[The value of PCR method in the species-level identification of a mucoid Salmonella sp. strain isolated from the urine culture of a case with asymptomatic nephrolithiasis]. / Nefrolitiazisli asemptomatik bir olgunun idrar kültüründen izole edilen mukoid Salmonella sp. susunun tür düzeyinde tanimlanmasinda PCR yönteminin degeri.

Colonies of the Salmonella strains usually show a smooth (S) character. Therefore, Salmonella strains producing mucoid colony are very rarely encountered in the literature. Identification of the mucoid Salmonella strains to the species level is difficult via conventional methods, since the mucus layer does not allow the bacterium to respond to the antigenic reactions. In this study we aimed to emphasize the identification of Salmonella serotypes by the polymerase chain reaction (PCR) when rough (R) or mucoid (M) Salmonella isolates are encountered in the laboratory. The urine culture of a 17-year-old female patient revealed growth of 100.000 cfu/mL gram-negative bacilli in mucoid colony morphology. The isolate was identified as Salmonella sp. by biochemical tests and Vitek 2 (bioMérieux, France) automated identification system. Agglutination tests showed negative reaction with the known antiserums. Absence of agglutination was attributed to the mucoid character of the isolate. Identification of the Salmonella sp. was confirmed by Vitek MS MALDI-TOF (bioMérieux, France) analysis method, however, the serotype of the strain could not be identified. In order to verify that the mucoid colony was Salmonella spp., species-specific PCR was performed using invA primers, and Salmonella sp. identification was verified by observing a 284 base-pair (bp) PCR amplicon. Subsequently, serogrouping was done by multiplex-PCR (mPCR), which could identify the O:B (O:4), O:C1 (O:7), O:C2-C3 (O:8), O:D (O:9, O:9,46, O:9,46,27), and O:E (O:3,10, O:3,19) somatic antigens. It was detected that the mucoid Salmonella sp. formed a band of approximately 615 bp in size and took place in group D. Another mPCR directed towards O:D1(O:9) and O:E1(3,10) somatic antigens to detect subgroups of group D mucoid Salmonella spp., revealed that the isolate formed a DNA band of approximately 624 bp in size and took place in group D1 which is usually isolated from human. Modified version of another mPCR was used to determine phase-1 flagellar antigen of common Salmonella serovars, as well as to determine the phase-1 flagellar antigen of mucoid Salmonella spp. in group D1. Thus, the isolate was serotyped as Salmonella Enteritidis (1.9,12:g,m:-). Antibiotic susceptibility test performed by disc diffusion method in line with the recommendations of CLSI, revealed that the isolate was susceptible to ampicillin, ciprofloxacin, ceftriaxone, trimethoprim-sulfamethoxazole and chloramphenicol. In conclusion, PCR is a reliable and rapid alternative method that contributes to the conventional serotyping of Salmonella when rough or mucoid strains that lack somatic and flagellar antigens, are isolated.

[A nine-year evaluation of cutaneous leishmaniasis patients in Diyarbakir Training and Research Hospital, Turkey]. / Diyarbakir Egitim ve Arastirma Hastanesinde dokuz yillik kutanöz leysmanyazis olgularinin degerlendirilmesi.

Leishmaniasis, which is a zoonotic disease caused by obligate intracellular parasites namely Leishmania spp., may present as visceral, cutaneous and mucocutaneous forms. Turkey is accepted as an endemic region for leishmaniasis. Cutaneous forms are more frequent in South and Southeastern Anatolia regions while visceral forms are more frequent in Aegean and Mediterranean regions. The aim of this study was to evaluate the cutaneous leishmaniasis (CL) cases identified in Diyarbakir Training and Research Hospital, retrospectively in a nine-year period, calling attention to the increase of cases in 2013, in our region. A total of 128 patients aged between 0-75 years, who were clinically diagnosed as CL in the dermatology outpatient clinic of our hospital between January 2005-August 2013 were evaluated in the study. Parasitologic diagnosis was based on the identification of Leishmania amastigote forms inside and outside the macrophages observed in Giemsa stained smears of serous liquid samples appropriately obtained from cutaneous lesions by scraping the edge of the ulcer or slightly removing the scab. Parasites were microscopically detected in 56 of 128 (43.7%) patients who were clinically pre-diagnosed as CL. Of those patients, 41 (73.2%) were female, 15 (26.8%) were male, and 34 (60.7%) were in 0-20, 10 (17.9%) were 21-41, and 12 (21.4%) were ≥ 42 years age group. In positive cases, lesions were found to be at the facial area of 34, arms and hands of 14, legs and feet of eight patients. Besides, 21 of 56 (37.5%) patients were detected with lesions on their various anatomic areas as hand and face or face and legs. When evaluating the distribution of 56 confirmed CL cases according to the study years, the case numbers were low in 2005 (n= 1; 2%) and 2006 (n= 2; 4%), there were no admission to our hospital in the period of 2007 to 2009, however the case numbers showed an increasing trend after 2010 [4 (7%) cases in 2010; 3 (5%) in 2011; 4 (7%) in 2012], reaching unusual number in 2013 (n= 42; 75%). When evaluating the CL cases according to their locations, 51 were from center and towns/villages of Diyarbakir, and five were from neighbouring countries (Mardin: 2, Urfa: 2, Adana: 1). It was noted that nine (37.5%) of the 24 cases detected in the city center of Diyarbakir were children of Syrian refugees. In conclusion, immigrations to endemic regions of Turkey from neighbouring countries where CL incidence is higher may lead to severe increases in case numbers, thus more powerful protective measures should be taken in those endemic areas.

[Four cases of cutaneous anthrax in Diyarbakir, Turkey]. / Diyarbakir'da saptanan dört kütanöz sarbon olgusu.

Anthrax which is a rare disease in developed countries, is still a serious public health problem in countries like Turkey where livestock is common. In this report, four cases of cutaneous anthrax detected in Kirkira village of Diyarbakir, Southeast Anatolia, Turkey, were presented. Three female and one male patients were admitted to our hospital with the complaints of skin lesions and high fever lasting for 10 days. Their history indicated that they injured their fingers during slaughtering of a dead cow meat. All patients had irregular edged necrotic vesiculobullous lesions on the erythematous and edematous base on their hand fingers, developed in 1 week following the contact. There was no systemic finding and the laboratory findings were within normal limits. Typical bamboo cane shaped gram-positive bacilli were observed on the Gram stained smears prepared from the vesicular lesions. Aerobic cultures in blood agar media revealed typical R type colonies, gray in color, creased, granulated and 2-3 mm in diameter within 24 hours of incubation. In one patient although the lesion was typical and characteristic gram-positive bacilli were detected in the Gram stained smears, no growth was seen in the cultures. The isolates (n= 3) were identified as Bacillus anthracis by conventional microbiological methods, and also confirmed by Vitek 2 (BioMerieux, France) automated identification system. Antibiotic susceptibility tests were performed by disc diffusion method according to the CLSI guidelines. The isolates were found susceptible to penicillin G, ampicillin, erythromycin, amikacin, chloramphenicol, tetracycline, vancomycin and ciprofloxacin. All of the patients were treated successfully with penicillin or ciprofloxacin accompanied by topical wound care. In the last years several case series of anthrax were reported especially from the East and Southeastern Anatolia regions of Turkey. These four cutaneous anthrax cases from Diyarbakir, Turkey were reported to withdraw attention to anthrax in that specific area. It was concluded that in areas where anthrax is endemic to educate people under risk, to take the necessary preventive measures and to rule out anthrax in the differential diagnosis of cases presenting with typical ulcers and had contact with animals or their products, are of crucial importance for the early initiation of appropriate treatment which would decrease related morbidity and mortality.

[Investigation of biofilm-associated antibiotic susceptibilities of methicillin-resistant staphylococci isolated from catheter-related nosocomial infections]. / Kateter ile iliskili hastane enfeksiyonlarindan izole edilen metisiline dirençli stafilokoklarda biyofilm ile iliskili antibiyotik duyarliliginin arastirilmasi

Risks for development of local and/or systemic infections are the most important complications of catheters that are widely used during hospitalization process. The aims of this study were to investigate and compare the antibiotic susceptibilities of methicillin-resistant staphylococci isolated from catheters, in planktonic and biofilm forms, and to evaluate the antimicrobial effects of antibiotics on those forms alone and in combinations. A total of 30 strains [15 methicillin-resistant Staphylococcus aureus (MRSA) and 15 methicillin-resistant coagulase-negative staphylococci (MR-CNS)] isolated from catheter cultures of patients hospitalized in different clinics and intensive care units in Baskent University Medical School Hospital between 2006-2009, were included in the study. The antibiotic sensitivities of MRSA and MR-CNS isolates were investigated in vitro in planktonic phase and on sessile cells after biofilm was formed. Vancomycin, ciprofloxacin, rifampicin, gentamicin, meropenem, tigecycline, linezolid, ceftazidime and cephazolin were used for antibiotic susceptibility testing. The sensitivity of planktonic cells to antibiotics was primarily investigated, so that minimal inhibitor concentration (MIC) and minimal bactericidal concentration (MBC) values were determined by broth microdilution method. Afterwards, each strain was transformed to sessile cell in a biofilm environment, and MIC and MBC values were also determined for sessile cells. Double and triple antibiotic combinations were prepared, the effectiveness of combinations were studied on both planktonic and biofilm cells with multiple-combination bactericidal testing (MCBT) method. The data set obtained from planktonic and biofilm cells for each antibiotic analyzed via two proportion z test. Statistically significant decreases were found in the sensitivities of sessile cells when compared to planktonic cells (p< 0.01). The tests performed with the use of double and triple antibiotic combinations also showed the susceptibility decrease between planktonic and biofilm forms to be significant in most of the combinations (p< 0.01). The comparison of double and triple antibiotic combinations against planktonic and sessile cells as determined by the inhibition of more than 90% of the strains, revealed no significant difference . Vancomycin and tigecycline were the most effective antibiotics for all isolates in planktonic and sessile cells. Combinations containing vancomycin and rifampicin showed the best activity both double and triple antibiotic combinations against biofilm. In conclusion, our data indicated that combination therapy, especially double combinations of antibiotics seem to be a rational approach for biofilm-related infections.

Retrospective Evaluation of Toxoplasma Serology in Patients Admitted to a Training and Research Hospital Between 2017-2021

Objective: In this study, it was aimed to retrospectively evaluate the anti-Toxoplasma IgG, IgM and avidity index results of patients who were requested for Toxoplasma serology in our hospital between 01.01.2017 and 31.12.2021. Methods: Anti-Toxoplasma antibodies are studied with Abbott Architect I2000 SR device that using the chemiluminescent microparticle immunoassay method (CMIA), according to the company's recommendations. The age, gender, nationality, sending clinic/polyclinic, and pregnancy status information of patients were scanned from the hospital system. Results: In the five-year period between 2017 and 2021, 29.58% of anti-Toxoplasma IgG tests requested from 12694 patients and 0.94% of anti-Toxoplasma IgM tests sent from 12546 patients were found positive. It is striking that the number of test requests is higher in women. IgG positivity is highest in women in the age group of 30-39 (9.97%), and in men in the age group of 60-69 (6.97%). IgM positivity is higher in both women and men in the 20-29 age group (0.48% and 0.38%, respectively). Anti-Toxoplasma IgG was positive in 27.78% and IgM in 0.64% of the pregnant women. IgG positivity in Turkish and Syrian pregnant women were determined as 25.88%; 47.10% and IgM positivity as 0.49% and 1.83%, respectively, and the difference was statistically significant (p<0.001). Conclusion: Our anti-Toxoplasma antibody positivity was found to be compatible with studies conducted in different centers in our country. The fact that IgM positivity in women is high in the 20-29 age group, which is the childbearing age, emphasizes the importance of screening before and during pregnancy. Consistent with other studies in the literature, the rate of seropositivity in Syrian pregnant women was found to be higher than Turkish. This is important in terms of showing the effect of socio-cultural behaviors on prevalence.

[The performance of two different chromogenic media for the diagnosis of extended spectrum beta-lactamase producing strains]. / Genislemis spektrumlu beta-laktamaz ureten suslarin tanisinda iki farkli kromojenik agarin performansi.

The aim of this study was to evaluate the performances of 2 different chromogenic media for the detection of extended spectrum beta-lactamase (ESBL) producing Escherichia coli and Klebsiella spp. isolated from different clinical samples of patients who were admitted to Baskent University Faculty of Medicine, Adana Application and Research Hospital between September to November 2007. A total of 365 strains [251 were ESBL positive and 114 were negative by double disc synergy (DDS) test] of which 255 were E. coli and 110 were Klebsiella spp. were included to the study. All the isolates have been inoculated onto Drigalski agar (prepared following the formula described by Stürenburg et al.) and chromID ESBL agar (bioMérieux, France) and the production of ESBL were evaluated at 4th and 24th hours for Drigalski agar, and at 24th hours for chromID ESBL agar. The strains which yielded contradictory results by DDS test and chromogenic media, were tested for the presence of TEM, SHV and CTX-M genes by polymerase chain reaction (PCR). The number of ESBL positive strains on Drigalski agar at 4th and 24th hours were 238 and 235, respectively, while chromID ESBL agar detected 259 ESBL positive strains at 24th hours. All (100%) of the 159 ESBL positive E. coli strains by DDS test were also found positive on chromID ESBL agar, and 150 (94.3%) were found positive on Drigalski agar. These rates were detected as 100% (92/92) and 92.3% (85/92) for Klebsiella spp. isolates. Eight of the strains (2 E. coli, 6 Klebsiella spp.) which yielded negative results by DDS test but positive on chromlD ESBL agar, harboured SHV (n = 1), CTX-M (n = 6) and TEM + CTX-M (n = 1) genes detected by PCR. As a result, the consistency of the results obtained by Drigalski agar at 4th and 24th hours has indicated that this medium may provide advantages in rapid diagnosis of ESBL producing bacteria in routine laboratories. The data obtained for chromogenic media seemed to be favourable for the rapid diagnosis of ESBL production, however comparative studies with the use of standard reference methods are needed in order to determine diagnostic sensitivity and specificity of these media.

[Activity of tigecycline on planktonic and sessile cells of Acinetobacter baumannii]. / Tigesiklinin Acinetobacter baumannii planktonik ve biyofilm hücrelerine etkisi.

Acinetobacter baumannii is an important pathogen, capable of survival for very long periods on various surfaces in the hospital environment. Tigecycline is a commonly used antimicrobial agent especially for the treatment of resistant infections. The aim of this study was to investigate the activity of tigecycline on both planktonic and sessile biofilm cells of A. baumannii strains isolated from blood cultures and to compare the efficiency in terms of biofilm synthesis. Tigecycline activity on 59 A. baumannii strains was examined by agar dilution technique. The ability of strains to form biofilm was evaluated by adherence on polystyrene surfaces in brain heart infusion broth supplemented with 0.25% glucose. Time-kill technique was used for determination of the time and concentration dependent activity of tigecycline on biofilm positive and negative strains. The planktonic cells in logarithmic growth phase were exposed to tigecycline at 0.5, 1, 2, 4, ve 8 x minimum inhibitory concentration (MIC) concentrations and colony counts were evaluated after 0, 2, 4, 6, 24 and 48 hours. The effect of tigecycline on sessile cells was studied on biofilm matrix composed around plastic beads. Tigecycline susceptibility rate of planktonic cells was 89.8% and MIC50 and MIC90 values were 1 and 2 microg/ml, respectively. Biofilm formation was detected in 52.5% of isolates and no significant correlation was found between MIC values and biofilm production of the strains (p > 0.05). Tigecycline showed a potent antibacterial activity against planktonic cells regardless of biofilm forming capability of strains. Biofilm inhibitory concentrations of sessile cells were elevated significantly. As a result, tigecycline showed a potent activity on planktonic A. baumannii cells however, the effect was decreased significantly on sessile cells in biofilm environment. The results suggest that, the possibility of decreased sensitivity of cells in biofilm environment should be considered as well as antibiotic sensitivity test results during the treatment of infections caused by A. baumannii.

Promoters of Colistin Resistance in Acinetobacter baumannii Infections.

Objectives: We aimed to describe the mechanisms of colistin resistance in Acinetobacter baumannii. Materials and Methods: Twenty-nine patients diagnosed with colistin-resistant A. baumannii infection were included to the study. The mutations in pmrCAB, lpxA, lpxC, and lpxD genes, expression of pmrCAB, carbapenemases, and mcr-1 positivity were studied. Results: Twenty-seven (93%) of the patients received IV colistin therapy during their stay, and the case fatality rate was 45%. All mutations in pmrC and pmrB were found to be accompanied with a mutation in lpxD. The most common mutations were I42V and L150F in pmrC (65%), E117K in lpxD (65%), and A138T in pmrB (58.6%). The colistin minimum inhibitory concentrations (MICs) of the isolates having any of these four mutations were higher than the isolates with no mutations (p < 0.001). The two most common mutations in pmrC (I42V and L150F) were found to be associated with higher expressions of pmrA and pmrC and higher colistin MIC values (p = 0.010 and 0.031). All isolates were blaOXA-23 positive. Conclusion: Coexistence of the lpxD mutation along with mutations in pmrCAB indicates synergistic function of these genes in development of colistin resistance in A. baumannii.

Prevalence of H. pylori in gastric biopsy specimen in the southeastern region of Turkey.

INTRODUCTION: Helicobacter pylori is a Gram-negative, microaerophilic bacterium that colonizes human gastric mucosa. Gastric ulcer, duodenal ulcer, chronic atrophic gastritis, mucosa-associated lymphoid tissue lymphoma, and stomach adenocarcinoma are associated with H. pylori as the etiological agent. Cytotoxin-associated gene A (cagA), which is one of the most important virulence factors of H. pylori, encodes a 120-145 kDa protein. The prevalence of cagA genes shows differences in H. pylori infections based on geographical area, and cagA-positive H. pylori strains play an important role in pathogenesis of gastric carcinoma. METHODOLOGY: The aim of this study was to detect the prevalence of cagA and vacA genes in H. pylori isolates in adult patient groups in the southeastern region of Turkey. The presence of H. pylori was investigated in gastric biopsy specimens using the culture method, and polymerase chain reaction (PCR) analysis was performed to detect the presence of the cagA and vacA s1 genes. RESULTS: H. pylori was detected in 65% (84/129) of patients who had gastrointestinal complaints. The number of vacA s1 and cagA genes of isolates were 44 (74.5%) and 31 (52.5%), respectively. CONCLUSIONS: H. pylori infection in southeastern region of Turkey with are comparable to those in developed countries. Patients with cagA- and vacA-positive H. pylori have a higher risk of severe inflammation and atrophy and should therefore be monitored for the development of gastric cancer.