Mikrobiyoloji bulteni最新文献

Central nervous system infections (CNS) are life-threatening infections in children, requiring urgent intervention and rapid diagnosis. In this study, we aimed to investigate the efficacy of syndromic tests in diagnosing CNS infections and the distribution of viral pathogens in pediatric patients. A total of 145 pediatric patients with a prediagnosis of CNS infection based on clinical findings by a pediatric infectious disease specialist were included in the study. Microscopic examination, biochemical tests, bacteriologic culture, and syndromic test (BioFire® FilmArray® Meningitis/Encephalitis Panel) were performed on cerebrospinal fluid samples obtained from the patients. Nearly half (44.8%) of the patients were younger than one year of age, the median age was 12 months (6-60 months), and the male-to-female ratio was 1.7, with 92 male and 53 female patients. Viral pathogens were observed in most of the 29 (18.8%) patients with syndromic test positivity (n= 23, 79.4%), while bacterial pathogens were detected in 20.6% (n= 6). No fungal pathogens were detected. Bacterial pathogens were Streptococcus pneumoniae [3.4% (5/145)] and Neisseria meningitidis [0.7% (1/145)]. Viruses were enterovirus [6.9% (10/145)], human herpesvirus-6 [5.5% (8/145)], herpes simplex virus type 1 [1.4% (2/145)], cytomegalovirus [0.7% (1/145)], human parechovirus [0.7% (1/145)], varicella zoster virus [0.7% (1/145)]. The main finding in cases with positive syndromic test was fever (n= 19, 65.5%), followed by vomiting (n= 15, 51.7%), convulsion (n= 14, 48.3%) and rash (n= 6, 20.6%). For turnaround time the median was 111 minutes and the mean was 119 minutes. Despite the lack of a performance study including sensitivity and specificity for syndromic testing or alternative tests for viral etiology, our study demonstrates the benefits of syndromic testing in children with presumed CNS infections, such as shortening the diagnostic period and guiding empirical treatment. It also constitutes an affirmative example of laboratory and clinical collaboration.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus has mutated at a high rate since the beginning of the pandemic, leading to the formation of different variants. Alpha, Beta, Gamma, Delta and Omicron have emerged as concerning variants identified by the World Health Organization (WHO). The Omicron variant and its sublineages became dominant worldwide in 2022. EG.5, a sublineage of Omicron, was associated with increased cases recently. In this study, we aimed to investigate the relationship between SARS-CoV-2 variants and the severity of the disease by using the whole genome sequence analysis method in patient samples diagnosed with coronavirus diseases 2019 (COVID-19) in our hospital and to contribute to SARS-CoV-2 surveillance in our country, in the period until the end of 2023, after the announcement of the EG.5 variant. The study included 68 patient samples that were found to be SARS-CoV-2 positive by polymerase chain reaction. Nasopharyngeal/oropharyngeal swab samples obtained from the patients were analysed by syndromic multiplex viral polymerase chain reaction panel. Whole genome sequence analysis was performed on SARS-CoV-2 positive patient samples with high viral load. Barcoded sequencing library was prepared and extracted DNA was sequenced on the Illumina next generation sequencing platform using COVIDSeq test kits (Illumina, USA). The library was loaded into a NextSeq 500/550 high output reagent cartridge v2 75 cycle, NextSeq 500/550 high output flow cell on the NextSeq 550 instrument (Illumina, USA). The DRAGEN COVID lineage programme available in the core domain was used to analyse the sequence data. The resulting combined fasta files were loaded into Nexclade and Pangolin COVID-19 Lineage Assigner programmes and class assignment, mutation calls and sequence quality checks were performed. Statistical evaluation was performed using Statistical Package for Social Sciences (Windows v20.0, Armonk, NY) programme. Sequence results of a total of 68 patients whose SARS-CoV-2 positivity was confirmed in our laboratory and whose samples were suitable for sequence study were analysed with clinical data. While EG.5 variant was detected in 15 (22.1%) of the samples included in the study, different sub-variants other than EG.5 were detected in 53 (77.9%) samples. The first three most frequently detected variants were XBB.1.16, EG.5.1 and FL.1.5.1, respectively. The subtypes of the EG.5 variant were determined as EG.5.1.1, EG.5.1.3, EG.5.1.6 and EG.5.1. Of the patients included in the study, 20 (29.4%) were hospitalised and followed up, 14 of whom had moderate to severe clinical conditions. Four hospitalised patients with comorbidities at an advanced age resulted in exitus. In the statistical evaluation, no significant difference was found between EG.5 and nonEG.5 Omicron variants in terms of age group, clinical symptoms and disease severity. It is recommended to continue genomic surveillance for the timely identification

According to the World Health Organization (WHO), leishmaniasis is a zoonotic/anthroponotic parasitic disease endemic in 99 countries. It is estimated that approximately 12 million people are infected with Leishmania spp. and 350 million people live at risk. Every year, two million new cases are added to these figures. One and a half million cases of zoonotic/anthroponotic cutaneous leishmaniasis and 500 000 cases of visceral leishmaniasis are reported annually. One person is estimated to to be infected with cutaneous leishmaniasis in every 20 seconds and visceral leishmaniasis causes 60 000 deaths. In this report, two pediatric cases diagnosed with visceral leishmaniasis were presented. In the study, bone marrow aspirations were performed to determine the etiology of the disease in an eight-month-old male patient with fever and hepatosplenomegaly who had been followed up in Manisa Celal Bayar University, Department of Pediatrics, Division of Pediatric Hematology with the diagnosis of severe glucose-6-phosphate dehydrogenase (G-6PD) deficiency since the neonatal period and in a nine-month-old female patient who had had a high fever and bicytopenia for two weeks. Bone marrow aspirations were cultured in NNN medium and their smears were stained and examined with Giemsa. rk-39 and Leishmania IFAT tests were performed by using patients' sera. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) analysis was also performed for Leishmania spp. Leishmania spp. amastigotes were observed in Giemsa-stained smear preparations, Leishmania spp. promastigotes were grown in NNN medium, rk39 rapid diagnostic kit was weakly positive, Leishmania IFAT was positive at a titer of 1/1024 and Leishmania tropica was identified as the causative agent by RT-qPCR analysis for both cases. These two cases suggested that fatal cases of visceral leishmaniasis may increase with the spread of visceralized isolates of L.tropica, the most common causative agent of cutaneous leishmaniasis in Türkiye, and this issue may create a significant public health problem.

Viral hepatitis are infections that can cause liver damage, become chronic, lead to cirrhosis, hepatocellular carcinoma and ultimately result in death due to their ability to spread in the community through blood and infected body fluids. The aim of this study was to determine the seroprevalence of hepatitis B (HBV), hepatitis C (HCV), and hepatitis D (HDV) transmitted through blood among individuals living in Trabzon province and to examine the factors potentially associated with seroprevalence. This cross-sectional study was conducted in Trabzon province, located in the northeast of Türkiye, including a total of 10 districts, including the central district. Since seroprevalence was calculated for HBV, HCV, and HDV in the study, the sample size was separately calculated for each, and the calculated maximum sample size of 1116 was accepted as the minimum sample size for the study. The study was completed with 1502 participants. Serological tests for HBV included HBsAg, anti-HBs, and anti-HBc IgG; for HCV, anti-HCV; and for HDV, anti-HDV were analysed. Data were evaluated for HBV risk factors using univariate analyses with Chi-square test and for multiple analyses using enter model logistic regression analysis. The mean age of the participants was 45.7 ± 16.6 years, with 767 (51.1%) being female. The prevalence of HBV seropositivity, indicating vaccination, was 23.0%, while the seroprevalence of HBV among unvaccinated adults was 27.4%. HBsAg positivity was 5.1%, and isolated anti-HBc IgG positivity was 4.2%. The proportion of individuals with HBsAg in the gray zone was 0.5%, while the positivity rates for anti-HBs and anti-HBc IgG (indicating past infection) were 17.6%. The prevalence of anti-HCV was six per thousand, while anti-HDV was not detected in the analyses. HBsAg positivity and co-infection with HCV were found in one person, and among the nine individuals positive for anti-HCV, isolated anti-HBc IgG positivity was detected in three. Increasing age, presence of a person with jaundice in the family, presence of diabetes mellitus, alcohol use and cupping therapy were identified as risk factors for HBV in the logistic regression analysis. Risk factors for HCV in univariate analyses were being over 40 years old, presence of hepatic steatosis and receiving dialysis treatment. The results of the study indicate that despite being included in our vaccination schedule and the administration of vaccines to high-risk adults, HBV still requires intensive attention as a public health problem. HCV, lacking a vaccine has been evaluated as an infectious agent that needs to be taken into consideration due to its potential risks and requires the complete implementation of individual and social precautions.

In recent years, as the paradigm of communication between cells has been clarified, the ability of bacteria to change their gene expression patterns in response to various extracellular signals has attracted great interest. In particular, intracellular and intercellular communication between bacterial populations, called quorum sensing (QS), is essential for coordinating physiological and genetic activities. QS studies are critical, particularly in elucidating the regulatory mechanisms of infectious processes in food-borne pathogens. Elucidating the QS mechanisms in Salmonella is effective in silencing the virulence factors in the fight against this bacterium. The aims of this study were; to create luxS gene mutants that play a vital role in the QS activity of Salmonella and to determine the effect of this mutation on the expression of virulence genes in the bacteria and to determine the impact of synthetic N-hexanoyl-homoserine lactone (C6HSL) on biofilm formation and AI-2 signaling pathway of Salmonella wild strain and luxS gene mutants. luxS gene mutants were constructed by recombining the gene region with the chloramphenicol gene cassette based on homologous region recombination. In the luxS mutants obtained in this way, the expression of eight different virulence genes (hilA, invA, inv, glgC, fimF, fliF, lpfA, gyrA), which have essential roles in Salmonella pathogenicity, was determined by quantitative real-time reverse transcriptase polymerase chain reaction (rRT-qPCR) method and compared with natural strains. As a result of these studies, it was determined that the expression of each gene examined was significantly reduced in luxS mutant strains. The relative AI-2 activities of Salmonella strains were analyzed depending on time. It was determined that the highest activity occurred at the fourth hour and the AI-2 activities of luxS mutants were reduced compared to the wild strain. Finally, it was determined that C6HSL increased the biofilm activity of Salmonella Typhimurium DMC4, SL1344 wild strains, and mutants, mainly at the 72nd hour. In conclusion, our results proved that C6HSL stimulated QS communication in all strains and increased biofilm of Salmonella formation and autoinducer activity. This situation determines that Salmonella responds to external signals by using QS systems. In addition, this research contributed to provide additional information on interspecies communication mechanisms to develop strategies to prevent biofilm formation of this pathogen.

An increasing number of different clinical infections caused by Corynebacteria have been reported in the last decade. The aim of this study was to evaluate the antibiotic resistance rates, biofilm formation capacities and to investigate the ''anti-quorum-sensing (anti-QS)'' activities of corynebacteria, which were divided into three groups according to the type of growth in culture (pure, with another pathogenic bacterium and polymicrobial growth). In total 240 Corynebacterium spp. isolates from different clinical specimens sent to the medical microbiology laboratories of Düzce University Faculty of Medicine Hospital and Başakşehir Çam and Sakura City Hospital between June 2021 and June 2022 were classified into three groups: pure, isolated with another pathogen and polymicrobial, according to their growth patterns in culture. Bacteria were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) Biotyper (Bruker, Germany) at an external centre. Antibiotic susceptibilities were determined by disc diffusion method and for vancomycin broth microdilution method was used. Results were interpreted according to EUCAST recommendations. The biofilm-forming properties of the isolates were determined quantitatively. Bioactive components of 17 isolates with strong biofilm formation were extracted and anti-QS activity was determined by agar diffusion method using Chromobacterium violaceum ATCC 12472 strain and then violacein pigment production was measured quantitatively. Of the 240 Corynebacterium spp. isolates, 138 (58%) were pure, 52 (22%) were isolated with another pathogen and 50 (20%) were part of a polymicrobial infection. Of the isolates, 140 were identified as C.striatum, 34 as C.amycolatum and 24 as Corynebacterium afermentans. When the antibiotic resistance rates of the Corynebacterium isolates were analysed according to the groups, the resistance rates to rifampicin and tetracycline antibiotics were found to be statistically significantly lower in the polymicrobial group than in the other groups. The resistance rates to penicillin, clindamycin, ciprofloxacin, moxifloxacin, rifampicin, tetracycline and linezolid were 96.7%, 88.3%, 86.3%, 73.8%, 62.5%, 59.2% and 0.8%, respectively. While all isolates were susceptible to vancomycin, linezolid resistance was detected in two C.afermentans isolates. When the biofilm formation ability was analysed, it was observed that 87 (36.3%) isolates formed biofilm. The biofilm formation rate of the isolates in the polymicrobial growth group was lower than the other two groups. The anti-QS activity of 17 isolates with strong biofilm formation was investigated and none of the Corynebacterium extracts tested were found to have anti-QS activity (inhibition of violacein pigment production without inhibiting bacterial growth) in the QS study with C.violaceum, whereas five isolate extracts had antibacterial activity (inhibition of bacterial growth). Four of the bacte

Aspergillus species are common hyphal fungi. In addition to allergies and mycotoxicosis, Aspergillus species can cause various infections known as aspergillosis. Aspergillosis of the respiratory tract, central nervous system, skin and soft tissues is well described. However, musculoskeletal infections due to invasive aspergillosis are not well described. Fungal joint infection due to invasive aspergillosis is a rare form of septic arthritis. In this case report, a patient who admitted to our hospital for liver transplantation and developed knee joint arthritis caused by Aspergillus flavus/Aspergillus oryzae during this process was presented. A 28-year-old male patient with autoimmune hepatitis was admitted to hospital with decompensated liver cirrhosis and encephalopathy. The patient, who was awaiting an emergency liver transplant, developed pain, swelling and limitation of movement in his right knee and appropriate consultations and tests were requested. Three joint fluid cultures taken one day apart and nine days later were positive for fungal growth. Macroscopic examination of the mould growth and microscopic examination with lactophenol cotton blue suggested a species belonging to the A.flavus complex and the isolate was identified as A.flavus/A.oryzae by matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) (EXS 2600, Zybio, China). As a result of ITS gene sequencing, the species was determined to be A.oryzae. As cases have been reported where A.flavus and A.oryzae species could not be distinguished by ITS gene sequencing, the pathogen was defined as A.flavus/oryzae. The patient died of liver disease during treatment with amphotericin B. There are few cases of arthritis caused by Aspergillus species in the literature. Aspergillus species found in joint infections are, Aspergillus fumigatus, A.flavus, Aspergillus niger and Aspergillus terreus species complexes, in order of frequency. A.flavus and A.oryzae are closely related. They are difficult to distinguish by conventional methods, MALDI-TOF MS or ITS region sequencing, which is commonly used for genus/species identification in fungi. The number of Aspergillus arthritis cases is low and the identification methods applied to the species reported as causative agents in most studies can identify at the species complex level. In addition, it can be assumed that species not previously reported as causative agents may be encountered as a result of developments in identification methods. In the few publications in the literature where A.flavus complex was reported as the causative agent of joint infections, it seems possible that some of the agents may be A.flavus and some may be A.oryzae, since the agents were identified at the complex level. There are a limited number of cases in the literature where A.oryzae is the causative agent, particularly in the respiratory tract. A PubMed search using the keywords "A.oryzae infections, arthritis, osteomyelitis" did not reveal