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1.  Early warning score: a dynamic marker of severity and prognosis in patients with Gram-negative bacteraemia and sepsis 
Background
Early Warning Score (EWS) is a physiological composite score of six bedside vital parameters, routinely used in UK hospitals. We evaluated the prognostic ability of EWS in Gram-negative bacteraemia causing sepsis.
Methods
We prospectively evaluated EWS as a marker of severity and prognosis in adult patients with Gram-negative bacteraemia. All adult patients with Gram-negative bacteraemia admitted to our tertiary Teaching hospital of the National Health Service in England were enrolled over 1 year period. The highest daily EWS score was recorded from 7 days before to 14 days after the date of onset of bacteraemia. The primary outcome was 28-day mortality.
Main results
A total of 245 consecutive adult patients with Gram-negative bacteraemia with sepsis were enrolled. On multivariate analysis, following variables were associated with death for every single unit change (odds ratio in the brackets): higher age (1.05), lower mean arterial pressure (1.03), lower serum bicarbonate (1.08), higher EWS (1.27), higher SOFA score (1.36), hospital-onset of infection (5.43) and need for vasopressor agents (16.4). EWS on day 0, 1, 2, and average 14-day score were significantly higher in patients who died by 28 days from the onset of bacteraemia [95 % CI 0.4–0.6] p < 0.001. A stepwise rise in EWS and failure of improvement in EWS by 2 points 48 h after the onset of bacteraemia were associated with poor outcome.
Conclusion
EWS is a simple and cost-effective bedside tool for the assessment of severity and prognosis of sepsis caused by Gram-negative bacteraemia.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-016-0139-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-016-0139-z
PMCID: PMC4830018  PMID: 27071911
Gram-negative bacteraemia; Early warning score; Clinical outcome
2.  A pilot study to assess bacterial and toxin reduction in patients with Clostridium difficile infection given fidaxomicin or vancomycin 
Background
To assess the effect of fidaxomicin and vancomycin on Clostridium difficile toxins and correlation with clinical and microbiologic outcomes.
Methods
Hospitalized patients with C. difficile infection were randomly assigned a 10-day course of fidaxomicin or vancomycin. Stool samples collected at baseline (day 0), mid-therapy (days 3–5), end of therapy (days 10–13) and follow-up (days 19–38) were assessed for quantity of toxins A and B as well as spore and vegetative cells counts. Correlation of toxins concentrations with microbiologic and clinical findings were evaluated.
Results
Among 34 patients 12 had detectable toxin concentrations at baseline seven were randomized to fidaxomicin and five to vancomycin. Overall both fidaxomicin and vancomycin resulted in drop of both toxins concentrations by midpoint of therapy. The drop in toxin A concentrations was maintained up to the follow-up period with fidaxomicin but not with vancomycin even in patients who developed recurrence. Patients who developed recurrence in the fidaxomicin group had lower concentrations of toxin B versus the recurrence patient of vancomycin group. Presence of vegetative cells and spores was significantly linked with high toxin A (P = 0.003 and <0.001 respectively) and toxin B (P = 0.007 and <0.001 respectively) concentrations across time points. Toxin B concentrations but not A significantly correlated with stool consistency (P < 0.001) and frequency (P = 0.05).
Conclusions
Fidaxomicin was associated with sustained reduction of both toxins up to 30 days post therapy versus vancomycin. Multiple clinical or microbiologic observations were correlated with toxin A or B concentrations.
doi:10.1186/s12941-016-0140-6
PMCID: PMC4830079  PMID: 27071986
Clostridium difficile toxins; Fidaxomicin; Vancomycin; Vegetative cells
3.  Comparison of Clinical Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing guidelines for the interpretation of antibiotic susceptibility at a University teaching hospital in Nairobi, Kenya: a cross-sectional study 
Background
The Clinical Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines are the most popular breakpoint guidelines used in antimicrobial susceptibility testing worldwide. The EUCAST guidelines are freely available to users while CLSI is available for non-members as a package of three documents for US $500 annually. This is prohibitive for clinical microbiology laboratories in resource poor settings. We set out to compare antibiotic susceptibility determined by the two guidelines to determine whether adoption of EUCAST guidelines would significantly affect our susceptibility patterns.
Methods
We reviewed minimum inhibitory concentrations (MIC) of various antibiotics routinely reported for Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Pseudomonas aeruginosa (P. aeruginosa) isolates from an automated microbiology identification system (VITEK-2) at the Aga Khan University Hospital Nairobi’s Pathology department. These MICs were then analyzed using both CLSI 2015 and EUCAST 2015 guidelines and classified as resistant, intermediate or susceptible. We compared the susceptibility and agreement between the CLSI and EUCAST categorizations.
Results
Susceptibility data from a total of 5165 E. coli, 1103 S. aureus and 532 P. aeruginosa isolates were included. The concordance rates of the two guidelines for E. coli, S. aureus and P. aeruginosa ranged from 78.2 to 100 %, 94.6 to 100 % and 89.1 to 95.5 % respectively. The kappa statistics for E. coli MICs revealed perfect agreement between CLSI and EUCAST for cefotaxime, ceftriaxone and trimethoprim–sulfamethoxazole, almost perfect agreement for ampicillin, ciprofloxacin, cefuroxime, gentamicin and ceftazidime, substantial agreement for meropenem, moderate agreement for cefepime and amoxicillin-clavulanate, fair agreement for nitrofurantoin and poor agreement for amikacin. For S. aureus the kappa statistics revealed perfect agreement for penicillin, trimethoprim–sulfamethoxazole, levofloxacin, oxacillin, linezolid and vancomycin, almost perfect agreement for clindamycin, erythromycin and tetracycline and moderate agreement for gentamicin. For P. aeruginosa the kappa analysis revealed moderate to almost perfect agreement for all the anti-pseudomonal antibiotics.
Conclusion
The results show comparable antibiotic susceptibility patterns between CLSI and EUCAST breakpoints. Given that EUCAST guidelines are freely available, it makes it easier for laboratories in resource poor settings to have an updated and readily available reference for interpreting antibiotic susceptibilities.
doi:10.1186/s12941-016-0135-3
PMCID: PMC4827198  PMID: 27068515
European Committee on Antimicrobial Susceptibility Testing (EUCAST); Clinical Laboratory Standards Institute (CLSI); Antimicrobial susceptibility testing (AST); Minimum inhibitory concentrations (MIC)
4.  Phenotypic and genotypic characteristics of carbapenem-resistant Enterobacteriaceae in a tertiary-level reference hospital in Turkey 
Background
Enterobacteriaceae are among the most common pathogens that are responsible for serious community-acquired, hospital-acquired, and health-care associated infections. The emergence and spread of carbapenem-resistant Enterobacteriaceae (CRE) have become an increasing concern for healthcare services worldwide. Infections caused by these bacteria have been associated with significant morbidity and mortality and treatment options have been limited. The rapid and accurate detection of carbapenem resistance in these bacteria is important for infection control. The aim of this study was to investigate the phenotypic and genotypic features of CRE strains isolated in a tertiary-level reference hospital in Turkey.
Methods
A total of 181 CRE strains were included in the study. Antimicrobial susceptibility rates were tested using Vitek 2 system. Modified Hodge test (MHT) was performed using meropenem and ertapenem discs. Metallo-β-lactamase antimicrobial gradient test (E-test MBL strips) were used for evaluation of metallo-β-lactamase production. A multiplex PCR was used for detection of carbapenems resistance genes (IMP, VIM, KPC, NDM-1 and OXA-48).
Results
The OXA-48 gene was detected in 86 strains, NDM-1 gene in six strains, VIM gene in one strain. IMP and KPC genes were not identified. Three strains produced both OXA-48 and NDM-1 and one strain produced both OXA-48 and VIM. In two patients more than one genus of OXA-48 positive CREs was isolated. Ninety-two of the isolates were multidrug-resistant. One hundred and ten isolates were MHT with meropenem (MEM-MHT) positive and 109 isolates were MHT with ertapenem (ERT-MHT) positive. Nine of the isolates were positive with E-test MBL strips. The sensitivity of MEM-MHT and ERT-MHT for detection of OXA-48 was 70.9 and 70.6 %, respectively. MEM-MHT was found highly discriminative for OXA-48 Escherichia coli (p < 0.001). The sensitivity of E-test MBL for NDM-1 was 66.7 %. A statistically significant correlation was observed between OXA-48 gene and MHT positivity and between NDM-1, VIM gene and E-test MBL positivity (p < 0.001).
Conclusions
OXA-48 gene is spreading rapidly to many different species of Enterobacteriaceae in the hospital environment. While OXA-48 is still the most common source of carbapenem resistance in Enterobacteriaceae in our country, NDM-1 is increasingly being isolated from patients without a history of foreign contact.
doi:10.1186/s12941-016-0136-2
PMCID: PMC4822248  PMID: 27048322
Enterobacteriaceae; Carbapenem resistance; OXA-48; NDM-1; VIM; Modified Hodge test; Multiplex PCR; Multidrug resistance
5.  Antimicrobial activity of mul-1867, a novel antimicrobial compound, against multidrug-resistant Pseudomonas aeruginosa 
Background
There is an urgent need for new antimicrobial compounds to treat various lung infections caused by multidrug-resistant Pseudomonas aeruginosa (MDR-PA).
Methods
We studied the potency of Mul-1867 against MDR-PA isolates from patients with cystic fibrosis, chronic obstructive pulmonary disease, and ventilator-associated pneumonia. The minimal inhibitory concentrations (MICs) and minimum biofilm eliminating concentrations (MBECs), defined as the concentrations of drug that kill 50 % (MBEC50), 90 % (MBEC90), and 100 % (MBEC100) of the bacteria in preformed biofilms, were determined by using the broth macrodilution method.
Results
Mul-1867 exhibited significant activity against MDR-PA and susceptible control strains, with MICs ranging from 1.0 to 8.0 µg/mL. Mul-1867 also possesses anti-biofilm activity against mucoid and non-mucoid 24-h-old MDR-PA biofilms. The MBEC50 value was equal to onefold the MIC. The MBEC90 value ranged from two to fourfold the MIC. Moreover, Mul-1867 completely eradicated mature biofilms at the concentrations tested, with MBEC100 values ranging between 16- and 32-fold the MIC. Mul-1867 was non-toxic to Madin-Darby canine kidney (MDCK) cells at concentrations up to 256 µg/mL.
Conclusion
Overall, these data indicate that Mul-1867 is a promising locally acting antimicrobial for the treatment and prevention of P. aeruginosa infections.
doi:10.1186/s12941-016-0134-4
PMCID: PMC4802586  PMID: 27001074
Biofilms; Mucoid; Non-mucoid; Multidrug-resistant; P. aeruginosa; Cystic fibrosis
6.  Real-world daptomycin use across wide geographical regions: results from a pooled analysis of CORE and EU-CORE 
Background
Pooled data from two large registries, Cubicin® Outcomes Registry and Experience (CORE; USA) and European Cubicin® Outcomes Registry and Experience (EU-CORE; Europe, Latin America, and Asia), were analyzed to determine the characteristics and clinical outcomes of daptomycin therapy in patients with Gram-positive infections across wide geographical regions.
Methods
Patients receiving at least one dose of daptomycin between 2004 and 2012 for the treatment of Gram-positive infections were included. Clinical success was defined as an outcome of ‘cured’ or ‘improved’. Post-treatment follow-up data were collected for a subset of patients (CORE: osteomyelitis and orthopedic foreign body device infection; EU-CORE: endocarditis, intracardiac/intravascular device infection, osteomyelitis, and orthopedic device infection). Safety was assessed for up to 30 days after daptomycin treatment.
Results
In 11,557 patients (CORE, 5482; EU-CORE, 6075) treated with daptomycin (median age, 62 [range, 1–103] years), the most frequent underlying conditions were cardiovascular disease (54.7 %) and diabetes mellitus (28.0 %). The most commonly treated primary infections were complicated skin and soft tissue infection (cSSTI; 31.2 %) and bacteremia (21.8 %). The overall clinical success rate was 77.2 % (uncomplicated SSTI, 88.3 %; cSSTI, 81.0 %; osteomyelitis, 77.7 %; foreign body/prosthetic infection (FBPI), 75.9 %; endocarditis, 75.4 %; and bacteremia, 69.5 %). The clinical success rate was 79.1 % in patients with Staphylococcus aureus infections (MRSA, 78.1 %). An increasing trend of high-dose daptomycin (>6 mg/kg/day) prescribing pattern was observed over time. Clinical success rates were higher with high-dose daptomycin treatment for endocarditis and FBPI. Adverse events (AEs) and serious AEs possibly related to daptomycin therapy were reported in 628 (5.4 %) and 133 (1.2 %) patients, respectively.
Conclusions
The real-world data showed that daptomycin was effective and safe in the treatment of various Gram-positive infections, including those caused by resistant pathogens, across wide geographical regions.
doi:10.1186/s12941-016-0130-8
PMCID: PMC4791778  PMID: 26976128
CORE; Daptomycin; Efficacy; EU-CORE; Gram-positive infections; High dose; MRSA; Real-world; Safety; Staphylococcus aureus
7.  Can one size fit all? Approach to bacterial vaginosis in sub-Saharan Africa 
Bacterial vaginosis (BV) is the most common vaginal disorder affecting women of reproductive age and is associated with increased risk of sexually transmitted infections such as human immunodeficiency syndrome (HIV-1). Sub-Saharan Africa has the highest BV and HIV-1 burden and yet very few studies have focused on understanding the aetiology of BV and its association with HIV in this region. It has been suggested that we need to accurately diagnose and treat BV to lower the risk of HIV infection globally. However, effective diagnosis requires knowledge of what constitutes a “healthy” cervicovaginal microbiome and current studies indicate that Lactobacillus crispatus might not be the only commensal protective against BV: healthy women from different countries and ethnicities harbour alternative commensals. Microbiotas associated with BV have also shown global variation, further complicating effective diagnosis via culture-based assays as some species are difficult to grow. Antibiotics and probiotics have been suggested to be key in controlling BV infection, but the efficacy of this treatment might rely on reconstituting endogenous commensals while targeting a specific species of BV-associated bacteria (BVAB). Alternatively, therapy could inhibit essential BV bacterial growth factors e.g. sialidases or provide anti-microbial compounds e.g. lactic acid associated with a healthy cervicovaginal microbiome. But without global investigation into the mechanism of BV pathogenesis and its association with HIV, selection of such compounds could be limited to Caucasian women from certain regions. To confirm this suggestion and guide future therapy we require standardised diagnostic assays and research methodologies. This review will focus on research papers that describe the global variation of BV aetiology and how this influences the identification of determinants of BV pathogenesis and potential probiotic and antimicrobial therapy.
doi:10.1186/s12941-016-0132-6
PMCID: PMC4787044  PMID: 26968525
Bacterial vaginosis; Sub-Saharan Africa; HIV; Aetiology
8.  Parasitic contamination of fresh vegetables sold at central markets in Khartoum state, Sudan 
Background
Fresh vegetables are considered as vital nutrients of a healthy diet as they supply the body with essential supplements. The consumption of raw vegetables is the main way for transmission of intestinal parasitic organisms. This study was aimed at detecting the parasitic contamination in fresh vegetables sold in two central open-aired markets in Khartoum state, Sudan.
Methods
In this prospective cross-sectional study, a total of 260 fresh vegetable samples and 50 water samples used to sprinkle vegetable(s) were collected from two central open-aired markets (namely; Elshaabi and Central markets) during November 2011 to May 2012. The samples were microscopically examined for detection of parasitic life forms using standardized parasitological techniques for protozoans and helminthes worms.
Results
Of the 260 fresh vegetable samples, 35 (13.5 %) were microscopically positive for intestinal parasites whereas 7/50 (14 %) of water samples used to sprinkle vegetable(s) were found positives. Remarkably, high level of contamination in fresh vegetable samples was recorded in lettuce (Lactuca sativa) 36.4 % (4/11) while cayenne pepper (Capsicum annuum) and cucumber (Cucumis sativus) were not contaminated. The identified protozoans and helminthes were Entamoeba histolytica/dispar, Entamoeba coli, Giardia lamblia, Ascaris lumbricoides, Strongyloides stercoralis, T. trichiura and hookworms. The most predominant parasite encountered was E. histolytica/dispar (42.9 %) whereas both T. trichiura and A. lumbricoides (2.9 %) were the least detected parasites. None of the fresh vegetables had single parasitic contamination. The highest percentages found in water samples used to sprinkle vegetable(s) was for Strongyloides larvae 60 % (3/5). It is worth-mentioned that the rate of contamination in Elshaabi market was higher compared with Central market. However, there was no significant correlation between the type of vegetables and existence of parasites in both markets and a high significant relationship was observed between the type of parasite and total prevalence in fresh vegetables (p = 0.000).
Conclusion
The study has identified a moderate rate of fresh vegetables contaminated with protozoan and helminthes. Contaminated fresh vegetables in central markets of Khartoum state may play a significant role in transmission of intestinal parasitic infections to humans, and the water used by greengrocers to sprinkle vegetable(s) can be implicated in vegetable contamination.
doi:10.1186/s12941-016-0133-5
PMCID: PMC4788893  PMID: 26968696
Parasitic contamination; Fresh vegetables; Intestinal parasites; Khartoum; Sudan
9.  Community acquired fungemia caused by Candida pulcherrima: diagnostic contribution of MALDI-TOF mass spectrometry 
Background
Community-onset candidemia constitute a distinct clinical entity the incidence of which is increasing. Contribution of non-albicans Candida species is rising.
Case presentation
We describe here the first reported case of community acquired fungemia due to Candida pulcherrima. Identification to the species level was performed by MALDI-TOF mass spectrometry. Treatment with fluconazole was successful.
Conclusion
This case confirms the pathogenic role of C. pulcherrima and the contribution of MALDI-TOF mass spectrometry for identification of rare Candida species.
doi:10.1186/s12941-016-0129-1
PMCID: PMC4782459  PMID: 26951431
Fungemia; Candida pulcherrima; Mass spectrometry
10.  In vitro selection of Staphylococcus aureus mutants resistant to tigecycline with intermediate susceptibility to vancomycin 
Background
Tigecycline (TIG) is an antibiotic belonging to the glycylcyclines class and appears to be a good choice to fight infections caused by Staphylococcus aureus. To date, TIG exhibits good activity against this microorganism. The aim of this work was to obtain in vitro mutants of S. aureus resistant to TIG and evaluate possible changes in their susceptibility patterns to other antibiotics.
Results
Two mutants of S. aureus resistant to TIG (MIC = 16 µg/mL) were selected in vitro from clinical isolates of methicillin-resistant S. aureus. In both mutants, corresponding to different lineage (ST5 and ST239), an increase of efflux activity against TIG was detected. One mutant also showed a reduced susceptibility to vancomycin, corresponding to the VISA phenotype (MIC = 4 µg/mL), with a loss of functionality of the agr locus. The emergence of the VISA phenotype was accompanied by an increase in oxacillin and cefoxitin MICs.
Conclusions
This study demonstrates that, under selective pressure, the increase of efflux activity in S. aureus is one of the mechanisms that may be involved in the emergence of tigecycline resistance. The emergence of this phenotype may eventually be associated to changes in susceptibility to other antibiotics such oxacillin and vancomycin.
doi:10.1186/s12941-016-0131-7
PMCID: PMC4782574  PMID: 26956508
MRSA; Tigecycline resistant; Efflux activity; VISA
12.  Characterization of Pseudomonas aeruginosa with discrepant carbapenem susceptibility profile 
Pseudomonas aeruginosa is the most common nosocomial pathogen, notorious for its multidrug resistance and causes life threatening infections. Carbapenems were considered as the last resort of drugs for the treatment of multi drug resistant P. aeruginosa infections. The emergence of resistance to carbapenems limits its use for treatment. Unlike other organisms, in P. aeruginosa intrinsic/chromosomal mediated resistance mechanisms plays a major role for carbapenem resistance rather than the carbapenemases. Carbapenemase producing organisms becomes resistant to both imipenem and meropenem. However, in our clinical settings, we have observed rare carbapenem resistant phenotypes such as imipenem resistant but meropenem susceptible (IRMS) and meropenem resistant but imipenem susceptible (MRIS) phenotypes. Thus we have chosen these rare phenotypes to look for the respective resistance mechanisms by phenotypic and molecular methods. From this study we found that, IRMS is primarily due to the mutations across various regions in the loops of oprD gene and MRIS is due to the over expression of mexAB efflux pumps. This study results confirms that, this rare phenotypes are due to the intrinsic/chromosomal mediated mechanisms, which occurred due to the antibiotic selection pressure. This study also provided data concerning alterations in outer membrane permeability which is often associated with the increased levels of antibiotic efflux. Consequently, this study provided the prevalence of the various resistance mechanisms that have deployed by the organism to resist antibiotics through different phenotypes.
doi:10.1186/s12941-016-0127-3
PMCID: PMC4765188  PMID: 26911874
Carbapenems; Pseudomonas aeruginosa; Porins; Efflux
13.  Is inhaled colistin beneficial in ventilator associated pneumonia or nosocomial pneumonia caused by Acinetobacter baumannii? 
Background
In the present study, our objective was to evaluate and compare the clinical and microbiological results in patients receiving systemic and systemic plus inhaled colistin therapy due to nosocomial pneumonia (NP) or ventilator associated pneumonia (VAP) caused by Acinetobacter baumannii.
Methods
A retrospective matched case–control study was performed at the ICUs at Izmir Katip Celebi University Ataturk Training and Research Hospital from January 2013 to December 2014. Eighty patients who received only systemic colistin were matched 43 patients who received systemic colistin combined with inhaled therapy.
Results
In 97.6 % of the patients colistin was co-administered with at least one additional antibiotic. The most frequently co-administered antibiotics were carbapenems (79.7 %). The patient groups did not differ significantly in terms of the non-colistin antibiotics used for treatment (p > 0.05). Acute renal injury was observed in 53.8 % and 48.8 % of the patients who received parenteral colistin or parenteral plus inhaler colistin, respectively (p = 0.603). There were no significant differences between the groups in terms of clinical success (p = 0.974), clinical failure (p = 0.291), or recurrence (p = 0.094). Only, a significantly higher partial clinical improvement rate was observed in the systemic colistin group (p = 0.009). No significant differences between the two groups in terms of eradication (p = 0.712), persistence (p = 0.470), or recurrence (p = 0.356) rates was observed. One-month mortality rate was similar in systemic (47.5 %) and systemic plus inhaled (53.5 %) treatment groups (p = 0.526).
Conclusions
Our results suggest that combination of inhaled colistin with intravenous colistin had no additional therapeutic benefit in terms of clinical or microbiological outcomes.
doi:10.1186/s12941-016-0123-7
PMCID: PMC4765191  PMID: 26911714
14.  Outbreak of plasmid-mediated NDM-1-producing Klebsiella pneumoniae ST105 among neonatal patients in Yunnan, China 
Background
In the past decade, the carbapenemase-producing Enterobacteriaceae (CPE) have been reported worldwide. Emergence of carbapenemase-producing strains among Enterobacteriaceae has been a challenge for treatment of clinical infection. The present study was undertaken to investigate the characteristics of carbapenem-resistant Klebsiella pneumoniae recovered from an outbreak that affected 17 neonatal patients in neonatal intensive care unit (NICU) of Kunming City Maternal and Child health Hospital, which is located in the Kunming city in far southwest of China.
Methods
Minimum inhibitory concentrations (MICs) for antimicrobial agents were determined according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI); Modified Hodge test and Carba-NP test were preformed to identified the phenotypes of carbapenemases producing; To determine whether carbapenem resistance was transferable, a conjugation experiment was carried out in mixed broth cultures; Resistant genes were detected by using PCR and sequencing; Plasmids were typed by PCR-based replicon typing method; Clone relationships were analyzed by using multilocus-sequence typing (MLST) and pulsed field gel electrophoresis (PFGE).
Results
Eighteen highly carbapenem-resistant Klebsiella pneumoniae were isolated from patients in NICU and one carbapenem-resistant K. pneumoniae isolate was detected in incubator water. All these isolates harbored blaNDM-1. Moreover, other resistance genes, viz., blaIMP-4, blaSHV-1, blaTEM-1, blaCTX-M-15, qnrS1, qnrB4, and aacA4 were detected. The blaNDM-1 gene was located on a ca. 50 kb IncFI type plasmid. PFGE analysis showed that NDM-1-producing K. pneumoniae were clonally related and MLST assigned them to sequence type 105.
Conclusions
NDM-1 producing strains present in the hospital environment pose a potential risk and the incubator water may act as a diffusion reservoir of NDM-1- producing bacteria. Nosocomial surveillance system should play a more important role in the infection control to limit the spread of these pathogens.
doi:10.1186/s12941-016-0124-6
PMCID: PMC4761218  PMID: 26896089
CPE; NDM-1; ST105; China
15.  Toxigenic profile of methicillin-sensitive and resistant Staphylococcus aureus isolated from special groups 
Background
Staphylococcus aureus is characterized by its pathogenicity and high prevalence, causing disease in both healthy and immunocompromised individuals due to its easy dissemination. This fact is aggravated by the widespread dissemination of S. aureus carrying toxigenic genes. The objective of this study was to determine the toxigenic profile of methicillin-sensitive S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) in patients with purulent skin and/or soft tissue infections seen at the Dermatology Department of the University Hospital of the Botucatu Medical School, asymptomatic adults older than 60 years living in nursing homes, and prison inmates of the Avaré Detention Center.
Methods
PCR was used for the detection of the mecA gene, enterotoxin genes (sea, seb, and sec), exfoliative toxins A and B (eta and etb), toxic shock syndrome toxin 1 (tst), panton–valentine leukocidin (lukS-PV and lukF-PV), and alpha- and delta-hemolysins or cytotoxins (hla and hld).
Results
The results showed a significant prevalence of toxigenic genes among S. aureus isolates from asymptomatic individuals, with the observation of a higher prevalence of cytotoxin genes. However, the panton–valentine leukocidin gene was only detected in MSSA isolated from patients with skin infections and the tst gene was exclusively found in MSSA isolated from prison inmates.
Conclusions
The present study demonstrated a significant prevalence of toxigenic genes in MSSA and MRSA strains isolated from asymptomatic S. aureus carriers. There was a higher prevalence of cytotoxin genes.
doi:10.1186/s12941-016-0125-5
PMCID: PMC4754922  PMID: 26880287
Staphylococcus aureus; MSSA; Toxins; Cytotoxins
16.  Intravenous Colistin in the treatment of multidrug-resistant Acinetobacter in neonates 
Background
Neonatal sepsis caused by multidrug-resistant gram-negative bacteria has been reported in different parts of the world. It is a major threat to neonatal care, carrying a high rate of morbidity and mortality. While Colistin is the treatment of choice, few studies have reported its use in neonatal patients.
Methods
A retrospective descriptive study of all neonatal patients who had multidrug-resistant Acinetobacter sepsis and were treated with Colistin over a 2-year period. Patients’ charts and hospital laboratory data were reviewed.
Results
During the study period, 21 newborns were treated with Colistin. All had sepsis evident by positive blood culture and clinical signs of sepsis. The median gestational age and birth weight were 33 weeks (26–39) and 1700 g (700–3600), respectively. Nine (43 %) were very low birth weight infants. Eighteen (86 %) were preterm infants. Nineteen (91 %) newborns survived. No renal impairment is documented in any of our patients. Fourteen (67 %) of our patients had elevated eosinophil counts following Colistin treatment, for those patients, the average eosinophilic counts ± standard deviation before and after Colistin therapy were 149.08 ± 190.38 to 1193 ± 523.29, respectively, with a p value of less than 0.0001.
Conclusion
Our study showed that Colistin was both effective and safe for treating multidrug-resistant Acinetobacter neonatal sepsis. This is a retrospective study. No universal protocol was used for the patients. The factors that might affect the response or cause side effects are difficult to evaluate.
doi:10.1186/s12941-016-0126-4
PMCID: PMC4751699  PMID: 26868136
Colistin; Sepsis; Neonate; Multidrug-resistant Acinetobacter; Eosinophilia
17.  The carbapenem-resistant Enterobacteriaceae threat is growing: NDM-1 epidemic at a training hospital in Turkey 
Background
Recently, new carbapenemases in Enterobacteriaceae strains and non-fermentative gram-negative bacilli have been reported. The New Delhi metallo‐β‐lactamase-1 (NDM-1) is a major problem around the world. The purpose of this article is to address the NDM-1 Klebsiella pneumoniae epidemic detected in eight cases in our hospital.
Methods
Bacteria identified in this epidemic were from patients already admitted to the intensive care unit of the Sakarya University Training and Research Hospital during efforts toward establishment of infection surveillance and control program. Antimicrobial susceptibility testing of strains was performed using the VITEK 2 system (bioMérieux, France), E-test gradient strips (bioMérieux, France), and the disc diffusion test. For the metallo-beta-lactamase activity, the combined disc diffusion test and modified Hodge test as phenotypic tests were performed. To identify the resistance gene, the Xpert Carba-R kit (Cepheid Inc., USA) and an in-house multiplex polymerase chain reaction (PCR) method designed for five common carbapenemase genes (IMP, VIM, KPC, NDM-1, and OXA-48) were employed. The clonal relationship of these strains was explored by the repetitive PCR (rep-PCR, DiversiLab System, bioMérieux, France) method.
Results
During the December 2014 to March 2015 period, NDM-1 positive K. pneumoniae strains were detected in eight patients. All of these strains were found to produce NDM-1, while two of them also revealed the presence of OXA‐48. The rep-PCR results reveal a clonal proximity of 95 % for six of the eight strains.
Conclusions
Our findings suggest the tendency of NDM-1-producing strains to spread in our country as well. A carbapenem-resistant K. pneumoniae threat may pose a great risk to our country. It is clear that more comprehensive infection control precautions should be implemented in our hospitals.
doi:10.1186/s12941-016-0118-4
PMCID: PMC4748493  PMID: 26860360
Carbapenemase; Multidrug resistance; Enterobacteriaceae; Antibiotic resistance
18.  Mortality predictors of Staphylococcus aureus bacteremia: a prospective multicenter study 
Background
Staphylococcus aureus is one of the causes of both community and healthcare-associated bacteremia. The attributable mortality of S. aureus bacteremia (SAB) is still higher and predictors for mortality and clinical outcomes of this condition are need to be clarified. In this prospective observational study, we aimed to examine the predictive factors for mortality in patients with SAB in eight Turkish tertiary care hospitals.
Methods
Adult patients with signs and symptoms of bacteremia with positive blood cultures for S. aureus were included. All data for episodes of SAB including demographics, clinical and laboratory findings, antibiotics, and outcome were recorded for a 3-year (2010–2012) period. Cox proportional hazard model with forward selection was used to assess the independent effect of risk factors on mortality. A 28-day mortality was the dependent variable in the Cox regression analysis.
Results
A total of 255 episodes of SAB were enrolled. The median age of the patients was 59 years. Fifty-five percent of the episodes were considered as primary SAB and vascular catheter was the source of 42.1 %. Healthcare associated SAB was defined in 55.7 %. Blood cultures yielded methicillin-resistant S. aureus (MRSA) as a cause of SAB in 39.2 %. Initial empirical therapy was inappropriate in 28.2 %. Although overall mortality was observed in 52 (20.4 %), 28-day mortality rate was 15.3 %. Both the numbers of initial inappropriate empirical antibiotic treatment and the median hours to start an appropriate antibiotic between the cases of fatal outcome and survivors after fever onset were found to be similar (12/39 vs 60/216 and 6 vs 12 h, respectively; p > 0.05). High Charlson comorbidity index (CCI) score (p = 0.002), MRSA (p = 0.017), intensive care unit (ICU) admission (p < 0.001) and prior exposure to antibiotics (p = 0.002) all were significantly associated with mortality. The Cox analysis defined age [Hazard Ratio (HR) 1.03; p = 0.023], ICU admission (HR 6.9; p = 0.002), and high CCI score (HR 1.32; p = 0.002) as the independent predictive factors mortality.
Conclusions
The results of this prospective study showed that age, ICU stay and high CCI score of a patient were the independent predictors of mortality and MRSA was also significantly associated with mortality in SAB.
doi:10.1186/s12941-016-0122-8
PMCID: PMC4748515  PMID: 26860463
Staphylococcus aureus; Bacteremia; Risk factors; Mortality; Sepsis
19.  MALDI-TOF MS based carbapenemase detection from culture isolates and from positive blood culture vials 
Background
Antibiotic resistance in bacteria leads to massive health problems. Incidence of carbapenem and multidrug resistance in Gram-negative bacteria are increasing globally and turn out to be a very urgent challenge in health care. Resistant bacteria play an important clinical role during hospital outbreaks as well as in sepsis. Rapid diagnostic tests are necessary to provide immediate information for antimicrobial treatment and infection control measures.
Methods
Our mass spectrometry-based assay was validated with 63 carbapenemase-producing Gram-negative bacterial isolates, and 35 carbapenem-resistant Gram-negative species with no carbapenemase production. These were analyzed from solid culture media and positive blood culture vials. After 4 h of incubation the carbapenemase products were analyzed with the MALDI-TOF MS. All the isolates were genotyped for carbapenemase genes by PCR and sequencing.
Results
For culture isolates the concordance of hydrolysis assay to genetic results was 98 % for OXA variants, KPC, VIM, IMP, GIM, and NDM. In contrast, only 14 of 29 Acinetobacter baumannii isolates carrying the OXA and NDM genes could be identified from blood culture. However, from blood culture vials our method allowed the detection of carbapenemases in 98 % of Pseudomonas and Enterobacteriaceae isolates harboring different genes.
Conclusions
This MALDI-TOF MS–based assay permitted the detection of carbapenemases either from solid culture media (98–100 %) or blood culture vials (96 %) for all non-A. baumannii isolates within 4 h. In case of A. baumannii isolates the assay was highly sensitive for the detection of carbapenemases directly from solid culture media.
doi:10.1186/s12941-016-0120-x
PMCID: PMC4736273  PMID: 26839024
MALDI-TOF MS; Carbapenemases; Acinetobacter baumannii; MDR Gram-negative bacteria; Hydrolysis
20.  The evaluation and application of multilocus variable number tandem repeat analysis (MLVA) for the molecular epidemiological study of Salmonella enterica subsp. enterica serovar Enteritidis infection 
Background
Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the most prevalent Salmonella serotypes that cause gastroenteritis worldwide and the most prevalent serotype causing Salmonella infections in China. A rapid molecular typing method with high throughput and good epidemiological discrimination is urgently needed for detecting the outbreaks and finding the source for effective control of S. Enteritidis infections.
Methods
In this study, 194 strains which included 47 from six outbreaks that were well-characterized epidemiologically were analyzed with pulse field gel electrophoresis (PFGE) and multilocus variable number tandem repeat analysis (MLVA). Seven VNTR loci published by the US Center for Disease Control and Prevention (CDC) were used to evaluate and develop MLVA scheme for S. Enteritidis molecular subtyping by comparing with PFGE, and then MLVA was applied to the suspected outbreaks detection. All S. Enteritidis isolates were analyzed with MLVA to establish a MLVA database in Shenzhen, Guangdong province, China to facilitate the detection of S. Enteritidis infection clusters.
Results
There were 33 MLVA types and 29 PFGE patterns among 147 sporadic isolates. These two measures had Simpson indices of 0.7701 and 0.8043, respectively, which did not differ significantly. Epidemiological concordance was evaluated by typing 47 isolates from six epidemiologically well-characterized outbreaks and it did not differ for PFGE and MLVA. We applied the well established MLVA method to detect two S. Enteritidis foodborne outbreaks and find their sources successfully in 2014. A MLVA database of 491 S. Enteritidis strains isolated from 2004 to 2014 was established for the surveillance of clusters in the future.
Conclusions
MLVA typing of S. Enteritidis would be an effective tool for early warning and epidemiological surveillance of S. Enteritidis infections.
Electronic supplementary material
The online version of this article (doi:10.1186/s12941-016-0119-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12941-016-0119-3
PMCID: PMC4731957  PMID: 26823185
S. Enteritidis; MLVA; PFGE; Epidemiological study
21.  Prevalence and characterization of extended-spectrum beta-lactamases producing Enterobacteriaceae in healthy children and associated risk factors 
Background
Community acquired infections due to extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) had been increased. The fecal flora of children in the community represents a huge potential reservoir for ESBLs which are located on highly transmissible plasmids. This study examined the prevalence of ESBL-PE fecal carriage, antimicrobial susceptibility pattern, possible risk factors, and characterized the genes encoding these ESBL enzymes in Lebanese children community.
Methods
A total of 125 rectal swabs were taken from healthy children aged from 1 to 5 years. Detection of ESBLs was carried out using combination-disc method test and multiplex PCR. A questionnaire concerning child’s lifestyle and risk factors for ESBL carriage was illustrated.
Results
Thirty-one of 125 participants (24.8 %) carried ESBL-PE. Regular consumption of meat, and chicken were significantly associated with high carriage rate of ESBL-PE, while dairy products (milk, yogurt, cheese) association was non-significant. Intimate hygiene habits were found also affecting the carriage rate. Multiple bla genes were the most common, 48.4 % (15/31) of ESBL-PE carried both blaCTX-M and blaTEM, and 22.6 % (7/31) carried blaCTX-M, blaSHV, and blaTEM, 29 % (9) carried blaCTX-M only. Concerning CTX-M-types, CTX-M-9 was the most predominant (24/31) and mostly in combination with CTX-M-15 type.
Conclusion
High rate of colonization in healthy children with ESBL-PE was observed, regular consumption of dietary products from animal source (meat or chicken) were associated with this colonization in the community in non-hospitalized children. To our best knowledge it is the first study about regular consumption of dairy product as a risk factor for ESBL-PE community carriage, the first data about the carriage rate of ESBL-PE in community children in Lebanon and Middle East, and for the wide dissemination of CTX-M-9 type in this population.
doi:10.1186/s12941-016-0121-9
PMCID: PMC4731960  PMID: 26823288
Extended-spectrum beta-lactamase; Children; TEM; SHV; CTX-M; CTX-9; Dairy products; Meat; Lebanon
22.  VacA, cagA, iceA and oipA genotypes status and antimicrobial resistance properties of Helicobacter pylori isolated from various types of ready to eat foods 
Background
Despite the high clinical standing of Helicobacter pylori, its exact routes of transmission and origin have not been determined. Based on the contentious hypothesis, foods play an important roles in the transmission of H. pylori to humans. The present study was carried out to investigate the vacA, cagA, oipA and iceA genotypes status of H. pylori isolated from the various types of ready to eat foods.
Methods
A total of 550 ready to eat food samples were cultured and tested. H. pylori-positive strains were analyzed for the presence of various genotypes and antimicrobial resistance pattern.
Results
Seventy four out of 550 (13.45 %) samples were positive for H. pylori. Olvie salad (36 %), restaurant salad (30 %), fruit salad (28 %) and soup (22 %) were the most commonly contaminated. H. pylori strains harbored the highest levels of resistance against amoxicillin (94.59 %), ampicillin (93.24 %), metronidazole (89.18 %) and tetracycline (72.97 %). The most commonly detected genotypes were vacA s1a (78.37 %), vacA m2 (75.67 %), vacA m1a (51.35 %) and cagA (41.89 %). The prevalence of iceA1, iceA2 and oipA genotypes were 13.51, 4.05 and 18.91 %, respectively. S1am2 (70.27 %), s1am1a (39.18 %) and m1am2 (31.08 %) were the most commonly detected combined genotypes. Of 40 different genotypic combinations, s1a/cagA+/iceA1/oipA− (12.16 %), s1a/cagA+/iceA1/oipA+ (10.81 %) and s1a/cagA−/iceA1/oipA+ (10.81 %) were the most prevalent.
Conclusions
The present investigation showed that some types of ready to eat food samples maybe the sources of resistant and virulent strains of H. pylori. Warily use of antibiotics with respect to the results of disk diffusion method and careful health monitoring on food and staffs of food producing companies maybe reduce the risk of H. pylori in foods.
doi:10.1186/s12941-015-0115-z
PMCID: PMC4719207  PMID: 26792758
Helicobacter pylori; Genotypes; Genotyping; Ready to eat foods
23.  Clonal dissemination of KPC-2 producing Klebsiella pneumoniae ST11 clone with high prevalence of oqxAB and rmtB in a tertiary hospital in China: results from a 3-year period 
Background
Carbapenemase-producing Klebsiella pneumoniae (CPKP) strains have emerged as a major problem for healthcare systems. The aim of this study was to determine the circulating clones and analyze the clinical and molecular characteristics of CPKP in our hospital.
Methods
A total of 74 carbapenemase producers collected from our hospital from 2012 to 2014 were analyzed for the prevalence of extended-spectrum β-lactamase (ESBLs), plasmid-mediated quinolone resistance genes (PMQRs), exogenously acquired 16S rRNA methyltransferase (16S-RMTase), and plasmid-mediated AmpC enzyme (pAmpCs) by PCR and DNA sequencing. The sequence types (STs) of the carbapenemase producers were analyzed by multi-locus sequence typing (MLST). And Pulsed-field gel electrophoresis (PFGE) was performed to investigate the genetic relationship of KPC-2 producing strains. Clinical data were retrieved from the medical records.
Results
KPC-2 (n = 72) was the predominant enzyme followed by NDM-1 (n = 2); The genes blaCTX-M, blaSHV, blaTEM-1, blaDHA-1, rmtB, armA, oqxA, oqxB, and qnrB were present in 29 (39.2 %), 27 (36.5 %), 46 (62.2 %), 2 (2.7 %), 25 (33.8 %), 1 (1.4 %), 60 (81.1 %) and 56 (75.7 %), 6 (8.1 %) isolates, respectively. MLST analysis revealed 10 different STs. The most dominant ST was ST11 (78.4 %, 58/74), followed by ST15 (8.1 %, 6/74). PFGE patterns of the KPC-2 producing K. pneumoniae isolates exhibited clonal dissemination of ST11 and ST15 clones as well as a genetic diversity of the remaining strains.
Conclusion
The intra- and inter-hospital cross-transmission of KPC-2-producing K. pneumoniae ST11 co-carrying oqxAB and rmtB in our hospital strongly suggested that rapid identification of colonized or infected patients and screening of carriers is quite necessary to prevent a scenario of endemicity.
doi:10.1186/s12941-015-0109-x
PMCID: PMC4717588  PMID: 26786830
KPC-2; ST11; OqxAB; MLST; Klebsiella pneumoniae
24.  Clinical features and characteristics of Clostridium difficile PCR-ribotype 176 infection: results from a 1-year university hospital internal ward study 
Background
Clostridium difficile infection (CDI) is a major cause of antibiotic-associated diarrhoea. Given an increasing CDI incidence and global spread of epidemic ribotypes, a 1-year study was performed to analyse the molecular characteristics of C. difficile isolates and associated clinical outcomes from patients diagnosed with CDI in the Internal Medicine department at University Hospital Motol, Prague from February 2013 to February 2014.
Results
A total of 85 unformed stool samples were analysed and CDI was laboratory confirmed in 30 patients (6.8 CDI cases per 10,000 patient bed days and 50.6 CDI cases per 10,000 admissions). The CDI recurrence rate within 3 months of treatment discontinuation was 13.3% (4/30). Mortality within 3 months after first CDI episode was 26.7% (8/30), with CDI the cause of death in two cases. 51.9% of C. difficile isolates belonged to PCR-ribotype 176. MLVA of ribotype 176 isolates revealed two clonal complexes formed by 10/14 isolates. ATLAS scores and Horn’s index were higher in patients with ribotype 176 infections than with non-ribotype 176 infections.
Conclusion
This study highlights the clinical relevance of C. difficile PCR-ribotype 176 and its capacity to spread within a healthcare facility.
doi:10.1186/s12941-015-0114-0
PMCID: PMC4690340  PMID: 26698842
Clostridium difficile; PCR-ribotype 176; Horn’s index; ATLAS score; Ribotyping; MLVA
25.  Characteristics of leptospirosis with systemic inflammatory response syndrome: a multicenter study 
Background
Leptospirosis is a common zoonotic infection in the world. In patients with leptospirosis, in case of presence of Systemic Inflammatory Response Syndrome (SIRS), clinical and laboratory findings can be mistaken for sepsis due to other causes of infection. The purpose of this study is to assess the clinical and laboratory parameters of patients with leptospirosis in terms of the presence of SIRS and to examine the association of these with mortality.
Methods
One hundred fifty-seven patients were included in the study. The patients were classified according to the presence or absence of SIRS and divided into SIRS (+) and SIRS (−). Patient files were retrospectively evaluated. Clinical features and laboratory data were compared, and risk factors associated with mortality were determined.
Results
SIRS (+) was found in 70 % (n = 110) of patients who had signs on admission. Comparison of the clinical symptoms and findings of organ systems in the SIRS (+) and SIRS (−) showed that abdominal pain and vomiting were significantly more common in the SIRS (+) than in the SIRS (−) (p = 0.025 and p = 0.046, respectively). BUN and serum creatinine levels were significantly higher in the SIRS (+) than in the SIRS (−) (p = 0.002 and p < 0.001, respectively). In follow-up posterior-anterior chest radiography, pathological findings improved in 58.8 % (n = 40) of patients in the SIRS (+) and 27.3 % (n = 9) of patients in the SIRS (−) (p = 0.003). The mortality rate of the SIRS (+) and SIRS (−) was not significantly different (p = 0.868).
Conclusion
In patients with positive SIRS findings, while examining the etiology of sepsis, leptospirosis should come to mind especially in endemic areas for differential diagnosis. Early initiation of antibiotic and supportive therapy can be lifesaving in these patients.
doi:10.1186/s12941-015-0117-x
PMCID: PMC4687284  PMID: 26690093
Leptospirosis; SIRS; Prognosis

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