (75.0%), tetracycline (66.7%), fluoroquinolones (41.7%) and co-trimoxazole (41.7%). One isolate was resistant to streptogramins. All isolates were susceptible to daptomycin, rifampin, linezolid and vancomycin. The clone isolated from the kennel owner and one of the dogs was resistant to beta-lactams, macrolides, gentamicin and tetracycline.
Conclusions
Pure-breed kennels keeping 6 or more females were determined to be a risk factor for the presence of MRSH strains. MRSH isolated from companion animals were frequently resistant to some classes of critically important antimicrobials, although they remain susceptible to antibiotics used exclusively in human medicine.
doi:10.1186/s12941-014-0056-y
PMCID: PMC4247881  PMID: 25431281
Staphylococcus haemolyticus; Methicillin-resistance; Kennels; Antimicrobial resistance; Companion animals
8.  Expression of enterotoxin-coding genes in methicillin-resistant Staphylococcus aureus strains isolated from Mexican haemodialysis patients 
Background
Methicillin-resistant Staphylococcus aureus (MRSA) causes severe catheter-related infections in haemodialysis patients ranging from local-site infections and septic thrombophlebitis to bacteraemia but the associated virulence factors and exotoxins remain unclear.
Findings
We employed an in vitro infection model using reconstituted human epithelium (RHE) to analyse the expression profiles of 4 virulence genes and 12 exotoxin-coding virulence genes in 21 MRSA strains isolated from catheter-related infections in 21 Mexican patients undergoing haemodialysis.
All 21 strains (100%) expressed the seg, seh, sei, eta, etb, or hla genes coding staphylococcal toxins. Eleven MRSA strains (52.3%) expressed the sea gene coding staphylococcal enterotoxin A, and two strains (9.5%) expressed the v8 gene coding serine protease. The tst, chp, and arcA genes coding toxic shock syndrome toxin 1, chemotaxis inhibitory protein, and arginine deiminase, respectively, were expressed in separate single strains (4.7%). The most frequent expression profile (42.8% of the strains) comprised seg, seh, sei, eta, etb, and hla.
Conclusion
It is likely that the SEG, SEH, SEI, ETA, ETB, and Hla toxins may play a role in MRSA catheter-related infections. Consideration of these toxins in the development of a vaccine or as targets for monoclonal antibody therapy could provide an improved therapeutic strategy for the treatment of catheter-related infections in haemodialysis patients.
doi:10.1186/s12941-014-0055-z
PMCID: PMC4245768  PMID: 25421262
MRSA, Haemodialysis catheter; Enterotoxins
9.  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
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.  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
12.  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
13.  Application of ATC/DDD methodology to eveluate of antibiotic use in a general hospital in Turkey 
Background
The aim of this study is to evaluate in-house antibiotic use in a state hospital in Turkey with its cost, using the ATC/DDD index, which is an accepted standard method.
Methods
This study was performed as a point prevalence study in a state hospital with 372 beds. All in-house patients using antibiotics on July 19, 2011 were included in the study. Indications for antibiotic use and information about the patients were recorded on special forms. Antibiotic use and cost analysis were evaluated using the ATC/DDD index, which is also suggested by the WHO to be used in similar studies.
Findings
147 patients out of 308 patients who were in-house were identified to use antibiotics with appropriate indications for prophylaxis or treatment in 61% of the patients. The rate of appropriate antibiotic use was identified to be in 78%, while this rate was 38.9% in surgical clinics. The daily cost of the antibiotics consumed on the date of the study was calculated as 4104.79 TL (=2476.80 USD).
Discussion
The rate of inappropriate use of antibiotics seems to be high in our hospital. This will result in both increased costs and also increased nosocomial infection rates with resistant species. Infectious disease specialists should take more active roles in the in-house antibiotic use, hospitals should prepare and implement their own principles of antibiotic use, and microbiology laboratories should be used more effectively. These measures would decrease the conspicuous shortcomings in the antibiotic use.
doi:10.1186/1476-0711-12-23
PMCID: PMC3847134  PMID: 24004538
Antibiotic; ATC/DDD index; Appropriate use of antibiotics
14.  Primary antibiotic resistance and associated mechanisms in Helicobacter pylori isolates from Senegalese patients 
Background
Antibiotic combination therapy for Helicobacter pylori eradication must be adapted to local resistance patterns, but the epidemiology of H. pylori resistance to antibiotics is poorly documented in Africa. The aim was to determine the antibiotic resistance rates, as well as the associated molecular mechanisms, of strains isolated in Dakar, Senegal.
Methods
One hundred and eight H. pylori strains were isolated between 2007 and 2009 from 108 patients presenting with upper abdominal pain to the Gastroenterology Department of Le Dantec Hospital. Antimicrobial susceptibility testing was performed for amoxicillin, clarithromycin, metronidazole, levofloxacin and tetracyclin using the E-test method. Mutations in the 23S rRNA gene of clarithromycin-resistant strains and in gyrA and gyrB of levofloxacin-resistant strains were investigated.
Results
Isolates were characterized by no resistance to amoxicillin (0%), tetracycline (0%), and very low rate of resistance to clarithromycin (1%), but a high rate of resistance to metronidazole (85%). The clarithromycin-resistant strain displayed the A2143G mutation. A worrying rate of levofloxacin resistance was detected (15%). N87I and D91N were the most common mutations in the quinolone-resistance-determining region of gyrA.
Conclusions
The first-line empirical regimen for H. pylori eradication in Senegal should include clarithromycin. Increasing rates of fluoroquinolone resistance detected should discourage the use of levofloxacin-containing regimens without prior antimicrobial susceptibility testing.
doi:10.1186/1476-0711-12-3
PMCID: PMC3552979  PMID: 23298145
Helicobacter pylori; Levofloxacin; Clarithromycin; Antibiotic resistance; Senegal
15.  Sensitization of Candida albicans biofilms to various antifungal drugs by cyclosporine A 
Background
Biofilms formed by Candida albicans are resistant towards most of the available antifungal drugs. Therefore, infections associated with Candida biofilms are considered as a threat to immunocompromised patients. Combinatorial drug therapy may be a good strategy to combat C. albicans biofilms.
Methods
Combinations of five antifungal drugs- fluconazole (FLC), voriconazole (VOR), caspofungin (CSP), amphotericin B (AmB) and nystatin (NYT) with cyclosporine A (CSA) were tested in vitro against planktonic and biofilm growth of C. albicans. Standard broth micro dilution method was used to study planktonic growth, while biofilms were studied in an in vitro biofilm model. A chequerboard format was used to determine fractional inhibitory concentration indices (FICI) of combination effects. Biofilm growth was analyzed using XTT-metabolic assay.
Results
MICs of various antifungal drugs for planktonic growth of C. albicans were lowered in combination with CSA by 2 to 16 fold. Activity against biofilm development with FIC indices of 0.26, 0.28, 0.31 and 0.25 indicated synergistic interactions between FLC-CSA, VOR-CSA, CSP-CSA and AmB-CSA, respectively. Increase in efficacy of the drugs FLC, VOR and CSP against mature biofilms after addition of 62.5 μg/ml of CSA was evident with FIC indices 0.06, 0.14 and 0.37, respectively.
Conclusions
The combinations with CSA resulted in increased susceptibility of biofilms to antifungal drugs. Combination of antifungal drugs with CSA would be an effective prophylactic and therapeutic strategy against biofilm associated C. albicans infections.
doi:10.1186/1476-0711-11-27
PMCID: PMC3508915  PMID: 23035934
Antifungal; Biofilms; Candida albicans; Calcineurine; Drug combination; Cyclosporine A; Drug resistance; Synergism
16.  In vitro antibiotic susceptibility testing of Brucella isolates from Egypt between 1999 and 2007 and evidence of probable rifampin resistance 
Background
Brucellosis poses a significant public health problem in Mediterranean countries, including Egypt. Treatment of this disease is often empirical due to limited information on the antibiotic susceptibility profiles of Brucella spp. in this region of the world. The aim of this study was to determine the antibiotic susceptibility profiles of Brucella blood isolates in Egypt, a country endemic for brucellosis.
Methods
Brucella spp. isolates were identified from the blood cultures of acute febrile illness (AFI) patients presenting to a network of infectious disease hospitals from 1999–2007. Minimum inhibitory concentrations were determined for tetracycline, gentamicin, doxycycline, trimethoprim-sulfamethoxazole, streptomycin, ceftriaxone, ciprofloxacin and rifampin using the E-test. Interpretations were made according to Clinical and Laboratory Standards Institute (CLSI) guidelines.
Results
A total of 355 Brucella spp. isolates were analyzed. All were susceptible to tetracycline, doxycycline, trimethoprim-sulfamethoxazole, streptomycin and ciprofloxacin; probable resistance to rifampin and ceftriaxone was observed among 277 (64%) and 7 (2%) of the isolates, respectively. Percentages of isolates showing probable resistance to rifampin were significantly lower before 2001 than in the following years (7% vs. >81%, p < 0.01).
Conclusions
Despite the high burden of brucellosis in Egypt and frequent empirical treatment, isolates have remained susceptible to the majority of tested antibiotics. However, this is the first report of high rates of probable resistance to rifampin among Brucella isolates from Egypt. Patients should be closely monitored while following standard treatment regimens. Continued surveillance, drug susceptibility studies and updated CLSI interpretive criteria are needed to monitor and update antibiotic prescribing policies for brucellosis.
doi:10.1186/1476-0711-11-24
PMCID: PMC3464789  PMID: 22929054
Brucella; Brucellosis; MIC; Rifampin; Ceftriaxone; E-test; Egypt
17.  Miliary tuberculosis occurred after immunosuppressive drug in PNH patient with completely cured tuberculosis; a case report 
Paroxysmal nocturnal hemoglobinuria (PNH) is a clonal disorder that presents with hemolytic anemia, marrow failure and thrombophilia. During acute attacks, corticosteroid can alleviate the hemolytic paroxysm, but the prolonged administration induces serious toxicity including immunosuppression. So American thoracic society (ATS) for tuberculosis (TB) recommends prophylactic anti-TB medication in patients with a long-term steroid therapy. However, in the patient who was treated for active TB in the past, there are no guidelines of the test for determining patients who have latent TB infection (LTBI) and no recommendations of TB prophylaxis if there is no evidence of reactivation at present. A 40-year-old male patient presented with fever and aggravated weakness for a week. He was diagnosed with PNH a month ago and took corticosteroid for 3 weeks. In the past, he was diagnosed with pulmonary TB and completely cured after treatment. According to guideline, he was not indicated with TB prophylaxis. However, he caught miliary TB, progressed to acute respiratory distress syndrome. We experience this embarrassing case, and emphasize the need to investigate multicentral TB prevalence and to make the guidelines of anti-TB medication in subgroups of hematologic diseases including PNH.
doi:10.1186/1476-0711-11-12
PMCID: PMC3464728  PMID: 22554314
Paroxysmal nocturnal hemoglobinuria; Miliary tuberculosis (TB); Tuberculosis (TB) prophylaxis
19.  Antimicrobial activity of polyhexamethylene guanidine phosphate in comparison to chlorhexidine using the quantitative suspension method 
Background
Polyhexamethylene guanidine phosphate (PHMG-P) belongs to the polymeric guanidine family of biocides and contains a phosphate group, which may confer better solubility, a detoxifying effect and may change the kinetics and dynamics of PHMG-P interactions with microorganisms. Limited data regarding PHMG-P activity against periodontopathogenic and cariogenic microorganisms necessitates studies in this area. Aim is to evaluate polyhexamethylene guanidine phosphate antimicrobial activity in comparison to chlorhexidine.
Methods
Quantitative suspension method was used enrolling Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli and Candida albicans, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Streptococcus mutans and Lactobacillus acidophilus.
Results
Both tested antiseptics at their clinically-used concentrations, of 0.2% (w/v) and 1% (w/v), correspondingly provided swift bactericidal effects against S. aureus, P. aeruginosa, E. coli andC. albicans, A. actinomycetemcomitans and P. gingivalis with reduction factors higher than 6.0. Diluted polyhexamethylene guanidine phosphate and chlorhexidine to 0.05% continued to display anti-bacterial activity and decreased titers of standard quality control, periopathogens to below 1.0 × 103 colony forming units/ml, albeit requiring prolonged exposure time. To achieve a bactericidal effect against S. mutans, both antiseptics at all concentrations required a longer exposure time. We found that a clinically-used 1% of polyhexamethylene guanidine phosphate concentration did not have activity against L. acidophilus.
Conclusion
High RF of polyhexamethylene guanidine phosphate and retention of bactericidal effects, even at 0.05%, support the use of polyhexamethylene guanidine phosphate as a biocide with sufficient anti-microbial activity against periopathogens. Polyhexamethylene guanidine phosphate displayed bactericidal activity against periopathogens and S. mutans and could potentially be applied in the management of oral diseases.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-015-0097-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-015-0097-x
PMCID: PMC4504446  PMID: 26182984
Periodontal disease; Chlorhexidine; Polyhexamethylene guanidine phosphate
20.  Prevalence of tetracycline resistance genes among multi-drug resistant bacteria from selected water distribution systems in southwestern Nigeria 
Background
Antibiotic resistance genes [ARGs] in aquatic systems have drawn increasing attention they could be transferred horizontally to pathogenic bacteria. Water treatment plants (WTPs) are intended to provide quality and widely available water to the local populace they serve. However, WTPs in developing countries may not be dependable for clean water and they could serve as points of dissemination for antibiotic resistant bacteria. Only a few studies have investigated the occurrence of ARGs among these bacteria including tetracycline resistance genes in water distribution systems in Nigeria.
Methodology
Multi-drug resistant (MDR) bacteria, including resistance to tetracycline, were isolated from treated and untreated water distribution systems in southwest Nigeria. MDR bacteria were resistant to >3 classes of antibiotics based on break-point assays. Isolates were characterized using partial 16S rDNA sequencing and PCR assays for six tetracycline-resistance genes. Plasmid conjugation was evaluated using E. coli strain DH5α as the recipient strain.
Results
Out of the 105 bacteria, 85 (81 %) and 20 (19 %) were Gram- negative or Gram- positive, respectively. Twenty-nine isolates carried at least one of the targeted tetracycline resistance genes including strains of Aeromonas, Alcaligenes, Bacillus, Klebsiella, Leucobacter, Morganella, Proteus and a sequence matching a previously uncultured bacteria. Tet(A) was the most prevalent (16/29) followed by tet(E) (4/29) and tet30 (2/29). Tet(O) was not detected in any of the isolates. Tet(A) was mostly found with Alcaligenes strains (9/10) and a combination of more than one resistance gene was observed only amongst Alcaligenes strains [tet(A) + tet30 (2/10), tet(A) + tet(E) (3/10), tet(E) + tet(M) (1/10), tet(E) + tet30 (1/10)]. Tet(A) was transferred by conjugation for five Alcaligenes and two E. coli isolates.
Conclusions
This study found a high prevalence of plasmid-encoded tet(A) among Alcaligenes isolates, raising the possibility that this strain could shuttle resistance plasmids to pathogenic bacteria.
doi:10.1186/s12941-015-0093-1
PMCID: PMC4481114  PMID: 26108344
Tetracycline resistance; Multidrug resistance; Water treatment; 16S rDNA library
21.  Comparative analysis of pulmonary and extrapulmonary tuberculosis of 411 cases 
Background
Tuberculosis is a disease that can involve every organ system. While pulmonary tuberculosis is the most common presentation, extrapulmonary tuberculosis (EPT) is also an important clinical problem. The current study aimed to outline and compare the demographic and clinical features of pulmonary and extrapulmonary tuberculosis cases in adults.
Methods
Medical records of 411 patients (190 women, 221 men) treated between January 2010 and July 2014 in provincial tuberculosis control dispensary was retrospectively reviewed. Demographic and clinical characteristics were compared for pulmonary and extrapulmonary tuberculosis cases.
Results
Of these 411 cases, 208 (50.6 %) had pulmonary tuberculosis (PTB) and 203 were diagnosed with extrapulmonary tuberculosis (EPTB) (49.4 %). The average ages for PTB and EPTB groups were 33.00-27.00 and 31.00-29.75, respectively (p = 0.513). Men were more frequently affected by PTB (59.6 %), while EPTB was more commonly detected in women (52.2 %) (p = 0.016). Main diagnostic modalities for PTB were sputum/smear analyses (72.7 %), clinical-radiological data (21.7 %) and biopsy (6.1 %); while biopsy (71.5 %), sputum/fluid analysis (18.8 %) and clinical-radiological data (4.9 %) were used for confirming EPTB (p < 0.0019). The most common sites of EPTB involvement were lymph nodes (39.4 %), followed by pleura (23.6 %), peritoneum (9.9 %) and bone (7.4 %).
Conclusıons
Extrapulmonary involvement of tuberculosis is common and females are more likely to be affected. Increased clinical awareness is important since atypical presentations of the disease may constitute diagnostic and therapeutic challenges.
doi:10.1186/s12941-015-0092-2
PMCID: PMC4504222  PMID: 26104066
Tuberculosis; Pulmonary; Extrapulmonary; Epidemiology
22.  Point-of-care multiplex PCR promises short turnaround times for microbial testing in hospital-acquired pneumonia – an observational pilot study in critical ill patients 
Background
The early beginning of an adequate antibiotic therapy is crucial in hospital-acquired pneumonia (HAP), but depends on the results of conventional microbiological diagnostics (cMD). It was the aim of this study to evaluate the performance and turnaround times of a new point-of-care multiplex polymerase chain reaction (mPCR) system for rapid identification of pathogens and antibiotic resistance markers. We assessed the applicability of the system under real-life conditions in critical ill patients with HAP.
Methods
We enrolled forty critical ill patients with clinical signs for HAP into an observational study. Two samples of respiratory secretions were collected during one course of aspiration and cMD and mPCR testing (Unyvero, Curetis AG, Holzgerlingen, Germany) were performed immediately. The mPCR device was operated as a point-of-care system at the intensive care unit. We compared turnaround times, results of pathogen identification and results of antibiotic resistance testing of both methods.
Results
Mean turnaround times (min-max) were 6.5 h (4.7–18.3 h) for multiplex PCR and 71 h (37.2–217.8 h) for conventional microbiology (final cMD results, incomplete results neglected). 60 % (n = 24) of the mPCR tests were completely valid. Complete test failure occurred in 10 % (n = 4) and partial test failure occurred in 30 % (n = 12). We found concordant results in 45 % (n = 18) and non-concordant results in 45 % (n = 18) of all patients. 55 % (n = 16) of the results were concordant in patients with a clinical pulmonary infection score (CPIS) > 5 (n = 29). Concordant results included three cases of multidrug resistant bacteria. MPCR frequently detected antibiotic resistance markers that were not found by cMD.
Conclusions
Unyvero allowed point-of-care microbial testing with short turnaround times. The performance of the system was poor. However, an improved system with a more reliable performance and an extended microbial panel could be a useful addition to cMD in intensive care medicine.
Trial registration
ClinicalTrials.gov NCT01858974 (registered 16 May 2013)
doi:10.1186/s12941-015-0091-3
PMCID: PMC4469099  PMID: 26071191
Pneumonia; Point-of-care systems; Microbiological techniques; Multiplex polymerase chain reaction; Molecular diagnostic techniques; Drug resistance
23.  Repurposing FDA approved drugs against the human fungal pathogen, Candida albicans 
Background
The high cost and prolonged timeline of new drug discovery and development are major roadblocks to creating therapies for infectious diseases. Candida albicans is an opportunistic fungal pathogen that is the most common cause of fatal fungal infections in humans and costs $2–4 billion dollars to treat in the US alone.
Methods
To accelerate drug discovery, we screened a library of 1581 existing FDA approved drugs, as well as drugs approved abroad, for inhibitors of C. albicans. The screen was done on YPD yeast growth media as well as on the serum plate assay developed in this study.
Results
We discovered that fifteen drugs, all which were originally approved for treating various infectious and non-infectious diseases, were able to kill Candida albicans. Additionally, one of those drugs, Octodrine, displays wide-spectrum anti-microbial activity. Compared to other selected anti-Candida drugs, Octodrine was shown to be one of the most effective drugs in killing serum-grown Candida albicans without significantly affecting the survival of host macrophages and skin cells.
Conclusions
This approach is useful for the discovery of economically viable new therapies against infectious diseases.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-015-0090-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-015-0090-4
PMCID: PMC4462072  PMID: 26054754
Antifungal; Drug-discovery; Off-label drug use; Small molecules
24.  Simple bedside score to optimize the time and the decision to initiate appropriate therapy for carbapenem-resistant Enterobacteriaceae 
Background
Epidemiological characteristics of patients with bloodstream infections (BSI) due to extended-spectrum β-lactamase producing (ESBL) and carbapenem-resistant (CRE) strains are often similar. Mortality rates for CRE BSI are 70 %, and mean time to initiation of appropriate therapy is ~5 days. A bedside score was developed to differentiate CRE-BSIs from ESBL-BSIs, in order to help decrease the time to initiation of appropriate therapy for CRE and mortality rates.
Findings
Score was developed based of data (2007–2010) abstracted from charts of adult patients from Assaf Harofeh Medical Center (AHMC, Zeriffin, Israel), and validated on a cohort of patients from Detroit Medical Center (DMC, MI, USA). A multivariate model for presence of CRE was generated. A clinical prediction score and ROC curve was derived. 451 patients with ESBL BSIs (285 from AHMC and 166 from DMC) and 74 patients with CRE BSIs (58 from AHMC and 16 from DMC) were included. The prediction score included chemotherapy in the past 3 months (19 points), presence of foreign invasive devices (10 points), no peripheral vascular disease (10 points), reduced consciousness or cognition at time of acute illness (9 points), time in hospital prior to BSI ≥ 3 days (7 points), and age younger than 65 years (6 points). A score of ≥32 to define “high CRE risk” had sensitivity of 59 %, specificity of 76 %, PPV of 34 % and NPV of 90 %.
Conclusions
The score’s 90 % NPV implies it could reduce un-necessary (and toxic) empiric use of anti-CRE therapeutics, but this should be studied prospectively and on broader populations in order to test its potential role in reducing mortality.
doi:10.1186/s12941-015-0088-y
PMCID: PMC4460756  PMID: 26041137
CRE; KPC; ESBL; Prediction score; Nosocomial infection; Multidrug resistant
25.  Ebola virus disease and the veterinary perspective 
Ebola virus disease (EVD) is a potentially fatal haemorrhagic disease of humans. The last and most serious outbreak of Ebola virus (EBOV) started in December 2013 in West Africa and also affected other continents. Animals such as fruit bats and non-human primates are potential sources of EBOV. This review highlights the clinical features of EVD in humans and animals and addresses the public health implications of EVD outbreaks from the veterinary perspective.
doi:10.1186/s12941-015-0089-x
PMCID: PMC4450609  PMID: 26018030
Ebolavirus; Ebolavirus disease; Prevention; Animals; Human and veterinary perspective

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