A rare case of necrotizing fasciitis of the abdominal wall due to Hungatella effluvii and Streptococcus constellatus.

We report a rare case of necrotizing fasciitis of the abdominal wall caused by Hungatella effluvii and Streptococcus constellatus. Necrotizing fasciitis has high mortality, so early diagnosis and aggressive treatment are essential for good clinical outcome. Identification of the microbial contribution to these infections is crucial for targeted antibiotic treatment.

Colistin resistance increases 28-day mortality in bloodstream infections due to carbapenem-resistant Klebsiella pneumoniae.

Mortality due to K. pneumoniae bacteremia is on rise, particularly in regions with high rates of carbapenem and colistin resistance. We aimed to define risk factors for colistin resistance and its impact on mortality. Patients diagnosed with "carbapenem-resistant K. pneumoniae (CRKp)" bacteremia between 2014 and 2018 were divided into two groups as "colistin susceptible (ColS)" and "colistin resistant (ColR)" based on broth microdilution method. Retrospective case-control study was conducted to compare characteristics and outcomes. Multiple logistic regression model was used to define independent risk factors for acquired colistin resistance and Cox proportional hazard model for 28-day mortality. A total of 82 patients (39 ColS and 43 ColR) were included. Mean age was 61.5 years, and 50 (61%) were male. Colistin resistance was significantly increased with duration of hospital stay (p = 0.007) and prior colistin use (p = 0.007). Overall, the 28-day mortality rate was 66%. Age (p = 0.014) and colistin resistance significantly increased 28-day (p = 0.009) mortality. Microbiological response to treatment within 7 days favors survival. PFGE analysis revealed an outbreak with K. pneumoniae ST78 and ST45 clones. Patients treated with combined antimicrobials had significantly lower 28-day mortality (p = 0.045) in comparison to monotherapy. However, types of combinations did not show significant superiority on each other. Colistin resistance increases 28-day mortality in CRKp bacteremia. Although combined regimens are more effective than monotherapy, existing antibacterial combinations have no apparent superiority to each other. New treatment options are pivotal.

First pediatric case of osteomyelitis caused by Robinsoniella peoriensis.

Robinsoniella peoriensis is a gram-positive, spore-forming, anaerobic rod. In our study, we isolated R. peoriensis from an open fracture of the left distal tibia of a three-year-old male patient. Tissue anaerobic culture was positive for R. peoriensis. It was identified with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry and confirmed via 16S rRNA gene sequencing. The patient responded to ampicillin-sulbactam and amikacin antibiotic therapy. Antimicrobial susceptibility testing should be performed to guide the choice of treatment. To the best of our knowledge, this is the first report of R. peoriensis osteomyelitis in a pediatric patient and first report from Turkey.

Methicillin-resistant Staphylococcus aureus in a Turkish hospital: characterization of clonal types and antibiotic susceptibility.

INTRODUCTION: The assessment of the clonal spread of methicillin resistant Staphylococcus aureus (MRSA) in nosocomial and community-acquired infections through characterization of the isolates is critical for tracking the evolution of the epidemics, implementing effective control measures, and preventing future outbreaks of MRSA. In this context, it is aimed with this study to determine the clonal relationships between the S. aureus isolates obtained from the patients receiving treatment in the intensive-care units of a state hospital in Turkey. METHODOLOGY: A total of 80 MRSA isolates obtained from the patients receiving treatment in three different intensive-care units were analyzed for their antibiotic susceptibilities, pulsed-field gel electrophoresis profiles, and multilocus sequence types. RESULTS: The dendrogram of the pulsed-field gel electrophoresis profiles revealed two major pulsed-field gel electrophoresis pulsotypes: A and B, which were further divided into two (A1 and A2) and four (B1-B4) subgroups, respectively. Multilocus sequence typeanalysis indicated that all isolates belonged to a single MRSA clone, sequence type 239. No significant difference was found between the antibiotic sensitivity profiles of strains isolated from different intensive-care units. All of the strains were sensitive to linezolid and vancomycin. CONCLUSIONS: It was concluded that the MRSA strains isolated from the patients receiving treatment at the intensive-care units of the hospital constituted two major pulse-field types and belonged to the ST239 lineage, one of the most extensively distributed MRSA lineages throughout the world.

Emergence of carbapenemase-producing and colistin resistant Klebsiella pneumoniae ST101 high-risk clone in Turkey.

Carbapenemase-producing and colistin resistant Klebsiella pneumoniae has become a worldwide healthcare problem. This study describes molecular characterization of carbapenemase-producing and colistin resistant clinical K. pneumoniae isolates.A total of 93 non-replicate carbapenem and colistin resistant K. pneumoniae were recovered from clinical specimens in a university hospital during 2017-2019. Detection of blaOXA-48, blaKPC, blaNDM-1, blaIMP, blaVIM-1 and mcr-1, -2, -3, -4, -5, -6, -7, and -8 genes was performed by PCR. The bacterial isolates were assigned to clonal lineages by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).All isolates harbored blaOXA-48 and only two isolates harbored blaOXA-48, and blaNDM-1 genes together. In colistin resistant K. pneumoniae, mcr-1 was detected in two (2.1%) isolates. Ninety three isolates of K. pneumoniae were categorized into three clusters and five pulsotypes. MLST revealed two different sequence types, ST101 (89/93) and ST147 (4/93).In our study ST101 was found to be a significantly dominant clone carrying blaOXA-48 and among our strains a low frequency of mcr-1 gene was determined. The emergence of colistin resistance was observed in K. pneumoniae ST101 isolates. ST101 may become a global threat in the dissemination of carbapenem and colistin resistance.

Clonal distribution of vancomycin-resistant Enterococcus faecium in Turkey and the new singleton ST733.

BACKGROUND: The aim of this study was to provide information about the spread and characteristics of the vancomycin-resistant Enterococcus faecium isolates (VREfm) in Turkey. METHODS: Seventy-one nonduplicate consecutive isolates of VREfm were obtained from various clinical specimens of inpatients treated at university or training hospitals in seven regions of Turkey. Further characteristics included antibiotic susceptibility testing, pulsed-field gel electrophoresis (PFGE) of SmaI-digested genomic DNA, and multilocus sequence typing (MLST) of selected isolates. The presence of vancomycin resistance and virulence genes (esp and hyl) was investigated by polymerase chain reaction (PCR). RESULTS: All VREfm isolates had MICs to vancomycin of ≥32 mg/L and contained the vanA gene. The presence of esp gene was identified in 64 and hyl in eight VREfm isolates. All VREfm showed the multiresistance phenotype, including ampicillin (99%), penicillin (99%), imipenem (99%), ciprofloxacin (87%), moxifloxacin (87%), erythromycin (97%), streptomycin (86%), gentamicin (82%), tetracycline (70%), and teicoplanin (99%). All were susceptible to tigecycline while quinupristin-dalfopristin (97%) and linezolid (93%) were the most active other agents. Analysis of the PFGE profiles showed that 53 (74.6%) VREfm isolates shared a similar electrophoretic profile, designed as type 1, and were closely related (>85%). The sequence type was identified by MLST in 44 VRE isolates with unrelated or closely related PFGE patterns. MLST revealed that nosocomial spread of VREfm resulted from dissemination of lineage C1 E faecium clones. Sequence types ST78, ST203, and ST117 were the most frequently isolated. This is the first report of ST733 around the world. CONCLUSIONS: Lineage C1 clones are disseminated among clinical VREfm isolates in seven different regions in Turkey. Regarding VREfm isolates, the worldwide epidemic strains are in circulation in Turkey.

Molecular typing of drug-resistant Mycobacterium tuberculosis strains from Turkey.

OBJECTIVES: Appropriate antibiotic therapy and prevention of cross-contamination are the most important subjects in tuberculosis (TB) control. The aim of this study was to investigate the major phylogenetic clades and transmission rate of multidrug-resistant (MDR) Mycobacterium tuberculosis isolates (n = 200) from patients with TB in Sivas and Konya Provinces of Turkey. METHODS: The phylogenetic relationship among the isolates was investigated by spoligotyping method. In addition, the 24-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing method was used to reveal cross-contamination. RESULTS: Spoligotyping revealed 13 different spoligotypes. A total of 188 strains (94.0%) were included in the cluster. The most prominent spoligofamily was the T family (43.0% of strains), followed by LAM (26.0%), H (8.0%), X and S (both 6.0%) and U (5.0%). Also, 12 strains (6.0%) belonged to the Beijing profile. MIRU-VNTR results showed 176 (88.0%) different genotypes among the isolates. In total, 24 strains (12.0%) were in the cluster. CONCLUSIONS: According to spoligotyping, there is a heterogeneous M. tuberculosis population in Turkey. MIRU-VNTR results showed that cross-contamination observed between MDR M. tuberculosis isolates in Turkey is controllable.

Detection of vancomycin-resistant enterococci in samples from broiler flocks and houses in Turkey.

Vancomycin-resistant enterococcus (VRE) is a global threat to public health. Knowledge about the occurrence of vanA-carrying enterococci in broiler and environmental samples is important as antibiotic resistance can be transferred to human bacteria. The aim of this study was to investigate the presence of VRE in broiler cloacal and environmental (house) samples and to genotype the isolates. In this study, 350 swabs were collected from broiler farms. All samples were plated onto enterococcus selective agar containing 6 mg/L vancomycin and 64 mg/L ceftazidime. Minimum inhibitory concentration (MIC) values were determined for vancomycin and teicoplanin. Vancomycin-resistant Enterococcus faecium (VREfm) was isolated from 6 out of 300 (2%) broiler cloacal samples and 13 out of 50 (26%) house samples. All E. faecium isolates had vanA genes. All VREfm isolates (19 isolates) were confirmed to be 95% similar to each other. In conclusion, although 20 years have passed since the ban on avoparcin in Turkey, the present study shows that VREfm isolates are still present in broiler production and especially in broiler houses, and most importantly, a major VREfm clone was isolated from broiler cloacal and house samples.

A diagnostic challenge in clinical laboratory: Misidentification of Neisseria subflava as Neisseria meningitidis by MALDI-TOF MS.

MALDI-TOF MS provides fast, easy to perform and cost-effective diagnosis in clinical microbiology laboratories, however in some cases results of MALDI-TOF MS should be confirmed with additional tests. This confirmation is especially important for causes of life-threatening infections like Neisseria meningitidis. In our laboratory, three isolates were identified as N. meningitidis by Bruker MALDI Biotyper (BD, USA) between April 2018 and March 2019 from clinical specimens of blood, sputum, and urine. 16S rRNA sequencing was performed for further investigation. Two of the isolates were identified as Neisseria subflava and only one was confirmed as N. meningitidis by sequencing. These results show that MALDI-TOF MS is not always reliable in the diagnosis of N. meningitidis and clinical microbiologists should confirm these results with additional tests. Also, clinical correlations should be determined. Accurate identification of this microorganism is very important because of the necessity of prophylactic antimicrobial usage and biosafety precautions. Enlarged databases of Neisseria species are needed to overcome this problem.

[Determination of the Subspecies of Francisella tularensis Isolated in Turkey by Molecular Methods]. / Türkiye'de Izole Edilen Francisella tularensis Alt Türlerinin Moleküler Yöntemlerle Belirlenmesi.

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.

[Investigation and Genotyping of Chlamydia psittaci ompA Gene in Pigeon (Columbia domestica) Feces]. / Güvercin (Columbia domestica) Diskilarinda Chlamydia psittaci ompA Geninin Arastirilmasi ve Genotiplendirilmesi.

Avian chlamydiosis, is a highly contagious, systemic disease occuring in domestic and wild birds. Chlamydia psittaci, the causative agent of the disease, is a gram-negative bacterium in the Chlamydiaceae family that can only live within the cell. The agent can be transmitted directly to humans by contact with infected animals or feces of infected animals. It can also be transmitted by inhalation of fecal dust. Since the disease has a zoonotic character, it is also important in terms of public health. By using the monoclonal antibodies against cell wall proteins (OMP) of C.psittaci, six (A-F) and two (WC and M56) serotypes were determined in mammals. The aim of this study was to investigate and genotype the presence of C.psittaci ompA gene in domestic pigeon feces grown in family management style in ten different districts in Ankara in winter and summer seasons. Within the scope of the study, 100 pigeon stool samples were collected from birdhouses in 10 different districts of Ankara (Beypazari, Haymana, Kizilcahamam, Cubuk, Pursaklar, Bala, Cankaya, Polatli, Golbasi and city center) in two different seasons. DNA extraction from fecal samples was performed by classical methods. The presence of the agent in the extracted DNA samples was investigated by polymerase chain reaction (PCR) analysis of the ompA gene. Two-way sequence analysis of the ompA gene was performed with the primers used in the study from the target DNA products amplified by PCR. The results of sequence analysis were compared with the international database and serotyping/genotyping was performed. In the study, C.psittaci ompA gene was detected in 6 (6%) samples of 100 pigeon stool samples. Among these positive samples, two were from Bala (one sample from winter, one sample from summer), two were from Haymana (one sample from winter, one sample from summer) and two were from Golbasi (one sample from winter, one sample from summer); where the same agent was isolated in the same aviaries in different seasons. In this study, no difference was found between the presence of C.psittaci in pigeon droppings and season. In addition when the sequence analysis of the isolated samples were compared with the World database; all isolates were found to be 100% genotype B and 99% genotype E. In this study, the sequence analysis of the ompA gene of C.psittaci from domestic pigeon feces was determined for the first time in Turkey. Although the presence of C.psittaci in domestic pigeons is low, it is a zoonotic bacterium and is important for the public health.

An unusual case of peritoneal dialysis-associated bacterial peritonitis caused by Weeksella virosa.

Weeksella virosa is an atypical Gram-negative bacterium that does not grow on MacConkey agar. In this report, we present a 4-year-old female patient with Addison's disease and end-stage renal failure secondary to focal sclerosing glomerulosclerosis. Continuous ambulatory peritoneal dialysis had been performed, and 3 months later, the patient developed fever, diarrhea, and vomiting. Peritoneal fluid culture and dialysis fluid culture were positive for W. virosa. It was identified with Phoenix (BD, USA) and confirmed via 16S rRNA sequencing. It cannot be identified by Maldi Biotyper (Bruker). The isolate was found to be resistant to cephalosporins, ciprofloxacin, and amikacin by gradient test. Intraperitoneal cefepime was initiated but since antimicrobial susceptibility testing revealed cephalosporin resistance, therapy was changed to intraperitoneal meropenem. Following the removal of peritoneal dialysis catheter, fever, abdominal distention, and vomiting were resolved. Piperacillin, aztreonam, and carbapenems can be used for empirical therapy. Antimicrobial susceptibility testing should be performed to guide the choice of treatment. Removal of peritoneal dialysis catheter is an important step of management of this infection. To our knowledge, this is the first report of W. virosa in a pediatric patient and first report from Turkey.

First molecular evidence of ocular transmission of Encephalitozoonosis during the intrauterine period in rabbits.

Many reports have been published on the suspected vertical transmission of Encephalitozoon cuniculi; however, prior to 2003, these reports were based on circumstantial evidence, such as histopathological, immunohistochemical, or serological diagnosis of the infection. In 2003, vertical transmission of the parasite was confirmed by detection of E. cuniculi DNA in fetuses with the nested polymerase chain reaction (PCR) technique. However, the passage of the parasite to eyes of fetus during the intrauterine stage still requires verification. In the current study, natively infected with parasite spores female rabbits were mated with non-infected males. All resulting offspring that died before ten postpartum days were investigated using molecular techniques to confirm the intrauterine transmission of the parasite to the offspring' eyes. In total, 119 DNA samples from rabbit offspring tissues were collected from blood, kidney, brain, eye (both eyes were used as single samples), lung, placenta, liver and heart were used for PCR. Parasitic DNA in the eyes of offspring was detected (54%) 6 of 11 naturally seropositive mother rabbits. PCR results were found to be positive for the eyes of 63% (19/30) of the offsprings from seropositive rabbits. Therefore, mother rabbits naturally infected with E. cuniculi showed the molecular presence of the parasite in their offspring' eyes. Sequence analysis confirmed the partial DNA sequence data of E. cuniculi and blast analysis identified the agent as genotype I. These results confirm transmission of E. cuniculi to rabbit offspring' eyes in the intrauterine period. This is the first molecular evidence to show ocular transmission of the infection via an intrauterine route in rabbits.

From days to hours: Can MALDI-TOF MS system replace both conventional and molecular typing methods with new cut off level for Vancomycin Resistant Enterococcus faecium.

Vancomycin-Resistant E. faecium (VRE) strains from clinical specimens were identified by conventional methods before. Following the phenotype-based identification, all strains were also identified using both BD Phoenix and VITEK MS bioMérieux System. Strains were typed with the Bruker MALDI-TOF MS system, pulsed field gel electrophoresis (PFGE) and 16S rRNA gene sequencing analysis and then the sensitivity compared for each. A cut off value of 850 assigned with Bruker MALDI-TOF MS system was found to give equal sensitivity to that of PFGE. Results obtained were compared with those of molecular typing. The main advantage of MALDI-TOF MS technology over the others was the much shorter analysis time which lasted only a few hours rather than days or a whole week. Also, the Bruker MALDI-TOF MS system was used for typing and compared with the gold standard method and this study is first to report the determined cut off level for typing of VRE strains.

The Antibiotic sensitivity of Stenotrophomonas maltophilia in a 5-year period and investigation of clonal outbreak with PFGE.

INTRODUCTION: Stenotrophomonas maltophilia, which is able to form a biofilm, has mostly been related to catheters when it is the agent in hospital infections; these infections generally present as bacteremia and pneumonia, which may progress with complications and result in death. METHODOLOGY: The study included 153 S. maltophilia strains isolated from clinical samples sent to our hospital laboratory between 1 January 2014 and 30 June 2018. The bacteria were identified and their antibiotic sensitivity was determined using the VITEK-2 automated system. PFGE (Pulsed Field Gel Electrophoresis): The strains isolated from 34 patient clinical samples and from 1 patient bedcover were taken for PFGE examination. RESULTS: The TMP/SXT and levofloxacin sensitivity of 153 S. maltophilia strains was examined. TMP/SXT resistance was determined to be 39% and levofloxacin resistance at 5%. Among 35 S. maltophilia strains, seven genotypes were identified using the PFGE method. While three strains showed a specific genotype profile, the other 32 were determined to consist of four clusters. The cluster rate was therefore 91.4% (32/35). CONCLUSIONS: There was a clonal relationship between the vast majority of the 35 S. maltophilia isolates, which suggests that there was a cross-contamination problem in the hospital. One strain (#4) was identified by dendrogram analysis showed a high rate of similarity to the other strains and was determined to be the common source of the cross-contamination.

Prevalence and diversity of rotavirus A genotypes cirulating in Turkey during a 2-year sentinel surveillance period, 2014-2016.

Human rotavirus A (RVA) is the main etiological agent of watery diarrhea among children under 5 years of age worldwide. The aims of this study were to investigate the prevalence and diversity of RVA genotypes circulating in Turkey during a 2-year sentinel surveillance study. A total of 1639 rotavirus antigen-positive stool samples were obtained from children younger than 5 years of age hospitalized with acute gastroenteritis. Rotavirus G and P genotypes were determined by reverse transcription polymerase chain reaction (RT-PCR) with consensus primers for the VP7 and VP4 genes, followed by semi-nested type-specific multiplex PCR. Rotavirus RNA was detected in 1396 (85.3%) of the samples tested. The highest detection rate (38.2%) was obtained among children in the 0-12 months age group, followed by children in the 13-24 months age group (36.2%). The most prevalent genotype was G1P[8] (24.6%) followed by G3P[8] (19.6%), G9P[8] (12.2%), G2P[4] (9.5%), G2P[8] (6.5%), and G4P[8] (4.8%). The proportions of uncommon and mixed genotypes were 21.5% and 1.14%, respectively. The large number of genotypes observed, including common, uncommon, and mixed types, indicates a high heterogeneity of RVA strains circulating in Turkey. The current study also exhibited dramatic fluctuations on the prevalences of the common genotypes, with increases in G3 and G1 and decreases in G9 and G2 from 2014-2016.

Outbreak of Hospital Infection from Biofilm-embedded Pan Drug-resistant Pseudomonas aeroginosa, Due to a Contaminated Bronchoscope.

Background: Colistin-resistant Pseudomonas aeruginosa (P. aeruginosa) has been defined as pandrug-resistant (PDR) strain. Outbreaks of PDR P. aeruginosa especially in pulmonary tract infections due to contaminated bronchoscopes have rarely been reported. The emergence of pandrug-resistant strains in both CF (Cystic Fibrosis) and non-CF clinical isolates over recent years remains of a great concern. Hospital wards contaminated with PDR P. aeruginosa infection, must be shot down until their eradication. Health Authorities must be informed immediately and infection control strategies must be implemented. Aim: To report such an outbreak and modify the infection control strategy in an academic hospital in Ankara Turkey. Methods: From October to December 2013, PDR-Pseudomonas aerogionsa were identified from bronchial cultures of 15 patients who had undergone bronchoscopy prior to the infection. Three batches of surveillance cultures were obtained from the environmental objects and healthcare workers related to the procedures. Pulsed-field gel electrophoresis (PFGE) was used for bacterial typing. Antimicrobial susceptibility was assessed by disc diffusion and E-test methods. Findings: A total of 70 specimens were obtained during the first surveillance operation. One Colistin-resistant P. aeroginosa was isolated from a bronchoscope. Although the disinfection protocols for bronchoscope were revised and implemented, seven additional bronchial cases were identified thereafter. The pathogen was identified from two subsequent surveillance cultures and was not eliminated until Ethylene oxide sterilization was added to the disinfection protocol. PFGE revealed that all 15 isolates from the patients and the three isolates from the bronchoscope shared a common pattern with minor variance. XbaI restriction enzyme turned out better than SpeI in interpreting bacterial pulse types with BioNumerics 6.0. The most suitable cut off value for SpeI was above 80% Dice similarity while for XbaI above 95%Dice similarity with BioNumerics 6.0. Conclusion: The outbreak of "Colistin" pan drug-resistant Pseudomonas aeroginosa was caused by a contaminated bronchoscope and was terminated by the implementation of a revised disinfection protocol for bronchoscope.

Detection and identification of cutaneous leishmaniasis isolates by culture, Polymerase chain reaction and sequence analyses in Syrian and Central Anatolia patients.

OBJECTIVES: To characterize the cutaneous leishmaniasis (CL) isolates of Syrian and Central Anatolia patients at species levels. Methods: Skin scrapings of 3 patients (2 Syrian, 1 Turkish) were taken and examined by direct examination, culture in Novy-MacNeal-Nicole (NNN) medium, internal transcribed spacer polymerase chain reaction and sequence analysis (PCR). Results:According to microscopic examination, culture and PCR methods, 3 samples were detected positive. The sequencing results of all isolates in the study were identified as Leishmania tropica. The same genotypes were detected in the 3 isolates and nucleotide sequence submitted into GenBank with the accession number: KP689599. Conclusion: This finding could give information about the transmission of CL between Turkey and Syria. Because of the Syrian civil war, most of the Syrian citizens circulating in Turkey and different part of Europe, this can be increase the risk of spreading the disease. So, prevention measurements must be taken urgently.

Molecular Typing and Antimicrobial Susceptibility of Staphylococcus aureus Strains Isolated from Raw Milk, Cheese, Minced Meat, and Chicken Meat Samples.

The objectives of this study were: i) to detect the presence of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in raw milk, cheese, beef minced meat, and chicken meat samples; ii) to evaluate the antimicrobial susceptibility of the isolates; and iii) to determine clonal relation among the isolates by using pulsed-field gel electrophoresis (PFGE) method. Therefore, a total of 160 food samples were randomly collected between August 2014 and May 2015 in Hatay province, located in the southern Turkey. Twenty (12.5%) of the samples were found to be contaminated with S. aureus. A total of 40 isolates from the 20 positive samples were confirmed to be S. aureus by multiplex PCR based on 16S rRNA and nuc gene. The mec A gene was not detected in any of the S. aureus strains. In the present study, 39 out of 40 (97.5%) isolates were found to be resistant to one or more antibiotics. All of isolates were susceptible to gentamicin, oxacillin, and vancomycin. The highest resistance rate was detected in penicillin (95%) and ampicillin (92.5%), followed by tetracycline (30%), erythromycin (20%), ciprofloxacin (12.5%). Nine major patterns were determined by PFGE. In 6 of these patterns, thirty-six strains (90%) had identical PFGE profiles.

[Comparison of MALDI-TOF and 16S rRNA methods in identification of viridans group streptococci]. / Viridans grup streptokok tanimlamasinda MALDI-TOF ve 16S rRNA yöntemlerinin karsilastirilmasi.

Accurate identification of viridans group streptococci (VGS) frequently encountered as a causative agent of infective endocarditis is always a challenge for the clinical microbiology laboratory. Clinical microbiology laboratories generally use semi automatic/full automatic systems, molecular methods and also conventional methods for the identification of these bacteria. There are recent published studies that have used MALDI-TOF (Matrix Assisted Laser Ionization Mass Spectrometry-Time of Flight) systems in the identification of VGS. The aim of the study was to compare the performance of the conventional methods, semi automatic and MALDI-TOF MS system used in identification of VGS in oral microbiota of persons under the risk of infective endocarditis, with the gold standard method 16S rRNA sequence analysis and to create a diagnosis algorithm for the identification of VGS in clinical microbiology laboratories according to the obtained data.The study was conducted with 51 VGS strains isolated from oral microbiota of the patients with rheumatologic cardiac, valve and/or prosthetic valve diseases, under the risk of development of infective endocarditis, who have admitted to Ankara Numune Training and Research Hospital, Department of Cardiology, between February-June 2015. Standard microbiology procedures, optochin susceptibility and bile solubility tests were done for the isolation of bacteria. Bacteria were also identified with APISTREP (bioMérieux, France) and MALDI-TOF MS Bruker Microflex (Bruker Biotyper; Bruker Daltonics, Bremen, Germany) methods. BSF-8 (5´-AGAGTTTGATCCTGGCTCAG-3´) and BSR-534(5´-ATTACCGCGGCTGCTGGC-3´) primers were used in the 16S rRNA sequence analysis of bacteria. ABI PRISM 3100 Avan t Genetic Analyzer (Applied Biossytems, Foster City, CA, USA) were used for the sequence analysis. Electropherograms were analyzed in SeqScape Software (Applied Biosystems, Foster City, CA, USA) and compared with the reference sequences in GenBank with BLASTN (NCBI). According to the result of optochin and bile solubility tests, with API STREP system, 16 (31,37%) of the isolates were identified as Mitis group, 15 (29.41%) as Anginosus group, 9 (17.5%) as Salivarius group, 7 (13,73%) as Sanguinis group and 4 (7.84%) as Bovis group among optochin and bile resistant alpha hemolytic streptococci. Moreover, of the same isolates 20 (39.22%) were identified as Mitis group, 14 (27.45%) as Anginosus group, 13 (25.49%) as Salivarius group and 4 (7.84%) as Sanguinis group with MALDI-TOF system. In the identification with 16S rRNA, 25 (49.02%) of the isolates were identified as Mitis group, 13 (25.49%) as Anginosus group, 12 (23.53%) as Salivarius group and 1 (1.96%) as Sanguinis group. According to the results, it was determined that 33 (64.70%) of the isolates identified in MALDI-TOF MS system and 31 (60.78%) of the isolates identified in API STREP system were compatible with 16S rRNA sequence analysis method. For Mitis group, API STREP test sensitivity was 48.00% and specificity was 84.62% and MALDI-TOF system sensitivity was 80.00% and specificity was 100%. As VGS identification is a complicated process, we believe a single method will be insufficient for the identification of these isolates in clinical microbiology laboratories. We suggest that MALDI-TOF system can be used for VGS diagnosis, however, optochin test and/or molecular methods should also be included in the diagnosis algorithm when necessary.