[The Relationship of Enterotoxigenic Bacteroides fragilis and Fusobacterium nucleatum Intestinal Colonization with Colorectal Cancer: A Case-Control Study Performed with Colon Biopsies]

In recent years, it has been shown that some bacteria may be associated with colorectal cancer (CRC). In this study, it was aimed to investigate the role of Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis (ETBF) in the etiology of CRC by comparing the amounts of these bacteria in colon biopsy tissues of patients with CRC and healthy individuals. The amounts of F.nucleatum and ETBF were determined by quantitative polymerase chain reaction (qPCR) in colon biopsy samples taken from 35 CRC and 35 healthy individuals, and the results were compared in the patient and control groups. The detection rate and amounts of F.nucleatum were found to be statistically significantly higher in tissues of female patients with CRC compared to male patients (p= 0.003, p= 0.013, respectively). There was no statistically significant difference between the tissues of female and male patients with CRC in terms of detection rate and amount of ETBF (p= 0.521, p= 0.515, respectively). It was found that in the 50-74 age group, the amount of ETBF was statistically significantly higher in women and men with CRC compared to the controls (p= 0.005, p= 0.047, respectively), while the amount of F.nucleatum was statistically significantly higher in female patients compared to controls. However, no difference was found between male patients and controls (p= 0.009, p= 0.083). It was determined that the detection rate and amount of F.nucleatum in the tissues of patients with CRC, regardless of age and gender, were not statistically different from the controls (p= 0.473, p= 0.995, respectively), however, the detection rate of ETBF and the amount of ETBF were found to be statistically significantly higher (p= 0.002, p= 0.004, respectively). It has been determined that ETBF can play a role in the etiology of CRC in both men and women, and F.nucleatum only in women, in the age range of 50-74 years, when routine screenings for CRC are performed.

Could Prior COVID-19 Affect the Neutralizing Antibody after the Third BNT162b2 Booster Dose: A Longitudinal Study

Vaccination is an essential public health measure for preventing the spread of illness during this continuing COVID-19 epidemic. The immune response developed by the host or the continuation of the immunological response caused by vaccination is crucial since it might alter the epidemic’s prognosis. In our study, we aimed to determine the titers of anti-S-RBD antibody and surrogate neutralizing antibody (snAb) formed before and after the third dose of the BNT162b2 vaccination (on the 15th, 60th, and 90th days) in healthy adults who did not have any comorbidity either with or without prior SARS-CoV-2 infection. In this longitudinal prospective study, 300 healthy persons were randomly included between January and February 2022, following two doses of BNT162b2 immunization and before a third dosage. Blood was drawn from the peripheral veins. SARS-CoV-2 NCP IgG and anti-S-RBD IgG levels were detected by the CMIA method, and a surrogate neutralizing antibody was seen by the ELISA method. Our study included 154 (51.3%) female and 146 (48.7%) male (total 300) participants. The participants’ median age was 32.5 (IQR:24–38). It was discovered that 208 individuals (69.3%) had never been infected with SARS-CoV-2, whereas 92 participants (30.7%) had SARS-CoV-2 infections in the past. Anti-S-RBD IgG and nAb IH% levels increased 5.94- and 1.26-fold on day 15, 3.63- and 1.22-fold on day 60, and 2.33- and 1.26-fold on day 90 after the third BNT162b2 vaccine dosage compared to pre-vaccination values (Day 0). In addition, the decrease in anti-S-RBD IgG levels on the 60th and 90th days was significantly different in the group without prior SARS-CoV-2 infection compared to the group with past SARS-CoV-2 infection (p < 0.05). In conclusion, it was observed that prior SARS-CoV-2 infection and the third BNT162b2 vaccine dose led to a lower decrease in both nAb and anti-S-RBD IgG levels. To evaluate the vaccine’s effectiveness and update immunization programs, however, it is necessary to perform multicenter, longer-term, and comprehensive investigations on healthy individuals without immune response issues, as there are still circulating variants.

Development of in House ELISAs to Detect Antibodies to SARS-CoV-2 in Infected and Vaccinated Humans by Using Recombinant S, S1 and RBD Proteins

(1) Background: The aim of this study was to produce in-house ELISAs which can be used to determine SARS-CoV-2-specific antibody levels directed against the spike protein (S), the S1 subunit of S and the receptor binding domain (RBD) of S in SARS-CoV-2 vaccinated and infected humans. (2) Methods: Three in-house ELISAs were developed by using recombinant proteins of SARS-CoV-2, namely the S, S1 and RBD proteins. Specificity and sensitivity evaluations of these tests were performed using sera from SARS-CoV-2-infected (n = 70) and SARS-CoV-2-vaccinated (n = 222; CoronaVac vaccine) humans in Istanbul, Turkey. The analyses for the presence of SARS-CoV-2-specific antibodies were performed using the in-house ELISAs, a commercial ELISA (Abbott) and a commercial surrogate virus neutralization test (sVNT). We also analyzed archival human sera (n = 50) collected before the emergence of COVID-19 cases in Turkey. (3) Results: The sensitivity of the in-house S, S1 and RBD ELISAs was found to be 88.44, 90.17 and 95.38%, while the specificity was 72.27, 89.08 and 89.92%, respectively, when compared to the commercial SARS-CoV-2 antibody test kit. The area under curve (AUC) values were 0.777 for the in-house S ELISA, 0.926 for the S1 ELISA, and 0.959 for the RBD ELISA. The kappa values were 0.62, 0.79 and 0.86 for the S, S1 and RBD ELISAs, respectively. (4) Conclusions: The in-house S1 and RBD ELISAs developed in this study have acceptable performance characteristics in terms of sensitivity, specificity, AUC and kappa values. In particular, the RBD ELISA seems viable to determine SARS-CoV-2-specific antibody levels, both in infected and vaccinated people, and help mitigate SARS-CoV-2 outbreaks and spread.

Evaluation of <em>Echinococcus</em> DNA by polymerase chain reaction (PCR) in cystic <em>Echinococcosis</em> of the liver

OBJECTIVES

The aim of this study was to determine the DNA and genotypes of Echinococcus granulosus in liver cyst hydatids isolated in humans.

MATERIAL AND METHODS

This study was conducted prospectively at the Department of General Surgery of the Cerrahpaşa School of Medicine, University of İstanbul-Cerrahpaşa, between January 2015 and June 2016 in 30 patients who were operated on for cystic Echinococcosis. E. granulosus DNA was analyzed using the Polymerase Chain Reaction (PCR) method in the cyst samples (protoscolex and/or germinative membrane) obtained during the operation, and genotype was determined in the PCR positive samples by sequence analysis. At the same time, indirect hemagglutination (IHA) was used to test for the presence of antibodies in the patients' blood.

RESULTS

E. granulosus DNA was found in 29 out of 30 cystic Echinococcosis of the liver samples. All of the 29 cystic Echinococcosis samples were found to be G1 (sheep) species. Also, IHA was positive in 22 patients and negative in eight patients.

CONCLUSION

In the present study, G1 species was the most commonly seen liver cystic Echinococcosis species. We suggest that a vaccine, which could be developed against prevalent regional genotypes, would be efficacious in the prevention of the disease with a cause of mortality and morbidity.

[Evaluation of the Diagnostic Performance of SARS-CoV-2 Rapid Antigen Tests in COVID-19 Patients]

The gold standard in the definitive diagnosis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is nucleic acid amplification tests (NAAT) due to their high sensitivity and specificity in detecting viral ribonucleic acid. However, while leaving two years behind in the pandemic, resources have come to the point of exhaustion in terms of both the economy and the manpower working in the field of health services. Therefore, the need for rapid, simple and accurate tests to diagnose SARS-CoV-2 infection continues. In this study, it was aimed to compare the performance characteristics of SARS-CoV-2 rapid antigen tests (RAgT) in the diagnosis of coronavirus disease 2019 (COVID-19) cases with the real-time reverse transcription-polymerase chain reaction (rRT-PCR) method. In Istanbul University-Cerrahpaşa Faculty of Medicine COVID-19 Molecular Diagnosis Laboratory, SARS-CoV-2 RNA positive respiratory tract samples with viral loads of <25 Ct (cycle of treshold), 25-29 Ct, 30-35 Ct and 35<Ct, a total of 205 patient samples were selected in four groups. SARS-CoV-2 positive samples were studied by lateral flow method (LFA) using twelve commercial RAgTs of different companies and their performances were evaluated. In addition, 90 samples were selected from various respiratory tract samples archived, which were sent to our laboratory for the identification of the non-COVID-19 pathogen(s) causing the respiratory tract infection between 2020-2022 and their specificities for RAgTs were evaluated to avoid cross reactivity. The sensitivities of the SARS-CoV-2 RAgTs included in the study, ranged from 40.4-97.5%, while the sensitivity of most of the kits (8/12), at <25 Ct values, was <90%, which is the minimum limit in the European Centre for Disease Prevention and Control (ECDC)'s guideline for the use of SARS-CoV-2 RAgTs. The specificities of RAgTs were found to be between 90-100%. When the concordance of SARS-CoV-2 RAgTs with rRT-PCR positivity was evaluated with the kappa coefficient, the concordance of only one RAgT was found to be statistically significant (Kappa= 0.88). SARS-CoV-2 RAgTs have a potential use as a diagnostic tool in symptomatic people, as a routine screening tool in community living environments, and in situations such as ending the isolation of the patients. Each country should carry out validation studies before the use of these tests, taking into account of their socio-economic situation, healthcare infrastructure and current epidemiological data of COVID-19.

Inactive SARS-CoV-2 vaccine generates high antibody responses in healthcare workers with and without prior infection

Background and Objectives

Healthcare workers (HCWs) were among the first groups to be vaccinated in Turkey. The data to be obtained by the vaccination of HCWs would guide wide spread vaccination programs.

Materials and Methods

The study included 330 HCWs working at Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty Hospital and vaccinated with inactive CoronaVac (Sinovac Life Sciences, China) SARS-CoV-2 vaccine in two doses (28 days apart). Anti-Spike /RBD IgG levels were measured 14 days after the first dose and 28 days after the second dose. Chemiluminescent microparticle immunoassay (CMIA) (ARCHITECT IgG II Quant test, Abbott, USA), which is 100% compatible with plaque reduction neutralization test (PRNT), was used.

Results

Of the participants, 211 (63.9%) were female, 119 (36.1%) were male, and mean age was 39.6 ± 7.7 years. In those without prior COVID-19 history; (n = 255) antibody positivity was detected as 48.2% (95% CI: 42.1–54.3) 14 days after the first dose of vaccine, and 99.2% (95% CI: 98.1–100) at day 28 after the second dose. Antibody titers were significantly lower in patients with hypertension (p = 0.011). In those with prior history of COVID-19 (n = 75); both the antibody positivity rates after the first vaccine (48.2% vs 100%, p = 0.000) and the anti-spike/RBD antibody levels after the second vaccine (with a ≥ 1050 AU/mL titer equivalent to PRNT 1/80 dilution) was significant than infection-naive group (25.9% vs. 54.7%, p = 0.000). Antibody positivity after two doses of vaccination for all study group was 99.4% (95% CI: 98.6–100).

Conclusions

Two doses CoronaVac produce effective humoral immunity in HCWs. Antibody response is significantly higher in those with prior history of COVID-19 than infection-naive group. Given no significant benefit of the second dose, a single shot of vaccination may be sufficient for those with prior history of COVID-19. Monitoring humoral and cellular immune responses, considering new variants, is required to validate this approach.

Effects of hypertonic alkaline nasal irrigation on COVID-19

Objective

The causative agent of COVID-19 is a novel member of coronaviridaes, SARS-CoV-2. It has been reported that the spike (S) protein of SARS-CoV-2 is responsible of infectivity. The S protein is demonstrated to be inactivated under environmental condition, such as hypertonicity and alkaline pH. The aim of the study was to investigate the effect of hypertonic alkaline nasal irrigation (HANI) on SARS-CoV-2.

Methods

Sixty patients divided into two groups. The patients in Group 1 used hydroxychloroquine (HCQ), and the patients in Group 2 used HCQ and HANI. Nasopharyngeal samples were collected at the beginning, on 3rd and 7th day of the PCR test positivity. The nasopharyngeal viral load (NVL) changes analyzed with quantitative PCR.

Results

NVL decrease in weekly period was statistically significant for both groups, when the difference between NVL day 0 and 3rd in Group 1 and NVL difference between day 0 and 3rd in Group 2 were compared. The difference between Groups 1 and 2 in terms of NVL change was statistically significant (P < 0.05).

Conclusion

We demonstrated a significant decrease in nasopharyngeal SARS-CoV-2 load with HANI solution and suggest that HANI may be promising modality for the COVID-19 treatment.

Level of evidence

IB.

Salmonella Spp. and Shigella Spp. detection via multiplex real-time PCR and discrimination via MALDI-TOF MS in different animal raw milk samples

Aims

The aim of this study was to provide epidemiological data about the presence of Salmonella spp. and Shigella spp. in raw milk samples collected from different animals.

Methods

A total of 231 raw milk samples from 48 cows, 65 goats, 65 sheep, and 53 donkeys were studied. The ISO 6579:2002 and ISO 21567:2004 methods, antimicrobial susceptibility tests, and serotyping were performed. Species and subspecies discriminations were made via matrix-assisted laser desorption/ionization-time of flight mass spectrometry. After DNA isolation from all samples, Salmonella spp. and Shigella spp. were detected using real-time polymerase chain reaction (PCR) kits.

Results

Five samples (2.16%) showed positivity out of 231 raw milk samples for Salmonella spp., and 2 (0.87%) samples were detected to be positive by multiplex real-time PCR design.

Conclusion

We found that raw milk samples were not free of Salmonella spp. and Shigella spp. and need to be tested routinely to avoid public health problems. Rapid and reliable real-time PCR method can be developed and used for this purposes instead of slow bacterial culture processes.

Hepatitis A virus vaccination in childhood-onset systemic lupus erythematosus

Objectives: Vaccination of systemic lupus erythematosus patients with non-live vaccines may decrease vaccine-preventable infections and mortalities. In the present study, we aimed to compare the immunogenicity and safety of inactivated hepatitis A vaccination in childhood-onset systemic lupus erythematosus and healthy subjects. Methods: A total of 30 childhood-onset systemic lupus erythematosus and 39 healthy participants who were seronegative for hepatitis A received two doses of the hepatitis A vaccine in a 0- and 6-month schedule. Hepatitis A virus (HAV) IgG antibodies were measured before vaccination and 7 months after the vaccination. Results: Although anti-HAV IgG antibody titers after vaccination were found to be somewhat lower in children with systemic lupus erythematosus than that of the healthy subjects ( p < 0.05), the difference in seroconversion rate was insignificant between childhood-onset systemic lupus erythematosus patients ( n = 24/30, 80%) and healthy controls ( n = 33/39, 84.6%). There was no increase in median Systemic Lupus Erythematosus Disease Activity Index (SLEDAI)-2K scores and anti-ds DNA levels after the vaccination procedure. Seroconversion rates in childhood-onset systemic lupus erythematosus patients were not affected by medication, high disease activity (SLEDAI-2K >6) and anti-ds DNA positivity. None of the patients experienced any flare or adverse reaction throughout the study. Conclusions: According to these results, we conclude that inactivated hepatitis A vaccine is safe and well tolerated in childhood-onset systemic lupus erythematosus patients, with no adverse events or increase in activity. Immunogenicity to the hepatitis A vaccine was adequate, with a seropositivity rate of 80%.

Patterns of EPIYA motifs among cagA-positive Helicobacter pylori strains: a case-control study in a Turkish population with Eurasian geographical features

Geographical variation in the frequency of various gastroduodenal pathologies was shown to be related to the geographical diversity of H. pylori CagA Glu-Pro-Ile-Tyr-Ala (EPIYA) patterns. We examined the EPIYA patterns of H. pylori and the association of EPIYA patterns with gastric cancer (GC) for the first time, to the best of our knowledge, in Turkey. The patient group (PG) contained 60 patients [38 GC and 22 duodenal ulcer (DU) patients]. The control group (CG) was 110 individuals [94 gastritis patients and 16 persons with a normal gastrointestinal system (NGIS)]. Specific primers were used for the detection of cagA including empty-site-positive and EPIYA-A, -B, -C, -D PCR. Bands of EPIYA-A, -B, -C were confirmed by DNA sequencing. One hundred and forty-two (83.5 %) strains [60 in the PG (38 GC, 22 DU), 82 in the CG (72 gastritis, 10 NGIS)] were positive for the cagA gene. EPIYA-C with multiple repeats was detected in 34 (23.9 %) strains, and 22 (64.7 %) were from GC patients. EPIYA-C with one repeat was detected in 89 (62.7 %) strains, and 54 (60.7 %) were from gastritis patients. EPIYT was detected in 10 strains, and EPIYA-D was not detected. The number of EPIYA-C with multiple repeats was significantly higher for the PG than for the CG (P < 0.0001). In GC patients, the number of EPIYA-C with multiple repeats was significantly higher than one repeat (P < 0.0001). In conclusion, our study showed that multiple EPIYA-C repeats increases the GC risk by 30.6-fold and the DU risk by 8.9-fold versus the CG. This indicates that Western-type H. pylori strains in Turkey have similar EPIYA motifs to those of neighbouring countries and Western populations.

Investigation of the relationship between the duration of postoperative mechanical ventilation and complication incidence following coronary artery bypass graft

BACKGROUND

The relationship between prolonged intubation period and postoperative complication incidence following cardiac surgery was investigated.

MATERIAL/METHOD

Evaluated were 237 adult patients who underwent coronary artery bypass graft operation, of whom 115 (group I) had intubation periods of more than 24 hrs (mean: 56.1+/-39.1 hrs) and 122 (group II) less than 24 hrs (mean: 16.25+/-14.6 hrs). Preoperative and postoperative pulmonary function test values as well as postoperative changes in the two groups were compared.

RESULTS

Mean hospital stay for group I and II patients were determined as 24.6+/-2.04 and 10.61+/-3.04 days, respectively (p<0.0001). The preoperative pulmonary function test results compared with the predicted values for both groups were similar. A significant decrease was determined in the postoperative pulmonary function test values in both groups, but the decrease in group I was significantly higher than in group II. Pulmonary complications developing in groups I and II were 26.09% (30 patients) and 7.38% (9 patients), respectively (p<0.0001). Also, total general complications were 39.14% (45 patients) and 13.12% (16 patients), respectively.

CONCLUSION

Under similar conditions, the patients whose partial bypass time and aortic clamp period were significantly longer needed to be ventilated for more than 24 hours, being related to late complications following bypass operation, and the complication risk of this group was 3.5 times higher than for those who remained intubated less than 24 hours.

Comparison of the BBL-mycobacteria growth indicator tube method with culture in the diagnosis of tuberculosis and evaluation of the resistance patterns of isolated strains to four major drugs

The BBL-mycobacteria growth indicator tube system (MGIT) is used for a rapid detection of the presence of mycobacteria. Our study aimed to compare MGIT with the Löwenstein-Jensen (LJ) reference method in clinical samples with suspected pulmonary and extrapulmonary tuberculosis, and to evaluate the primary and secondary resistance patterns by determining the resistances of the isolated strains to four major antimycobacterial drugs. 648 clinical samples from different clinics, with suspected pulmonary or extrapulmonary tuberculosis based on clinical, radiological, histopathological and immunological findings, were included in the investigation. The samples were first stained with Ziehl-Neelsen (ZN) and then cultured in LJ medium according to the standard bacteriological procedure and in the MGIT as recommended by the manufacturer. Conventional biochemical tests and p-nitro-alpha-acethylamino-beta-hydroxypropiophene of the Bactec system were used to identify the isolated mycobacterial strains. The susceptibilities to streptomycin, isoniazid, rifampicin, ethambutol were tested by the BBL-MGIT antibiotic susceptibility test and the resistances of the strains found to be resistant to any of the drugs were confirmed by the agar proportion method. Mycobacterium spp. were isolated in 61 (9.4%) out of 648 samples. Eventually, 58 out of 61 strains were classified as Mycobacterium tuberculosis and the other 3 as Mycobacterium tuberculosis complex. 32 of these were ZN positive. The growth time was determined as 12.2 days by the MGIT method and 24.1 days by the LJ method (p < 0.001). 29 strains were ZN negative. Their growth time was 23 days by the MGIT method and 37 days by the LJ method (p < 0.001). Drug resistance was detected in 23 (37.7%) of 61 cases (of whom 39 were new and 22 were former patients); of these resistances, 8 (20.51%) were primary and 15 (68.18%) were secondary. In double drug resistance, secondary resistance was found only to isoniazid + rifampin (4 cases) whereas both primary and secondary resistances were found to one drug. The highest cumulative drug resistance - both primary and secondary - was found to isoniazid. In conclusion, the MGIT was found to be advantageous because it enables rapid bacterial identification of tuberculosis and detection of antimicrobial resistance due to its high sensitivity and specificity. It is quicker than the LJ method. Its antibiotic susceptibility can be tested and it is easy to perform. We recommend to include it in routine laboratory work. In addition, our study suggests that the high ratio of secondary resistance in the public might be related to inappropriate and insufficient treatment of tuberculosis, and noncompliance, which appear to cause an important increase in primary tuberculosis as a result of new contaminations.

Antimicrobial resistance surveillance of gram-negative bacteria isolated from intensive care units of four different hospitals in Turkey. Evaluation of the prevalence of extended-spectrum and inducible beta-lactamases using different E-test strips and direct induction methods

BACKGROUND

The aim of this study was to determine the antimicrobial resistance of gram-negative rods (GNRs) isolated from surgical intensive care units and to establish the prevalence of extended-spectrum beta-lactamases (ESBLs) and inducible beta-lactamases (IBLs). We also wished to determine the widespread beta-lactam substrate in ESBL-positive GNRs by two different E-test strips and to discuss the value of the routine utilization of these substrates together.

METHODS

Out of 348 nosocomial gram-negative strains isolated with similar methods, 236 strains with resistance to the beta-lactam group of antimicrobials using the E-test method were included in this study. Two different strips were used for the detection of ESBLs: cefotaxime/cefotaxime + clavulanic acid (CT/CTL) and ceftazidime/ceftazidime + clavulanic acid (TZ/TZL). For IBLs, the double-disk method was used.

RESULTS

The order of frequency of the strains, starting with the most frequent, was Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. In the 236 strains, the ESBL positivity rate was found to be 19.5% with TZ/TZL and CT/CTL strips, while it was 13.2% for IBL in 348 strains. Seventy-one percent of ESBL-positive strains gave parallel results with TZ/TZL and CT/CTL. ESBL positivity with only TZ/TZL or only CT/CTL was found to be 18 and 8%.

CONCLUSIONS

Our study showed that except for imipenem, amikacin and ciprofloxacin, there was a high resistance to other antimicrobials, and multiresistance rates were increased in the strains in which ESBLs and IBLs were detected. In particular, the increasing prevalence of ESBLs in K. pneumoniae and IBLs in P. aeruginosa emphasizes the importance of the problem of infection control and antibiotic administration policies. Although it was seen that the prevalence of substrate templates in the detection of ESBL positivity was similar, we think that it is more useful to use two different strips together to obtain precise results.