Neutralization of Wild-Type and Alpha SARS-CoV-2 Variant by CoronaVac® Vaccine and Natural Infection- Induced Antibodies.

One of the immune responses desired to be achieved by SARS-CoV-2 vaccination is to create neutralizing antibodies (nAbs), thus preventing the development and spread of infection. The aim of this study was to investigate the seropositivity rate, anti-spike antibody levels, and neutralizing capacity of these antibodies against wild type (WT) and alpha variants in serum samples of individuals who had been naturally infected or vaccinated with CoronaVac®. Total anti-spike antibody levels were determined in all samples. Neutralization assays were performed by the reduction of the cytopathic effect in Vero-E6 cells with infectious WT and alpha SARS-CoV-2 variants. Although both naturally infected and vaccinated individuals were all seropositive for antispike antibodies, 84.8% of the vaccinated group, and 89.3% of the naturally infected group had detectable nAbs. The nAbs titers were significantly higher in the naturally infected group for both WT and alfa variant of the virus as compared to the vaccinated individuals. In this study, it was observed that all individuals became seropositive six weeks after exposure to the vaccine or the virus. Moreover, naturally infected individuals had higher levels of nAbs than those vaccinated. The presence of nAbs against the alpha variant in both naturally infected and vaccinated individuals suggests that these antibodies may also be protective against infections, which may be caused by other variants, such as delta and omicron.

[Comparision of Colistin Broth Disc Elution, Rapid Resapolymyxin NP and Broth Microdilution Methods in Determining Colistin Sensitivity in Acinetobacter, Pseudomonas and Enterobacterales species]. / Acinetobacter, Pseudomonas ve Enterobacterales Türlerinde Kolistin Duyarliliginin Belirlenmesinde Kolistin Sivi Disk Elüsyon, Hizli Resapolimiksin NP ve Sivi Mikrodilüsyon Yöntemlerinin Karsilastirilmasi.

In recent years, with the increase of carbapenem resistance in Acinetobacter, Pseudomonas, Enterobacterales species, the use of colistin in treatment has gradually increased. Since the broth microdilution method which is recommended as a reference method in colistin susceptibility tests, is laborious and expensive and other susceptibility tests do not give reliable results, all these cause laboratories to search for new methods for the determination of colistin susceptibility testing. In this study, it was aimed to compare the broth microdilution method which is the reference method with the colistin broth disc elution and rapid resapolymyxin NP tests for the determination of the susceptibility of colistin in Acinetobacter, Pseudomonas, Enterobacterales species which are common healthcare-associated infection agents.Colistin susceptibility of a total of 157 isolates isolated from patients hospitalized in Ankara City Hospital [Klebsiella pneumoniae (n= 74), Acinetobacter spp. (n= 33), Escherichia coli (n= 26), Pseudomonas aeruginosa (n= 24)] were tested by broth microdilution, colistin broth disc elution and rapid resapolymixin NP methods. The categorical and basic agreement was evaluated by comparing the broth microdilution results with the rapid resapolymyxin NP results and the colistin broth disc elution. When compared with broth microdilution, the categorical agreement of colistin broth disc elution test for Enterobacterales, Acinetobacter, Pseudomonas species was found to be 93%, 48%, 100%, respectively. When the essential agreement was evaluated the values of 95%, 45%, 100% were found, respectively. Very major error rates were found to be 10%, 70% and 0%, respectively. The categorical agreement of the rapid resapolymyxin test for Enterobacterales, Acinetobacter, Pseudomonas species was 85%, 36%, 100%, while very major error rates were found to be 10%, 88% and 0%, respectively. When compared with the reference method, both tests showed high categorical and essential agreements for P.aeruginosa. Accepted level of categorical and essential agreement was found in colistin broth disc elution method for Enterobacterales species, and low categorical agreement was found in rapid resapolymyxin NP test. For Acinetobacter species, both tests detected low categorical agreement and high rate of very major error. In addition, compared to the broth microdilution method, both colistin broth disc elution and rapid resapolymyxin NP tests were found to be cost-effective and easy to prepare. It was considered to be an additional advantage to have the results in rapid polymyxin NP test in four hours. In conclusion, in our study, it was shown that both colistin broth disc elution and rapid resapolymyxin NP test methods can be used in determining the susceptibility of colistin for P.aeruginosa and Enterobacterales species but both methods were found to be unsuccessful for Acinetobacter species.

Chronic lower extremity wound infection due to Kerstersia gyiorum in a patient with Buerger's disease: a case report.

BACKGROUND: Kerstersia gyiorum is an extremely rare pathogen of human infection. It can cause chronic infection in patients with underlying conditions. It can easily be misdiagnosed if proper diagnostic methods are not used. CASE PRESENTATION: A 47-year-old male patient with a history of Buerger's Disease for 28 years presented to our hospital with an infected chronic wound on foot. The wound was debrided, and the specimen was sent to Microbiology laboratory. Gram staining of the specimen showed abundant polymorphonuclear leukocytes and gram-negative bacilli. Four types of colonies were isolated on blood agar. These were identified as Kerstersia gyiorum, Proteus vulgaris, Enterobacter cloacae, Morganella morganii by Maldi Biotyper (Bruker Daltonics, Germany). The identification of K. gyiorum was confirmed by 16S ribosomal RNA gene sequencing. The patient was successfully recovered with antimicrobial therapy, surgical debridement, and skin grafting. CONCLUSIONS: This is the first case of wound infection due to K. gyiorum in a patient with Buerger's Disease. We made a brief review of K. gyiorum cases up to date. Also, this case is presented to draw attention to the use of new and advanced methods like MALDI-TOF MS and 16S rRNA gene sequencing for identification of rarely isolated species from clinical specimens of patients with chronic infections and with chronic underlying conditions.

Breast abscess due to Salmonella Typhimurium in a patient with rheumatoid arthritis: a case report.

BACKGROUND: This is the first report of breast abscess due to Salmonella enterica serotype Typhimurium. Staphylococcus aureus is known as the most common cause of breast abscess. Salmonella spp. may occasionally form localized abscesses after dissemination to various organ systems following a bacteraemia. But breast abscess related to Salmonella spp is a very rare complication. CASE PRESENTATION: A 43-year-old female patient referred to our hospital with a lump, fever and mild pain in her breast. The patient was not pregnant or lactating at that time. She had a history of rheumatoid arthritis for 5 years and was under immunosuppressive therapy. Ultrasonography of the breast revealed an abscess. The abscess was drained and sent for culture to medical microbiology laboratory. The microorganism was identified as Salmonella enterica serotype Typhimurium and found to be sensitive to all antibiotics tested. The patient was cured after surgical debridement and antibiotic therapy. The abscess did not recur again. CONCLUSIONS: This case is presented to draw attention to non-typhoidal Salmonella as rare causes of breast abscess and submission of specimens to the microbiology laboratory for accurate diagnosis and treatment especially in patients with underlying immunosuppressive diseases.

Phenotypic and genotypic characteristics of carbapenem-resistant Enterobacteriaceae in a tertiary-level reference hospital in Turkey.

BACKGROUND: Enterobacteriaceae are among the most common pathogens that are responsible for serious community-acquired, hospital-acquired, and health-care associated infections. The emergence and spread of carbapenem-resistant Enterobacteriaceae (CRE) have become an increasing concern for healthcare services worldwide. Infections caused by these bacteria have been associated with significant morbidity and mortality and treatment options have been limited. The rapid and accurate detection of carbapenem resistance in these bacteria is important for infection control. The aim of this study was to investigate the phenotypic and genotypic features of CRE strains isolated in a tertiary-level reference hospital in Turkey. METHODS: A total of 181 CRE strains were included in the study. Antimicrobial susceptibility rates were tested using Vitek 2 system. Modified Hodge test (MHT) was performed using meropenem and ertapenem discs. Metallo-ß-lactamase antimicrobial gradient test (E-test MBL strips) were used for evaluation of metallo-ß-lactamase production. A multiplex PCR was used for detection of carbapenems resistance genes (IMP, VIM, KPC, NDM-1 and OXA-48). RESULTS: The OXA-48 gene was detected in 86 strains, NDM-1 gene in six strains, VIM gene in one strain. IMP and KPC genes were not identified. Three strains produced both OXA-48 and NDM-1 and one strain produced both OXA-48 and VIM. In two patients more than one genus of OXA-48 positive CREs was isolated. Ninety-two of the isolates were multidrug-resistant. One hundred and ten isolates were MHT with meropenem (MEM-MHT) positive and 109 isolates were MHT with ertapenem (ERT-MHT) positive. Nine of the isolates were positive with E-test MBL strips. The sensitivity of MEM-MHT and ERT-MHT for detection of OXA-48 was 70.9 and 70.6 %, respectively. MEM-MHT was found highly discriminative for OXA-48 Escherichia coli (p < 0.001). The sensitivity of E-test MBL for NDM-1 was 66.7 %. A statistically significant correlation was observed between OXA-48 gene and MHT positivity and between NDM-1, VIM gene and E-test MBL positivity (p < 0.001). CONCLUSIONS: OXA-48 gene is spreading rapidly to many different species of Enterobacteriaceae in the hospital environment. While OXA-48 is still the most common source of carbapenem resistance in Enterobacteriaceae in our country, NDM-1 is increasingly being isolated from patients without a history of foreign contact.

[Investigation of oxacillinase genes in nosocomial multidrug-resistant Acinetobacter baumannii isolates by multiplex PCR and evaluation of their clonal relationship with Rep-PCR]. / Nozokomiyal çok ilaca dirençli Acinetobacter baumannii izolatlarinda oksasilinaz genlerinin multipleks PCR ile arastirilmasi ve klonal iliskilerinin Rep-PCR ile degerlendirilmesi.

Acinetobacter baumannii is a major nosocomial pathogen which can cause infections with high morbidity and mortality in hospitalized patients. In recent years A.baumannii has become a serious clinical problem because of the development of resistance to many antibiotics, and especially to carbapenems. The aims of this study were to investigate the oxacillinase genes responsible for carbapenem resistance in multidrug resistant (MDR) A.baumannii strains and to evaluate the clonal relationship between these strains. A total of 62 MDR A.baumannii strains isolated from various clinical specimens (24 tracheal aspirate, 14 wound, 10 blood, 7 urine, 2 abscess, 2 sputum, 2 catheter tip, 1 pleural fluid) of hospitalized patients in intensive care units (n= 42) and other inpatient clinics (n= 20) between February-March 2012, were included in the study. Identification and antibiotic susceptibility of A.baumannii isolates were performed by Vitek-2 automated system (bioMérieux, France), and the identified bacteria were confirmed by Maldi Biotyper (Bruker Daltonics, Germany) system. Imipenem, meropenem, colistin and tigecycline were additionally tested by E-test strips (bioMérieux, France). The presence of carbapenemase-producing OXA genes (blaOXA-23-like, blaOXA-40-like, blaOXA-51-like and blaOXA-58-like) were detected by multiplex PCR (hyplex® CarbOxaID test system, Amplex Diagnostics, Germany) and the clonal relationship between isolates were investigated by rep-PCR method (DiversiLab, bioMérieux, France). In our study, all isolates were found resistant to ampicillin-sulbactam, piperacillin, piperacillin-tazobactam, ceftazidime, cefepime, imipenem, meropenem, ciprofloxacin, levofloxacin and tetracycline, while the resistance rates for amikacin, gentamicin, trimethoprim-sulfamethoxazole, netilmicin and tigecycline were 88.7%, 88.7%, 82.3%, 43.5% and 27.4%, respectively. All A.baumannii isolates were susceptible to colistin. All of the strains were positive for blaOXA-23-like and blaOXA-51-like genes, while blaOXA-40-like and blaOXA-58-like genes were not detected in any of them. Simultaneous cultures from environmental samples collected from inpatient clinics in which MDR A.baumannii strains isolated were negative in terms of A.baumannii growth. In evaluation of clonal relationship between isolates, 48 strains (77.4%) showed greater than 95% similarity and formed a big cluster, named Cluster A. The remaining 14 isolates formed 3 small clusters (each had 2 isolates), named Cluster B, C and D, showing greater than 95% similarity. Majority of isolates (58.3%) in Cluster A were from patients in the surgical intensive care unit, and the first isolate from this cluster was also from a patient in the same unit. In our opinion, isolates from Cluster A may have spread to other clinics from surgical intensive care unit through transferred patients or medical and non-medical devices and equipment. Nosocomial MDR A.baumannii isolates in our hospital are highly resistant to antibiotics and all harboured blaOXA-23-like genes. The rep-PCR analysis of these isolates indicated that a large portion of A.baumannii strains were clonally closely related, and they probably from the same source and common ancestor, and separated shortly from each other. This data emphasizes that the choices of treatment are quite limited for inpatients, and the need for improvement of the infection control measures in our hospital.

[Characterization and determination of antibiotic resistance profiles of a single clone Acinetobacter baumannii strains isolated from blood cultures]. / Kan kültürlerinden izole edilen tek klonlu Acinetobacter baumannii suslarinin karakterizasyonu ve antibiyotik direnç profi llerinin incelenmesi.

Acinetobacter baumannii which is a significant cause of nosocomial infections, increases the rate of morbidity and mortality in health care settings especially in intensive care units (ICUs). The aim of this study was to determine the antibiotic resistance profiles of A.baumannii strains isolated from blood cultures of inpatients from different ICUs, wards and hospital environment and evaluate their clonal relationships and epidemiologic features. A total of 54 A.baumannii strains (47 from the blood cultures and 7 from the hospital environment), identified between 01 January 2012-28 December 2012 at the Clinical Microbiology Laboratory of Ankara Numune Training and Research Hospital, Turkey, were included in the study. Identification of A.baumannii isolates and their antimicrobial [sulbactam-ampicillin (SAM), piperacillin (PIP), piperacillin-tazobactam (TZP), ceftazidime (CFZ), cefoperazone-sulbactam (SCF), cefepime (CEF), imipenem (IMP), meropenem (MER), amikacin (AMK), gentamicin (GEN), netilmicin (NT), ciprofloxacin (CIP), levofloxacin (LVF), tetracycline (TET), tigecycline (TG), colistin (COL), trimethoprim-sulfamethoxazole (SXT)] susceptibility testing were performed by Vitek 2 (bioMérieux, France) system. The clonal relationship between the A.baumannii isolates was analysed by pulsed-field gel electrophoresis (PFGE). In our study colistin, tigecycline and netilmicin were found to be the most effective agents against A.baumannii isolates. All of the clinical isolates (n= 47) were found susceptible to COL, however all were resistant to SAM, PIP, TZP, CEF, IPM, CFZ, MER and CIP. While 1.85%, 14.8%, 14.8%, 16.6%, 59.2% and 22.2% of the isolates were susceptible to SCF, AMK, NT, GEN, TG and SXT, respectively; 1.85%, 1.85%, 9.2%, 16.6%, 38.8% and 27.7% of the isolates were intermediate to SCF, TET, AMK, NT, LVF and TG, respectively. Similarly, all of the environmental A.baumannii isolates (n= 7) were resistant to SAM, PIP, TZP, CFZ, CEF, IPM, MER and CIP, and all were susceptible to TG and COL. The resistance rates of the environmental isolates to SCF, AMK, GEN, NT, LVF, TET and SXT were determined as 57.1%, 85.7%, 85.7%, 28.8%, 28.6%, 85.7% and 57.1%, respectively. PFGE analysis done by the use of ApaI enzyme revealed the presence of one major clone. Dendogram analysis indicated that environmental and clinical isolates were in the same clone indicating that the outbreak was possibly originated from the same internal ICUs. Our data emphasized that multidrug resistant A.baumannii isolates were quite common in our hospital, and enviromental cross-contamination throughout the year was confirmed by molecular methods. Despite the precautions such as continous education on effective hand washing, use of gloves and hospital cleaning, established in our hospital, this single clonal spread was attributed to staff shortage and poor adherence to infection control rules. In conclusion, for the prevention of dissemination of multidrug resistant A.baumannii strains and control of nosocomial infections, infection control strategies should be established and strict compliance to these rules should be provided.

[Evaluation of the toxoplasmosis seroprevalence in pregnant women and creating a diagnostic algorithm]. / Gebelerde toksoplazmoz seroprevalansinin degerlendirilmesi ve bir tani algoritmasinin olusturulmasi

Toxoplasma gondii, an obligatory intracellular protozoon is widely distributed around the world and can infect all mammals and birds. While acquired toxoplasmosis is usually asymptomatic in healthy subjects, acute infection during pregnancy may lead to abortion, stillbirth, fetal neurological and ocular damages. For the prevention of congenital toxoplasmosis it is recommended that a screening programme and a diagnostic algorithm in pregnant women should be implemented while considering the cost effectiveness. Thus, it is necessary to determine the seroprevalence of toxoplasmosis in pregnant women and the actual risk of T.gondii transmission during pregnancy in a certain area. The aims of this study were to detect the T.gondii seropositivity in the pregnant women admitted to our hospital and to create a diagnostic algorithm in order to solve the problems arising from interpretation of the serological test results. A total of 6140 women aged 15-49 years who were admitted to our hospital between April 1st, 2010 to July 31st, 2013, were evaluated retrospectively. In the serum samples, T.gondii IgM, IgG and IgG avidity tests were performed by VIDAS automated analyzer using TOXO IgM, TOXO IgG II and TOXO IgG avidity kits (bioMerieux, France). It was noted that, both T.gondii IgM and IgG tests were requested from 4758 (77.5%) of the pregnant women, while only IgM test from 1382 (22.5%) cases. Sole IgM positivity was found as 0.2% (11/6140), IgG as 26.4% (1278/4758) and both IgM + IgG as 0.9% (44/4758). T.gondii IgG avidity tests were requested from 12 of 44 women who were found both IgM and IgG positive and eight of them revealed high avidity and four low avidity. Avidity test was ordered for the 91 (7.1%) of 1278 sole IgG positive cases and four of them were found to have low avidity. IgG avidity test was ordered for 554 (16.2%) of IgM and/or IgG negative subjects, however, the test was not performed according to rejection criteria of the laboratory. It was noticed that no re-testing was requested for none of the seronegative cases (3428/4758; 72%) during their follow-up. In our study, total Toxoplasma seropositivity rate among pregnant women was detected as 28% (1330/4758), showing statistically significant increase (p< 0.05) with age. There was no significant difference (p> 0.05) in the seropositivity rate between the years (2010-2013). Following the evaluation of the test orders, the problems related to test orders and interpretation of the test results were determined and a diagnostic algorithm to be used in our hospital, was established to minimize such problems in toxoplasma serology. It was concluded that a diagnostic algorithm related to toxoplasmosis serology should be implemented for the appropriate evaluation of the risk of acute toxoplasmosis during pregnancy. Such an approach is necessary to support the clinical diagnosis and to minimize the anxiety in pregnant women about congenital toxoplasmosis.

[Phenotypic and genotypic traits of vancomycin-resistant enterococci in a public hospital: the first vanB-positive Enterococcus faecium isolates]. / Bir Devlet Hastanesinde Vankomisine Dirençli Enterokok Suslarinin Fenotipik ve Genotipik Olarak Degerlendirilmesi: Ilk vanB-Pozitif Enterococcus faecium Izolatlari

Thirty eight vancomycin resistant enterococci (VRE) were isolated in one year surveillance study for hospital infection control programme in a state hospital in Ankara, Turkey. All isolates were identified as Enterococcus faecium by VITEK2 system (bioMerieux, France). Vancomycin and teicoplanin resistant 30 strains were defined as vanA phenotype while vancomycin-resistant teicoplanin-susceptible eight strains were defined as vanB phenotype. vanA genes were found in 30 strains while vanB genes were found in five strains by using PCR method. Those five strains were the first vanB positive E.faecium strains in our country. VRE strains revealed six different band patterns by PFGE, while six isolates could not be classified. All isolates with vanB type resistance were found in the same cluster. Source of vanB positive strains was considered as the hemodialysis unit. When the previous national reports related to vancomycin-resistant enterococci were considered, this was the first report of vanB positive E.faecium isolates in our country. This emphasized that both the diversity of VRE and the isolation rate was increasing. In order to eliminate the spread of VRE, effective surveillance studies should be performed and protective measures should be established promptly.

Synergistic Activities of Colistin Combinations with Meropenem, Sulbactam, Minocycline, Disodium Fosfomycin, or Vancomycin Against Different Clones of Carbapenem-Resistant Acinetobacter baumannii Strains.

Aims: Colistin became the primary treatment option for Acinetobacters that had developed a high rate of resistance to carbapenems which were the first-line therapy in the past, and now Acinetobacters become resistant to nearly all antibiotics. Because of the resistance potential to colistin and the concerns about toxicity, especially for high doses, colistin combination therapies are preferred nowadays. In this study, we aimed to investigate whether combinations of colistin with meropenem, sulbactam, fosfomycin, vancomycin, and minocycline are synergic or not and to determine minocycline susceptibility rate, which is not in use in our country. Results: For the studied 23 Acinetobacter strains, the highest synergy was between colistin and vancomycin, which was shown in 4 (17.4%) strains. The synergy of colistin with meropenem and fosfomycin was detected for 1 (4.3%) strain, the synergy of colistin with minocycline was detected for 2 (8.6%) strains, and no synergy was detected for colistin-sulbactam combination. All the strains were susceptible to minocycline. Conclusion: None of the antibiotic combinations was antagonistic. They had synergistic and additive interactions. Thus, these combinations can be used in clinical practices. The remarkable synergistic interaction of colistin-vancomycin combination and high susceptibility to minocycline highlight the need for more researches on these subjects.

High-risk Oncogenic Human Papilloma Virus Infection of the Foreskin and Microbiology of Smegma in Prepubertal Boys.

OBJECTIVE: To evaluate the prevalence and genotypes of human papillomavirus (HPV) infection and microbiological status of the foreskin in asymptomatic prepubertal boys. METHODS: A total of 100 prepubertal healthy boys who underwent a standard circumcision procedure were included in the study. High-risk HPV status was determined by real-time polymerase chain reaction for the genotypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68. The swabs were immediately sent to microbiology laboratory for culture and sensitivity tests. RESULTS: The median age at the time of surgery was 5.7 years (range, 2 months-9 years). High-risk HPV was detected in 9 foreskins (9%). Positive samples showed are HPV16 (n = 3), 31 (n = 2), 39 (n = 3), and 51 (n = 1). There were a total of 72 organism isolates: 54 gram-positive (75%) and 17 gram-negative (23.6%) bacteria and 1 (1.4%) Candida. The most commonly isolated gram-negative bacterium was Escherichia coli (41.2%), whereas the commonly isolated gram-positive bacterium was Enterecoccus sp. (57.4%). CONCLUSION: Our results showed that subclinical high-risk HPV infections are found in the foreskin, which could be a reservoir for HPV-associated diseases, and smegma seems not to be a risk factor for drug-resistant infection in children.

Comparison of the surface and core bacteria in tonsillar and adenoid tissue with Beta-lactamase production.

Adenoidectomy and tonsillectomy, indicated for children with recurrent or persistent symptoms of infection or hypertrophy, are among the most frequent operations performed in children. This study was carried out for investigating the microbial flora of the tonsils and adenoids regarding to core and surface microorganisms and also pathogen microrganisms' beta-lactamase production rate. Cultures were taken from the core and surface of tonsils and adenoids of the 91 patients at the time of the surgery for tonsillectomy and adenoidectomy. Aerobic and anaerobic cultures were inoculated and identified. Beta-lactamase production was detected also. The most frequently isolated aerobic microorganisms were Streptococcus viridans and Neisseria spp. The number of the microorganisms isolated from the tonsil core compared to the surface of the tonsils was found statistically insignificant (P > 0.05). The number of the adenoid surface aerobic microorganisms was found higher from the adenoid core (P < 0.05). The amount of adenoid and tonsil core anaerobic microorganisms were alike. The patients' preoperative antibiotherapy whether using beta-lactam or beta-lactamase resistant were compared for beta-lactamase producing bacteria production and the number of beta-lactamase producing bacteria were found statistically insignificant (P > 0.05). The togetherness of Staphylococcus aureus and other beta-lactamase producing bacteria was found statistically significant (P < 0.05). This study demonstrates that there is polymicrobial aerobic-anaerobic flora in both adenoids and tonsils. There was a close relationship between the bacteriology of the tonsil and adenoid flora. Staphylococcus aureus and and other beta-lactamase producing bacteria may be responsible for treatment failures in patients with tonsillitis.