Rize’deki Topraklardan İzole Edilen Bacillus Suşlarında Plazmit Kaynaklı Antibiyotik ve Ağır Metal Direnci

Toprak örneklerinden izole edilen 15 adet Bacillus suşu 17 farklı antibiyotiğe (ampisilin, metisilin, eritromisin, norfloksasin, sefalotin, gentamisin, siprofloksasin, streptomisin, tobramisin, kloramfenikol, trimetoprimsulfametaksozol, tetrasiklin, vankomisin, oksasilin, neomisin, kanamisin ve novabiosin) ve 10 farklı ağır metale (bakır, kurşun, kobalt, krom, demir, cıva, çinko, nikel, manganez ve kadmiyum) karşı dirençliliği ve plazmit DNA içeriği bakımından incelenmiştir. Toplam olarak 11 suş (%67) en azından bir antibiyotiğe dirençli bulunmuştur. En yaygın direnç metisilin ve oksasilin’e karşı gözlemlenmiştir. En yaygın dirençli suşlar ise Bacillus sp. B3 ve Bacillus sp. B11 olarak tespit edilmiştir. Bakır, krom, çinko, demir ve nikel’e karşı direnç belirlenmesine rağmen, cıva direnci gösteren 3 suş hariç (B3, B11 ve B12) cıva ve kobalta karşı direnç belirlenmemiştir. Yedi adet Bacillus suşunun plazmit içerdiği tespit edilmiştir. İzole edilen plazmitler Bacillus subtilis W168 suşuna transforme edilmiş, ağır metal ve antibiyotik direnç belirleyicilerinin plazmit üzerinde taşındığı bulunmuştur. Bu sonuçlar hem antibiyotik hem de ağır metal direnci ile plazmit içeriği arasında bir ilişki olduğunu göstermektedir.Fifteen Bacillus strains which were isolated from soil samples were examined for resistance to 17 different antibiotics (ampicillin, methicillin, erythromycin, norfloxacin, cephalotine, gentamycin, ciprofloxacin, streptomycin, tobramycin, chloramphenicol, trimethoprim-sulfamethoxazole, tetracycline, vancomycin, oxacilin, neomycin, kanamycin and, novabiocin) and to 10 different heavy metals (copper, lead, cobalt, chrome, iron, mercury, zinc, nickel, manganese and, cadmium) and for the presence of plasmid DNA. A total of eleven strains (67%) were resistant to at least one antibiotic. The most common resistance was observed against methicillin and oxacillin. The most resistance strains were found as Bacillus sp. B3 and Bacillus sp. B11. High heavy metal resistance against copper, chromium, zinc, iron and nickel was detected, but mercury and cobalt resistance was not detected, except for 3 strains (B3, B11, and B12) which showed mercury resistance. It has been determined that seven Bacillus strains have plasmids. The isolated plasmids were transformed into the Bacillus subtilis W168 and it was shown that heavy metal and antibiotic resistance determinants were carried on these plasmids. These results showed that there was a correlation between plasmid content and resistance for both antibiotic and heavy metal resistance

Evaluating molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae isolates with MLST, MALDI-TOF MS, PFGE

Background: This study aimed to evaluate antibiotic resistance genes and virulence genes and the clonal relationship of the carbapenem-nonsusceptible Klebsiella pneumoniae strains by molecular methods which are isolated from various clinical specimens from patients treated in tertiary care hospital in Turkey. Methods: Identification of 32 carbapenem non-susceptible K. pneumoniae were determined by VITEK-2 (BioMérieux, France) automated system. Thirteen colistin-resistant strains were tested with the broth microdilution method. Various antibiotic resistance genes and virulence genes frequently seen in carbapenem-resistant strains were screened by PCR. Immunochromatographic tests used in the rapid diagnosis of carbapenemases were compared with PCR results. In addition, PFGE, MLST and MALDI-TOF MS methods were used to determine the clonal relationship among these strains. Results: PCR demonstrated that 31 of the strains carried at least one of the carbapenemase genes. In one strain, the coexistence of bla OXA−48+NDM was shown. The most common resistance genes were determined as bla SHV (84.3%), bla CTX−M−1 (46.8%), bla OXA−48 (40.6%), bla KPC (40.6%), bla TEM (31.2%), bla NDM (18.8%) respectively. Among the virulence genes; magA (68.7%) was the most common, followed by kpn (59.3%) and K2 (9.3%). Immunochromatographic tests were found to be 100% compatible with PCR results. All colistin-resistant isolates were also found to be resistant by colistin broth microdilution. In PFGE analysis, 25 different genotypes were determined and clustering isolates were collected in 5 different clusters and the clustering rate was 35.4%. In MLST analysis, ST101 type was determined as the most common ST type with a rate of 29%. ST101 is followed by ST16, ST307, ST14, ST147, ST309, ST377, ST395 and ST2096, respectively. The compatibility rate between MALDI-TOF MS and VITEK-2 was found 94.3%, in bacterial identification. In MALDI-TOF MS typing, the maximum similarity between the strains was less than 70% and clustering not shown. Conclusion: In addition to OXA-48, which is endemic in our country, it has been determined that KPC, which is more common in the world, is becoming increasingly common in our region. ST101 type was determined as the most common type between the strains. To the best of our knowledge, this is the first study that compares these three methods in our country. There may be differences between bacterial identifications made with VITEK-2 and MALDI-TOF MS. In this study, it was observed that MALDI-TOF MS analyses were not compatible with the typing of strains according to PFGE and MLST analysis results.Recep Tayyip Erdogan University Scientific Research Projects Uni

Sex-hormone-binding globulin early in pregnancy for the prediction of severe gestational diabetes mellitus and related complications

Aims: The aim of this study was to evaluate the predictive value of sex-hormone-binding globulin (SHBG) for the diagnosis of gestational diabetes mellitus (GDM), and to clarify the association between SHBG levels and GDM complications/medication requirements. Material and Methods: Among the participants (n = 93) who provided blood samples between 13 and 16 weeks’ gestation, 30 cases subsequently developed GDM. Complications and medical interventions were noted. The best cut-off point of SHBG and diagnostic performance were calculated. Results: The mean age was 28.45 - 5.0 years. SHBG levels were lower in the GDM group (n = 30) when compared with non-GDM (n = 63) cases (<0.01). Among the GDM women, SHBG was lower in the insulin therapy group (n = 15) compared with medical nutritional therapy alone (n = 15) (P < 0.01). A good predictive accuracy of SHBG was found for GDM requiring insulin therapy (area under the curve: 0.866, 95% confidence interval: 0.773–0.959). An SHBG threshold for 97.47 nmol/L had a sensitivity of 80.0%, specificity 84.6%, positive predictive value 50.0% and negative predictive value 95.7%. The calculated odds ratio for SHBG < 97.47 nmol/L was 12.346 (95% confidence interval: 1.786–83.33). Conclusions: SHBG is valuable for screening women early in pregnancy for GDM risk; however, a standard assay for analyses and a threshold level of serum SHBG for a constant gestational week has to be determined

Isolation, characterization, and genetic diversity of Paenibacillus larvae from AFB suspected specimens in the Central and Eastern Black Sea Regions

American foulbrood is an important bacterial disease affecting the larvae of honey bees (Apis mellifera L.) caused by Paenibacillus larvae. Due to easy transmission of disease and the ability of bacteria to create spores, it is a bacterium resistant to both physical and chemical conditions. The study aims to isolate, perform microbiological analyses, and determine biochemical properties and genotypes P. larvae strains from AFB samples collected from Turkey's Central and Eastern Black Sea regions. An isolation study was conducted on adult bees, larvae, honey, and primary honeycomb samples from suspected colonies in the regions under study. After the purification of bacterial isolates from samples, P. larvae strains were identified using biochemical and molecular methods. The genetic diversity and ERIC types of P. larvae isolates were determined by rep-PCR DNA genotyping using BOX A1R and MBO REP1 primers and multiplex-PCR. A phylogenetic tree of P. larvae strains was constructed in the study. All P. larvae isolates were determined as ERIC I type. According to the rep-PCR results of P. larvae strains, 15 of the 28 isolates were Ab genotype (54%), 7 (25%) Aβ genotype, 4 (14%) AB genotype, 1 (3.5%) αB genotype, and 1 (3.5%) ab genotype. From an epidemiological viewpoint, it was determined that Ab and Aβ genotypes were widely distributed, while other genotypes (AB, αB, and ab) showed less spread. The results of the study will guide researchers in taking relevant measures to prevent and control American foulbrood. © 2023, The Author(s), under exclusive licence to Plant Science and Biodiversity Centre, Slovak Academy of Sciences (SAS), Institute of Zoology, Slovak Academy of Sciences (SAS), Institute of Molecular Biology, Slovak Academy of Sciences (SAS)

Antibacterial activity of bryophyte species against Paenibacillus larvae isolates

This study was performed to determine the antibacterial activity of methanol extracts of 23 bryophyte species against Paenibacillus larvae isolates that cause American foulbrood diseases in honeybee larvae. The honey and larva samples were collected from nine different locations of Rize in Turkey. A total of 22 gram-positive spore-forming bacteria were isolated from the larva and honey samples. According to the results of morphological, biochemical, and molecular (16S rRNA gene sequencing) tests, 10 isolates of the 22 gram-positive spore-forming bacteria were identified as P. larvae. A total of 10 bryophyte species (Polytrichum formasum,Polytrichum commune, Calliergonella cuspitada, Calliergonella lindbergi, Metzgeria conjugata, Isothecium alopecuroides, Syntrichia calcicola, Syntrichia intermedia, Tortella densa,and Grimmia alpestris) among 23 bryophytes showed good antimicrobial activity against P. larvae isolates according the results of agar-well diffusion method and minimal inhibition concentration experiments

Excitation energy-dependent nature of Raman scattering spectrum in GaInNAs/GaAs quantum well structures

The excitation energy-dependent nature of Raman scattering spectrum, vibration, electronic or both, has been studied using different excitation sources on as-grown and annealed n- and p-type modulation-doped Ga(1 − x)In(x)N(y)As(1 − y)/GaAs quantum well structures. The samples were grown by molecular beam technique with different N concentrations (y = 0%, 0.9%, 1.2%, 1.7%) at the same In concentration of 32%. Micro-Raman measurements have been carried out using 532 and 758 nm lines of diode lasers, and the 1064 nm line of the Nd-YAG laser has been used for Fourier transform-Raman scattering measurements. Raman scattering measurements with different excitation sources have revealed that the excitation energy is the decisive mechanism on the nature of the Raman scattering spectrum. When the excitation energy is close to the electronic band gap energy of any constituent semiconductor materials in the sample, electronic transition dominates the spectrum, leading to a very broad peak. In the condition that the excitation energy is much higher than the band gap energy, only vibrational modes contribute to the Raman scattering spectrum of the samples. Line shapes of the Raman scattering spectrum with the 785 and 1064 nm lines of lasers have been observed to be very broad peaks, whose absolute peak energy values are in good agreement with the ones obtained from photoluminescence measurements. On the other hand, Raman scattering spectrum with the 532 nm line has exhibited only vibrational modes. As a complementary tool of Raman scattering measurements with the excitation source of 532 nm, which shows weak vibrational transitions, attenuated total reflectance infrared spectroscopy has been also carried out. The results exhibited that the nature of the Raman scattering spectrum is strongly excitation energy-dependent, and with suitable excitation energy, electronic and/or vibrational transitions can be investigated

Evaluation of antimicrobial and antibiofilm activities of lactic acid bacteria (LAB) against citrobacter spp. isolates

Bu çalışmanın amacı; Citrobacter izolatlarına karşı laktik asit bakterilerinin antimikrobiyal ve antibiyofilm aktivitelerini belirlemektir. Bu çalışmada kullanılan Citrobacter izolatları (C1, C2, C3) BD PhoenixTM otomasyon sistemi ile Citrobacter braakii olarak tanımlanmıştır. Biyofilm oluşumu Kongo kırmızılı agar ve mikrotitrasyon plak metodu kullanılarak incelenmiştir. Antibiyogram test sonuçlarına göre, tüm izolatlar amfisilin ve amoksilin-klavulanata karşı dirençli bulunmuştur. Antimikrobiyal aktivite test sonuçları laktik asit bakterilerinden elde edilen ekstraktların (Lactococcus lactis (L1), Lactobacillus fermentum (L2), Enterococcus faecalis (L3), Lactobacillus casei (L4), Lactobacillus plantarum (L5), Enterococcus faecium (L6), Lactobacillus curvatus (L7), Enterococcus durans (L8) Lactococcus garviae (L9), Enterococcus faecalis (L10)) Citrobacter braakii üzerinde antimikrobiyal ve antibiyofilm etkinliğinin olduğu saptanmıştır. En yüksek antimikrobiyal etki C2 izolatı üzerinde ve en düşük etki C3 izolatı üzerinde belirlenmiştir. Antibiyofilm test sonuçlarına göre L1, L2, L4, L6, L7, L8 ekstraktlarının en yüksek dozlarının tüm Citrobacter izolatlarında biyofilm oluşumunu engellendiği görülmüştür.The aim of this research was to evaluate the antimicrobial and antibiofilm effects of LABs against Citrobacter isolates. In this study, Citrobacter isolates (C1, C2, C3) which were identified as Citrobacter braakii with the BD PhoenixTM automation system. Biofilm formation investigated by Congo red agar method and microtiter plate method. Acording to antibiogram test results, all isolates was resistance to ampicillin, amoxicillin-clavulanate. Antimicrobial activity test results revealed that extracts of LABs (Lactococcus lactis (L1), Lactobacillus fermentum (L2), Enterococcus faecalis (L3), Lactobacillus casei (L4), Lactobacillus plantarum (L5), Enterococcus faecium (L6), Lactobacillus curvatus (L7), Enterococcus durans (L8) Lactococcus garviae (L9), Enterococcus faecalis (L10)) extracts have an antimicrobial effect on Citrobacter braakii. The highest antimicrobial effect determined on C2 isolate and the lowest effect determined on C3. According to antibiofilm test results, it was observed that high doses of L1, L2, L4, L6, L7, L8 extracts inhibited biofilm formation in all Citrobacter isolates

Evaluation of patients with fibrotic interstitial lung disease: Preliminary results from the Turk-UIP study

OBJECTIVE: Differential diagnosis of idiopathic pulmonary fibrosis (IPF) is important among fibrotic interstitial lung diseases (ILD). This study aimed to evaluate the rate of IPF in patients with fibrotic ILD and to determine the clinical-laboratory features of patients with and without IPF that would provide the differential diagnosis of IPF. MATERIAL AND METHODS: The study included the patients with the usual interstitial pneumonia (UIP) pattern or possible UIP pattern on thorax high-resolution computed tomography, and/or UIP pattern, probable UIP or possible UIP pattern at lung biopsy according to the 2011 ATS/ERSARS/ALAT guidelines. Demographics and clinical and radiological data of the patients were recorded. All data recorded by researchers was evaluated by radiology and the clinical decision board. RESULTS: A total of 336 patients (253 men, 83 women, age 65.8 +/- 9.0 years) were evaluated. Of the patients with sufficient data for diag-nosis (n=300), the diagnosis was IPF in 121 (40.3%), unclassified idiopathic interstitial pneumonia in 50 (16.7%), combined pulmonary fibrosis and emphysema (CPFE) in 40 (13.3%), and lung involvement of connective tissue disease (CTD) in 16 (5.3%). When 29 patients with definite IPF features were added to the patients with CPFE, the total number of IPF patients reached 150 (50%). Rate of male sex (p<0.001), smoking history (p<0.001), and the presence of clubbing (p=0.001) were significantly high in patients with IPE None of the women <50 years and none of the men <50 years of age without a smoking history were diagnosed with IPE Presence of at least 1 of the symptoms suggestive of CTD, erythrocyte sedimentation rate (ESR), and antinuclear antibody (FANA) positivity rates were significantly higher in the non-IPF group (p<0.001, p=0.029, p=0.009, respectively). CONCLUSION: The rate of IPF among patients with fibrotic ILD was 50%. In the differential diagnosis of IPF, sex, smoking habits, and the presence of clubbing are important. The presence of symptoms related to CTD, ESR elevation, and EANA positivity reduce the likelihood of IPF

The genetic history of the Southern Arc: a bridge between West Asia and Europe

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe

Internal bacterial diversity of lasiocampa trifolii (Denis & Schiffermüller, 1775) (Lepidoptera: Lasiocampidae): A possible novel okibacterium sp.

Böceklerin bağırsak sistemlerinde bulunan mikroorganizmaların bu böceklerin sindirim ve beslenme süreçlerinde faydalı olduğu bilinmektedir. Bu anlamda, böceklerin bağırsak sistemindeki bakterilerin tanımlanması, özellikle ekonomik olarak zararlı veya faydalı böcek türlerinin besleyici ve sindirim özelliklerinin belirlenmesi açısından özellikle önemlidir. Bu çalışmada, Lasiocampa trifolii'nin (Denis & Schiffermüller, 1775) (Lepidoptera: Lasiocampidae) dahili bakteriyel florası kültür bağımlı teknikler kullanarak belirlenmiştir. Bu böceğin larvaları, çeşitli otlar ve çalılar, meşe, kavak ve süpürge çimi gibi bitki yapraklarıyla beslenmektedir. Larvalar Mayıs-Haziran (2019) aylarında Türkiye'nin Kırşehir bölgesinden toplanmış ve bakteri izolasyonu için laboratuvara getirilmiştir. Dört adet 3-4. instar larvalar bakteri izolasyonu için kullanılmıştır. İzole edilen bakteriler, 16S rRNA dizin analizi kullanılarak tanımlanmıştır. On bir bakteri izole edilmiş ve bunlar Bacillus sp. TT1, Micrococcus luteus TT2, Arthrobacter sp. TT3, Corynebacterium sp. TT4, Arthrobacter agilis TT5, Micrococcus luteus TT6, Micrococcus luteus TT7, Arthrobacter sp. TT8, Okibacterium sp. TT9, Staphylococcus haemolyticus TT10 ve Bacillus sp. TT11 olarak tanımlanmıştır. İzolat TT9’un, Okibacterium cinsi içinde yer alan yeni bir tür olarak değerlendirilebilmesi için daha ileri moleküler çalışmaların yapılması gerekmektedir. Bu bakteri bu çalışma ile şimdiye kadar herhangi bir hayvandan ilk kez izole edilmiştir. Elde edilen sonuçlar beslenme ve böcek hastalıkları açısından tartışılmıştır.Microorganisms in the intestinal systems of insects are known to be useful in the digestive and feeding processes of these insects. In this sense, the identification of bacteria in the intestinal systems of insects is especially important for determining the nutritional and digestive properties of economically harmful or useful insect species. In this study, the internal bacterial flora of Lasiocampa trifolii (Denis & Schiffermüller, 1775) (Lepidoptera: Lasiocampidae) was determined based on culture-dependent technique. The larvae of this insect are fed with leaves of plants such as various herbs and shrubs, oak, poplar and broom grass. The larvae were collected from Kirsehir region of Turkey in May-June (2019) and brought to the laboratory for bacterial isolation. Four 3-4. Instar larvae were used for bacterial isolation. The isolated bacteria were identified using 16S rRNA sequence analysis. Eleven bacteria were isolated, and these were identified as Bacillus sp. TT1, Micrococcus luteus TT2, Arthrobacter sp. TT3, Corynebacterium sp. TT4, Arthrobacter agilis TT5, Micrococcus luteus TT6, Micrococcus luteus TT7, Arthrobacter sp. TT8, Okibacterium sp. TT9, Staphylococcus haemolyticus TT10 and Bacillus sp. TT11. Further molecular studies are required for isolate TT9 to be considered as a new species within the genus Okibacterium. This has the first time been isolated from any animal so far. The results are discussed in terms of nutrition and diseases of insects