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ABSTRACT: Adenoviruses which are one of the causative agents of acute respiratory tract infections at all age groups worldwide, can lead to epidemic, endemic or sporadic infections year-round. Adenovirus infections in lower respiratory tract can be presented as bronchitis, bronchiolitis and pneumonia. The aim of this study was to investigate the presence of adenoviruses as the etiologic agent of lower respiratory tract infections (LRTIs) in children by cell culture, polymerase chain reaction (PCR) and direct fluorescence antibody (DFA) test. The results of the laboratory tests were evaluated in the light of patients' clinical findings. The study consisted of 206 patients aged between 0-5 years old and who were admitted to the hospital with the complaints of LRTI between January 2011 and April 2012. The clinical, radiological and laboratory findings of the patients were recorded. Nasopharyngeal specimens were taken with flocked swab from all patients and adenoviruses were investigated by shell-vial cell culture, real-time PCR and DFA test, simultaneously. Of all the samples 89.3% were taken in January, February and March and 38% of the patients have one or more chronic underlying diseases as chromosomal abnormalities, congenital heart disease, heart failure, asthma, cystic fibrosis, leukemia, kidney failure and prematurity. Adenovirus was detected in 12 (5.8%) of the samples by PCR, seven (3.4%) of the samples by cell culture method. While seven samples were found positive with both PCR and cell culture, 194 samples yielded negative results in both tests. Five samples, which were found positive by PCR, were not grown in cell culture method. Twelve of the 153 samples examined with DFA test, could not be evaluated due to insufficient amount of cells, however 2.8% (4/141) of the samples were found positive for adenovirus antigens by DFA method. Those samples were also positive ones in the other two methods. Compared with cell culture, the sensitivity, specificity, positive and negative predictive values of PCR were 100%, 97.5%, 58.3% and 100%, respectively; those values were 57%,100%,100% and 97.7%, respectively for DFA testing. Compared to PCR the sensitivity of cell culture is very low (16.6%) after three days of incubation, however, it increased to 58.3% after five days' of incubation. There was no significant relationship between adenovirus positivity and the presence of chronic diseases, the radiological findings and the laboratory findings. Of all adenovirus positive samples 83.3% were obtained in January, February and March. Our data indicated that the etiological agent was adenovirus in approximately 6% of children with LRTI. The most important step for the isolation of adenovirus from respiratory tract, is high quality and sufficient amounts of sample. The flexible flocked swabs made it easy to take nasopharyngeal swab from children. Although cell culture is still the gold standard for the diagnosis of adenovirus infections, PCR which is a fast method with high sensitivity and specificity can also be used. However, specific care should be taken during the DNA extraction stage, since the amount of the nucleic acid in the sample is critical for the best results. Even though the low sensitivity of DFA restricts its use in routine diagnosis of adenovirus infections, it should always be kept in mind that the quality of the clinical samples is most reliably evaluated by this method.
Mikrobiyoloji bülteni 04/2013; 47(2):282-94. · 0.40 Impact Factor
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ABSTRACT: Enterococci which are part of the commensal flora of the human gastrointestinal and genitourinary tracts, are increasing in importance as the cause of hospital-acquired infections. Identification of Enterococcus spp. at the species level is of great importance, for appropriate treatment of patients, infection control and to supply epidemiological data. Conventional methods for the identification of enterococcus isolates at species level is difficult and time consuming. Correct identification of enterococcus isolates in clinical microbiology laboratory by conventional methods is replaced by semi-automated or automated identification and molecular methods. The aim of this study was to evaluate the performance of Phoenix automated system (BD Diagnostic Systems, USA), API Rapid ID 32 Strep System (bioMerieux, France) and Enterococcus MGRADE LightCycler kit (Roche Molecular Biochemicals, Germany) used in real-time polymerase chain reaction (Rt-PCR), for the species level identification of enterococcus strains isolated from clinical specimens. A total of 90 vancomycin susceptible enterococci isolated from different patients were identified by all of the three commercial systems, together with conventional methods. Of the strains, 59 were identified as E.faecalis, 28 were E.faecium, and one of each as E.raffinosus, E.hirae and E.casseliflavus with conventional methods. One E.faecalis strain identified by the conventional system was identified as E.faecium by Phoenix system and one E.faecium strain as E.durans. One E.raffinosus strain identifed by the conventional method was identified as E.avium by API. Conventionally identified four E.faecalis strains were determined to be E.faecium by Rt-PCR and one E.faecium, one E.raffinosus and one E.casseliflavus as E.faecalis. Accordingly, the consistency of Phoenix, API Rapid ID 32 Strep and LightCycler Enterococcus MGRADE systems with the conventional methods were detected as 97.8% (88/90), 98.9% (89/90), and 92.2% (83/90), respectively. In conclusion, all of those three commercial assays are appropriate methods to be used for the identification of enterococci at the species level in the routine clinical microbiology laboratories, due to their high compliance with the conventional method, and their ability to yield the results at the same day.
Mikrobiyoloji bülteni 01/2013; 47(1):141-6. · 0.40 Impact Factor
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Volkan Korten,
Güner Söyletir,
Ata Nevzat Yalçın, Dilara Oğünç,
Başak Dokuzoğuz,
Harika Esener,
Sercan Ulusoy,
Alper Tünger,
Bilgehan Aygen,
Bülent Sümerkan,
Dilek Arman,
Murat Dizbay,
Murat Akova,
Gülşen Hasçelik,
Haluk Eraksoy,
Seniha Başaran,
Iftihar Köksal,
Gülçin Bayramoğlu,
Halis Akalın,
Melda Sınırtaş
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ABSTRACT: The aim of this study was to determine the in vitro activities of doripenem, imipenem, and meropenem against clinical gram-negative isolates. A total of 596 clinical isolates were obtained from intensive care unit (ICU) and non-ICU patients in 10 centers over Turkey between September-December 2008. The origin of the isolates was patients with nosocomial pneumonia (42.4%), bloodstream infections (%40.4), and complicated intraabdominal infections (17.1%). Of the isolates, 51.8% were obtained from ICU patients. The study isolates consisted of Pseudomonas spp. in 49.8%, Enterobacteriaceae in 40.3%, and other gram-negative agents in 9.9%. The minimum inhibitory concentrations (MIC) for doripenem, imipenem and meropenem were determined for all isolates in each center using Etest® strips (AB Biodisk, Solna, Sweden). Of the isolates, 188 (31.5%) were resistant to at least one of the carbapenems. MIC50 of doripenem against Pseudomonas spp. Was 1 mg/L which was similar to that of meropenem and two-fold lower than imipenem. Susceptibility to carbapenems in P.aeruginosa was 64% for doripenem at an MIC level of 2 mg/L, 53.9% and 63% for imipenem and meropenem at an MIC level of 4 mg/L, respectively. Doripenem and meropenem showed similar activity with the MIC90 of 0.12 mg/L whereas imipenem was four-fold less active at 0.5 mg/L. Against other gramnegative pathogens, mostly Acinetobacter spp., MIC50 was 8 mg/L for doripenem and 32 mg/L for other two carbapenems. P.aeruginosa isolates were inhibited 84.2% with doripenem and 72.1% with meropenem at the MIC level of 8 mg/L. Doripenem generally showed similar or slightly better activity than meropenem and better activity than imipenem against pathogens collected in this study. Against Pseudomonas spp., doripenem was the most active of the three carbapenems. Doripenem and meropenem were equally active against Enterobacteriaceae and at least four-fold more active than imipenem. It was concluded that doripenem seemed to be a promising agent in the treatment of nosocomial pneumonia, blood stream infections and intraabdominal infections particularly in patients who were under risk of developing antimicrobial resistance.
Mikrobiyoloji bülteni 04/2011; 45(2):197-209. · 0.40 Impact Factor
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ABSTRACT: The identification of community-acquired methicillin-resistant Staphylococcus aureus (MRSA) is becoming a hard task since colonization with MRSA is lasting for years and the number of the health care facilities other than hospitals is continuously increasing. In this study we aimed to investigate the genetic properties and health-care association of MRSA strains isolated from skin and soft tissue infections of outpatients admitted to Akdeniz University Hospital. Thirty strains were phenotypically identified as MRSA and after assessing the risk factors, 28 (93.3%) of them were classified as health-care associated (HCA) and 2 (6.7%) of them as community-acquired (CA). All of the isolates were positive for nuc and mecA genes by polymerase chain reaction. Antimicrobial resistance rates of HCA-MRSA and CA-MRSA isolates were found as follows, respectively; 89.3% and 0% for rifampin, 89.3% and 50% for ciprofloxacin, 89.3% and 0% for gentamicin, 50% and 50% for erythromycin, 28.6% and 0% for clindamycin, whereas all of the isolates were susceptible to vancomycin, linezolid and trimethoprim-sulfamethoxazole. SCCmec type III was detected in 24 (85.7%) of HCA-MRSA strains. SCCmec type IV was detected in 1 (3.6%) of HCA-MRSA and in 2 (100%) of CA-MRSA strains. Panton-Valentin leucocidin (PVL) gene positivity was detected in only CA-MRSA isolates (2/2; 100%). MRSA isolates were grouped into 17 different genotypes (from A to R) of which pulsotype A was predominant among HCA isolates and CA-MRSA isolates were found to be clonally related with each other. This is the first study which investigated the genetic properties of MRSA strains in Antalya (a province located at Mediterranean Region, Turkey). In this study HCA risk factors were investigated and CA-MRSA rate was only 6.7% among all MRSA strains isolated from outpatients. As a result of detailed investigation of HCA risk factors, it was possible to detect the exact rate of CA-MRSA among outpatients. Thus it is of clinical and epidemiological importance to know the origin of MRSA isolates since this will affect the empirical treatment choice. Genetic studies supplied by appropriate demographic data will help to clarify the evolution and epidemiology of MRSA in the community and in the hospital setting.
Mikrobiyoloji bülteni 10/2010; 44(4):533-45. · 0.40 Impact Factor
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ABSTRACT: The aim of this study was to determine the extended-spectrum beta-lactamase (ESBL) types by isoelectric focusing (İEF) and polymerase chain reaction (PCR) methods in 56 Escherichia coli strains isolated from urine samples of patients with community-acquired urinary tract infection and determined as ESBL positive with the phenotypic screening tests (E test and combined disk method). IEF revealed that most of the strains produced 1 to 3 different bands, mostly at the isoelectric points 8.2 (n= 44, 79%) compatible with CTX-M. Twenty four (43%) isolates had CTX-M and TEM enzyme bands together, 16 (29%) isolates had only CTX-M enzyme bands, 3 (5%) isolates had CTX-M, TEM, SHV bands, one had CTX-M and SHV enzyme bands together, and one had only TEM band. Eleven E.coli strains did not yield any enzyme bands. PCR analysis revealed that 93% (n= 52) of the isolates had CTX-M, 64% (n= 36) had TEM and 11% (n= 6) had SHV, while 29 (52%) had CTX-M + TEM, three had CTX-M + SHV, and three had CTX-M + TEM + SHV genes together. PER-1 type beta-lactamases were not detected by PCR method. PCR analysis of the eleven strains that yielded no band in IEF showed that 5 strains had CTX-M + TEM, 3 had CTX-M and 3 had TEM enzyme genes. The consistency between IEF and PCR methods for the determination of CTX-M, TEM and SHV enzymes was 85%, 78% and 67%, respectively. Genes encoding ESBL's are usually located on transferrable plasmids that may also carry other resistance determinants. Thus detection of beta-lactamase enzyme types in ESBL positive bacteria is important for the choice of appropriate antimicrobial agents for treatment.
Mikrobiyoloji bülteni 07/2010; 44(3):367-74. · 0.40 Impact Factor
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ABSTRACT: Imipenem and meropenem are broad spectrum antimicrobial agents that are especially useful in the treatment of nosocomially acquired Pseudomonas aeruginosa and Acinetobacter spp. infections. Previous reports have noted that susceptibility tests could show false resistance to imipenem. For this reason, Centers for Disease Control and Prevention has recommended that all carbapenem resistant or intermediate resistant isolates should be tested with an additional method to verify the results. This study was aimed to evaluate the imipenem and meropenem susceptibilities by disk diffusion, E-test and broth microdilution in P. aeruginosa and Acinetobacter baumannii strains found to be resistant or intermediate to imipenem-meropenem by BD Phoenix automated susceptibility testing system. Between January 2006-January 2007, 85 non-duplicate isolates of A. baumannii and 51 non-duplicate isolates of P. aeruginosa which were determined as resistant or intermediate resistant to imipenem and/or meropenem by BD Phoenix automated identification and susceptibility system (Becton Dickinson, Sparks, MD, USA) were collected in Akdeniz University Hospital Central Laboratory. All strains were tested by E-test (AB Biodisk, Sweden), disk diffusion and reference broth microdilution (BMD) method following CLSI recommendations. All 51 isolates of P. aeruginosa determined as imipenem and/or meropenem resistant or intermediate resistant by BD Phoenix, were found to be imipenem and/or meropenem resistant or intermediate resistant by the reference BMD method. Minor error rates were same for all testing systems (1.9%) except for the meropenem results of BD Phoenix system (5.9%). No major errors were produced by any system. For A. baumannii, only one very major error was detected for meropenem by BD Phoenix system. Number of minor errors determined for meropenem by all testing systems compared to the reference test, ranged from 2 (2.4%) to 3 (3.5%). It was concluded that carbapenem susceptibility test results obtained by BD Phoenix system for P. aeruginosa and A. baumannii isolates, could be reported without an additional susceptibility testing method unless indicated on case basis.
Mikrobiyoloji bülteni 04/2010; 44(2):197-202. · 0.40 Impact Factor
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ABSTRACT: Tuberculin skin test (TST) which is used in the diagnosis of tuberculosis disease and evaluation of latent tuberculosis cases, is an easily applied, reproducible and low cost test. This study was carried out to determine the tuberculin reactivity in BCG vaccinated and unvaccinated population, to investigate the variables (BCG vaccination, the number of BCG scars, age, sex) affecting tuberculin reactivity. It was also aimed to determine the annual risk of tuberculosis infection (ARTI). The study which was a cross-sectional epidemiological one, was carried out during July 2006-January 2007 in Antalya district center and the number of objects to be applied with TST was determined by Power analysis method. A total of 408 participants; 147 children aged 5-7, 165 young adults aged 14-25 and 96 elderly people aged over 60, were included to the study. TST was applied by Mantoux method using 0.1 ml of purified protein derivative (PPD) RT 23/tween 80 antigen containing 5 tuberculin unit (TU). Evaluation of the test is done according to the domestic tuberculin skin test evaluation criteria. It was determined that 83.5% (341/408) of the cases were vaccinated with BCG and the diameter of TST was significantly higher in the vaccinated group when compared to the unvaccinated group (p= 0.005). Mean tuberculin reactivity (diameter of the TST induration) was 2.70 +/- 2.96 mm in 5-7 years age group, 6.44 +/- 4.11 mm in 4-25 years age group and 4.48 +/- 3.72 mm in > or = 60 years age group. Mean TST diameter was statistically significantly higher in 14-25 years age groups compared to 5-7 years (p= 0.003) and > or = 60 years (p= 0.002) age groups. Among the BCG unvaccinated group TST positivity was none in 5-7 years, 2% in 14-25 years and 7% in > or = 60 years age group. These rates were none in 5-7 and > or = 60 years age groups and 1% in 14-25 years age group in the BCG vaccinated population. It was also observed that TST diameters increased with increasing number of BCG scars and there was no difference in sex dependent TST reactivity. Average ARTI was determined to be 6%. It was concluded that to determine the risk of tuberculosis, annual variation in the ratio of ARTI has to be determined by nationwide evaluation of tuberculin skin test.
Mikrobiyoloji bülteni 02/2009; 43(1):27-35. · 0.40 Impact Factor
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ABSTRACT: Plasmid mediated AmpC beta-lactamases are reported from Enterobacteriaceae with increasing frequency. There have been reports of treatment failures in patients infected with these organisms and given broad-spectrum cephalosporins. The aim of this study was to investigate the presence of plasmid mediated AmpC beta-lactamases in Escherichia coli and Klebsiella spp. A total of 41 strains of cefoxitin resistant or intermediate E. coli (n= 27) and Klebsiella spp. (n= 14) were collected from january 2005 to January 2006 at Akdeniz University Hospital Central Laboratory. Three-dimensional test was used as a phenotypic confirmatory test. Analytical isoelectric focusing electrophoresis was used to measure the pl values of the beta-lactamases. Plasmid mediated AmpC enzyme genes were amplified using multiplex polymerase chain reaction and sequenced by Beckman Coulter CEQ 8000. AmpC beta-lactamases were only detected in two isolates (7.4%) of E. coli. These isolates produced CMY-2 like enzymes and have either CTX-M or TEM enzyme. Transferable AmpC beta-lactamases are associated with multiple antibiotic resistance. Therefore detection of these enzymes in gram-negative bacteria has a clinical importance, since it can often provide valuable information to clinicians leading to more effective and appropriate use of antimicrobials.
Mikrobiyoloji bülteni 11/2008; 42(4):545-51. · 0.40 Impact Factor
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Deniz Gür,
Zeynep Gülay,
Ozay Arikan Akan,
Zerrin Aktaş,
Ciğdem Bal Kayacan,
Ozlem Cakici,
Bayri Eraç,
Meral Gültekin, Dilara Oğünç,
Güner Söyletir,
Nilgün Unal,
Sevil Uysal
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ABSTRACT: Increasing resistance due to extended-spectrum beta-lactamases (ESBLs) and multiple resistance mechanisms in gram-negative hospital isolates restrict the role of beta-lactam antibiotics in empirical treatment of serious infections. As the prevalence of ESBL producing strains and resistance rates to antimicrobial agents can vary in each center, local surveillance studies are required to guide therapy. In this study, in vitro rates of resistance to ceftriaxone, ceftazidime, cefepime, imipenem, cefoperazone/sulbactam and piperacillin/tazobactam were evaluated in 1196 gram-negative hospital isolates in a multicenter in vitro study with the participation of six different centers in Turkey between the period of June 2004-January 2005. The isolates included Escherichia coli (n= 457), Klebsiella pneumoniae (n= 390), Pseudomonas aeruginosa (n= 194) and Acinetobacter boumannii (n= 155). In addition, frequency of ESBL production and types of enzymes were determined in blood isolates of E. coli and K. pneumoniae. MICs and ESBL production were investigated by E-test (AB Biodisk, Solna) and the results were evaluated by using CLSI breakpoints. PCR analysis was used for typing of the ESBLs. In E. coli, 26% and in K. pneumoniae 32% of the isolates were ESBL producers. Among the blood isolates of E. coli and K. pneumoniae, 31.7% and 33.3% produced ESBLs, respectively. CTX-M (71.4%) was the most prevalent enzyme, followed by TEM (49.4%) and SHV (46.7%) derived enzymes. CTX-M-15 (69.4%) was the most frequent CTX-M type in blood isolates followed by CTX-M-3 (28.6%) and CTX-M-1 (2%). Resistance to imipenem was not observed in E. coli isolates, however it was 1.3% in K. pneumoniae, 28.9% in P. aeruginosa and 52.2% in A. baumannii strains. Resistance to cefoperazone/sulbactam was found as 6%, 17.7%, 27.9% and 41.3% in E. coli, K. pneumoniae, P. aeruginosa and A. baumannii isolates, respectively, whereas resistance rates to piperacillin/tazobactam were 10.2%, 22.3%, 22.7% and 78.7%, respectively. These results indicate that ESBL production and rates of resistance to beta-lactam antibiotics are high in hospital isolates of gram-negative bacteria in Turkey, however, they show variations in different hospitals and CTX-M enzymes are prevalent in these isolates.
Mikrobiyoloji bülteni 11/2008; 42(4):537-44. · 0.40 Impact Factor
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Burçin Sener,
Ferda Tunçkanat,
Sercan Ulusoy,
Alper Tünger,
Güner Söyletir,
Lütfiye Mülazimoğlu,
Nezahat Gürler,
Lütfiye Oksüz,
Iftihar Köksal,
Kemalettin Aydin,
Ata Nevzat Yalçin, Dilara Oğünç,
Asli Acar,
Jörg Sievers
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ABSTRACT: To determine the prevalence of antimicrobial resistance among Streptococcus pneumoniae and Haemophilus influenzae isolated in Turkey as part of Survey Of Antibiotic Resistance, a surveillance programme in the Africa and Middle East region examining the antimicrobial susceptibility of key bacterial pathogens involved in community-acquired respiratory tract infections (CARTIs).
Susceptibility was evaluated against a range of antimicrobial agents using disc diffusion and Etest methods.
Six centres in five cities collected 301 S. pneumoniae and 379 H. influenzae isolates between October 2004 and November 2005. Among S. pneumoniae, the prevalence of isolates with intermediate susceptibility (MICs 0.12-1 mg/L) and resistance to penicillin (MICs >or=2 mg/L) was 24.6% and 7.6%, respectively; there was a wide variation between cities (2.4% to 36.9% intermediate and 0% to 23.8% resistant phenotypes). Macrolide-azalide resistance rates exceeded those of penicillin resistance in all cities. Overall, 5.0% of isolates were co-resistant to penicillin and erythromycin and 10.0% were multidrug-resistant (joint resistance to erythromycin, co-trimoxazole and tetracycline). Agents tested to which over 90% of countrywide S. pneumoniae isolates remained susceptible were amoxicillin/clavulanate (98.7%), chloramphenicol (94.7%) and cefprozil (90.6%). Overall, the percentage of H. influenzae isolates producing beta-lactamase was 5.5%, differing widely across the country with the highest prevalence of beta-lactamase production detected in Trabzon (14.0%) and no beta-lactamase-positive isolates found in Izmir. H. influenzae had the highest per cent susceptibility to amoxicillin/clavulanate (99.5%) and ofloxacin (99.2%) while >20% were resistant to co-trimoxazole.
Prevalence of penicillin and macrolide-azalide resistance among S. pneumoniae appears to be on the increase in Turkey while overall beta-lactamase production in H. influenzae remains relatively low. To adequately monitor the spread of drug-resistant phenotypes among these two important CARTI pathogens, ongoing collection of resistance surveillance data is required-where possible locally as resistance patterns can vary substantially between cities and institutions.
Journal of Antimicrobial Chemotherapy 09/2007; 60(3):587-93. · 5.07 Impact Factor
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ABSTRACT: We evaluated the performance of Helicoblot 2.1 which differentiates the reactivity to each of the various Helicobacter pylori antigens, and compared the results with those obtained by standard techniques (rapid urease test and histological examination of gastric biopsy) in symptomatic children of different ages living in Antalya, Turkey.
Eighty-eight children (mean age, 9.15 years) were divided into two groups. The first group included 66 children who were found to be infected with H. pylori. The second group included 22 children who were negative for H. pylori. Serum samples collected from all patients were tested for H. pylori IgG antibodies by immunoblot assay (Helicoblot 2.1).
The sensitivity, specificity, positive and negative predictive values for detection of H. pylori infection were 80%, 100%, 100% and 85%, respectively. In children under 7 years of age, the sensitivity of the test was found to be lower than other age groups (P<0.05). No relationship was found between peptic ulcer and cagA antibody positivity (P>0.05).
Helicoblot 2.1 is a useful non-invasive diagnostic tool for H. pylori infection in children over 6 years of age.
Pathology 04/2003; 35(2):157-60. · 2.38 Impact Factor
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ABSTRACT: To investigate the effect of granulocyte colony-stimulating factor (G-CSF) in the treatment of Escherichia coli peritonitis with and without ceftriaxone in a nonneutropenic rat model.
The rats were divided into five groups: control group (C) receiving physiological saline; peritonitis group (P) infected intraperitoneally with a live bacterial suspension of E. coli; peritonitis and antibiotic group (PA) receiving ceftriaxone 3 h after being infected; peritonitis, antibiotic, and G-CSF group (PAG) receiving G-CSF and antibiotic 3 h after infection; and peritonitis and G-CSF group (PG).
All rats in group C survived. Any animals which did not survive died within 24h after inoculation. A significantly higher rate of survival, 95%, was observed with antibiotic treatment alone (PA), in comparison to the G-CSF-treated groups, PAG and PG, 52% and 57%, respectively.
No beneficial effect of G-CSF treatment was seen in the E. coli peritonitis and antibiotic therapy remains the basic treatment for this disease.
Surgery Today 02/2003; 33(7):504-8. · 1.22 Impact Factor
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ABSTRACT: We report a case of bacteremia caused by Brevibacterium species which is one of the coryneform bacteria, in a patient with chronic lymphocytic leukemia. We conclude that, if a coryneform bacteria is isolated from sterile body sites, it must be carefully evaluated, and especially in immunocompromised patients, Brevibacterium species should be considered as potential pathogens.
Haematologia 02/2002; 32(2):151-3.
