Role of quantitative planar lung perfusion scintigraphy and tomography in identifying target lobes in patients with emphysematous phenotype of advanced chronic obstructive pulmonary disease: a retrospective cross-sectional study.

Background: Chronic obstructive pulmonary disease (COPD) is a common, preventable, and treatable disease. Despite optimal medical therapy and pulmonary rehabilitation, bronchoscopic and surgical lung volume reduction may still be necessary. Identifying the target lobe is crucial for the success of these treatments. This study aims to compare the role of quantitative planar lung perfusion scintigraphy (QPLPS) with quantitative lung computed tomography (StratX®), which is used in identifying the target lobe before the Zephyr® endobronchial valve (EBV) placement in patients with the emphysematous phenotype of advanced COPD. Methods: A single-center retrospective cross-sectional study was performed in the Department of Pulmonology at the University of Health Sciences Turkey, Yedikule Chest Diseases and Thoracic Surgery Education and Research Hospital between June 2019 and June 2022. The study included 46 patients with the emphysematous phenotype of advanced COPD, who were all candidates for Zephyr® EBV therapy. The target lobes were assessed using the QPLPS and StratX® and the agreement between the methods was analyzed by the Kappa statistic method. Additionally, demographic characteristics, respiratory function tests, distributions of emphysema, and 6-minute walk test results of patients were recorded. Results: The median age was 67 (42-80) years and 42 (91.3%) were male. In QPLPS, the perfusion percentages were 7.47%±3.31%, 9.59%±2.67%, and 13.32%±2.59% for the 1st, 2nd and 3rd target lobes, respectively while in StratX®, the voxel densities were 68.28%±9.16%, 63.79%±7.42%, and 60.69%±5.35%. In StratX®, the fissure integrity (FI) at the target lobe was 76.25%±21.18%, 84.68%±17.67%, and 86.19%±13.19%, respectively. There was a significant agreement between the methods in identifying the first, second, and third target lobes in all patients (Kappa coefficient: 0.897, 0.700, and 0.522), and also in identifying the first and second target lobes in patients with heterogeneous (Kappa coefficient: 0.879, and 0.735), and homogeneous subgroups (Kappa coefficient: 0.919, and 0.672). Conclusions: There is an agreement between QPLPS and StratX® in identifying the target lobe in patients with severe emphysema, including those with homogeneous diseases. However, StratX® may be preferred, considering that it also predicts FI.

Management of airway complications following lung transplantation: first interventional bronchoscopy report from Türkiye.

Background/aim: Lung transplantation is the treatment of last resort for many chronic lung diseases. Airway complications (AC) following lung transplantation, such as bronchial stenosis, dehiscence, malacia, and fistula, account for frequent hospital admissions, additional treatment costs, decreased quality of life, and reduced survival rates. Beyond surgical and medical preventive efforts, interventional bronchoscopy (IB) can be used in the management of these complications. The aim of the study is to evaluate the efficacy of IB on the management of AC following lung transplantation. Materials and methods: A retrospective analysis was done using the data of lung transplant patients with AC referred to the interventional pulmonology unit between December 2012 and December 2019. Results: From a total of 116 lung transplants, the data of 14/116 (12%) patients and 14/220 (6.3%) anastomoses in the same lung transplant group with AC requiring IB were analyzed. In these 14 patients, the diseases leading to lung transplantation were interstitial lung diseases (ILD) (50.0%), bronchiectasis (28.6%), pulmonary arterial hypertension (PAH) (7.1%), chronic obstructive pulmonary disease (COPD) (7.1%), and COPD + bronchiectasis (7.1%). Airway stenosis was the most common airway complication, and it developed mostly in the right bronchial system.The 14 patients underwent 27 total sessions of IB with an average of 2-3 per patient. Airway patency was successfully achieved in 74.1% of the procedures. Mechanical dilatation with a balloon and/or a rigid tube was the most preferred procedure (81.5%). Permanent airway patency was achieved in eight (57.4%) patients. No early complications were encountered (0%). The late complication rate was 48.1%. The most frequent late complication was restenosis, which cannot be directly attributed to IB. Conclusion: IB is safe to perform on lung transplant patients with AC. It has low procedural complication rates and can be performed repeatedly. Because of the high rate of restenosis, interventional pulmonologists should find out treatment modalities with lower rates of restenosis.

Resistance Genes and Mortality in Carbapenem-resistant Klebsiella pneumoniae Bacteremias: Effects of the COVID-19 Pandemic

Background: Emerging carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) (CRKP) bacteremias are presenting significant public health risks due to limited treatment options and increased mortality. K. pneumoniae isolates exhibit carbapenem resistance rates that vary from 25% to 50% throughout the European continent, including our country. Aims: To assess the characteristics of CRKP bacteremia, a condition that has recently demonstrated an increasing prevalence in our center. We sought to ascertain the resistance rates of isolated strains to antibiotics other than carbapenems, identify the responsible carbapenemase genes, evaluate the efficacy of antibiotics, determine mortality rates, explore clonality among strains, and investigate the influence of the COVID-19 pandemic on all these factors. Study Design: Retrospective observational study. Methods: This study included patients aged 18 and older who had experienced meropenem-resistant K. pneumoniae bacteremia. Meropenem resistance was confirmed by employing the Kirby-Bauer disk diffusion method. Meropenem minimum inhibitory concentration (MIC) levels were determined using the gradient test, while colistin MIC levels were ascertained using the disk elution technique. Carbapenemase genes were evaluated via colony polymerase chain reaction (PCR), and clonality analysis was performed using the arbitrarily primed PCR technique. Results: The study comprised 230 patients, with a mean age of 63.1 ± 15.9 years, of whom 58.7% were male. Oxacillinase-48 (OXA-48) was detected in 74.8% of the patients, New Delhi metallo-beta-lactamase (NDM) in 12.6%, OXA-48 + NDM in 7.8%, and KPC in 4.8%. The 14-day and 30-day mortality rates were 57% and 69.6%, respectively. Multivariate analysis of the 30-day mortality revealed several crucial factors, including bacteremia development in the intensive care unit, the occurrence of bacteremia during the COVID-19 pandemic, polymicrobial bacteremia, the use of indwelling intravenous catheters, a platelet count of ≤ 140,000/µl, procalcitonin levels of ≥ 6 µg/l, and a Charlson comorbidity score ≥ 3. Notably, the OXA-48 and KPC genes were upregulated significantly during the COVID-19 pandemic, while the NDM gene groups were downregulated. Additionally, both 14-day and 30-day mortality rates increased significantly. Conclusion: In this study, the most prevalent carbapenemase gene was OXA-48; however, there has been a recent increase in KPC genes. No dominant epidemic strain was identified through clonality analysis. The clustering rate was 68% before the pandemic, increasing to 85.7% during the pandemic. The significance of infection control measures is underscored by the rise in both clustering and mortality rates during the COVID-19 pandemic.

The comprehensive evaluation of oral and fecal microbiota in patients with acromegaly.

PURPOSE: The alteration of the microbiota in the mouth and gut could potentially play a role in the pathogenesis of various diseases, and conversely, these diseases may have an influence on the composition of the gut microbiota. Acromegaly disease can potentially affect physiological processes in the mouth and gut. The present study was designed to investigate the relationship between acromegaly and the oral and gut microbiota, as data on this topic are scarce. METHODS: This was a multicenter, cross-sectional study. Our study included individuals diagnosed with acromegaly (who were treated and followed up, and also as an another group of patients with newly diagnosed acromegaly) and healthy participants. All three groups were assessed and compared based on age, sex, serum IGF-1, body mass index BMI as well as their stool and oral microbiota We collected demographic information from the patients, collected fecal and oral samples, performed DNA isolation followed by 16 S rRNA sequencing, and then performed bioinformatic analysis. We also analyzed the oral and fecal samples with respect to medical and surgical treatment and disease control status, specific treatments received for acromegaly, presence of comorbidities, hypopituitarism status, presence of intestinal polyps. RESULTS: One hundred and three patients with acromegaly, 15 newly diagnosed patients with acromegaly without comorbidities and 34 healthy controls were included in the study. The Firmicutes/Bacteroidetes ratio was significantly lower in patients with acromegaly who received treatment (medical and/or surgical) than in healthy controls. In addition, a significant difference was found in the fecal and oral microbiota of patients with acromegaly with disease control compared to healthy controls. Furthermore, a significant difference was found in the fecal and oral microbiota of patients with acromegaly without disease control. Nevertheless, it was not possible to establish a clear relationship between disease control status, the presence of intestinal polyps, the presence of type 2 diabetes and the composition of the oral and gut microbiota in acromegalic patients who had received different forms of treatment. CONCLUSION: Patients with acromegaly show distinct gut microbiota profiles, and it is evident that factors beyond the GH/IGF-1 axis play a role in shaping the gut microbiota of individuals with acromegaly.

A first study of meat-borne enterococci from butcher shops: prevalence, virulence characteristics, antibiotic resistance and clonal relationship.

IntroductionEnterococcus, which used to be thought of as a harmless commensal living in the digestive tract, has now become a highly resistant and highly contagious pathogen that makes nosocomial infections much more common. This study examined enterococci species and their antibiotic resistance phenotypes and genotypes and virulence gene content in Turkish ground beef samples. Methodology A total of 100 ground beef samples were analyzed between May 2020 and May 2021. The isolated strains were identified via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and confirmed using polymerase chain reaction (PCR) after which they were divided into several species using PCR and tested for antibiotic resistance against 19 antimicrobial agents using the disc diffusion method. The genetic similarity analysis, pulsed-field gel electrophoresis (PFGE) was performed. Results A total of 93 isolates in ground beef were identified, comprised of E. faecalis 72.04%; E. hirae- 11.82%; E. casseliflavous- 7.52%; E. faecium- 5.3%; E. gallinarium- 3.23%. The virulence genes observed in Enterococcus species were distributed as follows: gelE 88.1%, ace 53.7%, efaA 40.8%, asaI 19.3%, esp 6.4%, and cylA 1.07%. A high antibiotic resistance was recorded for tetracycline (43.01%), followed by ampicilin (17.2%), and chloramphenicol (13.9%). 17.2% of Enterococcus isolates were multidrug-resistant. The study determined the high prevalence of antibiotic resistance genes, specifically for tet(L) 10 (10.7%), aac(6')Ie-aph(2")-la 3 (3.2%), and ermB 3 (3.2%). The presence of efflux pump genes were identified in 74.1% of Enterococcus isolates. Genetic characterization of 67 E. faecalis isolates by PFGE revealed 41 pulsed-field gel electrophoresis (PFGE) patterns that were grouped into 15 clusters, which presented more than one strain with 100% similarity. Conclusion Isolates obtained from several areas and butchers had comparable patterns of PFGE, suggesting that the presence of circulating E. faecalis poses a potential public health concern in diverse districts. To mitigate the health hazards associated with the contamination of enterococci from raw to cooked meats, it is necessary to enhance the disinfection of butcheries, promote excellent hand hygiene among butchers, and implement appropriate meat storage and handling methods to prevent bacterial development.

Ceftazidime-avibactam resistance determination in carbapenem-resistant Klebsiella pneumoniae infections before its use in practice.

INTRODUCTION: To ensure the appropriate usage of ceftazidime-avibactam (CAZ-AVI), recently introduced in our hospital, we aimed to determine susceptibility rates, enzyme analysis, and clonal relationship among strains, together with clinical data. METHODOLOGY: Between June 1 and September 30, 2021, demographic and microbiological data of the patients were recorded. In the obtained samples, meropenem and colistin minimal inhibitory concentration (MIC) levels, carbapenem resistance genes, and the clonal relationship were studied by molecular methods. CAZ-AVI was not used in any of the patients. RESULTS: 140 carbapenem-resistant Klebsiella pneumoniae were isolated from 57 patients. Resistance to CAZ-AVI was found in 76 (54.3%) strains. Out of 57 patients, 31 (54.4%) isolates could be reached. Meropenem MIC level was ≥ 32 µg/mL in 26 (83.9%), and colistin MIC level was ≥ 4 µg/mL in 17 (54.8%) isolates. Enzyme analysis revealed NDM in 20 (64.5%), OXA-48 in 17 (54.8%), and KPC in seven (22.6%). NDM + OXA-48 was determined in 10 (32.2%) strains. NDM was determined in all CAZ-AVI resistant strains, OXA-48 in 16.1% (2/5) strains. Seven genotypes were detected. The largest cluster was genotype 3 clusters (11 isolates). Of 31 patients, 22 (71.0%) died. CAZ-AVI was susceptible in one of the patients who survived and four who died. CONCLUSIONS: Before using a new antibiotic, each center should determine the basal data and phenotypic/genotypic resistance ratios specific to that antibiotic. While a high NDM rate and low CAZ-AVI sensitivity limit the use of the drug in our center, it is clear that CAZ-AVI use in sensitive strains will decrease mortality.

Investigation of some changes and clonal relationship in enterococci isolates due to relocation of a hospital.

Objectives: To investigate the isolation rates, antimicrobial resistance rates, minimum inhibitory concentration values of antimicrobial agents, and clonal relationships of Enterococcus faecalis and Enterococcus faeciumdue to the relocation of a hospital to a newly constructed building. METHODS: The comparative, prospective study was conducted at adult general intensive care units of the Mus State Hospital, Mus, Turkey, in two phases; before the relocation from January 25 to December 1, 2014, and after the relocation from February 10 to May 24, 2015. Rectal swab samples were collected 72 hours post-hospitalisation. Identification of Enterococcus faecalis and Enterococcus faeciumisolates was determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and antimicrobial resistance with minimum inhibitory concentration values was detected with Vitek 2 system. The clonal relatedness among the strains was investigated by pulsed-field gel electrophoresis. Data was analysed using SPSS 23. RESULTS: Of the 69 patients, 37(53.62%) were related to pre-relocation phase; 20(54.1%) females and 17(45.9%) males with mean age 62.81±21.71 years. There were 32(46.37%) patients in the post-relocation phase; 13(40.6%) females and 19(59.4%) males with mean age 62.69±21.35 years (p>0.05). Of the 84 enterococci strains isolated, 51(60.7%) were Enterococcus faecium; 28(55%) before relocation and 23(45%) after relocation (p=0.77). The remaining 33(39.3%) isolates were Enterococcus faecalis; 16(48.5%) before relocation and 17(51.5%) after relocation (p=0.73). Multiple strains were located in 7(18.9%) patients before relocation and in 7(21.9%) after relocation. In 1(3.1%) patient after relocation, 2(8.7%) Enterococcus faecium isolates with different resistance and pulsed-field gel electrophoresis patterns were detected. There were no significant differences between the isolation and antibiotic resistance rates before and after relocation (p>0.05), and a clonal relation between the isolates was not detected (p>0.05). Decreased minimum inhibitory concentration values were noted for some antibiotics. CONCLUSIONS: Clonal relationship between the isolates and change in the rates of isolation and antimicrobial resistance of Enterococcus faecalis and Enterococcus faecium was not detected due to relocation. Minimum inhibitory concentration values could be used to reveal relocation-related changes in isolates obtained from patients hospitalised in intensive care units.

[A New Case of Fournier's Gangrene Caused by Actinotignum schaalii]. / Actinotignum schaalii'nin Etken Oldugu Yeni Bir Fournier Gangreni Olgusu.

Actinotignum schaalii (formerly known as Actinobaculum schaalii) is an anaerobic or facultative anaerobic gram-positive bacillus that can be found commensally in the urogenital region. It can be overlooked because it grows slowly and is difficult to identify with classical microbiology laboratory techniques. Colonies become visible after 48-72 hours of incubation on blood agar in anaerobic or CO2-rich media. While it typically causes urinary tract infection in older individuals, cases of bacteremia, vertebral osteomyelitis, endocarditis and cellulitis have been reported. Fournier's gangrene caused by A.schaalii has been reported very rarely so far. Fournier's gangrene has been defined as necrotizing fasciitis of the external genitalia, perineal and perianal region. Diabetes, immunosuppression, peripheral vascular disease, urethral anomalies, chronic alcoholism and smoking are important predisposing factors. In addition, approximately 25% of the cases have no known or identifiable etiology. The bacteria causing the infection may originate from skin, urogenital or intestinal microbiota. In this case report, a new case of Fournier's gangrene caused by A.schaalii was presented. A 65-year-old male patient admitted to the emergency department with the complaints of pain, swelling, redness in the left testis and also nausea, vomiting and chills that started three days ago. Physical examination revealed increased diameter of the scrotum, intense hyperemia of the skin and foci of necrosis. It was learned that the patient had no known chronic disease other than benign prostatic hyperplasia. The patient reported smoking of 25 packs of cigarettes per year. Routine laboratory tests revealed leukocyte= 32.41 x 109/L, neutrophil= 89.9%, procalcitonin= 1.62 ug/L, CRP= 265.07 mg/L and the patient was operated with the diagnosis of Fournier's gangrene. Gram staining of the abscess specimen obtained during the operation showed gram-positive bacilli both inside and outside the leukocytes. After 24 hours, grampositive bacilli were detected in the Gram staining of thin, transparent/gray colonies grown on 5% sheep blood and chocolate agar. The isolate was identified as A.schaalii by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) VITEK® MS (bioMérieux, France) microbial identification system. VITEK®2 ID ANC (bioMérieux, France) bacterial identification card was also used for comparison but the bacteria could be identified. As a result of the sequence analysis performed for confirmation, it was shown to be 100% homologous with Actinobaculum schaalii (GenBank accession no: FJ711193.1). For susceptibility tests, 5% sheep blood Schaedler agar was used and incubated in anaerobic environment. According to the minimal inhibitory concentration (MIC) results evaluated after 48 hours, penicillin was found to be 0.032 mg/L, clindamycin 0.125 mg/L, ciprofloxacin 0.19 mg/L, ceftazidime 4 mg/L, and amoxicillin 0.19 mg/L. The primary cause that initiated the infection in the case could not be identified, but it was thought that the presence of prostatic hyperplasia and smoking history may have contributed to the occurence or the progress of the disease. It is noteworthy that the ciprofloxacin MIC result was quite low compared to other studies. In addition, this study revealed the value of MALDI-TOF MS based methods in identification. In conclusion, it is thought that a significant proportion of A.schaalii infections may be overlooked due to the difficulty in growth and identification. Increasing the diagnostic power of clinical microbiology laboratories for poorly identified bacteria and renewing the databases of commercial identification systems are important for the early and accurate diagnosis and treatment of serious infections that may occur with such agents.

Stenotrophomonas maltophilia outbreak originating from a pull-out faucet in a pediatric intensive care unit in Turkey: Insights from clinical records and molecular typing.

BACKGROUND: Nosocomial Stenotrophomonas maltophilia-related cases are rising and pose a threat to immunocompromised patients. Twelve patients from our pediatric intensive care unit (PICU) presented with S maltophilia-associated bloodstream infection. METHODS: This outbreak investigation includes 12 patients from PICU between the ages of 2 months and 4 years (mean 16 months, 7 male). To identify the origin, samples from all possible sources throughout the hospital were collected and ran through DNA isolation and Pulse Field Gel Electrophoresis. RESULTS: 120 samples were collected during the outbreak. 31 samples (26%) were positive for S maltophilia. 30 S maltophilia isolates were analyzed, 10 different genotypes were identified. Clustering isolates were grouped into 3 different clusters (tolerance and optimization 1.0, cutoff 90%). The largest cluster was genotype 1, which included 19 isolates, those belong to patients' samples and a sample from a pull-out faucet inside the PICU. The Pull-out faucet was the origin of the bloodstream infection. DISCUSSION: Pull-out faucets allow biofilm production, due its structure. Pulse Field Gel Electrophoresis identifies the transmission dynamics of the outbreak, with its high discriminatory power. CONCLUSIONS: Water sources should be monitored on a regular basis. Pull-out faucets enable bacterial overgrowth; therefore, we recommend water surveillance during outbreak investigations.

An Outbreak of Vancomycin-Resistant Enterococci in a City Hospital Intensive Care Unit: Molecular Characterization of Resistance.

Background and Objectives: Vancomisin-resistant Enterococci (VRE), is a resistant microorganism that colonizes and causes infections in hospitalized patients. The aim of this study was to show the spread of vancomycin-resistant Enterococcus faecium (VREfm) step-by-step in all intensive care units, which started with the growth of VREfm on 2 December 2021 in the blood culture of a patient hospitalized in the anesthesia intensive care unit of our hospital and was found to have reached epidemic size in the surveys. Materials and Methods: Rectal swab samples were taken from all patients hospitalized in intensive care units, VRE colonization was determined, the VanA and VanB resistance genes associated with the vancomycin resistance of VREfm isolates were determined by PCR method, and clonal association analysis was performed by Arbitrarily Primed-PCR (AP-PCR) and PFGE (pulsed-field gel electrophoresis). Results: In our study, VRE were detected in 61 of 2601 rectal swab samples. In total, fifty-four (85.52%) of the VRE isolates were Enterococcus faecium, three (4.91%) was Enterococcus faecalis, three (4.91%) was Enterococcus gallinorum, and one (1.63%) was Enterococcus casseliflavus. It was determined that all of the 54 VREfm isolates, which were the most detected among all VRE isolates, carried the vanA gene. In the clonal association analysis of the isolates by AP-PCR and PFGE methods, it was found that they had 12 different genotypes, 48 of them were included in any cluster, the clustering rate was 88.8%, and the largest cluster was the genotype 1 cluster, with 36 isolates. Of the 54 patients with VREfm isolated recently, 18.51 percent of the clinical samples were isolated before the survey, and 9.25% were isolated after the survey. It was determined that 100% of VREfm isolates were resistant to ampicillin, levofloxacin, ciprofloxacin, high-level gentamicin, trimethoprimsulfamethoxazole, and teicoplanin, 7.4% to tigecycline, and 1.85% to linezolid. Conclusions: In our study, in the clonal association analysis performed by isolating VREfm in rectal swab samples, it was found that 88.8% of the samples were indistinguishably similar, and that the increase in the number of VREfm infections after the index case in our hospital was associated with the epidemic. VREfm infections cause long-term hospitalization, costs and also deaths, which shows the seriousness of the event, and the importance of the combination of epidemiological and molecular analysis in epidemic research.

Carbapenem-resistant Klebsiella pneumoniae outbreak with monoclonal spread: Evaluation of resistance genes and ceftazidime-avibactam susceptibility.

PURPOSE: The aim of this study was to investigate ceftazidime-avibactam (CAZ-AVI) susceptibility, carbapenemase genes, and clonal relationship in carbapenem-resistant Klebsiella pneumoniae (CrKp) isolates. METHODS: A total of 28 non-repetitive CrKp isolates with positive carbapenemase production determined by the modified carbapenem inactivation method (mCIM), were included in the study. Identification of the isolates was performed with MALDI-TOF MS (VITEK-MS, bioMerieux, France). The automated system (VITEK-2, bioMerieux) and gradient diffusion test (Etest, bioMerieux) were used to determine antibiotic susceptibility. The mCIM was performed according to CLSI (2021) recommendations. CAZ-AVI susceptibility was carried out using the standard disc diffusion method. Results were evaluated according to EUCAST 2022 criteria. The blaOXA-48, blaNDM, blaKPC, blaIMP and blaVIM genes were investigated by multiplex PCR. The clonal relationship between isolates was determined by both AP-PCR and PFGE methods. RESULTS: Of the total 28 isolates, 89.3% were susceptible to CAZ-AVI. blaOXA-48 gene was found in 85.7% of the isolates, blaOXA-48+blaNDM gene in 10.7%, and blaNDM gene in 3.6%. blaKPC, blaIMP and blaVIM genes were not detected. Three clusters with three different genotypes were determined by the PFGE method. The largest cluster was Genotype A (n:24), followed by Genotype B (n:3), and Genotype C (n:1). AP-PCR was highly compatible with PFGE. The isolates of Genotype A, mostly from the intensive care unit (ICU), were evaluated as outbreak strains with monoclonal dissemination. CONCLUSIONS: OXA-48 remains the most frequently detected enzyme in CrKp strains in our country. The ceftazidime-avibactam susceptibility rate of 89.3% indicates that this antibiotic is still effective against CrKp isolates. The unnoticed outbreak detected in our study revealed the severity of intra-hospital cross-contamination affecting different wards, including the ICU. Therefore, in order to limit the spread of CrKp isolates, it is of great importance to implement strict infection control measures, and molecular surveillance programs, especially in the ICU.

[Pasteurella multocida Pneumonia with Hemoptysis in an Immunocompetent Case]. / Immün Kompetan Bir Olguda Hemoptizi ile Seyreden Pasteurella multocida Pnömonisi.

Pasteurella species are gram-negative bacilli found in healthy pets' oropharynx and gastrointestinal tract flora. In humans, skin and soft tissue infections develop most frequently with the bite or scratching of animals such as cats or dogs. At the same time, they cause infections in the respiratory tract, mainly in patients with chronic lung disease or immunosuppressive patients. In this case report, a rare case of pneumonia caused by P.multocida bacteria in a patient with bronchiectasis was presented. A young male patient was admitted to the emergency department of our hospital with complaints of hemoptysis, cough with phlegm, and weight loss. The patient's blood pressure was 140/82 mmHg and SO2= 94%. Rales and rhonchi were detected in the lower left lung during the examination. Standard thorax tomography revealed prominent cystic structures and pneumonic infiltrates in the left lower lobe. Laboratory findings were normal. The Coronavirus disease-2019 (COVID-19) quantitative real-time polymerase chain reaction (qRt-PCR) test was found to be negative in the nasopharyngeal swab sample taken from the patient. Fiberoptic bronchoscopy was performed on the patient to investigate the presence of endobronchial lesion or foreign body aspiration. Culture and cytological evaluation was requested from the bronchial lavage taken. Gram-negative coccobacilli were seen among dense polymorphonuclear leukocytes in the Gram stain of the sample. Acid-fast bacilli were not detected with Ehrlich Ziehl Neelsen stain. In the lavage culture evaluated after 24 hours, colonies growing in blood and chocolate media were stained and gramnegative coccobacilli were observed. The isolate was identified as 96.0% P.canis with the automated Vitek 2 (Biomerieux, France) system. It was determined that the isolate was susceptible to levofloxacin, trimethoprim-sulfamethoxazole, amoxicillin-clavulanic acid, penicillin, ciprofloxacin and cefotaxime in the antibiogram performed by disc diffusion test according to EUCAST v13.0 guideline criteria. Sequence analysis of the isolate obtained from the culture was performed on the ABI Prism 310 Genetic Analyzer (Applied Biosystems, USA). Sequence analysis of the isolate revealed 99.85% homology with P.multocida (GenBank accession no: NG_115137.1). Although Pasteurella multocida pneumonia is not commonly observed, the presence of underlying bronchiectasis in this patient facilitated the establishment of the bacteria. In order not to miss the diagnosis of pneumonia due to P.multocida, microbiological evaluation and molecular typing should be performed in the samples taken from the respiratory tract in patients with chronic respiratory diseases such as bronchiectasis.

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 blaOXA-48+NDM was shown. The most common resistance genes were determined as blaSHV (84.3%), blaCTX-M-1 (46.8%), blaOXA-48 (40.6%), blaKPC (40.6%), blaTEM (31.2%), blaNDM (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.

Cessation of Rectal Screening for Vancomycin-Resistant Enterococci: Experience from a Tertiary Care Hospital from Türkiye.

OBJECTIVE: Here, we compared the impact of different polices on the epidemiology of Vancomycin-resistant Enterococcus faecium bloodstream infections (VRE-BSIs) in a tertiary care hospital including two hospital buildings (oncology and adult hospitals) in the same campus. MATERIAL AND METHODS: All patients who were hospitalized in high-risk units were screened weekly for VRE colonization via rectal swab between January 2006 and January 2013. After January 2013, VRE screening was only performed in cases of suspicion of VRE outbreak and during point prevalence studies to evaluate the epidemiology of VRE colonization. Contact precautions were in place for all VRE-positive patients. The incidence density rates of hospital-acquired (HA)-VRE-BSIs were compared between two periods. RESULTS: While the rate of VRE colonization was higher in the second period (5% vs. 9.5% (p < 0.01) for the adult hospital, and 6.4% vs. 12% (p = 0.02 for the oncology hospital), there was no increase in the incidence rate HA-VRE BSIs after the cessation of routine rectal screening in either of the hospitals. CONCLUSION: Screening policies should be dynamic and individualized according to the epidemiology of VRE as well as the workforce and cost. Periodical rectal screening of VRE can be discontinued if suspicion of an outbreak can be carefully monitored.

Serum Specific Antibodies Do Not Seem to Have an Additional Role in the Diagnosis of Hypersensitivity Pneumonitis.

BACKGROUND: We aimed to investigate the contribution of serum IgG testing to the history of exposure in the diagnosis of fibrotic hypersensitivity pneumonitis. METHODS: A single-center, retrospective, cross-sectional study including 63 patients pathologically diagnosed with fibrotic hypersensitivity pneumonitis in line with the guidelines of the American Thoracic Society. Descriptive statistics were presented and Kappa statistic was performed to evaluate the compatibility between panel and the history of exposure. RESULTS: The median age was 63 (22-81) years and 34 (54%) were male. Forty-six patients (73%) had a positive history of exposure. Thirty-nine patients (61.9%) had a positive HP/Avian panel. The most common exposure agent was mold (34.9%), followed by parakeet (31.7%). The antibody detected the most was penicillium chrysogenum lgG (36.5%), followed by aspergillus fumigatus (31.8%). There was no compatibility between HP/Avian panel and history of exposure (kappa coefficient= 0.18, p= 0.14). When the exposure was only assessed based on the history, 4 (6.35%) patients were diagnosed as fibrotic hypersensitivity pneumonitis with low confidence, 6 (9.52%) with moderate confidence, 11 (17.46%) with high confidence and 42 (66.67%) with definite confidence; whereas 4 (6.35%) patients were diagnosed as fibrotic hypersensitivity pneumonitis with low confidence, 6 (9.52%) with moderate confidence, 9 (14.29%) patients with high confidence and 44 (69.84%) patients with definite confidence if exposure was evaluated with history and/or panel. CONCLUSIONS: Serum specific precipitating antibody panel does not seem to provide additional value to the history of exposure in the diagnosis of fibrotic hypersensitivity pneumonitis.

The role of endobronchial ultrasonography elastography in the diagnosis of hilar and mediastinal lymph nodes.

BACKGROUND: Endobronchial ultrasonography (EBUS) is a minimally invasive diagnostic tool in the diagnosis of mediastinal lymph nodes (LNs) and has sonographic features. We aimed to investigate the diagnostic accuracy of EBUS elastography, which evaluates tissue compressibility integrated into EBUS, on malignant vs. benign mediastinal-hilar LNs. METHODS: A single-center, prospective study was conducted at the University of Health Sciences Yedikule Chest Diseases and Thoracic Surgery Training and Research Hospital between 01/10/2019 and 15/11/2019. The features of 219 LNs evaluated by thoracic computed tomography (CT), positron emission tomography (PET)/CT, EBUS sonography and EBUS elastography were recorded. The LNs sampled by EBUS-guided fine needle aspiration were classified according to EBUS elastography color distribution findings as follows: type 1, predominantly nonblue (green, yellow, and red); type 2, part blue, part nonblue; type 3, predominantly blue. The strain ratio (SR) was calculated based on normal tissue with the relevant region. RESULTS: The average age of 131 patients included in the study was 55.86 ± 13 years, 76 (58%) were male. Two hundred and nineteen lymph nodes were sampled from different stations. Pathological diagnosis of 75 (34.2%) LNs was malignant, the rest was benign. When EBUS B-mode findings and pathological results were compared, sensitivity was 65.33%, specificity 63.19%, positive predictive value (PPV) 48%, negative predictive value (NPV) 77.8%, and diagnostic yield (DY) 64%. When the pathological diagnoses and EBUS elastography findings were compared, while type 1 LNs were considered to be benign and type 3 LNs malignant, sensitivity 94.12%, specificity 86.54%, PPV 82.1%, NPV 95.7%, and DY 89.5%. SR of malignant LNs was significantly higher than benign LNs (p < 0.001). When the classification according to color scale and SR were compared, no difference was found in DY (p = 0.155). DISCUSSION: The diagnostic accuracy of EBUS elastography is high enough to distinguish malignant LN from benign ones with the SR option. When compared with EBUS-B mode sonographic findings, it was found to have a higher diagnostic yield.

Investigation for the presence of bacteria and antimicrobial resistance genes in sea snails (Rapana venosa).

INTRODUCTION AND OBJECTIVE: The aims of this study were to search for the presence of bacteria in sea snails (Rapana venosa) by using culturomics and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and the antibiotic resistance/susceptibility of the sea snails. MATERIAL AND METHODS: The anti-microbial susceptibilities of Gram-negative bacteriawas assessed by the Kirby-Bauer disk diffusion method, the presence of the mcr genes (mcr-1 to -5), the major carbapenemase and ß-lactamase resistant genes in Gram-negative bacteria, using mPCR method and 16S rRNA sequence analysis of A. hydrophila isolates. RESULTS: Bacterial growth accounted for 100% and 94.2% in the samples of intestine and meat, respectively, in the snails. The main organisms identified by MALDI-TOF MS were A. salmonicida subsp. salmonicida at 33.7%, followed by Raoultella ornithinolytica at 9.6% (10/104) and Staphylococcus warneri at 7.7% in meat and intestine samples. Aeromonas hydrophila/punctata (caviae), Aeromonas sobria, Klebsiella aerogenes, Klebsiella oxytoca, Raoultella planticola, Shewanella putrefaciens and Vibrio vulnificus are intrinsic or chromosomally-mediated resistant against ampicillin. No mcr genes (mcr-1 to -5), the major carbapenemase and ß-lactamase resistant genes were found. Aeromonas salmonicida subsp. salmonicida showed very low levofloxacin and meropenem resistance levels at 2.9%. When the sequence was searched in the Blast database, the genome of A. hydrophila/punctata (caviae) isolate showed high similarity with the A. hydrophila sequences. CONCLUSIONS: Conclusions. The findings obtained not only provide data about the proportion of bacteria in the gut and meat of the sea snails and their antibiotic resistance/susceptibility, but also show the absence of carbapenemase, colistin, and ß-lactamase resistant genes among bacterial isolates from sea snail gut microbes.

The Effects of Antiperspirant Aluminum Chlorohydrate on the Development of Antibiotic Resistance in Staphylococcus epidermidis.

This study investigates the effects of the antiperspirant aluminum chlorohydrate on the development of antibiotic resistance in commensal Staphylococcus epidermidis isolates. The isolates were exposed to aluminum chlorohydrate for 30 days. The bacteria that developed resistance to oxacillin and ciprofloxacin were isolated, and the expression levels of some antibiotic resistance genes were determined using quantitative reverse transcriptase PCR. Before and after exposure, the minimum inhibitory concentration (MIC) values of the bacteria were determined using the microdilution method. A time-dependent increase was observed in the number of bacteria that developed resistance and increased MIC values. Consistent with the ciprofloxacin resistance observed after exposure, an increase in norA, norB/C, gyrA, gyrB, parC, and parE gene expression was observed. In addition to aluminum chlorohydrate exposure, oxacillin resistance was observed in all test bacteria in the group only subcultured in the medium, suggesting that phenotypic resistance cannot be correlated with chemical exposure in light of these data. The increase in mecA gene expression in selected test bacteria that acquired resistance to oxacillin after exposure compared with control groups suggests that the observed resistance may have been related to aluminum chlorohydrate exposure. To our knowledge, this is the first time in the literature that the effects of aluminum chlorohydrate as an antiperspirant on the development of antibiotic resistance in Staphylococcus epidermidis have been reported.

Fibrinogen-Aα THR312ALA Polymorphism is Associated to Chronic Thromboembolic Pulmonary Hypertension in Turkey.

BACKGROUND: Chronic thromboembolic pulmonary hypertension is a condition that occurs after mechanical obstruction of the pulmonary arteries by thrombus. Since the frequency and demographics of chronic thromboembolic pulmonary hypertension differ between countries, it is thought that genetic factors may play a role in its development. The aim of this study is to reveal the status of VKORC1, CYP2C9*3, CYP2C9*7, and fibrinogen-Aα THR312ALA gene polymorphisms in chronic thromboembolic pulmonary hypertension patients in Turkey. METHODS: In this prospective cross-sectional study, a total of 46 chronic thromboembolic pulmonary hypertension patients and 106 healthy volunteers were included. Polymerase chain reaction-restriction fragment length polymorphism method was used to determine candidate gene polymorphisms for chronic thromboembolic pulmonary hypertension. The general population parameters of each locus were calculated, and the relationship between dominant, codominant, and recessive genotype models and chronic thromboembolic pulmonary hypertension was analyzed. RESULTS: For the fibrinogen-Aα gene, those with the THR/THR genotype were found to have a 13.51 (95% CI: 2.688-33.333) times less susceptibility rate to the disease than those with the ALA/THR genotype, the susceptibility of THR/ALA genotype to the disease was 5.026 (95% CI: 1.774-14.242) times more than those with ALA/ALA genotype. There was no difference between patient groups for VKORC1, CYP2C9*3 genes (P >.05). Since the CYP2C9*7 patient group was monomorphic for the ILE allele, the patient/control odds ratio and 95% CI could not be calculated. CONCLUSION: This study shows that there is an association between the fibrinogen-Aα gene ALA polymorphism at the amino acid position of 312 and the development of chronic thromboembolic pulmonary hypertension, but not between the CYP2C9 and VKORC1 gene polymorphisms.

Does marking as sterile mean really sterile? Stenotrophomonas maltophilia outbreak caused by a blood-gas injector containing liquid heparin.

An outbreak investigation was initiated after detecting an increase in the number of patients with Stenotrophomonas maltophilia bloodstream infections (SM-BSIs) througout the hospital. S. maltophilia was isolated from the cultures of blood-gas injectors containing liquid heparin. The incidence density of SM-BSIs decreased significantly after prohibiting the use of those injectors.