[A Case of Thyroid Gland Abscess Caused by Brucella melitensis]. / Brucella melitensis'in Neden Oldugu Bir Tiroid Bezi Apsesi Olgusu.

Brucellosis is a zoonotic disease endemic in many developing countries, including Türkiye. Among the species that are pathogenic for humans; Brucella melitensis is isolated from livestock animals like sheep and goats, Brucella abortus from cattle and Brucella suis from pigs. Laboratory diagnosis of infection caused by Brucella species with gram-negative coccobacillus morphology; can be made through characteristic culture features, serological tests and molecular methods. Brucellosis, which has a wide distribution of clinical signs and symptoms; can cause various complications by affecting many organs and systems. Among all complications, the probability of thyroid abscess is less than 1%. In this case report; an example of thyroid abscess, one of the rare complications of brucellosis that is not frequently encountered in the literature, was presented. During the physical examination of a 45-year-old female patient who admitted with the complaint of pain in the neck area, fever, neck swelling, redness and pain that increased with palpation were detected. Leukocytosis, lymphopenia, high sedimentation and CRP, low TSH and high T4 values were detected in laboratory tests and subacute thyroiditis was considered as the preliminary diagnosis. Surgical abscess drainage was planned as the patient's clinical findings progressed during follow-up and spontaneous pus discharged from the midline of the neck. The abscess aspirate sample taken during surgical intervention and the blood culture samples taken before were evaluated microbiologically. Microorganisms that did not grow on EMB agar but grew on 5% sheep blood and chocolate agar at the 72-96th hour of incubation of culture plates; were detected to have gram-negative coccobacillus morphology and positive for catalase, oxidase and urease. Although the Wright test was negative with a titer of 1/20, the Rose Bengal test was positive, Coombs test was positive with a titer of 1/160 and the Brucellacapt test was positive with a titer of >1/5120. Microorganisms growing on culture plates were identified as B.melitensis at the species level with specific antisera. As a result of antibiotic susceptibility tests evaluated according to the European Committee on Antimicrobial Susceptibility Testing version 14.0 (EUCAST v14.0), the isolate was susceptible to rifampicin, doxycycline, gentamicin and trimethoprim-sulfamethoxazole at standart dosing regimen and susceptible to ciprofloxacin and levofloxacin at increased exposure. The patient, who was started on doxycycline and rifampicin combination treatment, was discharged without any complaints. In the diagnosis of infection due to Brucella species, which is one of the pathogens that early diagnosis and initiation of treatment greatly affects the prognosis; in addition to culture, which is the gold standard method, serological tests are also very important. If diagnosis is delayed, complications may develop due to involvement in almost every part of the body, depending on the affected organs and systems. In areas where brucellosis is endemic, patients with symptoms such as neck swelling, shortness of breath and difficulty in swallowing, thyroid tissue involvement due to brucellosis should definitely be considered etiologically.

Two novel phages, Klebsiella phage GADU21 and Escherichia phage GADU22, from the urine samples of patients with urinary tract infection.

Phages are found in a wide variety of places where bacteria exist including body fluids. The aim of the present study was to isolate phages from the urine samples of patients with urinary tract infection. The 10 urine samples were cultured to isolate bacteria and also used as phage sources against the isolated bacteria. From 10 urine samples with positive cultures, 3 phages were isolated (33%) and two of them were further studied. The Klebsiella phage GADU21 and Escherichia phage GADU22 phages infected Klebsiella pneumonia and Escherichia coli, respectively. Among the tested 14 species for host range analysis, the Klebsiella phage GADU21 was able to infect two species which are Klebsiella pneumonia and Proteus mirabilis, and Escherichia phage GADU22 was able to infect four species which are Shigella flexneri, Shigella sonnei and Escherichia coli. Among different isolates of the indicator bacteria for each phage, GADU21 infected half of the tested 20 Klebsiella pneumonia isolates while GADU22 infected 85% of the tested 20 E. coli isolates. The genome sizes and GC ratios were 75,968 bp and 44.4%, and 168,023 bp and 35.3% for GADU21 and GADU22, respectively. GADU21 and GADU22 were both lytic and had no antibiotic resistance and virulence genes. GADU21 was homologue with Klebsiella phage vB_KpP_FBKp27 but only 88% of the genome was covered by this phage. The non-covered parts of the GADU21 genome included genes for tail-fiber-proteins and HNH-endonuclease. GADU22 had 94.8% homology with Escherichia phage vB_Eco_OMNI12 and had genes for immunity proteins. Phylogenetic analysis showed GADU21 and GADU22 were members of Schitoviridae family and Efbeekayvirus genus and Straboviridae family and Tevenvirinae genus, respectively. VIRIDIC analysis classified these phages in new species clusters. Our study demonstrated the possibility to use infected body fluids as phage sources to isolate novel phages. GADU21 is the first reported Klebsiella phage isolated from human body fluid. The absence of virulence and antibiotic resistance genes in their genomes makes the phages a potential therapeutic tool against infections.

Preparation of Piroxicam nanosuspensions by high pressure homogenization and evaluation of improved bioavailability.

OBJECTIVE: Inflammation is a natural response of the organism, involving events responsible for releasing chemical mediators and requiring treatments of symptoms such as pain, redness, heat, swelling, and loss of tissue function. Piroxicam (PRX) is a non-steroidal anti-inflammatory drug with the effect of nonselective COX inhibitor activity; however, it shows poor bioavailability caused by the poor and slow water solubility. In this study, we developed PRX nanosuspensions with 200-500 nm in diameter to increase the bioavailability of PRX by improving its solubility. METHODS: PRX nanosuspensions were fabricated by High pressure homogenization method with PVA, SDS and Tween 80. The nanosuspensions were characterized by XRD, FTIR, DSC, and in vitro release. In vivo pharmacokinetic properties and anti-inflammatory effects were also investigated in rabbits. RESULTS: PRX nanosuspensions significantly increased the solubility (14.89 ± 0.03 mg/L for pure PRX and 16.75 ± 0.05 mg/L for PRX nanosuspensions) and dissolution rate as compared to the pure PRX (p < 0.05). Orally administered PRX nanosuspension (AUC 0-t is 49.26 ± 4.29 µg/mL × h) significantly improved the bioavailability of PRX (AUC 0-t is 28.40 ± 12.11 µg/mL × h). The anti-inflammatory effect of PRX nanosuspension was also investigated in rabbits and it was observed that PRX nanosuspension treatment significantly improved the inhibition of COX-2 and NFκB expression as compared to the PRX treatment (p < 0.05). CONCLUSIONS: The results in this study indicate that PRX nanosuspension is a promising nanomedicine for enhancing the anti-inflammatory activity of PRX and has a high potential for the treatment of inflammation.

Myroides odoratimimus: a New Threat with Persistent Infections, Multidrug Resistance, and the Potential for Hospital Outbreaks.

Myroides species have recently been reported more frequently in outbreaks in clinics and intensive care units (ICUs). In this study, we aimed to investigate the epidemic potential, antibiotic resistance profile, and risk factors of M. odoratimimus isolates that are increasingly being isolated from the ICUs of our hospital. Data from patients whose Myroides spp. were isolated from their clinical specimens over a 5-year period (September 2016 to January 2022) were retrospectively analyzed. Bacterial identification was performed using a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). The presence of antibiotic resistance genes was analyzed using polymerase chain reaction (PCR). Possible clonal associations between isolates were investigated using enterobacterial repetitive intergenic consensus (ERIC)-PCR. As a result, 66 isolates were identified as M. odoratimimus and one isolate was identified as M. odoratus. The blaMUS resistance gene was detected in all M. odoratimimus isolates, whereas sul2 was detected in ten isolates and tetX was detected in 11 isolates. No other resistance genes, such as blaTUS, were detected. Additionally, two different clonal association patterns were discovered in the 24 selected isolates through the ERIC-PCR method. The increase in the immunosuppressive patient population indicate the possibility of encountering this agent and other opportunistic pathogens more frequently in the future.

Role of Vitamin D, ACE2 and the Proteases as TMPRSS2 and Furin on SARS-CoV-2 Pathogenesis and COVID-19 Severity.

BACKGROUND: COVID-19, the 21st century pandemic disease caused by SARS-CoV-2, has shown a wide clinical spectrum ranging from asymptomatic to deadly serious pneumonia. OBJECTIVE: In our study, the relationship between the pathogenesis and clinical severity of COVID-19 and vitamin D, ACE2, Furin and TMPRSS2 was investigated. METHODS: Serum 25(OH)D, 1,25(OH)2D and ACE2 protein were measured in 85 COVID-19 cases, divided into 5 groups, according to disease severity, from asymptomatic to severe and including a healthy control group. Expression levels of ACE2, VDR, TMPRSS2 and Furin mRNAs in PBMC were also measured. The relationship of the parameters within each group, the severity of the disease and the effect on the patients' fate were investigated. RESULTS: Statistically significant differences were found between the severity of COVID-19 and all study parameters, except for serum 25(OH)D. A strong negative correlation was found between serum ACE2 protein, 1,25(OH)2D, and ACE2 mRNA, and disease severity, length of hospital stay and death/survival rate. Vitamin D deficiency increased the death risk by 5.6-fold (95% CI 0.75-41.47), and the levels of 1,25(OH)2D lower than 1 ng/mL increased the risk of death by 3.8-fold (95% CI 1.07-13.30). CONCLUSION: This study suggests that vitamin D supplementation could be beneficial in the treatment and/or prevention of COVID-19.

Clinical and microbiological comparison of knotless/barbed and silk sutures for impacted third-molar surgery.

BACKGROUND: Several types of suture materials are available for oral surgery. However, the most used non-resorbable suture in oral surgery is 3/0 silk. The aim of the present study was to compare the effectiveness of knotless/barbed sutures with silk sutures during the postoperative period after the third molar surgery in terms of clinical and microbiological parameters. METHODS: The study comprised 38 patients who underwent surgical extraction of a mandibular impacted third molar. The patients were divided into two groups. The mucoperiosteal flap was closed using 3/0 knotless/barbed sutures for the test group and 3/0 silk sutures for the control group. The duration of suturing was recorded during surgery. Pain level, postoperative edema, and trismus were measured at 3 and 7 days after surgery. The status of plaque formation on the sutures was scored using the Plaque Index at 3 and 7 days after the surgery. At 7 days, the suture materials were removed and submitted to the laboratory for microbiological analysis. The level of pain during suture removal was also recorded by a Visual Analog Scale. RESULTS: The duration of suturing in the barbed sutures group was found significantly lower than in silk sutures (P<0.05). There was no significant difference between the suture types in terms of trismus and edema at 3 and 7 days after surgery (P>0.05). On the third day after surgery and during suture, removal pain scores were statistically significantly lower in the barbed suture group than in the silk suture group (P<0.05). The Plaque Index values of the barbed sutures were statistically significantly lower than that of the silk sutures at 3 and 7 days after surgery (P<0.05). Aerobic, anaerobic, and aerobic/anaerobic mean colony forming units (CFUs) were statistically significantly lower in the barbed suture group than in the silk suture group (P<0.05). CONCLUSIONS: Barbed sutures increase the ease of operation and patient comfort with less postoperative pain than silk sutures. Additionally, less plaque accumulation and lower bacterial colonization were found on the barbed/knotless sutures than on the silk sutures.

Toll-like receptor-4 expression and oxidative stress in ocular rosacea.

Purpose: To investigate systemic and ocular toll-like receptor (TLR)-4 expression and its association with oxidative stress markers in ocular rosacea (OR). Methods: This prospective study included 40 patients with rosacea with ocular involvement and 20 healthy volunteers. Tear break-up time (TBUT), Schirmer test, meibomoscore, and ocular surface disease index (OSDI) scores were estimated for all participants. TLR-4 expression in conjunctival epithelium and peripheral blood mononuclear cells was quantified using real-time polymerase chain reaction (RT-PCR). In the tears and serum samples of all participants, antioxidant status (TAS), total oxidant status (TOS), and arylesterase (ARE) activation levels were measured using a fully automated spectrophotometric method, and the oxidative stress index (OSI) was calculated. Results: TLR-4 expression levels and oxidative stress status (TOS and OSI values) were significantly higher (p < 0.01), and antioxidant status (TAS and ARE values) were significantly lower (p < 0.01) in both ocular and blood samples of patients with OR compared with those in controls. A significant positive correlation was found between the ocular and blood values in all parameters (p < 0.05). According to the clinical associations of these results, we found negative correlations between TLR-4, OSI, and TBUT and between TLR-4 and Schirmer, whereas a positive correlation was observed between TLR-4, OSI, and meiboscore and between TLR-4, OSI, and OSDI (p < 0.05). No correlation was found between the OSI and Schirmer results (p = 0.92). Conclusions: TLR-4 and oxidative stress both play important roles in OR pathophysiology and are closely related to clinical findings.

HIV Seroprevalence in Mogadishu, Somalia: a Retrospective Study between 2015 and 2019.

BACKGROUND: Acquired immunodeficiency syndrome (AIDS) remains a major global public health problem. This study aimed to obtain current epidemiological data on the Human immunodeficiency virus (HIV) infections in Mogadishu, Somalia. METHODS: This study included 92,270 anti-HIV test results reported for 82,954 different individuals between 2015 and 2019. HIV tests were performed using the Architect HIV Ag/Ab Combo assay and retested with the Elecsys HIV combi PT assay. RESULTS: HIV seropositivity was found to be 0.32% (269/82,954) in all individuals over a period of four years. Anti-HIV seropositivity in the 0 - 14, 15 - 19, 15 - 24, 15 - 49, and > 15 age groups were as follows: 0.17% (11/6,441), 0.17% (12/7,131), 0.15% (35/24,132), 0.37% (212/56,895), and 0.34% (258/76,513), respectively. In HIV-infected patients, anti-HBs, HBsAg, anti-HCV, and anti-TP (syphilis) seropositivity was found to be 30.3% (56/185), 9.54% (23/241), 1.24% (3/242), and 3.45% (2/58), respectively. CONCLUSIONS: The findings from this study provide comprehensive data on the HIV epidemiology in Somalia. We believe that the results presented in this study will contribute to the risk analysis and planning of preventive policies of national and global health organizations.

Evaluation of the relationship between progression and SARS-CoV-2 viral load in COVID-19 cases in Ankara, Turkey.

INTRODUCTION: Patients infected with SARS-CoV-2 may present with varying clinical pictures. This study aimed to examine the relationship between viral load cycle threshold value, clinical prognosis and other laboratory parameters in initial swab samples on the day of hospitalization. METHODOLOGY: This retrospective and cross-sectional study included 112 patients, who were diagnosed with SARS-CoV-2 via the Bio-Rad CFX96 TouchTM system. Cycle threshold values for the RdRp gene obtained from reverse transcriptase polymerase chain reaction positive patients were recorded. RESULTS: The mean age of the 112 patients was 47.57 ± 17 years. No relationship was found in symptoms, pneumonia, oxygen need, follow-up in intensive care unit, and mortality between patient groups with cycle threshold values of < 30 and ≥ 30. Frequencies of thrombocytopenia (50%) and elevated LDH levels were higher in patients with cycle threshold values of ≥ 30 (p = 0.02 and p = 0.04, respectively). There was a weak but significant correlation between cycle threshold values and CRP levels (Pearson's r = 0.207, p = 0.029). CONCLUSIONS: Symptoms or clinical prognosis were not significantly related to the SARS-CoV-2 viral load levels tested at admission or for the first time within the scope of this study. Thrombocytopenia and elevated LDH rates were higher in patients with cycle threshold values of ≥ 30. A weak but significant correlation was found between the viral load and CRP levels. Large-scale studies are needed to further elucidate this subject matter.

[Investigation of The Efficacy of Three Different Protein Extraction Protocols and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Identification of Nontuberculous Mycobacteria]. / Tüberküloz Disi Mikobakterilerin Tanimlanmasinda Üç Farkli Protein Ekstraksiyon Protokolü ve Matriks Destekli Lazer Desorpsiyon IyonizasyonUçus Zamanli Kütle Spektrometresi Etkinliginin Arastirilmasi.

There are more than 160 defined nontuberculous mycobacteria (NTM) species within Mycobacterium genus. In recent years, the number of NTM species associated with human infections and the infections caused by them have been reported at increasing rates. The identification of these species by phenotypic methods is difficult, laborious, and unlikely to obtain reliable results. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) MALDI-TOF MS has proven to be a good method for the identification of bacteria and yeasts in routine laboratory practices. However, Mycobacterium species differ from other bacteria by their cell wall structures, less ribosomal protein content, and slower growth rates. A standardized and efficient protein extraction protocol for MALDI-TOF MS analysis of mycobacteria is essential. The aim of our study was to investigate the efficacy of different protein extraction protocols and the MALDI-TOF MS method in the diagnosis of NTM species. A total of 73 NTM isolates, grown in both solid and liquid media and previously identified with line probe assay, were evaluated with MALDI-TOF MS (Bruker Daltonics GmbH and Co. KG, Germany). Stock isolates were homogenized and decontaminated by N-Acetyl L-cysteine (NALC)/Sodium hydroxide (NaOH) method. For solid media, isolates were inoculated on Löwenstein-Jensen medium and incubated at 35˚C in a normal atmosphere. For liquid media culture, BD BACTEC MGIT 960 automated system (Becton, Dickinson, Sparks, MD, USA) was performed according to the manufacturer's instructions. For the identification of all isolates by MALDI-TOF MS, the manufacturer's recommended protein extraction protocol (Protocol 1) was compared with the two other protocols, using a simplified extraction procedure (Protocol 2), and freezing temperature (Protocol 3). In the liquid media analysis, the rates of the isolates identified by MALDI-TOF MS (score≥ 2.0) for Protocol 1, 2, and 3 were found as 84.93% (n= 62), 63.01% (n= 46), and 43.83% (n= 32), respectively. In the solid media analysis, the rates of the isolates with an identification score of ≥ 2.0 for the protocols with the same order were determined as 87.67% (n= 64), 52.05% (n= 38), and 31.50% (n= 23), respectively. Isolates grown in both solid and liquid media were identified in the same species level in all three protocols, regardless of the identification values and misidentification was not presented. When the reliable identification score was evaluated as ≥ 2.0 in our study, the manufacturer's recommended MYCOEX IVD procedure was found to be the most effective method for the isolates grown in both liquid and solid media. In conclusion, MALDI-TOF MS has the potential to be a reliable, easy-to-use and fast method that can be used in routine practice for the identification of NTM species with its standardized protein extraction protocols.

[In Vitro Activity of Ceftazidime-avibactam and Colistin Against Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates]. / Karbapenem Dirençli Klebsiella pneumoniae Klinik Izolatlarina Karsi Seftazidim-avibaktam ve Kolistinin In Vitro Etkinligi.

Infections caused by multi drug-resistant gram-negative bacilli are increasingly reported worldwide. Colistin, tigecycline and aminoglycosides are almost the only and last choice antibiotics in the treatment of infections caused by carbapenem-resistant Enterobacterales members. Ceftazidime-avibactam is a novel antibiotic combination consisting of a broad-spectrum cephalosporin and avibactam with good antimicrobial activity against carbapenem-resistant Enterobacterales members. The aim of this study was to assess the in vitro activity of ceftazidime-avibactam and colistin against carbapenem-resistant Klebsiella pneumoniae isolates and to obtain local antimicrobial surveillance data. A total of 150 carbapenem-resistant K.pneumoniae isolates obtained from various clinical samples of the patients hospitalized in our hospital between 2018-2021 were included in the study. Duplicate isolates were excluded from the study. The isolates were recovered from blood (n= 72), tracheal aspirate (n= 40), wound (n= 20), biopsy and abscess (n= 10), steril body fluid (n= 5), and peripheral venous catheter (n= 3) samples. Isolates were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS, Bruker Daltonics, Germany). The minimum inhibitory concentration (MIC) values of the isolates for meropenem, colistin, ceftazidime, and ceftazidime-avibactam were determined by broth microdilution method. Susceptibility of the isolates to the tested antibiotics was evaluated by the European Committee of Antimicrobial Susceptibility Testing (EUCAST) criteria. The presence of carbapenemases (VIM, IMP, NDM, KPC, and OXA-48) was investigated by polymerase chain reaction (PCR) using specific primers. The mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5 genes were evaluated by PCR for plasmid-mediated colistin resistance. All K.pneumoniae isolates were found to be positive for at least one of the carbapenemase genes evaluated in the study. The blaOXA-48 gene was detected in 107 (71.3%), blaKPC gene in 25 (16.7%); blaNDM gene in 7 (4.7%), co-production of blaOXA-48 and blaKPC genes in 10 (6.7%), co-production of blaOXA-48 and blaNDM genes in 1 (0.6%) isolate. None of the isolates harbored the blaVIM and blaIMP genes. None of the mcr genes screened in the study were detected among the isolates. The susceptibility of the isolates to ceftazidime-avibactam and colistin was 92.7% (139/150) and 48% (72/150), respectively. The MIC50 and MIC90 values for meropenem, ceftazidime, ceftazidime-avibactam, and colistin of the isolates were determined as 32/256, > 128/> 128, 1/8, and 4/16 µg/ml, respectively. Of the ceftazidimeavibactam resistant isolates, seven were positive for blaNDM, three for blaKPC, and one for both blaOXA-48 and blaNDM genes. High ceftazidime-avibactam MIC levels (> 128 µg/ml) were detected in metallo-betalactamase producing isolates. Consequently, our data suggested that ceftazidime-avibactam exhibited as a good alternative therapeutic choice for carbapenem-resistant K.pneumoniae isolates. It is noteworthy that high rate of colistin resistance was detected in K.pneumoniae isolates. Another notable finding of this study is the increase in K.pneumoniae isolates producing blaKPC for our country. To prevent the development of resistance which is observed even in last-choice therapeutic antibiotics, the principles of rational antibiotic use should be followed. The appropriate antimicrobial susceptibility testing should be routinely performed for surveillance of ceftazidime-avibactam and colistin.

Candidemia Among Coronavirus Disease 2019 Patients in Turkey Admitted to Intensive Care Units: A Retrospective Multicenter Study.

Background: We evaluated the epidemiology of candidemia among coronavirus disease 2019 (COVID-19) patients admitted to intensive care units (ICUs). Methods: We conducted a retrospective multicenter study in Turkey between April and December 2020. Results: Twenty-eight of 148 enrolled patients developed candidemia, yielding an incidence of 19% and incidence rate of 14/1000 patient-days. The probability of acquiring candidemia at 10, 20, and 30 days of ICU admission was 6%, 26%, and 50%, respectively. More than 80% of patients received antibiotics, corticosteroid, and mechanical ventilation. Receipt of a carbapenem (odds ratio [OR] = 6.0, 95% confidence interval [CI] = 1.6-22.3, P = .008), central venous catheter (OR = 4.3, 95% CI = 1.3-14.2, P = .02), and bacteremia preceding candidemia (OR = 6.6, 95% CI = 2.1-20.1, P = .001) were independent risk factors for candidemia. The mortality rate did not differ between patients with and without candidemia. Age (OR = 1.05, 95% CI = 1.01-1.09, P = .02) and mechanical ventilation (OR = 61, 95% CI = 15.8-234.9, P < .0001) were independent risk factors for death. Candida albicans was the most prevalent species overall. In Izmir, Candida parapsilosis accounted for 50% (2 of 4) of candidemia. Both C parapsilosis isolates were fluconazole nonsusceptible, harbored Erg11-Y132F mutation, and were clonal based on whole-genome sequencing. The 2 infected patients resided in ICUs with ongoing outbreaks due to fluconazole-resistant C parapsilosis. Conclusions: Physicians should be aware of the elevated risk for candidemia among patients with COVID-19 who require ICU care. Prolonged ICU exposure and ICU practices rendered to COVID-19 patients are important contributing factors to candidemia. Emphasis should be placed on (1) heightened infection control in the ICU and (2) developing antibiotic stewardship strategies to reduce irrational antimicrobial therapy.

Investigation of Viral Load Cycle Threshold Values in Patients with SARS-CoV-2 Associated Pneumonia with Real-Time PCR Method.

INTRODUCTION: In this study, we aimed investigate the relationship of SARS-CoV-2 viral load cycle threshold (Ct) values with pneumonia. METHODOLOGY: A total of 158 patients in whom SARS-CoV-2 was confirmed in upper respiratory tract (URT) samples with molecular method and who had computed tomography (CT) of the chest, between April 2020 and June 2020 were included in this retrospective cross-sectional study. RESULTS: Mean age of 158 PCR positive patients was 45.22 ± 17.89 and 60.8% of them were male. Pneumonia was detected in 40.5% of the patients on their chest CT. A weak but significant correlation was found between SARS-CoV-2 Ct value detected with PCR in analysis of oropharyngeal/ nasopharyngeal (OP/NP) samples and chest CT score (Pearson's r: 0.197, p = 0.01). No correlation was found between the first detected viral load Ct value and age, gender and mortality. There was no significant correlation between chest CT score and mortality. While the areas remaining under ROC curve for Ct value in analysis of OP/NP samples in prediction of chest CT score ≥ 1, ≥ 5 and ≥ 10 were 0.564, 0.640 and 0.703 respectively. CONCLUSIONS: We found that the amount of SARS-CoV-2 viral load (inverse relationship with Ct) detected in OP/NP samples of patients with COVID-19 pneumonia did not reflect the increasing severity of pulmonary lesions on chest CT. Although primary target of SARS-CoV-2 is all epithelial cells of the respiratory tract we believe studies comparing viral loads in lower respiratory tract samples are needed to determine the severity of pulmonary disease.

Molecular Detection of Virulence Associated Genes in Coagulase Negative Staphylococci Isolated from Blood Culture.

BACKGROUND: Coagulase-negative staphylococci (CoNS) are one of the most important causes of infections. Unlike Staphylococcus aureus, less is known about their pathogenic mechanisms. In the present study, we aimed to evaluate the presence of virulence genes among 98 CoNS isolated from blood cultures of inpatients. METHODS: The isolates were identified by MALDI-TOF MS (Bruker Daltonics, Bremen, Germany). PCR was performed to detect 29 virulence factors using specific primers for icaA, icaB, icaC, icaD, icaADB, aap, fbe, aae, sesI, atIE, hla, hlb, hld, gehC, gehD, sea, seb, sec, sed, see, seg, seh, sei, tst, eta, etb, etd, etx, and pvl genes. The VITEK2 system (bio-Merieux, France) and the BD Phoenix™ System (Becton Dickinson, USA) were used for antimicrobial susceptibility testing. RESULTS: Staphylococcus epidermidis was found to be the most virulent CoNS species. All isolates were negative for eta, etb, etd, sea, seb, sed, see, seg, sei, and pvl virulence genes. We detected up to 15 virulence genes in a single isolate. The most common gene was icaC (73.5%), followed by icaA (57.1%), icaD (56.1%), aap (55.1%), aae (52.0%), sesl (51.0%), gehC (50.0%), hld (50.0%), hlb (49.0%), fbe (44.9%), atIE (37.8%), icaADB (37.8%), gehD (34.7%), icaB (31.6%), hla (30.6%), etx (2.0%), sec (1.0%), seh (1.0%), and tst (1.0%). CONCLUSIONS: We determined high rates of genes encoding biofilm formation. Only four isolates did not possess either the ica operon or aap gene. Although we found low rates of toxin-related genes, our data indicates that apart from biofilm formation, the CoNS isolates could express various virulence genes similar to those of Staphylococcus aureus.

[Investigation of Azithromycin Minimum Inhibitory Concentration Values and Carbapenem Resistance in Salmonella and Shigella Clinical Isolates]. / Salmonella ve Shigella Klinik Izolatlarinda Azitromisin Minimum Inhibitör Konsantrasyon Degerlerinin ve Karbapenem Direncinin Arastirilmasi.

Increasing resistance to first-line antibiotics used in the treatment of infections caused by Salmonella and Shigella species is emerging. Azithromycin presents a good alternative treatment option for Salmonella and Shigella infections. However, there are limited data regarding the susceptibility of azithromycin in Turkey. In this study, we aimed to evaluate the susceptibility of Salmonella and Shigella species to azithromycin, to determine and compare the minimum inhibitory concentration (MIC) values and disk diffusion zone diameters. In addition, susceptibility to meropenem and first-line antibiotic options in isolates was also investigated. A total of 170 Salmonella, 76 Shigella clinical isolates collected between 2014 and 2018 in our hospital were tested for their susceptibility to azithromycin, meropenem, ampicillin, pefloxacin, trimetoprim-sulfamethoxazole, ceftazidime, and cefotaxime. Isolates were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry. The isolates were confirmed and serotyped by the reference laboratory using the conventional slide agglutination method. Susceptibility of the isolates to azithromycin and other antibiotics was evaluated by Kirby-Bauer disk diffusion method. MIC values of azithromycin were determined by the reference broth microdilution method. Combined disk diffusion test was used for the detection of extended spectrum beta-lactamase (ESBL) production. Polymerase chain reaction was performed for macrolide and carbapenem resistance genes and the detected resistance genes were confirmed by sequencing. Of the 76 Shigella isolates tested, 64 (84.2%) were identified as Shigella sonnei, 10 (13.2%) as Shigella flexneri, one (1.3%) as Shigella boydii, and one (1.3%) as Shigella dysenteriae. Among the 170 Salmonella isolates, 131 (77%) were identified as Salmonella enteritidis, 11(6.5%) as Salmonella Typhimurium, 8 (4.7%) as Salmonella Kentucky, 5 (2.9%) as Salmonella Paratyphi B, 4 (2.4%) as Salmonella Infantis, 3 (1.8%) as Salmonella Cholerasuis, and 8 (4.7%) as other serovars (Salmonella Agona, Salmonella Dabou, Salmonella Gallinarum, Salmonella Hadar, Salmonella Muenchen, Salmonella Newport, Salmonella Paratyphi C, Salmonella Senftenberg), respectively. ESBL production was determined as 7.9% (6/76) in Shigella isolates and 2.9% (5/170) in Salmonella isolates. A carbapenem resistant S.Senftenberg isolate positive for the blaOXA-48 resistance gene was detected in our study. Meropenem MIC value of the isolate was detected as > 32 µg/ml with gradient diffusion test. Among all isolates, only one S.boydii isolate was detected as resistant to azithromycin with a MIC value of 128 µg/ml. The isolate was positive for the existence of mphA gene by PCR. In the disk diffusion test, azithromycin inhibition zone diameters were ≥ 12 mm in all of the tested isolates, except for the azithromycin-resistant isolate, and the azithromycin MICs were determined as ≤ 16 µg/ ml by broth microdilution. Increasing resistance to commonly used antibiotics in Salmonella and Shigella species is emerging. The detection of a carbapenem-resistant Salmonella isolate in our study indicates that the spread of carbapenem resistance to other Enterobacterales species may cause global problems. Antimicrobial susceptibility testing of azithromycin for Salmonella and Shigella species has been difficult to establish due to the lack of approval in vitro breakpoints for all species. Consequently, our data shows that azithromycin exhibits as a good alternative therapeutic choice for the treatment of gastrointestinal diseases caused by Salmonella and Shigella species. Further studies are needed to provide appropriate in vitro breakpoints supported by clinical data.

Carbapenem and Colistin Resistant Klebsiella Pneumoniae ST14 and ST2096 Dominated in Two Hospitals in Turkey.

BACKGROUND: The determination of clonal interactions between microorganisms is very important in epidemiological studies. In the present study, we aimed to evaluate the resistance mechanisms and genetic relationships of carbapenem and colistin resistant Klebsiella pneumoniae (K. pneumoniae) strains isolated from inpatients at two university hospitals in Turkey. METHODS: A total of 38 K. pneumoniae clinical isolates were included in the study. Identification of isolates was confirmed by 16S rRNA sequencing. Antimicrobial susceptibility testing was performed with VITEK-2 system (bio-Mérieux, France). Modified Hodge test was used for the detection of carbapenemase activity in isolates. Carbapenem resistance genes (blaOXA-48, blaNDM, blaKPC, blaIMP, blaVIM) and colistin resistance genes (mcr-1, mcr-2 and mcr-3) were investigated by PCR. Enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and multilocus sequence typing (MLST) analysis were used to determine the genetic relatedness among the isolates. RESULTS: We detected that 58% of isolates were positive for only blaOXA-48, 5% were only positive for blaNDM, and 34% were positive for both blaOXA-48 and blaNDM. blaKPC, blaIMP, blaVIM, mcr-1, mcr-2, and mcr-3 were not detected among the isolates. Only one carbapenem resistant isolate was negative for the carbapenemase genes tested. A total of nine profiles were found by ERIC-PCR, and MLST results showed seven different sequence types-ST14, ST16, ST79, ST101, ST1543, ST2096, and ST2832. The seven STs were grouped by PHYLOVIZ Online into four clonal complexes. The most common ST was ST14 (81%) in Center 1 and ST2096 (94%) in Center 2. CONCLUSIONS: We determined MLST types of carbapenem and colistin resistant K. pneumoniae isolates from two different centers. Although the most common ST types were different in these centers, both ST types were clustered in CC14. To the best of our knowledge this is the first report of ST14 and ST2096 outbreaks in Turkey.

Does COVID-19 cause an increase in spleen dimensions? Possible effects of immune activation, hematopoietic suppression and microthrombosis.

PURPOSE: To radiologically examine how the spleen size, which has important functions in hematological and immunological balance, is affected in COVID-19. METHODS: Between July 1 and August 31, 2020, consecutive patients diagnosed with COVID-19 were analyzed. Among these patients, those who underwent chest computed tomography (CT) examination at the time of presentation, patients with follow-up CT due to clinical deterioration were included in the study. The CTs of the patients were evaluated in terms of spleen size and volume. RESULTS: A total of 160 patients (88 females, 55%) were included in the study. The mean time between the initial and follow-up CT was 7.2 ± 2.8 days. The splenic volume (244.3 ± 136.7 vs. 303.5 ± 156.3 cm3) and splenic index (421.2 ± 235.5 vs. 523.2 ± 269.4 cm3) values were significantly higher in the follow-up CT compared to the initial CT (p < 0.001). The increase in the splenic volume and splenic index values was 59.2 ± 52.4 cm3 and 101.9 ± 90.3 cm3 (p < 0.001), respectively. The COVID-19 severity score was significantly higher in the follow-up CT compared to the initial CT (3.7 ± 4.2 vs. 12.5 ± 5.7, respectively; p < 0.001). The spleen width measured separately on the initial and follow-up CTs showed a highest positive correlation (r = 0.982, p < 0.001). CONCLUSION: Our study indicates that spleen size increases slightly-moderately in the first stages of the infection, and this increase is correlated with the COVID-19 severity score calculated on the chest CT data, and in this respect, it is similar to infections presenting with cytokine storm.

Frequency of hepatic steatosis and its association with the pneumonia severity score on chest computed tomography in adult COVID-19 patients.

BACKGROUND: Recent studies of the coronavirus disease 2019 (COVID-19) demonstrated that obesity is significantly associated with increased disease severity, clinical outcome, and mortality. The association between hepatic steatosis, which frequently accompanies obesity, and the pneumonia severity score (PSS) evaluated on computed tomography (CT), and the prevalence of steatosis in patients with COVID-19 remains to be elucidated. AIM: To assess the frequency of hepatic steatosis in the chest CT of COVID-19 patients and its association with the PSS. METHODS: The chest CT images of 485 patients who were admitted to the emergency department with suspected COVID-19 were retrospectively evaluated. The patients were divided into two groups as COVID-19-positive [CT- and reverse transcriptase-polymerase chain reaction (RT-PCR)-positive] and controls (CT- and RT-PCR-negative). The CT images of both groups were evaluated for PSS as the ratio of the volume of involved lung parenchyma to the total lung volume. Hepatic steatosis was defined as a liver attenuation value of ≤ 40 Hounsfield units (HU). RESULTS: Of the 485 patients, 56.5% (n = 274) were defined as the COVID-19-positive group and 43.5% (n = 211) as the control group. The average age of the COVID-19-positive group was significantly higher than that of the control group (50.9 ± 10.9 years vs 40.4 ± 12.3 years, P < 0.001). The frequency of hepatic steatosis in the positive group was significantly higher compared with the control group (40.9% vs 19.4%, P < 0.001). The average hepatic attenuation values were significantly lower in the positive group compared with the control group (45.7 ± 11.4 HU vs 53.9 ± 15.9 HU, P < 0.001). Logistic regression analysis showed that after adjusting for age, hypertension, diabetes mellitus, overweight, and obesity there was almost a 2.2 times greater odds of hepatic steatosis in the COVID-19-positive group than in the controls (odds ratio 2.187; 95% confidence interval: 1.336-3.580, P < 0.001). CONCLUSION: The prevalence of hepatic steatosis was significantly higher in COVID-19 patients compared with controls after adjustment for age and comorbidities. This finding can be easily assessed on chest CT images.

Recent Increase in the Prevalence of Fluconazole-Non-susceptible Candida tropicalis Blood Isolates in Turkey: Clinical Implication of Azole-Non-susceptible and Fluconazole Tolerant Phenotypes and Genotyping.

Candida tropicalis is the fourth leading cause of candidemia in Turkey. Although C. tropicalis isolates from 1997 to 2017 were characterized as fully susceptible to antifungals, the increasing global prevalence of azole-non-susceptible (ANS) C. tropicalis and the association between high fluconazole tolerance (HFT) and fluconazole therapeutic failure (FTF) prompted us to re-evaluate azole susceptibility of C. tropicalis in Turkey. In this study, 161 C. tropicalis blood isolates from seven clinical centers were identified by ITS rDNA sequencing, genotyped by multilocus microsatellite typing, and tested for susceptibility to five azoles, two echinocandins, and amphotericin B (AMB); antifungal resistance mechanisms were assessed by sequencing of ERG11 and FKS1 genes. The results indicated that C. tropicalis isolates, which belonged to 125 genotypes grouped into 11 clusters, were fully susceptible to echinocandins and AMB; however, 18.6% of them had the ANS phenotype but only two carried the ANS-conferring mutation (Y132F). HFT was recorded in 52 isolates, 10 of which were also ANS. Large proportions of patients infected with ANS and HFT isolates (89 and 40.7%, respectively) showed FTF. Patients infected with azole-susceptible or ANS isolates did not differ in mortality, which, however, was significantly lower for those infected with HFT isolates (P = 0.007). There were significant differences in mortality (P = 0.02), ANS (P = 0.012), and HFT (P = 0.007) among genotype clusters. The alarming increase in the prevalence of C. tropicalis blood isolates with ANS and HFT in Turkey and the notable FTF rate should be a matter of public health concern.

Low level of antifungal resistance of Candida glabrata blood isolates in Turkey: Fluconazole minimum inhibitory concentration and FKS mutations can predict therapeutic failure.

BACKGROUND: Candida glabrata is the third leading cause of candidaemia in Turkey; however, the data regarding antifungal resistance mechanisms and genotypic diversity in association with their clinical implication are limited. OBJECTIVES: To assess genotypic diversity, antifungal susceptibility and mechanisms of drug resistance of C glabrata blood isolates and their association with patients' outcome in a retrospective multicentre study. PATIENTS/METHODS: Isolates from 107 patients were identified by ITS sequencing and analysed by multilocus microsatellite typing, antifungal susceptibility testing, and sequencing of PDR1 and FKS1/2 hotspots (HSs). RESULTS: Candida glabrata prevalence in Ege University Hospital was twofold higher in 2014-2019 than in 2005-2014. Six of the analysed isolates had fluconazole MICs ≥ 32 µg/mL; of them, five harboured unique PDR1 mutations. Although echinocandin resistance was not detected, three isolates had mutations in HS1-Fks1 (S629T, n = 1) and HS1-Fks2 (S663P, n = 2); one of the latter was also fluconazole-resistant. All patients infected with isolates carrying HS-FKS mutations and/or demonstrating fluconazole MIC ≥ 32 µg/mL (except one without clinical data) showed therapeutic failure (TF) with echinocandin and fluconazole; seven such isolates were collected in Ege (n = 4) and Gulhane (n = 3) hospitals and six detected recently. Among 34 identified genotypes, none were associated with mortality or enriched for fluconazole-resistant isolates. CONCLUSION: Antifungal susceptibility testing should be supplemented with HS-FKS sequencing to predict TF for echinocandins, whereas fluconazole MIC ≥ 32 µg/mL may predict TF. Recent emergence of C glabrata isolates associated with antifungal TF warrants future comprehensive prospective studies in Turkey.