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Korkoca H.,Mus Alparslan University | Berktas M.,Yuzuncu Yil University | Durmaz R.,Public Health Agency of Turkey | Gursoy N.C.,Inonu University
Kafkas Universitesi Veteriner Fakultesi Dergisi | Year: 2013

Aeromonads infect human through potable water and causes various infections. Their existence in animal are being assessed as potential risk for human health. The aim of this study was to investigate clonal relationship among 52 Aeromonas strains isolated from human with diarrhea (14 strains), healthy food workers (2 strains), animals (24 strains) and drinking water (12 strains) by pulsed-field gel electrophoresis (PFGE). Clonal relation was determined between one diarrheic human isolate and one cattle isolate. No clonal relation was determined between drinking water and human isolates. Two fish isolates, A. caviae and A. sobria, were not distinguished PFGE patterns. Consequently no predominant clone was determined while clonal related strains were determined. Particularly, it is necessary to elicit the epidemiological importance of animals in respect of human Aeromonas infections and extensive studies are required for identification of environmental isolates.


Metin O.,Dr Sami Ulus Maternity And Childrens Training And Research Hospital | Tanir G.,Dr Sami Ulus Maternity And Childrens Training And Research Hospital | Nur Oz F.,Dr Sami Ulus Maternity And Childrens Training And Research Hospital | Kalaycioglu A.T.,Public Health Agency of Turkey | And 5 more authors.
Mikrobiyoloji Bulteni | Year: 2014

Elimination of measles and rubella until the end of 2015 in parallel with the "World Health Organization (WHO) Europe Region's Measles Elimination" work-up has been targetted and "Measles Elimination Program" has been carried out since 2002 in Turkey. Due to the routine vaccination programmes the number of the vaccinated children have increased and epidemic incidences have been falling. However, imported measles cases from Europe and other neighboring countries have been observed in Turkey in the recent two years. Patients who applied to Dr. Sami Ulus Maternity and Children's Training and Research Hospital with a pre-diagnosis of measles between December 2012 and April 2013 were screened in this study. Seventy-eight patients who match the clinical definition of the disease (> 38°C fever and maculopapular rash and cough or nasal discharge or conjunctivitis) were evaluated. Forty-four children (25 male, 19 female; age range: 4-191 months, mean age: 58.6 ± 59.5 months) with a positive measles IgM test result were taken into consideration and the epidemiological and clinical features of these children were evaluated. In addition to fever and rash, cough, nasal discharge and conjunctivitis were seen in 36 (82%), 24 (55%), and 18 (41%) patients, respectively. Thirty five (80%) patients were diagnosed in December, 6 (14%) in January, 2 (4%) in February, and 1 (2%) in March. All patients included in the study were unvaccinated or too young to be vaccinated according to the routine vaccination calendar. The Index case was a three-year old unvaccinated girl who had a history of contact with the Syrian neighborhoods. During the study period; following contact with the index case, two doctors (born in 1986 with a history of single dose of vaccination at ninth month) and three children (without vaccination) were also diagnosed as measles. Eight (18%) patients were hospitalized because of complications. Four (50%) of them had pneumonia and the other four (50%) had lack of oral feeding and dehydration. Average duration of hospitalization for patients was 4 ± 1.7 (range: 2-6) days and all patients were discharged with full recovery. For molecular typing, viral RNAs were isolated from urine samples of two of the measles IgM positive patients, subjected to sequence analysis of 450 nucleotides comprising the most variable C-terminal region of the nucleoprotein (N) gene. Phylogenetic analysis revealed that those two strains belonged to genotype D8. This study represented the involvement of measles virus genotype D8 in an outbreak in Turkey for the first time. During a measles epidemic, following the index case; medical personnel should be informed about possible, probable, and definite case definitions and should apply for appropriate triage or fast-track (rapidly examination) if necessary, and routine announcements should be made precisely and accurately at proper times and unvaccinated medical personnel and any people in touch with the patient should be vaccinated. In order to reach the elimination goal declared by European WHO for 2015, susceptible populations should be identified and vaccinated in Turkey to obtain sufficient herd immunity for preventing outbreaks.


Kara S.S.,Gazi University | Polat M.,Gazi University | Tapisiz A.,Gazi University | Nar Otgun S.,Public Health Agency of Turkey | Tezer H.,Gazi University
Mikrobiyoloji Bulteni | Year: 2014

Pneumococci are one of the most common causes of bacterial meningitis in children. It's also responsible for the other invasive pneumococcal diseases (IPD) including bacteremia and pneumonia worldwide. Unvaccinated children are more prone to IPD. Although IPD tend to have a higher prevalence under 2 years of age and in children with primary/secondary immunodeficiencies, and various predisposing factors, older age groups with no underlying diseases also experience IPD. In this report, a pediatric case diagnosed with meningitis due to Streptococcus pneumoniae serotype 35F with no underlying condition and no history of pneumococcal vaccination was presented. An 11-year-old male patient was admitted to the hospital with the complaints of high (39.4°C) fever, headache, vomiting and sleepiness. On the basis of findings from physical examination and laboratory results, the patient was prediagnosed as bacterial meningitis and empirical ceftriaxone and vancomycin therapy was initiated. The cerebrospinal fluid culture of the patient yielded penicillin-susceptible pneumococci and the isolate was identified as serotype 35F by quellung reaction. Vancomycin treatment discontinued depending on the culture result, and the patient fully recovered with 14-days of ceftriaxone therapy without any complications during his follow-ups. Although effective antibiotics are available for IPD, vaccination is indispensable considering the high mortality rates. Seven serotypes (1, 5, 6A, 6B, 14, 19F, 23F) which are currently included in the vaccine, were the most common serotypes related to IPD globally. After mass infant vaccination has been introduced, invasive pneumococcal diseases due to the vaccine serotypes have tended to decrease in both vaccinated young children and non-vaccinated age groups due to herd immunity. Nevertheless, non-vaccine serotypes (NVTs) have emerged as the agents of IPD as a result of serotype replacement. 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in April, 2011 nationwide in our country. This case report was about a patient who had developed meningitis after the introduction of PCV13. There has been no data evaluating the pneumococcal serotype distribution after PCV13 in our country yet. On February, 2013, the Advisory Committee on Immunization Practices (ACIP) recommended routine use of PCV13 for children aged 6-18 years with underlying disease conditions. However, there is no recommendation for children with no underlying diseases in this age group. Vaccination can be extended for otherwise healthy children older than 6 years of age because of increasing trends in incidence of IPD both with vaccine and NVTs like serotype 35F. Recent studies have indicated the emergence of serotype 35F as a cause of IPD in children over 6 years of age and there have been also reports of IPD cases with 35F after the introduction of PCV13. Although serotype 35F is not yet a well-known serotype causing IPD, it might probably gain importance owing to its increasing frequency and virulence and might attract attention to be considered for inclusion in the future pneumococcal vaccines.


Multidrug-resistant (MDR) tuberculosis (TB) constitutes a restricting factor for the effective treatment of TB worldwide. Early diagnosis and appropriate treatment of patients are the most effective strategy in the control of MDR-TB. Therefore, knowledge of drug resistance patterns of the MDR-TB clinical isolates are necessary in planning of an appropriate treatment regimen for the patient. The aims of this study were to detect the susceptibilities of MDR-TB isolates to second-line anti-TB drugs by E-test method, and to compare their results with Löwenstein-Jensen (LJ) proportion method. A total of 122 MDR (resistant to isoniazid and rifampicin) Mycobacterium tuberculosis complex (MTC) strains isolated from samples of patients with pulmonary TB were included in the study. The isolates were identified by conventional methods and first-line anti-TB drug susceptibility testing was performed by the proportion method using LJ medium. The susceptibilities of the isolates to second-line anti-TB drugs [kanamycin (KN), ofloxacin (OFL), ethionamid (ETN), linezolid (LIN)] were tested by proportion method on LJ medium and E-test method on Middlebrook 7H11 medium. For this purpose, E-test strips (bioMerieux, Fransa) of KN (0.016-256 mg/ml), OFL (0.02-32 mg/ml), ETN (0.016-256 mg/ml), and LIN (0.016-256 mg/ml) were used. The susceptibility tests were evaluated in 5., 7., and 10. days after application of the E-test strips, and proportion method on LJ medium was evaluated 28 days later. Second line-anti-TB drug susceptibility results were obtained in 5 to 10 days by E-test. Of the MDR MTC strains 98% (119/122) were susceptible to KN, OFL and LIN, while 2% (3/122) of the strains were resistant to KN and ETN. The correlation between E-test and LJ proportion method was estimated as 96% for KN and ETN, 98% for OFL, and 100% for LIN. When compared with LJ proportion method, the specificity of E-test in the detection of susceptibility to KN, OFL, ETN and LIN were 60%, 38%, 60%, and 100%, respectively, while the sensitivity was 100% for all drugs. Our results indicated that E-test method exhibited high sensitivity and specificity (100%) for LIN, so it may be used alone in susceptibility testing for this drug, however since the specificity is low (38%) for OFL it should be used together with the proportion method. In conclusion, E-test method might contribute for initiation of an early and effective anti-TB drug treatment and control of infection by rapid diagnosis in MDR-TB cases.


Guldemir D.,Public Health Agency of Turkey | Kalaycioglu A.T.,Public Health Agency of Turkey | Basak Altas A.,Public Health Agency of Turkey | Korukluoglu G.,Public Health Agency of Turkey | And 2 more authors.
Japanese Journal of Infectious Diseases | Year: 2013

The aimes of the present study were to monitor genetic alterations in the hemagglutin (HA) gene and oseltamivir resistance-related alterations in the neuraminidase (NA) gene of influenza A(H1N1)pdm09 viral isolates detected during the post-pandemic period in Turkey. A total of 2601 clinical specimens obtained from suspected cases of influenza A(H1N1)pdm09 viral infections were analyzed by real-time reverse transcription polymerase chain reaction. Viral RNA was detected in 233 (9%) clinical specimens. Sequence analysis of the HA gene in 16 random isolates showed > 98.7% homology among each other and with the A/California/07/2009 vaccine strain. These 16 isolates had common (75%-100%) amino acid substitiutions at positions P83S, D97N, S203T, R205K, I216V, V249L, I321V, and E374K in the HA gene. In addition, two additional rare mutations were also observed at positions S162N (addition of a glycosylation site, 6.25%) and A186T (receptor binding region, 6.25%). On the basis of amino acid substitutions in the HA1 domain, majority of the Turkish isolates were classified in the genetic group v and others in the genetic groups ii, iii, and vi. In the present study, we observed an increase in the variety and ratio of mutations detected in the HA1 and HA2 domains of the HA gene; however, these alterations have not yet resulted in vaccine escape mutants in Turkey. In addition, analysis of the NA regions of the isolates revealed that oseltamivir resistance was not an issue in Turkey.


Coskun-Ari F.F.,Public Health Agency of Turkey | Guldemir D.,Public Health Agency of Turkey | Durmaz R.,Public Health Agency of Turkey | Durmaz R.,Kirikkale University
PLoS ONE | Year: 2012

The life-threatening illnesses caused by Streptococcus pneumoniae have been declined significantly after the use of pneumococcal conjugate vaccines. Continuous monitoring of the vaccine serogroups/types is necessary to follow the changing epidemiology of invasive pneumococcal diseases. Recently, the sequential multiplex PCR approach, which uses several different sets of reactions, has been commonly adopted for determining capsular serogroups/types of S. pneumoniae isolates. In our study, we focused on development of a one-step multiplex PCR assay detecting all 1, 3, 4, 5, 6A/B, 7F, 9V, 14, 18C, 19A, 19F and 23F serogroups/types targeted by PCV13. The content of multiplex PCR mix and the cycling conditions were optimized in a manner that allowed rapid and accurate serotyping of a pneumococcal isolate by performing only a single amplification reaction. In our study of 182 clinical isolates, the one-step multiplex PCR assay exhibited 100% sensitivity and specificity, suggesting that its utilization can significantly reduce the use of traditional antiserum method requiring expensive reagents. © 2012 Coskun-Ari et al.


Yamur G.,Istanbul Forensic Medicine Institute | Albayrak N.,Public Health Agency of Turkey | Das T.,Istanbul Forensic Medicine Institute | Yildirim M.,Istanbul Forensic Medicine Institute | And 2 more authors.
Mikrobiyoloji Bulteni | Year: 2014

Tuberculosis (TB) is one of those infections with high morbidity and mortality in all around the world. Hundreds of people died from this disease without diagnosed or due to resistant strains in Turkey. Therefore, it is important to identify postmortem cases who have died from tuberculosis. Molecular methods have been widely used as well as conventional methods in the diagnosis of tuberculosis. The aim of this study was to compare the two different real-time polymerase chain reaction (Rt-PCR) system in the postmortem diagnosis of Mycobacterium tuberculosis infections in paraffin-embedded tissues. A total of 40 paraffin-embedded tissue samples [lung (n= 35), brain (n= 2), heart (n= 2), lymph node (n= 1)] in which histopathologic findings consistent with TB (necrotizing granulomatous inflammation, gelatinous caseous pneumonia, necrotic fibrous nodul) obtained from 37 autopsy cases (31 male, 6 female; age range: 25-85 yrs) were included in the study. Paraffin-embedded tissues were deparafinized with xylene and ethyl alcohol and then DNA isolation was done with QIAsymphony DSP Virus/Pathogen Midi kit in the QIAsymphony device. DNA amplification process was performed by Rt-PCR using the kit Artus® M. tuberculosis RC-PCR in the Rotor-Gene® Q device (Qiagen, Germany). Likewise, after deparafinization process, samples placed in the cartridge and isolation and Rt-PCR was performed by Xpert® MTB/RIF (Cepheid, USA) system, simultaneosly. Seventeen and 20 out of the 40 paraffin-embedded tissues yielded positive results with Qiagen and Xpert system, respectively. M.tuberculosis DNA was found positive in 13 (32.5%) and negative in 16 (40%) of the samples by both of the systems, exhibiting 72.5% (29/40) of concordance. On the other hand, seven (17.5%) samples that were positive with Xpert system yielded negative result with the Qiagen, while four (10%) samples that were positive with Qiagen yielded negative result with the Xpert system. Of the 20 positive cases detected with Xpert MTB/RIF system, 15 were found rifampicin-susceptible, and three were rifampicin-resistant. In two samples in which M. tuberculosis DNA was low positive, rifampicin resistance could not be detected. The identification of M.tuberculosis infections in postmortem cases will contribute epidemiological data in Turkey. In these cases, effective sampling and diagnosing of M.tuberculosis infections by acid-fast stain and culture methods are crucial. However, in cases without microbiological sampling the detection of M.tuberculosis DNA in paraffin-embedded tissues with PCR, although there are differences between PCR systems has diagnostic value. In conclusion, our data indicated that Xpert MTB/RIF system is more favourable to detect M.tubercuiosis DNA in paraffin-embedded tissues, with the advantages of determination of rifampicin resistance, and detection of more positive results within a shorter time.


Bayrakdar F.,Public Health Agency of Turkey | Altas A.B.,Public Health Agency of Turkey | Korukloglu G.,Public Health Agency of Turkey
Mikrobiyoloji Bulteni | Year: 2016

Human metapneumovirus (HMPV), classified in Paramyxoviridae family, phylogen- iically consists of two major groups namely A and B, with genetic lineages of A1, A2 (comprises of sublineages A2a and A2b) and B1, B2. ththough detailed evaluation on phylogenetic analysis of HMPV has been described in other countries, there are no data from Turkey on this subject. The aim of this study was tedemonstrate for the first time, the phylogenetic diversity of HMPV strains circulating in Turkey during two consecutive epidemic seasons. A tot al of 2900 upper respiratory tract samples collected from patients with respiratory illness were evaluated between January 2011 and December 2013, without any special selection < riteria. The presence of respiratory viruses in the samples were detected by real-time multiplex polymerase < bain reaction (FTD® Respiratory Pathogens 21 Multiplex RT-PCR, Fast Track Diagnostics, Luxemburg), anl 76 (2.6%) samples positive for HMPV were included in the study. HPMV nucleocapsid (N) (nt: 454-871) and fusion (F) (nt: 3624-4130) g 2nes were selected for phylogenetic analysis. In sequence analysis, F an i N gene sequences could only be obtained successfully from 46 out of 76 HMPV positive samples. Aco -rding to sequences obtained, 54.2% belonged to B2, 17.4% to B1, 4.3% to A1, 4.3% to A2a, and 206 to A2b. In 2011, the A2b sublineage was predominant, while in 2012 and 2013, B2 lineages were prodominant together with the B1 lineage. The A1 lineage was observed only in 2013. For the F gene fiigment, nucleotide distance between group A and B was In the range of 0.138-0.168, however aminoaced distance amongst Turkish HMPVsequences were in the range of 0.028-0.042. For the N gene fragment, nucleotide distance between group A and B was in the range of 0.141-0.163, but aminoadd distance be .ween group A and B was in the range of 0.037-0.050. Nucleotide diversity was higher than aminoacid dr fcrsity between and within lineages found in this study. This result indicated that the functional constraint, on F and N genes prevent dramatic aminoacid changes, and indicated that the evolution of HMPV was slow. The seasonal peaks were obs :rved from April to July In 2011, from January to une in 2012 and from January to May in 2013. In additicn, our data emphasized that the HMPV prevalence was high in childrei 0-5 years old, and coinfections we ∗e common with the other respiratory viruses such as respiratory sync> jal virus, coronavi-rus, parainflueata virus 3, rhinovirus and enterovirus. In conclusion, this study showeo khat HMPV strains circulating in Turkey were similar to those circulating in Europe.


PubMed | Public Health Agency of Turkey
Type: Journal Article | Journal: Mikrobiyoloji bulteni | Year: 2015

Coronaviruses (CoV) are enveloped, spherical, single-stranded positive-sense RNA viruses causing mainly respiratory and intestinal infections in animals and humans. Until recently five types of human coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, HCoV-229E, SARS-CoV) have been known, however a novel CoV has been identified in 2012 in Saudi Arabia. This virus, namely MERS-CoV (Middle East Respiratory Syndrome Coronavirus), was classified within Coronaviridae family, Coronavirinae sub-family, Betacoronavirus genus, clade C. It causes acute respiratory infections in humans and transmits via respiratory route and close contact between humans. The aim of this study was to present the first MERS case from Turkey identified by molecular methods and the results of viral sequence analysis. A 42-year-old male Turkish citizen who worked as an employee in Jeddah, Kingdom of Saudi Arabia, admitted to hospital with the complaints of fever and malaise on 25-26 September 2014. Since his symptoms went on and got worse, he returned to Turkey, and hospitalized in a hospitals intensive care unit in Hatay on 6th of October with the symptoms of fever, malaise, sweating, cough and respiratory distress. He transferred to a university hospital on 8th of October and died on 11th October. The tracheal aspirate sample obtained before he died was sent to Virology Unit of Reference Laboratories of the Turkish Public Health Institution. Detection of viral RNA was performed by using a commercial real-time PCR kit (hCoV-EMC Real-Time RT-PCR, Fast Track Diagnostics, Luxembourg) targeting the MERS-CoV E protein (upE), ORF1a and ORF1b gene regions. The reference method Superscript III One Step RT-PCR (Invitrogen, USA) recommended by World Health Organization (WHO) was also applied for confirmation. Both of the methods yielded positive results for MERS-CoV RNA. For the amplification of nucleocapsid (N) and RNA-dependent RNA polymerase (RdRp) genes, hemi-nested PCR (Invitrogen, ABD) was conducted, followed by sequence analysis of 204 nucleotide part of N gene. Phylogenetic tree of N gene was obtained with the use of MEGA6 software. N gene was chosen as it comprised a two aminoacid deletion in the corresponding published sequence from the patient treated in London, United Kingdom. There was no nucleotide or aminoacid change in our isolate, namely ANK/1079/2014 when compared with human Betacoronavirus 2c EMC/2012 reference strain found in Genbank database. The target gene regions selected in our study (UpE, ORF1a, ORF1b, N and RdRp) which were also recommended by WHO, shown to have high specificity and sensitivity for the diagnosis and confirmation of MERS-CoV, and also recommended by WHO. The previous studies indicated that, the viral genomes detected in the earliest cases of humans (clade A) are genetically distinct from the others (clade B) which were isolated from dromedary camels and humans. In our study, according to phylogenetic analysis of partial N gene segment, isolate ANK/1079/2014 has taken place within clade A. In conclusion, MERS-CoV appears to have limited circulation in Arabian Peninsula and Middle-Eastern countries, it should be considered in mind that travel-related cases may export the virus outside these regions leading autochtonous infections in the other parts of the world.


PubMed | Public Health Agency of Turkey
Type: Journal Article | Journal: Mikrobiyoloji bulteni | Year: 2014

Acinetobacter baumannii which is a significant cause of nosocomial infections, increases the rate of morbidity and mortality in health care settings especially in intensive care units (ICUs). The aim of this study was to determine the antibiotic resistance profiles of A.baumannii strains isolated from blood cultures of inpatients from different ICUs, wards and hospital environment and evaluate their clonal relationships and epidemiologic features. A total of 54 A.baumannii strains (47 from the blood cultures and 7 from the hospital environment), identified between 01 January 2012-28 December 2012 at the Clinical Microbiology Laboratory of Ankara Numune Training and Research Hospital, Turkey, were included in the study. Identification of A.baumannii isolates and their antimicrobial [sulbactam-ampicillin (SAM), piperacillin (PIP), piperacillin-tazobactam (TZP), ceftazidime (CFZ), cefoperazone-sulbactam (SCF), cefepime (CEF), imipenem (IMP), meropenem (MER), amikacin (AMK), gentamicin (GEN), netilmicin (NT), ciprofloxacin (CIP), levofloxacin (LVF), tetracycline (TET), tigecycline (TG), colistin (COL), trimethoprim-sulfamethoxazole (SXT)] susceptibility testing were performed by Vitek 2 (bioMrieux, France) system. The clonal relationship between the A.baumannii isolates was analysed by pulsed-field gel electrophoresis (PFGE). In our study colistin, tigecycline and netilmicin were found to be the most effective agents against A.baumannii isolates. All of the clinical isolates (n= 47) were found susceptible to COL, however all were resistant to SAM, PIP, TZP, CEF, IPM, CFZ, MER and CIP. While 1.85%, 14.8%, 14.8%, 16.6%, 59.2% and 22.2% of the isolates were susceptible to SCF, AMK, NT, GEN, TG and SXT, respectively; 1.85%, 1.85%, 9.2%, 16.6%, 38.8% and 27.7% of the isolates were intermediate to SCF, TET, AMK, NT, LVF and TG, respectively. Similarly, all of the environmental A.baumannii isolates (n= 7) were resistant to SAM, PIP, TZP, CFZ, CEF, IPM, MER and CIP, and all were susceptible to TG and COL. The resistance rates of the environmental isolates to SCF, AMK, GEN, NT, LVF, TET and SXT were determined as 57.1%, 85.7%, 85.7%, 28.8%, 28.6%, 85.7% and 57.1%, respectively. PFGE analysis done by the use of ApaI enzyme revealed the presence of one major clone. Dendogram analysis indicated that environmental and clinical isolates were in the same clone indicating that the outbreak was possibly originated from the same internal ICUs. Our data emphasized that multidrug resistant A.baumannii isolates were quite common in our hospital, and enviromental cross-contamination throughout the year was confirmed by molecular methods. Despite the precautions such as continous education on effective hand washing, use of gloves and hospital cleaning, established in our hospital, this single clonal spread was attributed to staff shortage and poor adherence to infection control rules. In conclusion, for the prevention of dissemination of multidrug resistant A.baumannii strains and control of nosocomial infections, infection control strategies should be established and strict compliance to these rules should be provided.

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