Development of nucleic acid based lateral flow assays for SARS-CoV-2 detection.

SARS-CoV-2 is still threat for humanity and its detection is crucial. Although real time reverse transcriptase polymerase chain reaction is the most reliable method for detection of N protein genes, alternative methods for molecular detection are still needed. Thus, lateral flow assay models for 2019-nCoV_ N3 were developed for molecular detection. Briefly, gold nanoparticles were used as label and three sandwich models (1A, 1B, and 1.2) were designed. Prob concentrations on gold nanoparticles, types of sandwich model and membrane, limit of detection of target gene and buffer efficiency were studied. Model 1B has shown the best results with M170 membrane. Lower limit of detection was achieved by model 1.2 as 5 pM. All parameters have significant role for molecular detection of SARS-CoV-2 by lateral flow assays, and these results will be useful for nucleic acid based lateral flow assays for viral detection or multiple detection of mutated forms in various detection systems.

[Clinical Properties of COVID-19 Developed in the Patients with Tuberculosis]. / Tüberküloz Hastalarinda Gelisen COVID-19'un Klinik Özellikleri.

There are limited publications about the Coronavirus disease 19 (COVID-19) clinic developing in the patients with active tuberculosis (TB). In this study, it was aimed to determine some clinical features of patients diagnosed with TB who also had COVID-19. In this retrospective cross-sectional study, 71 patients with COVID-19 were evaluated out of a total of 595 patients diagnosed with TB in our province between 2015 and 2021. After contracting COVID-19, a total of nine (12.6%) TB patients were hospitalized, five (7%) patients were admitted to the intensive care unit, three (4.2%) were intubated, and one (1.4%) died due to severe COVID-19. The frequency of such health problems was found to be higher than the normal population living in the same province. None of these complications were observed in a total of 40 female TB patients, and the hospital and intensive care unit admission rates for men were significantly higher than for women. The results of this study showed that men with active TB had more health problems due to COVID-19 than the normal population. Comprehensive studies are needed to detail the resilience of female TB patients against COVID-19.

Diagnostic and treatment outcomes of patients with pulmonary tuberculosis in the first year of COVID-19 pandemic.

Background: The COVID-19 pandemic has put a significant strain on human life and health care systems, however, little is known about its impact on tuberculosis (TB) patients. Aims: To assess the impact of COVID-19 pandemic on pulmonary tuberculosis (PTB) diagnosis, treatment and patient outcomes, using the WHO definitions. Methods: A cross-sectional study was conducted in Malatya region, Turkey (population 800 000). Data on regional PTB test numbers, case notification rates and PTB patients' clinical characteristics and treatment outcomes were collected. Data from the first pandemic year (2020) were compared to data from the previous 3 years (2017-2019). The attitudes and experiences of patients were analysed. Results: Despite a non-significant 22% decrease in annual PTB case notifications (P = 0.317), the number of TB tests performed (P = 0.001) and PTB patients evaluated (P = 0.001) decreased significantly during the pandemic year compared with the previous 3 years. The proportion of patients with high (3/4+) sputum acid-fast bacilli grades (P = 0.001), TB relapse (P = 0.022) and treatment failure (P = 0.018) increased significantly. The median 64.5-day treatment delay detected in 2017-2019 increased significantly to 113.5 days in 2020 (P = 0.001), due primarily to patients' reluctance to visit a health care facility. Conclusion: In addition to the problems with case detection, this study shows notable deterioration in several indicators related to the severity, contagiousness and poor outcomes of TB, which had already been suppressed for decades.

Clinical Characteristics and Outcomes of Liver Transplantation Recipients With COVID-19 Pneumonia.

BACKGROUND: We aimed to evaluate the clinical characteristics and outcomes of mild-severe COVID-19 pneumonia cases in liver transplant (LT) recipients. METHODS: Ten LT recipients diagnosed as having COVID-19 pneumonia in a 6-month period in our transplantation center were included. Demographic and medical data of the recipients were retrospectively collected; clinical courses, treatment responses, and outcomes were evaluated. RESULTS: Ten LT recipients were male, had a median age of 57 years (min-max, 36-69 years; interquartile range [IQR], 13 years), and had right lobe from living donor LT performed in a median of 11 months (min-max, 1-72 months; IQR, 12 months). Five patients had severe pneumonia, and the remaining patients had mild/moderate pneumonia. The most frequent symptoms were fever (90%) and cough (70%). Favipiravir, enoxaparin sodium, and corticosteroid were initiated at the time of the diagnosis; immunosuppressive drug doses were reduced or discontinued in 3 cases. Lymphopenia median: 510/mL (min-max, 90-1400 mL; IQR, 610 mL), increased levels of C-reactive protein median: 4.72 (min-max, 0.31-23.4; IQR, 8.5), and ferritin median: 641 (min-max, 40 to ≥ 1650; IQR, 1108) were frequent. Four patients required antibacterial treatments because of emerging bacterial pneumonia and/or sepsis. All patients were hospitalized for a median of 10 days. One patient with sepsis died on the 26th day after intensive care unit admission, and the remaining 9 survived. No further complication was recorded for 1-month follow-up. CONCLUSIONS: Commencing favipiravir, enoxaparin sodium, and corticosteroid treatments; close follow-up of the developing complications; the temporary reduction or cessation of immunosuppression; a multidisciplinary approach; early awareness of the bacterial infections; and the initiation appropriate antibiotic treatments can contribute to success.

An evaluation of patients with a previous endemic coronavirus infection during the COVID-19 pandemic.

Few studies exist on the clinical manifestation of coronavirus disease 2019 (COVID-19) in patients who previously had a common cold due to an endemic coronavirus (eCoV). In a retrospective scan of the data obtained in our microbiology laboratory, 64 patients who were diagnosed with an eCoV infection between 2016 and 2020 were identified. National COVID-19 surveillance data showed that four (6.2%) of 64 patients were infected with severe acute respiratory syndrome coronavirus 2 by the end of 2020, while, simultaneously, the COVID-19 prevalence in the city of Malatya ranged from 7.8% (polymerase chain reaction-based diagnosis) to 9.2% (total diagnosis). The differences were found statistically significant (6.2% vs. 7.8%, p < .01; 6.2% vs. 9.2%, p < .001). Patient interviews and evaluation of medical records revealed that these four patients did not manifest any severe COVID-19 symptoms despite their substantial comorbidities, and they did not require hospitalization. Consequently, despite a low number of samples, we determined a lower frequency of COVID-19 among the patients who had a prior eCoV infection, and the results of this study support the previous findings that people with a prior eCoV infection develop a milder case of COVID-19. Our results may provide some insights for future studies aiming at vaccine development, but detailed investigations are still required.

Differential diagnosis of the granulomatous appendicitis: Retrospective analysis of 16 cases.

BACKGROUND: This study aims to present the usability of real-time polymerase chain reaction (PCR) and interferon-gamma release assay (IGRA) in the differential diagnosis of granulomatous appendicitis (GAp), especially in areas where tuberculosis (TB) is endemic. METHODS: Sixteen patients underwent appendectomy with presumed diagnosis of acute appendicitis were retrospectively analyzed for histopathological diagnosis of GAp. Real-time PCR method was used to show the whether presence of DNA of the tubercle bacilli in paraffin-embedded tissue blocks. IGRA test was used to investigate whether tubercle bacilli- specific interferon gamma was present in peripheral blood. RESULTS: Sixteen patients (male: 10 female: 6) aged between 21 and 82 years were included in this study. All patients had acute appendicitis and three of them also had appendiceal perforation. Histopathologically, necrotizing granulomatous inflammation was detected in all appendectomy specimens. Acid-fast bacilli were not detected in any of the pathology slides stained with Ehrlich-Ziehl-Neelsen. Real-time PCR was studied in paraffin-embedded tissue blocks of all patients with GAp, but the TB bacilli DNA was amplified in only three patients. IGRA test was studied in peripheral blood samples of 12 patients with GAp and results were as follows: negative (n=9), positive (n=2) and indeterminate (n=1). CONCLUSION: We believe that the use of anamnesis, histopathological findings, tissue PCR, blood IGRA and clinical findings together are important for differential diagnosis of GAp, especially where TB is endemic. We also suggest that all appendectomy specimens should be sent to the laboratory for histopathological evaluation even if specimens appear macroscopically normal.

Visualization and characterization of Enterococcus faecalis biofilm structure in bovine dentin using 2D and 3D microscopic techniques.

Bacterial biofilms are related to various dental and periodontal infectious diseases, and the characterization of this biological structure with micro-computed tomography (micro-CT) may offer valuable information for clinical and research applications. In this study, we aimed to develop a model to visualize three-dimensionally the biofilm structure on dentin using micro-CT. Dentin blocks were prepared and incubated in tryptic soy broth with Enterococcus faecalis (ATCC 29212). The control group did not receive any staining procedure, while groups 1 and 2 were stained with 100% and 50% barium sulfate, respectively. Transmission electron microscopy (TEM) and confocal laser scanning microscopy (CLSM) were used to detect biofilm formation, barium sulfate penetration, and microbial cell density in the biofilm. Micro-computed tomography (micro-CT) (SkyScan 1172, Bruker Co., Belgium) was used to visualize biofilm formation on the dentin blocks. Biofilm thicknesses were measured from 10 different locations on the specimen surfaces, using CTAn v.1.14.4 software. Obtained data were statistically analyzed using Kruskal-Wallis and Dunn's tests. TEM photomicrographs showed that barium sulfate could penetrate the biofilm structure. CLSM analysis showed that viable and total cell densities were similar between the control and barium sulfate-treated groups (P > 0.05), indicating barium sulfate had no significant influence on cell density. In barium sulfate-treated blocks, biofilm could be discriminated from the dentin, and its thickness could be measured with micro-CT. This study showed that bacterial biofilm on dentin could be characterized by micro-CT after barium sulfate staining without causing any significant side effect on viable and total cell densities.

Risk factors for fecal carriage of extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli and Klebsiella pneumoniae strains among patients at hospital admission.

AIM: Extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Enterobacteriaceae are substantial problems in hospital-acquired infections worldwide. We analyzed the risk factors for fecal carriage of ESBL-positive and/or CR E. coli and K. pneumoniae (EcKp) strains in a hospital in Turkey, an endemic country for both resistances. MATERIALS AND METHODS: A prospective cross-sectional study including the rectal swab samples of 168 patients, obtained at the day of admission, was conducted. ESBL-producing and CR EcKp were investigated with phenotypic tests and PCR, and the clonal relatedness of isolates was studied. Risk analysis was performed with logistic regression method. RESULTS: A total of 67 (39.8%) and 21 (12.5%) patient samples tested positive for ESBL-producing and CR EcKp, respectively. CTX-M (n = 27) and OXA-48 (n = 12) were the dominant ESBL and carbapenemase types, and 4.5%-10.7% of the isolates were clonally-related. Among 15 potential risk factors studied, longer lengths of hospital stay and antimicrobial use, and receiving total parenteral nutrition in the last 6 months were determined as independent risk factors for fecal carriage of ESBL-producing and/or CR EcKp, while prior antimicrobial treatment was only a risk factor for ESBL producers. CONCLUSION: Certain conditions in patients' medical backgrounds may be associated with increased likelihood of resistant bacterial colonization. Notably, questioning these situations at admission can help to identify potential carriers and proactively administer appropriate infection control measures.

[Performance of MALDI-TOF MS for the identification of gram-negative bacteria grown on eosin methylene blue (EMB) agar: A simple method for improving the effectiveness of identification]. / MALDI-TOF MS'nin EMB agarda üreyen gram-negatif bakterileri tanimlama performansi: Tani etkinligini arttiran basit bir yöntem.

Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is a new method that is increasingly used in microbiology laboratories due to its ability of reliable and rapid identification (ID) of bacteria and fungi. However, some problems emerge in the routine clinical diagnosis since only one gram-negative selective medium has been suggested up to date. Though EMB agar is one of the traditional gram-negative selective media, there is no data in the scientific literature, about the ID performance of MALDI TOF MS with the gram-negative bacteria grown on this medium. In this study, we tested the ID performance of MALDI-TOF MS for gram-negative isolates on EMB agar and aimed to develop a rapid and easy sample preparation method for improving this performance. A total of 468 clinical isolates of gram-negative bacteria, consisting of 37 different species from 20 genera, were included in this study. The isolates were identified using the Vitek MS MALDI-TOF MS (Bio Mérieux, France) both directly from EMB agar, and also through a two-step colony washing (once with physiologic saline, and three times with 70% ethanol) method. The performances of these two IDs were compared. In the direct reading from EMB medium, 382 (81.6%) of 468 studied isolates were correctly identified at species level; no ID was detected for 80 (17%) isolates, and 6 (1.2%) isolates (four at the genus level) were misidentified Performance of MALDI-TOF MS directly from EMB agar was excellent (100%) for 14 species including Stenotrophomonas maltophilia, Klebsiella oxytoca, Salmonella spp., and Proteus mirabilis; and lowest for Providencia spp. (62.5%), Escherichia coli (70.5%) and Acinetobacter spp. (70.7%). Following the washing procedure which was performed about 20 min with simple laboratory equipment, 434 (92.7%) isolates were correctly identified at species level; 30 (6.4%) strains could not be identified, and four (0.85%) isolates (two at the genus level) were misidentified. Statistical analyses indicated that the washing procedure defined here significantly increased the overall ID performance of MALDI-TOF MS with EMB agar (p= 0.001), particularly with improving the IDs of those markedly dye-absorbing genera, such as E.coli and A.baumannii. In this study, EMB agar which has no data until today on its suitability for mass spectrometric identification has been shown to be useful for bacterial identification with MALDI-TOF MS. In addition, the unidentified gram-negative bacteria in the direct reading from the EMB medium have been shown to be identified after the colony washing method as described here. Determination of the different medium alternatives will contribute to effective usage of MALDI-TOF MS in microbiology laboratories.

[Co-production of OXA-48 and NDM-1 Carbapenemases in Providencia rettgeri: the first report]. / Providencia rettgeri'de OXA-48 ve NDM-1 karbapenemaz genlerinin birlikte üretimi: ilk bildirim.

Our country is the epicenter of the OXA-48-like carbapenemase-producing Klebsiella and Escherichia coli; and in the recent years, the concern has been increasing due to both spreading of this resistance to other members of Enterobacteriaceae family and acquiring other carbapenemases by the OXA-48-producing strains. In this study, OXA-48 and NDM-1 co-production was presented in Providencia rettgeri. Two P.rettgeri strains that were resistant to all antimicrobials except colistin and tigecyclin, were isolated from two patients in the burn unit of our hospital, including one from the urine sample of a 68 years female in April 2017, and the other from a burn wound swab of a 35 years old male, in November 2017. Minimal inhibitory concentrations (MICs) of the isolates for imipenem and meropenem were measured as ≥ 32 µg/ml; and for colistin and tigecyclin were 1 ve 0.5 µg/ml, respectively. Multiplex PCR analysis showed that both strains were carrying blaOXA-48 and blaNDM-1 carbapenemases, and blaTEM extended spectrum beta-lactamase genes. By using DNA sequence analysis, the TEM gene was typed as blaTEM-1. The Pulsed Field Gel Electrophoresis (PFGE) analysis indicated that these two strains which were consecutively isolated from two different patients in a single unit within about seven months were genetically indistinguishable. No significant data that could explain the spread of these isolates was obtained from our retrospective analysis of the medical records including the results of environmental surveillance cultures, and patients' history. Nevertheless, hospital infection control committee enforced the infection control measures in that unit, and no further isolation was observed within three months period following the last isolation, neither from environmental nor from clinical samples. With this study, it was emphasized that the co-production of OXA-48 and NDM-1 carbapenemases which was reported from only three Enterobacteriaceae species up to date was ongoing for spreading to other species by using horizontal route, and also showing a potential to be a growing problem in the hospitals, by clonal expansion (vertical route). Effectively using of the molecular epidemiological methods will provide useful data to better understand the transmission dynamics of such rare, but problematic species in hospitals.

Hospital Outbreak of a Colistin-Resistant, NDM-1- and OXA-48-Producing Klebsiella pneumoniae: High Mortality from Pandrug Resistance.

Colistin resistance causes substantial problems in the treatment of serious infections with carbapenem-resistant (CR) gram-negative bacteria. In this study, we report a fatal hospital outbreak from the spread of a pandrug-resistant Klebsiella pneumoniae clone. An outbreak investigation was conducted after consecutive isolation of nine CR-K. pneumoniae (CR-Kp) strains from eight patients in two intensive care units of a university hospital within 2 weeks. Carbapenem and colistin resistance genes were investigated with PCR, clonal relationships of isolates were studied with pulse-field gel electrophoresis, and multilocus sequence types were determined. The outcomes of the affected patients were analyzed. Genotyping showed a predominant CR-Kp clone consisting of seven strains from six patients. These strains were in ST11 type, an international high-risk clone. They were resistant to all antimicrobials, including colistin, and positive for NDM-1 and OXA-48 carbapenemases, but negative for plasmid-borne colistin resistance genes. One patient had colonization and the remaining five died due to the infection within mean 12 days. No environmental or staff links could be established, and the outbreak was stopped by augmenting infection-control measures. Colistin-resistant K. pneumoniae could clonally expand in the hospital setting, and this spread might be associated with high mortality due to the lack of an appropriate treatment option. Immediate implementation of infection-control measures may be the best way to limit fatal consequences of the spread of such incurable pathogens.

Is airborne transmission of Acinetobacter baumannii possible: A prospective molecular epidemiologic study in a tertiary care hospital.

BACKGROUND: Understanding the dynamics of aerial spread of Acinetobacter may provide useful information for production of effective control measurements. We investigated genetic relationships between air and clinical isolates of Acinetobacter baumannii in an intensive care unit (ICU) setting. METHODS: We conducted a prospective surveillance study in a tertiary care hospital for 8 months. A total of 186 air samples were taken from 2 ICUs. Clonal characteristics of air isolates were compared with the prospective clinical strains and the previously isolated strains of ICU patients over a 23-month period. RESULTS: Twenty-six (11.4%) air samples yielded A baumannii, of which 24 (92.3%) isolates were carbapenem-resistant. The Acinetobacter concentration was the highest in bedside sampling areas of infected patients (0.39 CFU/m3). Air isolates were clustered in 13 genotypes, and 7 genotypes (including 18 air strains) were clonally related to the clinical strains of 9 ICU patients. One clone continued to be cultured over 27 days in ICU air, and air isolates could be clonally related to 7-week retrospective and approximately 15-week prospective clinical strains. CONCLUSIONS: The results of this study suggest that infected patients could spread significant amounts of Acinetobacter to ICU air. These strains could survive in air for some weeks and could likely still infect new patients after some months. Special control measurements may be required against the airborne spread of Acinetobacter in ICUs.

[Evaluation of the diagnostic performance of Xpert MTB/RIF test for the detection of Mycobacterium tuberculosis and rifampin resistance in clinical samples]. / Klinik örneklerde Mycobacterium tuberculosis'in saptanmasi ve rifampin direncinin tespitinde Xpert MTB/RIF testinin tanisal performansinin degerlendirilmesi.

Rapid and accurate detection of active tuberculosis (TB) cases is one of the most important goal of tuberculosis control programme. For this purpose, new methods are being developed to isolate, serotype and determine the drug resistance of the agent. Xpert MTB/RIF test (CepheidGeneXpert® System, USA) that has been recently developed, is a real-time polymerase chain reaction-based method which detects Mycobacterium tuberculosis complex and resistance of the strain to rifampicin (RIF) from the clinical sample directly within a couple of hours. However, there are not sufficient data about the performance of that test for extrapulmonary samples and pulmonary samples other than sputum. The aims of this study were to investigate the sensitivity, specificity, positive and negative predictive values of Xpert MTB/RIF test in detection of M. tuberculosis and the performance in the determination of rifampicin resistance of the isolates from pulmonary and extrapulmonary clinical samples. A total of 2160 clinical samples, in which 1141 (52.8%) were pulmonary and 1019 (47.2%) were extrapulmonary samples, sent to our laboratory between July 2013 to December 2014, were included in the study. Sixty seven of the evaluated samples (3.1%) were positive with microscopy (acid-fast stain; AFS), 116 samples (5.1%) were positive with culture and 98 samples (4.5%) were positive with Xpert MTB/RIF test. When the culture was considered as the reference method, the sensitivity and specificity of Xpert MTB/RIF test were determined as 73.3% and 99.3%, respectively for all samples; 77.5% and 99.5%, respectively for pulmonary samples and 63.9% and 99.2%, respectively for extrapulmonary samples. Among AFS positive samples, the sensitivity was 100% and specificity was 66.7%; whereas among AFS negative samples those values were 40.4% and 99.4%, respectively. Among all the samples involved in the study, RIF resistance was determined only in three samples with Xpert MTB/ RIF test and that was also proved phenotypically (100% concordance). According to mycobacterial culture results, positive and negative predictive values of Xpert MTB/RIF test were determined as 86.7% and 98.5%, respectively for all samples. Those were determined as 92.5% and 98.3%, respectively for extrapulmonary samples and were determined as 74.2 and 98.7%, respectively for pulmonary samples. According to the results obtained in our study, sensitivity of Xpert MTB/RIF test for extrapulmonary samples was found to be at moderate level; sensitivity of the test was found to be decreased especially in AFS negative samples with less bacilli load. Nonetheless, specificity of Xpert MTB/RIF test to the agent in all samples was found to be extremely high. In our study, although RIF-resistant strains were detected in few of the samples, Xpert MTB/ RIF test could differentiate all resistant and sensitive strains. Additionally, detection of M. tuberculosis and RIF resistance in our laboratory takes approximately 20.96 days with culture, this period decreases to a couple of hours with Xpert MTB/RIF test. Because of the advantages such as being practical, rapid and requiring minimal safety measures, it was concluded that Xpert MTB/RIF test may contribute to rapid diagnosis of TB also in extrapulmonary samples, with the confirmation of culture method.

Laboratory-acquired skin infections in a clinical microbiologist: Is wearing only gloves really safe?

Laboratory-acquired infection is one of the leading occupational health hazards. On a laboratory worker's hands, carbuncles occurred. Staphylococcus aureus was isolated from pus samples of the carbuncles, with the same pulsed field gel electrophoresis band pattern with one of the recently studied strains in the laboratory. Incorrect or inadequate application of infection control measures may result in pathogen acquisition from the clinical samples, and wearing only gloves is not sufficient for the biosafety of laboratory workers in clinical diagnostic laboratories.

The Effect of Chronic Alcoholism on the Conjunctival Flora.

AIM: We aimed to investigate the effect of alcohol abuse on the conjunctival flora. MATERIALS AND METHODS: The cases were evaluated as two groups. The study group consisted of 55 heavy-drinking males diagnosed with alcohol abuse, while the control group consisted of 55 males without a history of alcohol abuse. Samples were taken from the inferior fornix conjunctiva with sterile cotton-tipped swabs (Amies transport medium) for culture. The samples were inoculated into blood agar, chocolate agar, eosine methylene blue agar and Saboraud-Dextrose agar (Oxoid/UK) with the dilution method. RESULTS: The microorganisms that grew in study group subjects were Coagulase Negative Staphylococcus (CNS) in 30 (54.5%), Staphylococcus aureus in 14 (25.5%), Moraxella spp. in 3 (5.5%), Streptococcus spp. in 3 (5.5), Bacillus spp. in 3 (5.5%), Corynebacterium spp. in 3 (5.5%), Candida spp. in 3 (5.5%), Haemophilus spp. in 2 (3.6%), Acinetobacter spp. in 2 (3.6%), Neisseria spp. in 1 (1.8%) and Micrococcus spp. in 1 (1.8%). The results for control group were CNS in 31 (56.4%), Bacillus spp. in 7 (12.7%), S. aureus in 5 (9.1%), and Corynebacterium spp. in 2 (3.6%). Moraxella spp., Streptococcus spp., Candida spp., Haemophilus spp., Acinetobacter spp., Neisseria spp. and Micrococcus spp. microorganisms grew in the conjunctival flora samples of the study group but not in the control group. S. aureus colonization was significantly higher in the study group than the control group (p < 0.05). CONCLUSION: The S. aureus colonization rate was statistically significantly higher in the study group. Some microorganisms only grew in the conjunctival flora samples of the study group. These findings indicate that the conjunctival flora in persons with chronic alcoholism is different than the normal population.

[Carriage of Streptococcus pyogenes in primary school children: M-protein types, pyrogenic toxin genes, and investigation of the clonal relationships between the isolates]. / Ilkokul çocuklarinda Streptococcus pyogenes tasiyiciligi: M-protein tipleri, pirojenik toksin genleri ve izolatlar arasi klonal iliskinin arastirilmasi.

M-protein and pyrogenic toxins are the most important virulence factors of Streptococcus pyogenes, and they play significant role in the pathophysiology of acute rheumatoid fever and scarlet fever, respectively. In this study, the pharyngeal carriage of S.pyogenes of the primary school children, clonal relationship of the strains, M-protein types, and the presence of pyrogenic toxin genes were aimed to be investigated. A total of 668 throat cultures obtained from children (age range: 6-16 years) in two primary schools in our region, were included in the study. The clonal relationships of the isolated group A streptococci (GAS) strains were investigated by DiversiLab assay (BioMérieux, France), and the clonal relatedness was confirmed by pulsed-field gel electrophoresis (PFGE) method. M-protein (emm) typing was performed by DNA sequencing as suggested by Centers for Disease Control and Prevention (CDC). The genes encoding pyrogenic toxins, speA and speC, were investigated by an in-house multiplex polymerase chain reaction (PCR) method. S.pyogenes was isolated from 134 (20.05%) of the throat samples. The GAS carriage rate of the students aged ≥10 was statistically higher than those 7-9 years age group (%22 vs %16.4, p<0.05). The M protein gene could be characterized only among 123 isolates by DNA sequencing, and 20 different emm types were detected. The most frequent emm type was emm1 (n=38, 30.9%) followed by emm12 (n=18, 14.6%), emm89 (n=10, 8.1%), emm118 (n=9, 7.3%), and emm4 (n=7, 5.7%). Pyrogenic toxin genes were found in 25 (18.6%) of the isolates, including speA in 11 isolates (8.2%) and speC in 12 isolates (8.9%) and both genes were detected in 2 isolates (1.5%). Sixty-two different Rep (Repetitive extragenic palindromic)-PCR profiles were detected in 134 S.pyogenes isolates by DiversiLab method. Thirteen different clusters were formed by a total of clonally related 36 isolates revealing a strain clustering ratio of 26.9%. Clonal relationship of all isolates in the same cluster was confirmed by PFGE method. In this study, relatively high percentage of GAS carriage was observed among primary school children in our region. The coverage rate of the 30-valent vaccine was determined to be over 90% with respect to M-protein types. Since the pyrogenic toxin-encoding genes were found in one fifth of the isolates from the studied subjects, we concluded that the carrier population may also have high risk for scarlet fever. We also concluded that, the clonal relationship ratio determined among the isolates may be a risk in school transmission of GAS.

Prevalence of the Helicobacter pylori in the tonsils and adenoids / Prevalência do Helicobacter pylori em amígdalas e adenoides

INTRODUCTION: There is an ongoing debate about the existence and effects of Helicobacter pylori (Hp) in adenotonsillar tissue. OBJECTIVE: A clinical study was conducted to assess the existence of Hp in the adenoid and/or adenotonsillar tissues, which were surgically excised due to chronic adenotonsillitis. METHODS: Phosphoglucosamine mutase gene for the detection of Hp and cytotoxin-associated gene as virulence gene were examined in 84 adenotonsillar tissues obtained from 64 patients and patients' serum by using polymerase chain reaction. RESULTS: Hp IgG was detected in 57 (89%) patients' serum. A total of seven tissue samples from 64 patients (10.9%) were found positive for Hp DNA, of which five were adenoids and two were tonsil tissues. All polymerase chain reaction positive samples were also positive for the cytotoxin-associated gene, which is a virulence determinant for the organism. CONCLUSION: This study suggests that children are exposed to Hp at an early age of their life in this province. Hp may have a role in the pathogenesis of chronic adenotonsillitis, especially in endemic areas. .

INTRODUÇÃO: Há um debate atual sobre os efeitos da Helicobacter pylori (HpHp) no tecido adenotonsilar. OBJETIVO: Conduzimos um estudo clinico para avaliar a existência de Hp nos tecidos adenoideano e/ou adenotonsilar, os quais foram removidos cirurgicamente em decorrência de adenotonsilite crônica. MÉTODO: No total, 84 amostras de tecido obtidos de 64 pacientes foram analisadas para o gen fosfoglucosamina mutase para a detecção de Hp. Os casos positivos foram a seguir examinados para o gen associado à citotoxina, relacionado à virulência, usando-se o método de Reação de Polimerase em Cadeia (PCR). RESULTADOS: A IgG de Hp foi detectado em 57 (89%) soros de pacientes. Sete amostras de tecido de sessenta e quatro pacientes (10.9%) resultou positivo para o DNA de Hp, das quais cinco eram adenóides e duas eram tecido tonsilar. No PCR todas as amostras foram também positivas para o gen associado à citotoxina, o qual é um determinante de virulência. CONCLUSÃO: Esse estudo sugere que as crianças são expostas ao Hp nos primeiros anos de vida nessa província e que o Hp pode ter um papel na patogênese da adenotonsilite crônica, principalmente em áreas endêmicas. .

A rapidly fatal sepsis caused by listeria monocytogenes type-4b in a patient with chronic renal failure.

INTRODUCTION: Listeria monocytogenes is a significant zoonosis causing invasive infections in the susceptible persons. The current paper presented a patient who died due to a rapidly-progressing multiple organ failure (MOF) as a result of severe sepsis caused by L. monocytogenes. CASE PRESENTATION: A 70-years-old patient with chronic renal failure was admitted to the infectious diseases clinic due to diarrhea for one day. He was hospitalized and the body fluid samples were collected for laboratory analyses. Within few hours, his vital findings worsened, and he developed respiratory arrest. Ceftriaxone and gentamycin were administrated. However, he died due to disseminated intravascular coagulation, septic shock and meningoencephalitis at the 22nd hour of admission. Causative agent was identified as L. monocytogenes serotype-4b in post-mortem period. DISCUSSION: L. monocytogenes can cause progressive and rapidly fatal infections in the vulnerable persons, with multisystem involvement. Since this bacterium is not susceptible to cephalosporines, it will be better to consider effective antimicrobials in the treatment of the possible cases.

Prevalence of the Helicobacter pylori in the tonsils and adenoids.

INTRODUCTION: There is an ongoing debate about the existence and effects of Helicobacter pylori (Hp) in adenotonsillar tissue. OBJECTIVE: A clinical study was conducted to assess the existence of Hp in the adenoid and/or adenotonsillar tissues, which were surgically excised due to chronic adenotonsillitis. METHODS: Phosphoglucosamine mutase gene for the detection of Hp and cytotoxin-associated gene as virulence gene were examined in 84 adenotonsillar tissues obtained from 64 patients and patients' serum by using polymerase chain reaction. RESULTS: Hp IgG was detected in 57 (89%) patients' serum. A total of seven tissue samples from 64 patients (10.9%) were found positive for Hp DNA, of which five were adenoids and two were tonsil tissues. All polymerase chain reaction positive samples were also positive for the cytotoxin-associated gene, which is a virulence determinant for the organism. CONCLUSION: This study suggests that children are exposed to Hp at an early age of their life in this province. Hp may have a role in the pathogenesis of chronic adenotonsillitis, especially in endemic areas.

Oral amoxicillin-clavulanic Acid treatment in urinary tract infections caused by extended-spectrum Beta-lactamase-producing organisms.

BACKGROUND: Extended-spectrum ß-lactamases (ESBLs) are increasing problems. The involvement of ESBL-producing organisms is associated with higher rates of carbapenem usage in urinary tract infections (UTIs). Though some strains are susceptible to amoxicillin-clavulanic acid (AMC) in vitro, there is very less data about the consequences of AMC usage for such infections. OBJECTIVES: The purpose of this study was to evaluate the clinical and microbiological outcomes of AMC treatment in UTIs caused by AMC-susceptible ESBL-producing organisms. PATIENTS AND METHODS: A retrospective cohort study was conducted in a tertiary care hospital. Forty-six out of 652 patients (F/M ratio: 32/14; mean age: 43.9 years) with ESBL-positive UTIs were eligible for this study. These patients had cystitis (n = 23), vesicoureteral reflux (n = 7), hyperactive bladder (n = 6), and prostatitis (n = 10). Data was collected via chart review and was statistically analyzed. RESULTS: AMC-susceptible ESBL-producing Escherichia coli, Klebsiella pneumoniae and K. oxytoca were identified as the causative agents in 31, 14, and 1 patients, respectively. Thirty-nine (84.7%) out of 46 patients were successfully treated with oral AMC. Additionally, 2 (4.3%) patients' urine cultures turned to be negative, though their clinical complaints and leukocyturia had continued. In the remaining 5 (10.8%) patients, no positive clinical and microbiological response was obtained. Increased minimum inhibitory concentration levels of AMC (from 4 to > 256 µg/mL) were detected in these patients and the treatment failures were attributed to this developing resistance. We found that therapeutic failure was significantly more frequent in Klebsiella spp. than in E. coli (33.3% vs 6.5%, P = 0.029). Furthermore, no treatment failure was observed in pathogens with minimum inhibitory concentrations (MICs) ≤ 2 mg/mL, and the high AMC MIC (8 mg/mL) was associated with resistance development and therapeutic failure (71.4% vs. 5.1%, P = 0.0001). CONCLUSIONS: Our results suggested that amoxicillin-clavulanic acid may be a good oral antimicrobial which can be used for treatment of ESBL-positive UTIs, if the causative agent is susceptible to this antibiotic. However, some strains may develop resistance during therapy, especially in those exhibiting high AMC MICs.