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Infections due to methicillin-resistant Staphylococcus aureus (MRSA) are a growing concern for public health resulting in increase in morbidity, length of hospital stay, and cost of treatment. MRSA nasal swab screening may give clinicians additional information for decision of empiric antimicrobial agents. While increasing antibiotic resistance leads to new treatment approaches, bacteriophages are one of the most promising methods for these alternatives. It was aimed to determine the effectiveness of bacteriophages against MRSA isolates. Nasal swab samples were collected from outpatients without any evidence of infection who applied to Hatay, Mersin and Gaziantep family and immigration health centers. A series (35) were isolated from Turkish patients, and G series (64) were isolated from Syrian immigrants. Methicillin resistance was determined phenotypically and genotypically. Also, antibiotic susceptibilities of all isolates were determined against erythromycin, clindamycin, gentamicin, linezolid, rifampicin, and mupirocin. The total antimicrobial resistance rates of isolates were found to be 11%, 28%, 8%, 5%, 16%, 19%, and 29% respectively. The high susceptibility rate against ciprofloxacin (88.8%) was remarkable. The overall susceptibility of MRSA strains to ENKO, INTESTI, PYO, SES, and staphylococcal bacteriophages was 67.7%, 55.5%, 53.5%, 61.6% and 44.4%, respectively. The antibiotic susceptibility rates (except erythromycin) and efficacy of bacteriophages were higher in group A. Considering that high efficacy rates were not achieved in the study and the sensitivity rates of Turkish isolates to all phages were found to be higher than those of Syrian isolates, searching for phages in the geographic regions where the pathogen is common may be helpful to obtain suitable phages for treatment.

In our study, we evaluated the in vitro activities of plazomicin, amikacin, gentamicin, and tobramycin among fifty carbapenem resistant Klebsiella pneumoniae (CR-Kp) isolates. Aminoglycoside resistance genes in selected CR-Kp strains were also examined.Minimum inhibitory concentration (MIC) of meropenem, plazomicin, tobramycin, gentamicin, and amikacin were determined by gradient test (G-test) method. In all strains carbapenemase activity was assessed by polymerase chain reaction (PCR). Aminoglycoside modifying enzyme (AME) genes in 14 CR-Kp strains that are resistant to at least one of tobramycin, gentamicin, and amikacin among fifty CR-Kp isolates, and 16S ribosomal methylase genes in 6 CR-Kp strains with plazomicin MIC ≥ 128 mg/L were investigated by PCR method.The most frequently detected carbapenemase enzyme in the strains in our study was OXA-48 (88%). Aminoglycoside susceptibilities of all isolates were determined; plazomicin 84%, amikacin 66%, gentamicin 50%, tobramycin 18%. The most common AME gene positivities were found, 93% (n = 13) ant(3')-I, 78% (n = 11) aac(6')-Ib, 57% (n = 8) aac(3')-IV, 42% (n = 6) aac(3')-IIa, and 29% (n = 4) aph(3')-VI. Most of the isolates examined for the presence of AME carry at least two or more AME genes. The most common 16S ribosomal methylase gene was rmtH. In our study, MIC values of ≥ 256 µg/mL were found in 6 (12%) of 50 isolates against amikacin, tobramycin, and gentamicin, including plazomicin. At least two 16S ribosomal methylase gene positivity has been shown in these 6 strains.In our study, increased in vitro efficacy of plazomicin was shown in CR-Kp isolates comparing to other aminoglycosides. Plazomicin is an effective treatment option against CR-Kp isolates and needs to be sup-ported by clinical studies.

Antibiotic resistance is one of the most important public health problem and one of the most critical steps in preventing resistance is the monitorization of the resistance. Local, regional and global monitoring enables the spread of antibiotic resistance to be understood more clearly. In this study, it was aimed to evaluate the results of the pilot study for the establishment of molecular-based carbapenem surveillance system in Escherichia coli and Klebsiella pneumoniae isolates and to investigate the carbapenemase epidemiology in Turkey. Hospitals (n= 28) from 26 different statistical level II regions from Turkey were included in the study. The hospitals participated in the study submitted ten carbapenem susceptible and ten carbapenem resistant E.coli and K.pneumoniae isolates to our laboratory that were isolated in two different periiods of six-month either between 1 March-31 August or 1 April-30 September 2019. A total of 509 isolates were collected from 26 of the 28 participating hospitals in the study. Isolates were identified by matrix assisted laser desorptionization-time of flight mass spectrophotometry (MALDI TOF MS) (Bruker Daltonics, Germany) method and antibiotic susceptibility tests for imipenem, meropenem and colistin were studied by broth microdilution. Moreover, susceptibilities to amikacin, amoxicillin-clavulanic acid, ampicillin, aztreonam, cefepime, cefotaxime, ceftazidime, ciprofloxacin, ertapenem, gentamicin, piperacillin-tazobactam, tobramycin and trimethoprim-sulfamethoxazole were determined by disc diffusion method. The resistance genes were investigated in isolates which were found to be phenotypically resistant to carbapenem and colistin, in house method was used to investigate carbapenemase genes and a commercial colistin resistant real-time PCR kit (Biospeedy, Turkey) was used for colistin resistance genes. In total, 493 of the 509 isolates collected from hospitals were identified as E.coli (25.7%, n= 127) and K.pneumoniae (74.3%, n= 366) and included in the study. It was determined that 31% of the isolates evaluated were from community-acquired infections and 69% were either from healthcare-associated infections or from colonization sites. Among the tested isolates, 248 (50.3%) were susceptible to carbapenems and 245 (49.7%) were resistant. The types of carbapenemases in carbapenemase-producing isolates were OXA-48 (52.2%), KPC (16.1%), NDM-1 (15%), OXA-48 + NDM-1 (12.6%), KPC + NDM-1 (2.8%) and VIM (0.5%) and OXA-48+VIM (0.5%). Resistance to colistin was detected in 23.3% of the isolates but mcr1-8 genes were not detected. It was found that all colistin resistant isolates are resistant to at least one of the carbapenems. The importance of a molecular-based antimicrobial resistance surveillance system in our country was demonstrated with this pilot study. It is thought that continuous monitoring of these epidemiological features will contribute to the management of infections due to carbapenemase-producing organisms.

Antibiotic resistance genes can easily be transferred between bacteria in the biofilm. In the dairy industry, many bacterial species forming biofilms on the surfaces of equipment are widely reported. The experiments reported in this research paper aimed to investigate the carbapenem resistance and biofilm formation properties of Enterobacterales isolates which are spoilage microorganisms obtained from raw milk. In addition, the study determined that whether there was a relationship between the biofilm formation ability or the protein spectra of these isolates. In this study, ninety-two Enterobacterales isolates collected from 173 raw milk samples were investigated. Initially, the isolates were identified as Citrobacter braakii (n = 18), Citrobacter freundii (n = 12), Enterobacter asburiae (n = 1), Enterobacter cloacae (n = 3), Escherichia coli (n = 10), Hafnia alvei (n = 18), Klebsiella oxytoca (n = 1), Serratia fonticola (n = 24), Serratia liquefaciens (n = 4), and Serratia marcescens (n = 1) using MALDI-TOF MS. As a result, carbapenem resistance was determined in 6.5% of the isolates by CIM test, MHT, and the disk diffusion methods, but none of them had blaOXA-48, blaKPC, blaNDM-1, blaOXA23, blaOXA-58, blaOXA-51, blaVIM, and blaIMP genes. This may be due to the effect of other resistance mechanisms such as porin loss or increased flow pump activity. Furthermore, biofilm formation (weak and moderate) was detected in 97.8% of the Enterobacterales isolates. The mass spectra of the moderate biofilm producer isolate of Serratia spp. and the mass spectra of the weak biofilm producers of E.coli presented similarities.

In this study, it was aimed to determine the antibiotic resistance of Escherichia coli strains isolated from samples taken from various children's parks of Ankara and to confirm the resistance by molecular methods. Five hundred fifty-four samples, including soil samples from 140 different parks and 414 swab samples from slides, swings, ferris wheels, seesaws, and other toys from 176 different parks, were taken. Fourty E. coli strains isolated from these samples were included in the study. Antibiotic susceptibility tests of 40 E. coli isolates were performed by EUCAST recommendations. The resistance rates of E. coli isolates were found as ciprofloxacin 5%, ampicillin 17%, trimethoprim/sulfamethoxazole 15%, streptomycin 12.5%, tobramycin 5%, gentamicin 5%, cefotaxime 2.5%, and ceftazidime 2.5%. Intermediate rates were found as 95%, 90%, and 70% for tobramycin, gentamicin, and streptomycin respectively. blaCTX-M beta-lactamase gene was investigated for an isolate determined to be resistant to both cefotaxime and ceftazidime but blaCTXM gene could not be detected. Aminoglycoside resistance of strains has been investigated because of high intermediate sensitivity rates. For this purpose, aac(6 ')-Ib, aac(3 ')-IIa, aph(3 ')-VI, ant(3 ')-I, aac (3 ')-IV, ant(2 ')-Ia genes scanned, and were detected 97.5% of our isolates ant (3 ')-I, %25 aac(6 ')-Ib', 5% aac(3 ')IIa, 2.5% ant(2 ')-Ia. Also, aph(3 ')-VI, and aac(3 ')-IV genes could not be detected in any of the isolates. Consequently, it has been revealed that resistant E. coli strains isolated from children's parks can pose a potential risk in public health for transmission of resistant genes.

Francisella tularensis is a gram-negative, coccobasillus, facultative intracellular bacteria and causes a zoonotic disease, tularemia in humans. F.tularensis has four subspecies, which have different virulences for humans as F.tularensis subsp. tularensis, F.tularensis subsp. holarctica, F.tularensis subsp. mediasiatica and F.tularensis subsp. novicida. F.tularensis subsp. tularensis is the most virulent subspecies and mortality rate is high in human cases. F.tularensis subsp. holarctica, which has been reported in our country to date, has lower virulence than that of subsp. tularensis, and causes rare lethality among untreated patients. According to the erythromycin resistance and the properties of glucose-glycerol fermentation, F.tularensis subsp. holarctica has three biovar as biovar I, biovar II and biovar japonica. F.tularensis subsp. mediasiatica has been reported only in a few central asian countries and its virulence is similar to the F.tularensis subsp. holarctica F.tularensis subsp. novicida is avirulent for immunocompetent individuals but has been observed to cause infection in immunocompromised individuals. The aim of this study was to determine the F.tularensis subspecies in 259 F.tularensis strains isolated from clinical specimens, drinking water and a rodent sample and 517 F.tularensis PCR-positive DNA isolated from clinical specimens between years 2009 and 2014. Conventional PCR was performed using primers specific for the RD1 (Region Difference) region of F.tularensis. Subspecies were differentiated depending on the difference in PCR amplification product size. In our study, F.tularensis subsp. holarctica was detected in 764 samples yielding 922 base pair (bp) amplification product. The DNA samples obtained from one water and 11 lymph aspirates were determined as F.tularensis subsp. holarctica biovar japonica. The DNA sequence analysis of the amplification product of the RD1 region of the isolate from water sample was determined. The 1136 bp nucleotide sequence obtained from the DNA sequence analysis was 100% similar to F.tularensis subsp. holarctica biovar japonica (FCS075 strain-accesion number AF469618) when compared with GenBank data. The whole genome sequence of this isolate was also determined and recorded to GenBank with accesion number CP007148. None of the samples used in our study belonged to other sub-species. F.tularensis subsp. holarctica biovar japonica positive 11 lymph aspirate samples were sent to our center from Ankara (n= 1), Kayseri (n= 1) and Afyon (n= 9) provinces. The results of the current study revealed that F.tularensis subsp. holarctica biovar japonica caused a tularemia outbreak in a village in Afyon province at first time and it was observed sporadically in two other different provinces.

Influenza A(H1N1)pdm09 pandemic virus causing the 2009 global outbreak moved into the post-pandemic period, but its variants continued to be the prevailing subtype in the 2015-2016 influenza season in Europe and Asia. To determine the molecular characteristics of influenza A(H1N1)pdm09 isolates circulating during the 2015-2016 season in Turkey, we identified mutations in the hemagglutinin (HA) genes and investigated the presence of H275Y alteration in the neuraminidase genes in the randomly selected isolates. The comparison of the HA nucleotide sequences revealed a very high homology (>99.5%) among the studied influenza A(H1N1)pdm09 isolates, while a relatively low homology (96.6%-97.2%), was observed between Turkish isolates and the A/California/07/2009 vaccine virus. Overall 14 common mutations were detected in HA sequences of all 2015-2016 influenza A(H1N1)pdm09 isolates with respect to the A/California/07/2009 virus, four of which located in three different antigenic sites. Eleven rare mutations in 12 HA sequences were also detected. Phylogenetic analysis revealed that all characterized influenza A(H1N1)pdm09 isolates formed a single genetic cluster, belonging to the genetic subclade 6B.1, defined by HA amino acid substitutions S84N, S162N, and I216T. Furthermore, all isolates showed an oseltamivir-sensitive genotype, suggesting that Tamiflu (Oseltamivir) could still be the drug of choice in Turkey.

The selection of therapeutic agent to be used for the treatment of multidrug-resistant bacteria is a major concern. Polymyxin B use has been commenced in Turkey, although its clinical breakpoint is not listed in the EUCAST. This study aimed to determine the correlation between the MIC values of polymyxin B and colistin. A total of 505 isolates, including 122 isolates of Escherichia coli and 383 isolates of Klebsiella pneumoniae were included in the present study. All the isolates were assessed for colistin and polymyxin B using the broth microdilution method. The categorical agreement in the E. coli isolates was 98.4%, and the rate of very major error was 33.3%. The categorical agreement in the K. pneumoniae isolates was 99.5%, the rate of major error was 0.36%, and the rate of very major error was 0.98%. In the evaluation of the essential agreement, 1.6% error in E. coli and 2.3% error in K. pneumoniae were observed. It was concluded that polymyxin B should never be used in the treatment of the isolates reported as colistin-resistant, and if the MIC values are above 4 mg/L in E. coli and K. pneumoniae. Our results indicate importance of reporting both polymyxin B and colistin susceptibility results of clinical isolates.

Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae type B are responsible for about 80-85% of acute bacterial meningitis cases among adults and in our country it is mandatory to report bacterial meningitis cases caused by these agents. In recent years, disease control programs have focused especially on these three pathogens in our country. It is very important to know the causative agent of meningitis for prevention/control measures, choice of treatment regimen, and prediction of the severity and the course of the disease. Rapid diagnosis of meningococcal meningitis is especially vital. In addition, the identification of N.meningitidis serogroups in the community is also important for the decision of the type and combination of vaccine to be administered. The aim of this study was to optimize the real-time multiplex polymerase chain reaction (Rt-multiplex PCR) for the diagnosis of the disease and serogrouping of N.meningitidis in clinical samples in a direct, quick and reliable way. In this study, three Rt-multiplex PCR assays were optimized and standardized for the detection of N.meningitidis, H.influenzae and S.pneumoniae (NHS mix) and for the serogrouping of N.meningitidis (BCY mix and AWX mix) in our laboratory. Sensitivity of the Rt-multiplex PCR method was detected by reference strains and simulation studies. Forty three samples (41 cerebrospinal fluid (CSF), 1 serum and 1 clinical isolate) with the suspicion of acute bacterial meningitis and six nasopharyngeal isolates sent to National Reference Laboratory for Molecular Microbiology between July 2012-May 2014 were included in the present study. All samples were examined with the Rt-multiplex PCR methods. Clinical isolates were studied by both conventional and Rt-multiplex PCR methods. Oxidase, catalase test, Gram stain, API-NH and agglutination tests with specific antisera were performed in the National Respiratory Pathogens Reference Laboratory. The detection limit of the method, which was optimized and standardized in our laboratory was determined as 102 cfu/ml. The CT (threshold cycle) value in this dilution was detected approximately as 35. N.meningitidis was detected in 14 of the 41 CSF samples by the NHS mix. However, only 10 of the positive samples could be typed with BCY mix and AWX mix. Eight (80%) of them were serogroup B, one of each was (10%) serogroup A and serogroup W135, respectively. All the isolates (six nasopharyngeal and one clinical specimen) were identified as N.meningitidis serogroup B by Rt-multiplex PCR and the isolates were also confirmed by conventional methods. The CSF specimens with CT value > 35 could not be typed. We concluded that the Rt-multiplex PCR method is a rapid and reliable test for the direct diagnosis of acute bacterial meningitis due to NHS and serogrouping of N.meningitidis. Rapid diagnosis plays an important role for the treatment and control of the disease, and serogrouping of the agent plays an important role in terms of prevention/control and vaccination policies.

Genetic characterization of measles viruses (MVs) combined with acquisition of epidemiologic information is essential for measles surveillance programs used in determining transmission pathways. This study describes the molecular characterization of 26 MV strains (3 from 2010, 23 from 2011) obtained from urine or throat swabs harvested from patients in Turkey. MV RNA samples (n = 26) were subjected to sequence analysis of 450 nucleotides comprising the most variable C-terminal region of the nucleoprotein (N) gene. Phylogenetic analysis revealed 20 strains from 2011 belonged to genotype D9, 3 to D4, 2 strains from 2010 to genotype D4 and 1 to genotype B3. This study represents the first report describing the involvement of MV genotype D9 in an outbreak in Turkey. The sequence of the majority of genotype D9 strains was identical to those identified in Russia, Malaysia, Japan, and the UK. Despite lack of sufficient epidemiologic information, the presence of variants observed following phylogenetic analysis suggested that exposure to genotype D9 might have occurred due to importation more than once. Phylogenetic analysis of five genotype D4 strains revealed the presence of four variants. Epidemiological information and phylogenetic analysis suggested that three genotype D4 strains and one genotype B3 strain were associated with importation. This study suggests the presence of pockets of unimmunized individuals making Turkey susceptible to outbreaks. Continuing molecular surveillance of measles strains in Turkey is essential as a means of acquiring epidemiologic information to define viral transmission patterns and determine the effectiveness of measles vaccination programs designed to eliminate this virus. J. Med. Virol. 85:2128–2135, 2013. © 2013 Wiley Periodicals, Inc.

The serotonin (5-hydroxytryptamine) transporter (5HTt) gene has been reported to be associated with suicidal behavior. In this study, we have investigated the 50 promoter region (i.e., 5HTt gene-linked polymorphic region [5-HTTLPR]) and a 17-base pair variable number of tandem repeats polymorphism in the 5HTt gene for potential association with suicidal behavior in a Turkish population. Genotypes were determined for 182 subjects of suicide (86 attempted suicide and 96 completed suicide) and 181 healthy control subjects. Our results showed that allele frequencies at individual loci were not significantly different in the two groups. This absence of altered individual locus haplotype (allele) frequency suggests the lack of a significant genetic contribution by the 5-HTTLPR or variable number of tandem repeats variations to the expression of suicidal tendencies. However, our linkage disequilibrium analyses indicated that there may be a greater risk for suicidal behavior in carriers of the S10 and L12 alleles of 5-HTTLPR.

Bakkaloglu, Zekiye/0000-0001-9137-016X WOS: 000361745100005 PubMed: 26295292 Determination of the distribution of rotavirus genotypes is essential for understanding the epidemiology of this virus responsible for nearly half a million of deaths in patients with gastroenteritis worldwide. in the present study, we aimed to genotype the rotavirus strains isolated from diarrheal stool samples in children under 5 years old. A total of 1297 fecal samples were collected, and rotavirus antigen was detected in 73 of these samples. Antigen-positive samples were transferred to the Public Health Agency of Turkey, Molecular Microbiology Research Laboratory, and were tested for determination of genotypes G and P using semi-nested multiplex polymerase chain reaction method performed with consensus- and genotype-specific primers. Twelve specimens were found to be negative for rotavirus in genotyping method. All the positive-strains were in G1-4, G8-9, P(4), P(8), and P(9) genotypes. the most frequent GP genotype combinations were found to be G9P(8) in 21 strains (34.4%), G2P(4) in 14 strains (23.0%), and G1P(8) in 12 strains (19.7%). We found 10 distinct genotypes amongst a total of 61 strains. Among the strains isolated and genotyped in our study, 90.2% (55/61) and 67.2% (41/61) have already been included in the two existing commercial vaccines. in conclusion, these findings implicate the necessity of development of region-specific vaccines after evaluation of the local genotype distribution. Further studies on the large number of rotavirus strains would contribute to this process.

PubMedID: 25437502 Background: Group A rotaviruses are the most common causative agent of acute gastroenteritis among children less than 5 years of age throughout the world. This sentinel surveillance study was aimed to obtain baseline data on the rotavirus G and P genotypes across Turkey before the introduction of a universal rotavirus vaccination program. Methods: Rotavirus antigen-positive samples were collected from 2102 children less than 5 years of age who attended hospitals participating in the Turkish Rotavirus Surveillance Network. Rotavirus antigen was detected in the laboratories of participating hospitals by commercial serological tests such as latex agglutination, immunochromatographic test or enzyme immunoassay. Rotavirus G and P genotypes were determined by reverse transcription polymerase chain reaction (RT-PCR) using consensus primers detecting the VP7 and VP4 genes, followed by semi-nested type-specific multiplex PCR. Results: RT-PCR found rotavirus RNA in 1644 (78.2%) of the samples tested. The highest rate of rotavirus positivity (38.7%) was observed among children in the 13 to 24 month age group, followed by children in the age group of 25 to 36 months (28.3%). A total of eight different G types, six different P types, and 42 different G-P combinations were obtained. Four common G types (G1, G2, G3, and G9) and two common P types (P[8] and P[4]) accounted for 95.1% and 98.8% of the strains, respectively. G9P[8] was the most common G/P combination found in 40.5% of the strains followed by G1P[8] (21.6%), G2P[8] (9.3%), G2P[4] (6.5%), G3P[8] (3.5%), and finally, G4P[8] (3.4%). These six common genotypes included 83.7% of the strains tested in this study. The rate of uncommon genotypes was 14%. Conclusion: The majority of the strains analyzed belonged to the G1-G4 and G9 genotypes, suggesting high coverage of current rotavirus vaccines. This study also demonstrates a dramatic increase in G9 genotype across the country. © 2014 Durmaz et al.

Genetic characterization of measles viruses (MVs) combined with acquisition of epidemiologic information is essential for measles surveillance programs used in determining transmission pathways. This study describes the molecular characterization of 26 MV strains (3 from 2010, 23 from 2011) obtained from urine or throat swabs harvested from patients in Turkey. MV RNA samples (n = 26) were subjected to sequence analysis of 450 nucleotides comprising the most variable C-terminal region of the nucleoprotein (N) gene. Phylogenetic analysis revealed 20 strains from 2011 belonged to genotype D9, 3 to D4, 2 strains from 2010 to genotype D4 and 1 to genotype B3. This study represents the first report describing the involvement of MV genotype D9 in an outbreak in Turkey. The sequence of the majority of genotype D9 strains was identical to those identified in Russia, Malaysia, Japan, and the UK. Despite lack of sufficient epidemiologic information, the presence of variants observed following phylogenetic analysis suggested that exposure to genotype D9 might have occurred due to importation more than once. Phylogenetic analysis of five genotype D4 strains revealed the presence of four variants. Epidemiological information and phylogenetic analysis suggested that three genotype D4 strains and one genotype B3 strain were associated with importation. This study suggests the presence of pockets of unimmunized individuals making Turkey susceptible to outbreaks. Continuing molecular surveillance of measles strains in Turkey is essential as a means of acquiring epidemiologic information to define viral transmission patterns and determine the effectiveness of measles vaccination programs designed to eliminate this virus.