Etiological agents of community-acquired pneumonia in adult patients in Turkey; a multicentric, cross-sectional study.

This cross-sectional study was intended to investigate the etiology of community-acquired pneumonia (CAP) in adult patients receiving no prior antibiotic therapy. Etiological agents were identified in 137 (62.8%) of 218 patients, the most frequent being Streptococcus pneumoniae (14.7%), Mycoplasma pneumoniae (13.8%) and respiratory syncytial virus (10.1%). A single pathogen was detected in 50.9% of cases and mixed pathogens in 11.9%. Typical pathogens were determined in 35.8% of cases, atypical pathogens in 20.2% and viral pathogens in 20.6%. Chronic obstructive pulmonary disease was a common (42.7%) comorbidity. S. pneumoniae was the most common pathogen in adult patients with CAP. Atypical pathogens were more common in patients < 65 years old, M. pneumoniae being the most common in this age group. Our results suggest that initial empiric antibiotic treatment in patients with CAP should cover S. pneumoniae and M. pneumoniae in Turkey.

Peripheral blood natural killer cells in Crimean-Congo hemorrhagic fever.

BACKGROUND: The relationship of changes in the peripheral blood lymphocyte subgroups during Crimean-Congo hemorrhagic fever (CCHF) to prognosis has not been reported. OBJECTIVES: To determine peripheral blood lymphocyte subgroups in CCHF patients at the time of diagnosis and relate these to clinical outcome. STUDY DESIGN: Peripheral blood samples were obtained from the patients treated at the Karadeniz Technical University Hospital for CCHF in 2004. Lymphocyte subgroups were analyzed by flow cytometry on these samples and their association with patients' risk group (severe vs. non-severe) and mortality was recorded. RESULTS: There were significantly more peripheral blood natural killer (NK) cells in severe risk CCHF patients than in non-severe risk group CCHF patients. A positive correlation was found between NK cell count and aspartate transferase (AST), alanine transferase (ALT) and activated partial thromboplastin times (aPTT). In addition, NK cell counts were observed to be higher in two patients who died. CONCLUSION: Elevated NK cell counts may be a prognostic marker in CCHF patients.

Necrotizing fasciitis with ruminococcus.

Necrotizing fasciitis is a life- and limb-threatening soft tissue infection. Due to its underlying predisposition and rapid progression, treatment should be started quickly using antibiotherapy and surgical intervention. Although necrotizing fasciitis is mainly caused by streptococci and staphylococci, it may also be polymicrobial. Other peptostreptococci have been reported as necrotizing fasciitis agents in the literature, though we encountered no cases of necrotizing fasciitis caused by Ruminococcus productus. Here, we describe a case of necrotizing fasciitis caused by R. productus, a Gram-positive, obligatory anaerobe.

Voriconazole-induced neuropathy.

BACKGROUND: Fungal infections are common and life threatening among immunosupressive patients. Rare side effects may occur related to the use of voriconazole, which is the drug of choice in invasive aspergillosis. PATIENTS AND METHODS: Neuropathy was determined through clinical and electromyographic findings during the course of voriconazole therapy in 2 patients developing invasive aspergillosis. RESULTS: Since examinations revealed no neuropathy capable of ascription to any other cause and improvement followed the cessation of the drug, this suggested that neuropathy may be linked to voriconazole use. CONCLUSION: Neuropathy may be seen as a side effect during voriconazole treatment. Voriconazole-induced side effects should be borne in mind and patients carefully monitored during its use.

Molecular epidemiology of clinical Pseudomonas aeruginosa isolates carrying IMP-1 metallo-beta-lactamase gene in a University Hospital in Turkey.

Pseudomonas aeruginosa isolates carrying IMP- or VIM-type metallo-beta-lactamase (MBL) have been increasingly reported in hospitals worldwide. One hundred P. aeruginosa clinical isolates from unrelated inpatients hospitalized at a Turkish university hospital were screened for the presence of bla(IMP) and bla(VIM) genes by polymerase chain reaction (PCR). One (1%) isolate was found to carry a VIM-type MBL gene, whereas nine (9%) carried an IMP-1 MBL gene carried on a cassette inserted into a class 1 integron. Only four of the IMP producers were detected as MBL producers according to E-test MBL. Minimum inhibitory concentrations (MICs) of imipenem for the IMP-1 and VIM-type MBL-producers were highly variable (MIC values, 8-128 mug/ml). Imipenem resistance was not plasmid-mediated according to the transformation assays. Piperacillin/tazobactam was the only effective drug in antimicrobial susceptibility testing. No aztreonam-resistant IMP and VIM producers were detected to produce an extended-spectrum beta-lactamase (ESBL). Three class 1 integrons of approximately 2,300 bp, 1,800 bp, and 1,500 bp in size were detected in each of the nine IMP-positive isolates. Sequencing revealed three novel gene cassette arrays, aac(3)-1c-cmlA5, bla(IMP-1)-aadA7-like, and aacA7-smr-2-orfD. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) indicated that a clonal spread of IMP-1-producers had occurred in this hospital.

Cerebellar abscess and meningitis, caused by Shewanella putrefaciens and Klebsiella pneumoniae, associated with chronic otitis media.

Shewanella putrefaciens is a facultatively anaerobic, non-motile, Gram-negative, non-fermentative bacterium. It is found in various environments and has been isolated worldwide. S. putrefaciens is a rare cause of brain abscesses and meningitis. This is a case report of a cerebellar abscess and meningitis caused by Shewanella putrefaciens and Klebsiella pneumoniae in a river trap fisherman.

Detection and prevalence of inducible clindamycin resistance in staphylococci.

Staphylococcus aureus and coagulase-negative staphylococci (CNS) are recognized as causing nosocomial and community-acquired infections in every region of the world. The resistance to antimicrobial agents among staphylococci is an increasing problem. Clindamycin (CL) is considered to be one of the alternative agents in these infections. This study demonstrates a simple, reliable method (double-disc diffusion test) for detecting inducible resistance to CL in erythromycin-resistance (ER-R) isolates of S. aureus and CNS. A total of 883 (52.3%) isolates of S. aureus and 804 (47.7%) isolates of CNS were selected from recent (2003-2005) clinical isolates recovered in the laboratory of the authors; duplicate isolates were not included. A total of 214 (12.6%) S. aureus and 308 (18.3%) CNS isolates were selected based on ER-R and CL sensitivity using standard National Committee for Clinical Laboratory Standards disc diffusion testing. A total of 1687 staphylococcal isolates were included, consisting of 27.5% meticillin-resistant S. aureus, 24.8% meticillin-sensitive S. aureus, 36.1% meticillin-resistant CNS and 11.6% meticillin-sensitive CNS isolates: 30.9% of staphylococcal isolates (214 S. aureus and 308 CNS) that were erythromycin resistant and CL sensitive were tested for inducible resistance using the D-test. A D-shaped zone around the CL was observed for 70.9% of staphylococcal isolates (81.8% of S. aureus isolates and 63.3% of CNS isolates) with an ER-R and a clindamycin-sensitive (CL-S) phenotype. The organism was positive for inducible clindamycin resistance (CL-R). There was a 21.9% level of inducible macrolide-lincosamide-streptogramin B resistance phenotype among all the staphylococcal isolates. When the S. aureus and CNS strains among all the staphylococcal isolates were compared statistically, inducible CL-R in CNS strains was determined to be 23% more positive (P=0.028, odds ratio 0.77, 95% confidence interval 0.61-0.98). When a statistical comparison was performed among ER-R but CL-S staphylococcal isolates inducible CL-R in S. aureus strains was determined to be 2.6 times more positive (P=0.000, odds ratio 2.6, 95% confidence interval 1.68-4.04). A simple, reliable method of detecting inducible resistance to CL in ER-R isolates of S. aureus and CNS is described. Clinical microbiology laboratories should use the double-disc diffusion test as standard practice with all ER-R staphylococci. CL should not be used in patients with infections caused by inducibly resistant staphylococcal isolates. Therapeutic failures may thus be avoided.

Risk factors of catheter-related bloodstream infections in parenteral nutrition catheterization.

BACKGROUND: Intravascular catheters are integral to the practice of modern medicine. Potential risk factors for catheter-related bloodstream infection (CRBSI) include underlying disease, method of catheter insertion, and duration and purpose of catheterization. The administration of parenteral nutrition (PN) through intravascular catheters increases CRBSI risks. The purpose of this study was to evaluate the risk factors of CRBSI in patients with PN administration. METHODS: This study was conducted at the Karadeniz Technical University Hospital between October 2003 and November 2004. All the patients to whom PN was administered through intravascular catheters were prospectively monitored for the presence of CRBSI and risk factors. RESULTS: During the study period, 111 intravascular catheters through which PN was administered were monitored for a total of 1646 catheter-days. CRBSI was determined in 31 cases, a CRBSI rate of 18.8 per 1,000 catheter-days. When risk factors affecting CRBSI were investigated using logistic regression, an increase in APACHE II score (OR, 1.10; 95% CI, 1.01-1.21; p = .012), prolongation of catheterization (OR, 1.08; 95% CI, 1.02-1.14; p = .004), catheterization in emergent conditions (OR, 5.45; 95% CI, 1.20-24.82; p = .016), and poor patient hygiene (OR, 4.38; 95% CI, 1.39-13.78; p = .019) were all determined to be independent risk factors. Proper implementation of hand hygiene and maximal barrier precautions during the insertion of catheters reduced CRBSI levels (OR, 0.28; 95% CI, 0.09-0.88; p = .003 and OR, 0.26; 95% CI, 0.08-0.93; p = .017, respectively). CONCLUSIONS: It was concluded that the duration of catheterization should be shortened; that the intravascular catheter, which is inserted in urgent situations, should be removed as soon as possible; and that maximal sterile barrier precautions should be taken and due attention should be paid to hand hygiene.

[Isolation of Brucella melitensis from ejaculate culture of a brucellosis patient with epididymoorchitis]. / Ejekülat kültüründe Brucella melitensis üretilen epididimoorsitli bir bruselloz olgusu.

Brucellosis is a significant public health problem particularly in developing countries. People are frequently infected through milk, milk products, urine and pregnancy material of animals with brucellosis. Epididymoorchitis is the most frequent genitourinary complication of brucellosis and is often unilateral. In this report, a 35 years old male patient who was diagnosed as epididymoorchitis based on clinical presentation, laboratory findings and imaging techniques, has been presented. Brucella melitensis was isolated from blood, bone marrow and ejaculate cultures of the patient. The patient was treated with rifampicine and doxycycline combination therapy for six weeks and no complication has developed in the one year follow-up period. In areas where brucellosis is endemic, such as our country, Brucella infection should be considered in the differential diagnosis of epididymoorchitis and in addition to blood and bone marrow cultures, ejaculate cultures should also be evaluated.

Post-ERCP bacteremia caused by Alcaligenes xylosoxidans in a patient with pancreas cancer.

Alcaligenes xylosoxidans is an aerobic, motile, oxidase and catalase positive, nonfermentative Gram negative bacillus. This bacterium has been isolated from intestine of humans and from various hospital or environmental water sources. A.xylosoxidans is both waterborne and results from the poor-hygienic conditions healthcare workers are in. In this case report, the bacteremia which appeared in a patient with pancreas cancer after ERCP was described.

[Liver abscess and infective endocarditis cases caused by Ruminococcus productus]. / Ruminococcus productus'un etken oldugu karaciger apsesi ve enfektif endokardit olgulari.

The genus Ruminococcus which are anaerobe Gram positive cocci, previously classified as Peptostreptococcus, may colonize the upper respiratory tract, gastrointestinal tract, vagina and skin of humans and animals. In this report a case of liver abscess and a case of infective endocarditis caused by Ruminoccocus productus, which is very rarely encountered in the clinical practice were presented. The first case was a 32 years old male who was admitted to the hospital in 2002, with the complaints of fever lasting for 20 days and pain while breathing. The abdominal ultrasonography revealed the presence of a liver abscess, and the drainage material from the abscess yielded Ruminococcus productus, identified in BACTEC 9200 (Becton Dickinson, Sparks, Md) anaerobe system. As the isolate was found to be sensitive to penicilin, the empirical gentamicin and ampicillin/sulbactam therapy was continued. The second case was a 25 years old male who was admitted to the hospital in 2005, with the signs of fever lasting for 3-4 months, chills, bone and joint pains. As multiple vegetations were detected in echocardiography, blood cultures were collected and empirical therapy with ceftriaxone and gentamicin was initiated with the preliminary diagnosis of infective endocarditis. Bacteria which were isolated from blood cultures by BACTEC 9200 system have been identified as R. productus. As this strain was also sensitive to penicillin, the empirical therapy was changed to penicilin and gentamicin. These two cases indicated that R. productus should be considered in complicated infections even if it is a rarely isolated species from the clinical samples.

The influence of G-CSF addition to antibiotic treatment of experimental sepsis on pulmonary tissue.

AIM: To investigate the effects of G-CSF addition to antibiotic treatment of experimental sepsis on pulmonary lung tissue. MATERIALS AND METHODS: Fifty Sprague-Dawley rats were used. The first four groups received a bolus intraperitoneal injection of Pseudomonas aeruginosa. The first group (Group SAG) received a combined therapy of imipenem and G-CSF, the second group (Group SA) received only imipenem, the third group (Group SG) received only G-CSF, and no antibiotic or G-CSF was given to the fourth group (Group S). The fifth group (Group C) served as the control. Survival rates, peripheral leukocyte counts (PLC) and absolute neutrophil counts (ANC) were obtained, and lung tissues were examined under light microscopy. RESULTS: Survival rates at the 120th hour were 100% in groups SAG, SA and C; 20% in group SG; and 0% in group S. PLC and ANC values reached their highest levels at the 36th hour in the SAG group and at the 60th hour in the SA group. Pulmonary architecture was better preserved in the SAG, SA and SG groups--in that order--than in the S group. CONCLUSION: Particularly in the early phase of infection, the administration of G-CSF in combination with antibiotics would be appropriate for maximizing the effect of antibiotics as soon as possible and for minimizing the damage caused by inflammation.

[Prospective evaluation of blood cultures in Medical Faculty Hospital of Blacksea Technical University]. / Karadeniz TEKNIK Universitesi Tip Fakültesi hastanesinde kan kültürlerinin prospektif olarak degerlendirilmesi.

In this study, the rate of blood culture contamination, bacterial pathogens and their antimicrobial susceptibilities causing nosocomial and community acquired bloodstream infections were investigated prospectively during the period February 2003 to February 2004. In the study period, among the 5994 blood culture samples obtained from 3114 patients, 1091 (18%) yielded positive results. Seventy-four of them (1.2%) were evaluated as false positive, 514 (9%) were pseudobacteremia or contamination. According to patients' clinical features, 503 (8%) blood culture samples were associated with blood stream infections, and 358 of them (71%) were primary episodes. Twohundred and ninetyfour of primary episodes (82%) were hospital acquired and 64 were community acquired bloodstream infections. Staphylococcus aureus was the most frequently isolated agent in the hospital and community acquired bloodstream infections at the rates of 16% and 20%, respectively. In hospital acquired blood stream infections, Escherichia coil (9%) and Pseudomonas aeruginosa (8%); in community acquired bloodstream infections Streptococcus spp (17%) and E. coli (15%) were the other most frequently isolated bacterial agents. Methicillin resistance of S. aureus isolates was determined as 54% in hospital acquired blood stream infections and 25% in community acquired blood stream infections.

Investigation of atypical bacteria and virus antigens in respiratory tract infections by use of an immunofluorescence method.

In this study an immunofluorescence (IF) method was used to investigate the antigens of viruses and atypical bacteria in respiratory tract infections (RTI) in pediatric and adult age groups. In this prospective study of 2 years (1998-2000), IF was used to investigate the antigens of 7 viral and 3 atypical bacteria to be used for the etiological diagnosis of RTI. Sputum (33.6%) and nasopharyngeal aspirate specimens were obtained from pediatric patients (Group I, 76 cases) and adults (Group II, 135 cases) with RTI symptoms. Antigen detection rates were found to be 44.7% in Group I and 67.4% in Group II (P < 0.05). The following rates for specific antigens in Groups I and II, respectively, were as follows: Chlamydia pneumoniae, 17.1 and 13.3% (P > 0.05); Mycoplasma pneumoniae, 0 and 9.6% (P < 0.05); influenza A virus, 3.9 and 16.3% (P < 0.05); adenovirus, 3.9 and 14.8% (P < 0.05); parainfluenza virus type 1, 5.3 and 7.4% (P > 0.05); respiratory syncytial virus, 9.2 and 1.5% (P < 0.05); parainfluenza virus type 2, 3.9 and 3%(P > 0.05); and influenza B virus, 1.3 and 1.5% (P > 0.05). Mixed agents were found at a rate of 2.6 and 3.7% (P > 0.05) in Groups I and II, respectively. Parainfluenza virus type 3 and Legionella pneumophila antigens were not found. Since detecting etiological agents provides an important guide for determining the most appropriate antibiotic therapy, this IF method could be applied in clinical practice for arriving at a correct diagnosis and administration of effective treatment.

An epidemiological analysis of Stenotrophomonas maltophilia strains in a university hospital.

The aim of this investigation was to evaluate the epidemiology of Stenotrophomonas maltophilia in a university hospital of Turkey. From June 2000 to December 2001, S. maltophilia strains were collected, clinical presentations were noted, and MIC determinations were performed by means of E-test. Enterobacterial repetitive intergenic consensus sequences-PCR (ERIC-PCR) was used for molecular typing of the strains. Forty-four strains of S. maltophilia were isolated from 41 hospitalized patients in a teaching hospital. The majority of specimens were from the blood and respiratory tract. Antimicrobial sensitivities of these strains were as follows: 97.7 % trimethoprim-sulfamethoxazole, 15.9% ticarcillin, and 95.4% ticarcillin- clavulanate. The strains were evaluated using the ERIC-PCR method. It was of interest to note that epidemiological typing revealed three small outbreaks that were caused by a total of 12 strains. The remaining isolates generated singular DNA patterns. DNA amplification was possible in 38 isolates and yielded 26 different patterns in a period of 20 months, leading to the suggestion that commensal bacteria becomes selected in the presence of a suitable host.

Vitamin D and Tumor Necrosis Factor-Alpha Receptor Gene Polymorphisms in Various Hepatitis B Clinical Conditions in Turkey.

BACKGROUND: The aim is to define the role of single nucleotide polymorphism on the progress of hepatitis B virus (HBV) infection. We evaluated polymorphisms of TNF-α-308, Vitamin D receptor Apa I and Taq I gene in patients with HBV infection. METHODS: All subjects included were older than 18 years old. Sixty three patients had chronic HBV infection, 61 were HBsAg positive carriers and 59 were positive for anti-HBs and anti-HBc. Gene polymorphisms were evaluated by Amplification Refractory Mutation System PCR. For patients with chronic hepatitis, viral load, ALT levels, and histopathological evaluation of the liver were also compared. RESULTS: Gender distribution was not different among groups; however, anti-HBs positive patients were significantly older than the other patients. ALT levels and viral load were significantly higher in chronic hepatitis group than the asymptomatic carriers group. Vitamin D receptor Apa I gene and Taq I gene and TNF-α -308 gene variant alleles were not different in all three groups. Variant alleles of three genes were not different in subgroups of chronic hepatitis patients formed according to ALT levels, viral load, histological activity index, and fibrosis score. CONCLUSIONS: Role of single nucleotide polymorphism in clinical status of various HBV infection states was not shown in this study. Considering the other studies performed with this aim, which strengthens the notion that ethnicity is an important factor, future studies with more patients from different ethnic groups may help to clear the role of polymorphisms in the clinical progress of HBV infection.

The complete genome analysis of Crimean-Congo hemorrhagic fever virus isolated in Turkey.

Crimean-Congo hemorrhagic fever virus (CCHFV) is the causative agent of a tick-borne disease with high mortality rates in humans. The distribution of CCHFV includes over 30 countries in Asia, the Middle East, southeastern Europe, and Africa. It was first recognized in Turkey in 2002, with an increasing number of cases reported between 2002 and 2009. Recent analysis of complete genome sequences of CCHFV isolates has revealed that the genomic plasticity of the virus is surprisingly high for an arthropod-borne virus. We have determined the complete nucleotide and deduced amino acid sequences of strain CCHFV Turkey-Kelkit06 isolated from the blood of a patient in an endemic region of Turkey in 2006. The complete sequence length of the CCHFV Turkey-Kelkit06 strain is 19,186 nt, consisting of a 1673 nt S segment, a 5364 nt M segment, and a 12,149 nt L segment. Based on the analysis of S, M, and L segments, CCHFV Turkey-Kelkit06 clustered in Group V, which represents the Europe/Turkey geographic lineage. Although glycoproteins encoded by the M gene are the most variable part of the CCHFV Turkey-Kelkit06 strain, some functional domains of the glycoproteins are well conserved. Here, we report the complete sequence and genome organization of the CCHFV Turkey-Kelkit06 strain and its phylogenetic relationship to other strains of CCHFV. Collecting data on viral sequences among isolates from CCHF epidemics may provide valuable information regarding the molecular basis of the epidemic potential of the virus.

The efficacy of ribavirin in the treatment of Crimean-Congo hemorrhagic fever in Eastern Black Sea region in Turkey.

BACKGROUND: The efficiency of ribavirin for treatment of Crimean-Congo hemorrhagic fever (CCHF) is unknown. In the literature, prospective randomized studies investigating the efficacy of ribavirin are not found. OBJECTIVES: To investigate the efficacy of ribavirin in treatment of patients with CCHF. STUDY DESIGN: In this prospective randomized cohort study 136 cases were included between June 2004 and August 2007. The diagnosis was confirmed in the CCHF reference laboratory of Refik Saydam National Hygiene Central Institute of the Turkish Ministry of Health. Patients either received ribavirin plus supportive treatment (Group A) (n=64) or only supportive treatment (Group B) (n=72). For the evaluation of efficacy of ribavirin, various parameters were compared between Group A and Group B. RESULTS: As well as the similarity of demographic features between the two groups, there were no statistical differences in incubation time; hospitalization time; patients requiring platelet replacement therapy; the time taken for platelet levels to return to normal levels and mortality. In Group B, the rate of tick contact was higher (p=0.03). In Group A, leukocyte levels took longer to return to the normal levels (p=0.02). CONCLUSION: In our study, there was no positive effect determined on clinical or laboratory parameters in CCHF patients treated with ribavirin, also it was observed that leukocyte levels took longer to return to normal (p=0.02) and, while not statistically significant, the longer period of hospitalization (p=0.09) needed was observed as a negative effect. Because of these reasons, it is thought that the use of ribavirin makes no significant contribution to the prognosis of the CCHF disease.

MRSA genotypes in Turkey: persistence over 10 years of a single clone of ST239.

OBJECTIVES: Methicillin-resistant Staphylococcus aureus (MRSA) is a significant cause of life-threatening human infections. The clinical impact of MRSA is mounting, not only due to the ever-increasing prevalence but also due to the occurrence of new, community-acquired MRSA strains. The aim of this prospective, multi-centre study was to determine the prevalence and genetic relatedness of clinically relevant MRSA isolates, in Turkey. METHODS: During a 1-year period, data from 20 successive patients with invasive S. aureus infections were collected from eight university hospitals, geographically distributed over the six main regions of Turkey. Among these S. aureus isolates, the genetic association of MRSA isolates was investigated by pulsed-field gel electrophoresis (PFGE) and spa typing. A selected number of isolates were also analyzed by multilocus sequence typing (MLST). Furthermore, Panton Valentine leucocidin (PVL) genes were examined. RESULTS: In this study, the rate of methicillin resistance in S. aureus in patients with apparent infections (sepsis, meningitis, lung abscess or septic arthritis) ranged from 12 to 75% within the seven participating centres. Typing by pulsed-field gel electrophoresis and spa typing revealed the presence of 22 closely related genotypes. According to the PFGE and spa typing results, 53 out of 54 MRSA isolates were closely related. These isolates were of spa type t030 or a related spa type, contain an SCC mec type III element and belong to sequence type ST239. None of the isolates contained the PVL genes. CONCLUSIONS: Despite the broad surface area of Turkey, a single predominant clone of ST239 circulates in hospitals in different regions and only few new types of MRSA were introduced over the past years. These results place Turkey in the epicenter of ST239 prevalence.