Integron distribution and relationship to antimicrobial resistance in E. coli isolated from blood culture.

PURPOSE: The aim of this study was to evaluate the distribution of integrons in strains of E. coli isolated from blood culture and the relationship between integrons and antimicrobial resistance. METHODS: The study included 100 E. coli strains sent to the Medical Microbiology Laboratory from different clinics between September 2022 and June 2023. Antibiotic susceptibility was evaluated according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST). The presence of integrons was determined by the inhouse polymerase chain reaction (PCR). RESULTS: Integron positivity was detected in 45 (45%) of isolates, and class 1 integrons were found in 41 (41%), class 2 integrons in 2 (2%), and both class 1 integrons and class 2 integrons in 2 (2%). Class 3 integron positivity was not detected. In total, 63 cases of community origin and 37 cases of hospital origin were identified. When antibiotic resistance was evaluated, the highest sensitivity was noted for amikacin (1%), meropenem (5%), imipenem (6%), and the highest resistant antibiotics were ampicillin (82%), cepfuroxime sodium (65%), and amoxicillin/clavulanate (62%), respectively. Of the 16 antimicrobial substances evaluated, 10 had an antibiotic resistance rate of over 45%. In class 1 integron-positive samples, ampicillin resistance and trimethoprim/sulfamethoxazole resistance were higher than in negative samples (p = 0.02, p = 0.0001, respectively). Fifty-one (51%) samples were found to have multiple drug resistance (MDR). In total, 59.5% of hospital-acquired isolates and 46% of community-acquired isolates were considered to be MDR. The class 1 integron positivity in MDR samples was high (p = 0.038). CONCLUSION: The high MDR rates in both hospital-acquired and community-acquired isolates are alarming. In particular, class 1 integron monitoring is very important to prevent the spread of MDR isolates.

[Fungal Keratitis Associated with Curvularia lunata: First Case Report from Türkiye]. / Curvularia lunata'ya Bagli Gelisen Fungal Keratit: Türkiye'den Ilk Olgu Raporu.

Fungal keratitis is a medical emergency that is among the most common causes of blindness in developing countries. The type of the agent may vary depending on the geographical conditions under which the patient lives, trauma exposure, the use of contact lenses and profession. Curvularia spp. is a saprophytic genus that rarely causes systemic disease in humans and has 250 species identified to date. They proliferate in soil and plants and spread to the environment with their spores and the formation of blackish and fluffy colonies is its most well-known morphological feature. There may be difficulties in cultivating brown (dematiaceous) fungi. Due to the similarity between the genera, conventional methods remain inadequate for diagnosis. In this report, a case of fungal keratitis associated with C.lunata was presented. Seventy-five years-old female patient admitted to the hospital with the symptoms of stinging pain, blurred vision, and swelling in the right eye. Her symptoms had begun four days ago after her eye was hit by a plant. The patient who had a history of peripheral neuropathy due to diabetes mellitus (DM) was hospitalized with a preliminary diagnosis of keratitis, and in the cultures of the patient's corneal scraping samples, the filamentous, black pigment-forming colonies of the pathogen growing on 5% sheep blood agar and potato dextrose agar showing an aerial hyphal structure, were stained with lactophenol cotton blue and examined under the microscope. The microscopic examination revealed geniculate conidiophores with brown pigmentation. On top of these structures were tetralocular macroconidia, one of which appeared to be larger than the main axis. The fungus was subjected to molecular identification with the prediagnosis of Curvularia/Bipolaris. DNA extraction of the ITS region polymerase chain reaction amplification and Sanger sequencing were performed for molecular identification. Sanger sequencing identified the agent to be Curvularia lunata with a similarity rate of 99.79% (NCBI-GenBank Nucleotide ID: OR365075). In vitro antifungal susceptibility of C.lunata was evaluated by microdilution method. Itraconazole and amphotericin B showed higher activity against C.lunata compared to other antifungals while fluconazole was the least active antifungal. Intrastromal and subconjunctival voriconazole injection was applied to the patient who was unresponsive to empirically initiated oral moxifloxacin and different topical treatments (vancomycin, ceftazidime, flucanozole, ganciclovir, cyclopentolate hydrochloride, hyaluronic acid and trehalose). After injection, right penetrating keratoplasty was applied due to increased thinning of the ulcerated area. No pathogen was detected in cultures taken after keratoplasty. Rare fungi should be considered in cases of keratitis that are difficult to treat. Fungal keratitis caused by brown fungi are clinically similar to each other and effective treatment protocols cannot be implemented without a species identification. Identification of the pathogen will enable genus-specific treatment. This will also help prevent complications that may occur. This article aims to present a case of fungal keratitis associated with C.lunata.

[Evaluation of Malassezia furfur Biofilm Formation on Polypropylene Membrane]. / Polipropilen Membran Üzerinde Malassezia furfur Biyofilm Olusumunun Degerlendirilmesi.

The Malassezia yeast species colonize on the skin immediately after birth and could be found on the healthy skin flora for life. Although they are more frequently involved in the etiology of common skin infections in the community, particularly Malassezia furfur could cause life-threatening infections such as fungemia. Detection of biofilm during the colonization of these yeasts on the skin is an important criterion for its virulence. Since they are lipophilic yeasts, commonly used biofilm detection methods are not applicable to the Malassezia strains. The aim of the study was to describe the growth and measurement of M.furfur isolates on a polypropylene membrane to demonstrate their biofilm-forming capacities. Twenty-seven M.furfur strains colonized in the newborns were included in the study. Basically, sterile polypropylene membranes were placed on different polysorbates (tween 20, 40, and 80) which were spread on Sabouraud dextrose agar. Ten µl saline suspension of M.furfur was dropped on the polypropylene membrane and incubated in standard growth conditions for three days. Later, the visible colony was removed gently by washing with running water and the biofilm structure formed on the membrane was stained with safranin. The stained biofilm was photographed. Performing image analysis, the values obtained against background activity were digitized according to the specified protocol. Moreover, XTT reduction test was performed and the measured metabolic activity results were compared with the safranin-stained biofilm data. The safranin hydrolysis of the strains was measured spectrometrically. Twenty-five (92.6%) of the strains included in the study were stained with safranin, which indicated the presence of biofilm on the polypropylene membrane. The strains grown with tween 20 and tween 80 formed a higher biofilm layer density than those supplied with tween 40. Isolates with low and high biofilm-forming capacity were clearly separated by tween 20 (p< 0.05). XTT activity was detected in 26 (96.3%) isolates. No correlation was found between biofilm density obtained by the described method and XTT reduction. It was observed that hydrolysis of safranin did not affect the biofilm evaluation method. In this study, it was shown that as a result of sufficient diffusion through hydrophobic membranes, polysorbate-based growth factors could maintain measurement of the biofilm layer formed by lipophilic M.furfur strains. The best grouping properties for M.furfur were obtained with tween 20 which could determine low and high level of biofilm formation. Image analysis was used with high performance for this method. As conclusion, the utilization of different hydrophobic membranes and dyes would lead to the development of new techniques for the application in other lipophilic yeasts.

Evaluation of Viral and Bacterial Pathogens in the Central Nervous System Infections with Multiplex PCR.

OBJECTIVE: To evaluate the bacterial and viral causes of central nervous system (CNS) infection by multiplex PCR. STUDY DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: Department of Medical Microbiology, Pamukkale University Faculty of Medicine, Turkey, from March 2016 to December 2021. METHODOLOGY: Cerebrospinal fluid (CSF) samples of patients prediagnosed with CNS infection were included in the study. Viral pathogens were detected with the Multiplex real-time PCR panel (FTD Neuro9, Fast Track Diagnostics, Luxembourg) and bacterial pathogens with the multiplex real-time PCR panel (FTD Bacterial Meningitis, Fast Track Diagnostics, Luxembourg). The identification of bacteria growing in samples was done by conventional methods and with the Phoenix™ (Becton Dickinson Diagnostics, USA) automated system. RESULTS: CSF samples of 440 patients were evaluated using multiplex PCR panel. The viral factors included adenovirus (14.2%), human herpes virus 7 (1.5%), varicella zoster virus (1.3%), herpes simplex virus 1 (1.3%), cytomegalovirus (1.3%), Epstein-Barr virus (0.8%), human herpes virus (0.8%), herpes simplex virus 2 (0.3%), varicella zoster virus (0.3%), and parvovirus B19 (0.3%); and bacterial factors included Streptococcus pneumoniae (7.0%) and Neisseria meningitidis (0.9%). The bacterial growth was detected in the CSF culture was 4.9%. Among the growing bacteria, there were six different types that were not found on the multiplex PCR panel. CONCLUSION: The use of a comprehensive bacterial multiplex PCR panel containing common pathogens will be more effective in pathogen detection. Care should be taken, especially when interpreting the viral Multiplex PCR. KEY WORDS: Viral multiplex PCR, Bacterial multiplex PCR, Bacteria culture.

Determination of COVID-19 PCR positivity and mutation status in coronaVac vaccinated individuals in Turkey.

BACKGROUND: CoronaVac is an inactivated virus-based COVID-19 vaccine used in Turkey and approved for emergency use by the World Health Organization (WHO). In this study, it was aimed to retrospectively evaluate the mutation status and clinical status in individuals who received two doses of CoronaVac vaccine and were infected with COVID-19 at least two weeks after the second dose. METHODS: 164 people were included in the study and COVID-19 diagnosis and mutation analyses were determined by RT-PCR using the Bioseepdy SARS CoV-2 Double Gene RT-qPCR Kit and the Biospeedy SARS-CoV-2 Variant Plus kit in accordance with the protocol determined by the manufacturer. RESULTS: 116 (70.7%) UK (Alpha, B.1.1.7) mutation and 3 (1.8%) South Africa (Beta, B.1.351), Brazil (Gamma, P.1) mutations were determined in 164 double doses CoronaVac vaccinated patients; 45 (27.5%) patients were mutation negative. Nine patients (5.5%) developed pneumonia. Eight patients (4.9%) had CT findings compatible with corona virus infection. Seven (4.3%) of the patients received treatment in the intensive care unit, and 5 (3%) of the patients were intubated. DISCUSSION: In conclusion, people who receive two doses of CoronaVac vaccine can be reinfected with mutant viruses, vaccine significantly reduces the need for hospitalization, CT findings and intensive care.

Rotavirus and adenovirus prevalence in patients with acute viral gastroenteritis in Denizli, Turkey, 2017-2021.

This study aims to determine retrospectively the prevalence of rotavirus and enteric adenovirus in patients with gastroenteritis symptoms and the distribution of pathogens by gender, age, seasons, and years. The stool samples sent to Pamukkale University Healthcare Research and Practice Hospital's Medical Microbiology laboratory between January 2017 and December 2021 were evaluated for rotavirus/adenovirus antigen positivity. Rotavirus and adenovirus antigens were studied with the Rotavirus-Adenovirus Combo Rapid Cassette Test (Acro Biotech) kit. Rotavirus was detected in 683 (8.2%) of the 8315 stool samples evaluated, and 180 (2.2%) samples were positive for adenovirus. Coinfection was detected in 21 (0.25%) samples. Rotavirus was found at the highest rate in 2019 (p = 0.001). The adenovirus was detected in 2020 at a lower rate than in other years (p = 0.0001). The rotavirus was observed at a higher rate in 0-<3, 3-<6, and 6-<13 age groups and adenovirus was detected at a higher rate in 3-<6 and 6-<13 age groups compared to other age groups (p = 0.001, p = 0.003, respectively). The highest rate of incidence of the rotavirus was found in spring and adenovirus in winter. In the etiology of gastroenteritis, especially in children, adenovirus and rotavirus should not be ignored in winter and spring. The prevalence of rotavirus was observed to have decreased in 2020 and onwards, and the prevalence of adenovirus decreased in 2020.

Evaluating bacterial contamination of free bone fragments falling to the ground and the effectiveness of antiseptic solutions.

OBJECTIVES: This study aims to determine the contamination incidence rate of bone fragments that have been dropped on the floor of the operating theatre, as well as how effective antimicrobial solutions are at decontaminating them. METHODS: Bone fragments obtained after 30 total knee arthroplasties were used in the study. Inert pieces of bone emerging after the bone cuts during total knee arthroplasty were divided into 1 × 1 cm fragments. The bone fragments were first left in free fall on the floor of the operating theatre and then were kept in a number of antimicrobial solutions for 15 s. Subsequently, they were microbiologically and histopathologically examined. A swab culture was also taken from the floor of the operating theatre. RESULTS: It was determined that 63.3% of osteochondral fragments in the non-intervened group were contaminated. Growth was likewise detected in all swab cultures. Microorganisms growing in the swab culture and the non-intervened group were similar and mostly Staphylococcus epidermidis and Klebsiella pneumoniae. When the growth rates of the 10% povidone-iodine and 4% chlorhexidine gluconate groups were compared with the growth rate of the non-intervened group, a statistical difference was found. No difference was determined between the growth rates of the sodium hypochlorite and the non-intervened groups. The histopathological analysis revealed no statistical difference between the groups in terms of bone marrow, vascular structure, fat tissue, and osteoblastic activity results in the osteochondral fragments CONCLUSION: Bone tissues dropped from a sterile area on the floor of the operating theatre are highly contaminated. An effective decontamination without bone cell toxicity was achieved using povidone-iodine. Although chlorhexidine gluconate solution had an effective decontamination effect compared to the non-intervened group, it was not 100% effective. Sodium hypochlorite solution was not effective in the decontamination of grafts under our working conditions.

[A case with scalp pruritus caused by Dermanysus gallinae (order: mesostigmata)]. / Dermanysus gallinae'nin (Takim: mesostigmata) neden oldugu saçli deride kasintili olgu.

Dermanyssus gallinae is one of the important hematophagous ectoparasite species of poultry like chicken, pigeon and wild bird species. These ectoparasites in the form of nymphs or adults who can not find their hosts are also seen in mammals and even in humans. For this reason, they are considered as important for public health. The ectoparasite causes a clinical condition named gamasoidosis among pet owners and people who live or work close to animal shelters, barns and chicken farms. Pruritus dermatitis is also caused by D.gallinae in humans and can cause false diagnosis. In this report, a case of D.gallinae which leads to severe itch in the hairy head skin was presented. A 66-year-old female patient admitted to University Hospital with complaints of "bugs in her hair and itching of the skin increasing in the evenings" that have persisted for a month. In the dermatological examination of the patient, it was noted that her hair and scalp were usual. Routine laboratory tests were normal. However, a large number of mites were found in her headscarf that she brought with her to the examination. Later, it was learned that the patient feeds chicken in her garden in the village where she lives. The collected mite samples were were kept in glass test tubes that contained glycerol and alcohol. The mites were identified as D.gallinae by morphological identification with light microscopy by using 10x, 20x and 40x magnifications. The mites were described as D.gallinae (Order: Mesostigmata, local name: poultry red mite, perch mite, poultry mite) with the morphological examination. Long-acting 1% permethrin shampoo was applied to remove the mites on the patient and during the controls, it was changed as 5% permethrin and 10% crotamiton lotion. For environmental sanitation, carbamates (such as carbolineum, trichlorfon, malathion, tetrachlorvinphos, etc.), organophosphates and acaricide insecticides with pyrethroids spraying or powder formulations were recommended. It was recommended to repair the slits and cracks where the parasite in the shelter could be stored. The patient was informed on (i) how to clean the household items with susceptible acaricides, (ii) removal of unused infected animal shelters, cages and nests from human habitat, (iii) raising of ambient temperature above 45°C, (iv) ventilation of the living spaces and (v) washing the clothes with detergent. In order to be effectively protected from the risk of infection and the detriments that are brought by this parasite, it is imperative to stay away from the hosts and the infected areas such as chicken farms, to obey the hygiene regulations, and to properly conduct the disinfestation of the shelters. In addition, it is also helpful to receive a true story from the patient, with details of contact with birds for the protection and treatment.