The effect of pre-pregnancy obesity on gut and meconium microbiome and relationship with fetal growth.

OBJECTIVE: To investigate the effect of pre-pregnancy obesity on maternal and newborn microbiomes and fetal growth. METHODS: Individuals who gained body weight in accordance with the recommendations during pregnancy and normal gestastional age are included in the study and were separated into two groups, normal (n = 20) and obese (n = 20), based on their body mass index (BMI) value of pre-pregnancy. Maternal stool samples collected during the first trimester of pregnancy and meconium samples collected at birth were evaluated using 16S rRNA gene-based microbiome analysis. RESULTS: The stool samples of mothers who were obese before pregnancy harbored a higher (59.9 versus 52.3%) relative abundance of Firmicutes and a lower (7.1 versus 4.1%) relative abundance of Proteobacteria than the stool samples of mothers with normal body weight pre-pregnancy. In contrast, in the meconium samples of mothers who were obese pre-pregnancy, compared to those of mothers who had a normal body weight pre-pregnancy, the phylum Firmicutes was less (56.0 versus 69.0%) abundant and Proteobacteria (9.0 versus 8.5%) was more abundant. There was a negative correlation between pre-pregnancy BMI, birth weight, weight/height ratio and alpha diversity indices (Shannon and Chao1). CONCLUSIONS: Pre-pregnancy obesity can affect pregnant and newborn gut microbiota, which might related to fetal growth of the newborn.

The effect of gestational weight gain on serum total oxidative stress, total antioxidant capacity and gut microbiota.

This study aimed to investigate the effect of gestational weight gain on total oxidative stress (TOS), total antioxidant capacity (TAC), oxidative stress index (OSI), dietary antioxidant intake, and the gut microbiome. The study was carried out on 40 pregnant women divided as follows: a) normal prepregnancy weight and gestational weight gain of 11.5-16.0 kg (n=10) b) normal prepregnancy weight and gestational weight gain of >16.0 kg (n=10) c) obese before pregnancy and gestational weight gain of 5-9 kg (n=10) and d) obese before pregnancy and gestational weight gain of >9.0 kg (n=10). Serum TOS and TAC levels, dietary antioxidant intake, and microbiome diversity of the gut microbiome were evaluated during the third trimester of pregnancy. A positive correlation was found between body mass index (BMI) in the third trimester and serum TOS levels and OSI. In women with normal prepregnancy weight, an increase in the Firmicutes and Bacteroidetes phyla was observed when gestational weight gain was above the recommended values (p<0.05). In women who were obese before pregnancy, an increase only in the Bacteroidetes phylum was observed when gestational weight gain was above the recommended values (p<0.05). A positive correlation was found between Firmicutes/Bacteroidetes and OSI, and a negative correlation was found between Firmicutes/Bacteroidetes and dietary antioxidant intake (p<0.05). Prepregnancy body weight, high serum TOS level, and dietary antioxidant intake are determinant factors for microbial diversity, with increased serum TOS levels caused by increased gestational weight gain.

Respiratory viruses in the healthy middle ear and middle ear with otitis media with effusion.

To investigate the presence of respiratory viruses in the middle ear cavity of the individuals with a healthy middle ear and the children with otitis media with effusion (OME). A total of 72 middle ear samples were collected from 25 children with OME (Group 1) and 47 individuals with no middle ear disease (Group 2). Multiplex real-time polymerase chain reaction was used to investigate the presence of 20 different respiratory viruses. Virus results were compared with bacteriomes of the same populations. At least one respiratory virus was detected in 56% of the patients in Group 1 and 12.8% of the individuals in Group 2. The viral co-infection rate for Group 1 and 2 was 8% and 2.1%, respectively. In Group 1, adenovirus was the most frequently detected virus with a rate of 24%, either alone (16%) or concurrent with other viruses (8%), followed by influenza B (12%), rhinovirus, and bocavirus (8%) each. Parainfluenza 4, coronavirus OC43, and RSV A/B were detected in 4% of the sample each. In Group 2, rhinovirus was detected in two samples (4.3%) followed by adenovirus, coronavirus OC43, coronavirus E299, and coronavirus NL63 with a rate of 2.1% each. The detection rate of respiratory viruses was significantly higher in children aged 6 to 11 years. There was no positive association between virus and bacteria found in the middle ear cavity. The current study has provided comprehensive data indicating the presence of diverse respiratory viruses in the healthy middle ear cavity. Our results also suggest that respiratory viruses might have a contribution to OME pathogenesis.

Mycobiome in the Middle Ear Cavity with and Without Otitis Media with Effusion.

Objective: No data have yet been published revealing the composition and the diversity of fungal communities (mycobiome) in the human middle ear cavity. The presented study investigated the mycobiome in the middle ear cavities of individuals with healthy middle ears and patients with otitis media with effusion. Methods: A total of 77 middle ear and four adenoid samples were collected from 47 individuals (35 children and 12 adults) in Group 1 and from 20 children in Group 2. The mycobiome profile was analyzed with nuclear ribosomal internal transcribed spacer 2 (ITS2) based metabarcoding using an Illumina MiSeq metagenomics kit. Results: ITS2-based metabarcoding detected 14 different genera and 17 different species with a mean relative abundance of ≥1% in the samples analyzed. Mycobiome profile was similar between the adenoid tissue and the middle ear cavity, between Groups 1 and Group 2, and between children and adults. Fusarium, Stemphylium, Candida, and Cladosporium were the most abundant genera detected in all samples. The mean relative abundances of the genera Candida and Fusarium were remarkably higher in Group 2 compared to Group 1. Conclusion: The species Candida glaebosa, Candida cretensis, Aspergillus ruber, Penicillium desertorum, and Rhizopus arrhizus were significantly more abundant in patients with otitis media with effusion (OME), raising the possibility that they affect the pathogenesis of OME.

Mutations Observed in the SARS-CoV-2 Spike Glycoprotein and Their Effects in the Interaction of Virus with ACE-2 Receptor.

Coronaviruses (CoVs) classified in the Coronaviridae family infect a very large spectrum of vertebrate group. Seven CoVs that cause human disease consist of Alpha-CoVs, which are HCoV-229E, and NL63 and beta-CoVs, which are MERS-CoV, SARS-CoV, HCoV-OC43, HCoV-HKU1, and SARS-CoV-2. SARS-CoV-2 is an enveloped, positive-polarity, single-stranded RNA virus responsible for a new Coronavirus disease 2019 (COVID-19). The mutagenic ability of the SARS-CoV-2 directs its evolution and genome variability, thus allowing viruses to escape from host immunity and develop drug resistance. Tracing viral mutations is also important for the development of new vaccines, antiviral drugs, and diagnostic systems. During replication in the host cell, genomic mutations occur in the virus and these mutations are transferred to new generations. For this reason, systematic monitoring of mutations in the SARS-CoV-2 genome allows observation of the national and international molecular epidemiology of the virus. SARS-CoV-2 spike (S) glycoprotein is vital in the binding of the virus to the host cell receptor that is angiotensin converting-enzyme 2 (ACE2), membrane fusion, vaccine studies and immune response to the virus. Therefore, mutations in the gene encoding the S glycoprotein and especially the possible variations in the receptor binding domain (RBD) in S gene are important issues to be emphasized. In this article, information about the mutations observed in the SARS-CoV-2 S glycoprotein and their possible effects are presented.

Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology.

PURPOSE: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes. METHODOLOGY: Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument. RESULTS: Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves. CONCLUSION: The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.

Porphyromonas somerae sp. nov., a pathogen isolated from humans and distinct from porphyromonas levii.

Porphyromonas levii is an anaerobic, pigmented gram-negative bacillus originally isolated from bovine rumen. We describe 58 human clinical strains of P. levii-like organisms, isolated from various human clinical specimens that are phenotypically similar to the type strain of P. levii, a rumen isolate (ATCC 29147). Our biochemical, comparative 16S rRNA sequence analyses, and DNAlpha-DNA relatedness studies indicate that the human P. levii-like organisms are similar to each other but genetically different from the P. levii type strain isolated from bovine rumen. We therefore propose the name Porphyromonas somerae to encompass the human P. levii-like organisms. P. somerae was predominantly isolated from patients with chronic skin and soft tissue or bone infections, especially in the lower extremities.

Nasopharyngeal carriage, antimicrobial susceptibility, serotype distribution and clonal relatedness of Streptococcus pneumoniae isolates in healthy children in Malatya, Turkey.

The aims of this study were to assess the nasopharyngeal colonisation rate, serogroup and antibiotic susceptibility patterns of Streptococcus pneumoniae strains isolated from healthy children. Of 848 children, 162 (19.1%) were found to be carriers. The carrier rate was significantly higher in the 7-year-old age group. Children from the slums of the city had higher carriage rate (23.7%) than those in the centre of the city (17.7%), but this was not statistically significant. The number of intermediate penicillin-resistant strains was 17 (10.5%). No high-level penicillin-resistant S. pneumoniae strain was found. The rates of resistance to co-trimoxazole, erythromycin, tetracycline and clindamycin were 11.7%, 4.9%, 4.3% and 3.7%, respectively. All isolates were uniformly susceptible to rifampicin, moxifloxacin, levofloxacin and vancomycin. Fourteen different serogroups were identified. The most prevalent serogroups in descending order were 9, 19, 23, 10, 6 and 18, accounting for 76.3% of the isolates. Arbitrarily primed polymerase chain reaction typing of 105 isolates revealed that 25 (23.8%) of the isolates were clonally indistinguishable. This value was 20.9% in children from the central area and 36.8% in those from the slum of the city. There was no relationship between serogroups and genotypes, i.e. strains within the same serogroup yielded the same or different genotypes, and vice versa. In conclusion, serogrouping results give a preliminary idea about the possible coverage of a future pneumococcal vaccine. Penicillin G is still a suitable agent for the empirical treatment of pneumococcal infections in our population. Living in the slum of the city may lead to both increased carriage and clustering rates of S. pneumoniae among healthy children.

The prevalence of fecal colonization of enterococci, the resistance of the isolates to ampicillin, vancomycin, and high-level aminoglycosides, and the clonal relationship among isolates.

The gastrointestinal tract carriage of enterococci was searched in 150 hospitalized patients and 100 outpatients, and clonal relatedness of the isolates and their resistance to ampicillin, vancomycin, and high-level streptomycin and gentamicin were investigated. A stool sample or rectal swab collected from each patient was inoculated into appropriate media within an hour. Enterococcus species were identified by using conventional biochemical tests, API-20 Strep assay, and BBL crystal kit. Antibiotic susceptibility tests were performed using Kirby-Bauer disk diffusion method. A polymerase chain reaction (PCR) was used to detect vanA and vanB genes. Pulsed-field gel electrophoresis (PFGE) and arbitrarily primed-polymerase chain reaction (AP-PCR) methods were used for molecular typing of the strains. Enterococci were isolated from 90 (60%) of the specimens collected from 150 inpatients. Of these 90 isolates, 37 (41%) had high-level gentamicin resistance, 36 (40%) had high-level streptomycin resistance, and 50 (55.6%) had ampicillin resistance. Fecal colonization was found in 30% of the outpatients. Resistances to ampicillin, high-level streptomycin, and gentamicin were 13%, 10%, and 3%, in these patients' isolates, respectively. No vancomycin-resistant enterococci were detected by both agar diffusion and PCR assays in our study. Both typing procedures were applied on 78 Enterococcus strains isolated from inpatients. AP-PCR typing showed that 30 (50.8%) of the 59 E. faecium and 5 (50%) of the 10 E. faecalis strains were clonally related. These values were found to be 12 (20.3%) and two (20%) by PFGE, respectively. The typing procedures did not find any clustered strains in the six E. durans and three E. avium isolates. Neither PFGE nor AP-PCR result was significantly different among the sensitive and resistant strains. Our results indicate that the high prevalence of colonization with ampicillin and highlevel aminoglycoside-resistant enterococci is an important problem in our medical center. The high clonal diversity among the isolates indicates limited spread of antibiotic-resistant strains between patients.

Prevalence of enterotoxigenic Bacteroides fragilis in patients with diarrhea: a controlled study.

In this age matched controlled study performed in Malatya, a city in east region of Turkey, enterotoxigenic Bacteroides fragilis (ETBF) was investigated in stool specimens obtained from children and adults with and without diarrhea. A nested polymerase chain reaction (PCR) method was used to detect the enterotoxin gene of B. fragilis in a total of 418 stool samples, including 221 samples from 117 children (aged 0-16 years) and 104 adults (aged >16 years) with diarrhea, and 197 samples from 102 children and 95 adults as control group that was the same age group with those having diarrhea. ETBF was detected in 13 of 117 diarrheal children (11.1%) and 8 of 102 control children (7.8%) (P>0.05). In children aged 1-5 years, the rate of ETBF was significantly higher in patients than in controls (25% versus 9.5%, respectively; P<0.05). On the other hand ETBF was detected similar rates (2.2% and 2.4%, respectively) in children younger than 1 year in both patients and controls. ETBF positivity was not significantly difference between patient and control groups who were older than 5 years of age and adults. The frequency of ETBF in the controls was slightly higher in older persons than in younger ones; however, it was not significant. The rate of ETBF as the only enteropathogen in the patients with ETBF was significantly higher than in controls with ETBF (88% versus 39%, respectively; P<0.02). We found that in east region of Turkey, the prevalence of ETBF was higher in the childhood diarrhea, particularly in aged 1-5. As the only enteropathogen, ETBF may play an important role in diarrheal diseases. Persons after 6 years old can be carrier for ETBF regardless diarrhea.

Spread of a single clone Acinetobacter baumannii strain in an intensive care unit of a teaching hospital in Turkey.

Acinetobacter baumannii is an important nosocomial pathogen, especially in immunocomprimised patients and those hospitalized in intensive care units. After the first isolation of A. baumannii strains from the bronchial aspirates of two patients in the intensive care unit (ICU) of our hospital as a pure culture, screening studies were performed to define possible source(s). A. baumannii strains isolated from bronchial aspirates and blood cultures of the patients in ICU were collected as a possible part of the outbreak. A total of 23 screening samples collected from equipment (7), hands (4) and gloves (2) of the staff, and from ten different body regions of the patients in the ICU were cultured. Antimicrobial susceptibility test of the isolates was performed by the standardized disk-diffusion method. All isolates were subtyped by antibiogram, arbitrarily primed polymerase chain reaction (AP-PCR) and pulsed-field gel electrophoresis (PFGE) typing methods. A total of 26 A. baumannii strains including eight clinical and 18 screening isolates were identified. All isolates were susceptible only to meropenem, tobramycin, and imipenem. There was at least a 96% resistance rate to the other antibiotics tested. Antibiogram typing showed that 24 of the 26 isolates were epidemiologically related, two were unique. AP-PCR yielded two types, one of which had 21 isolates, the other had five. PFGE fingerprinting revealed that all isolates were clonally related, including four closely related and 22 indistinguishable strains. Based on the results of PFGE which has been accepted as a reference method it can be concluded that A. baumannii strains isolated from our intensive care unit originated from a single type of strain.

Prevalence of group A streptococcal carriers in asymptomatic children and clonal relatedness among isolates in Malatya, Turkey.

In our study, the prevalence of nasopharyngeal Streptococcus pyogenes was 130 (14.3%) of 909 healthy children. Isolates were found to be susceptible to all antibiotics tested. Pulsed-field gel electrophoresis and arbitrarily primed PCR revealed that 34 (32.4%) of the 105 isolates and 41 (40.6%) of the 101 isolates typed, respectively, were clonally indistinguishable.

Bacteriology of chronic maxillary sinusitis and normal maxillary sinuses: using culture and multiplex polymerase chain reaction.

BACKGROUND: Although many investigations have been performed on bacteriology of chronic sinusitis and normal sinuses, there still is much discussion. Also a new bacterial agent, Alloiococcus otitidis determined in the nasopharynx and middle ear specimens can be thought as a causative agent of sinusitis. METHODS: The bacteriology of chronic maxillary sinusitis and maxillary sinuses with normal radiogram and endoscopic findings were studied by culture methods for aerobic and anaerobic bacteria. Multiplex polymerase chain reaction (PCR) was used to investigate four bacteria in study and control groups. There were 27 specimens in the study group and 28 specimens in the control group. RESULTS: In the study group, the bacteria commonly isolated were Staphylococcus aureus (11.1%), alpha-hemolytic streptococci (11.1%), Streptococcus pneumoniae (11.1%), Haemophilus influenzae (7.4%), coagulase-negative staphylococci (7.4%), and anaerobes (33.3%). Coagulase-negative staphylococci (14.3%), alpha-hemolytic streptococci (10.7%), and anaerobes (35.7%) were isolated also in the control group. PCR was used to investigate S. pneumoniae, H. influenzae, Moraxella catarrhalis, and A. otitidis in the study and control groups. None of these bacteria was determined in the control group whereas detection rates of these bacteria in the study group were 11.1, 11.1, 3.7, and 7.4%, respectively. It should be considered that PCR yielded faint amplification band for A. otitidis. CONCLUSION: Using multiplex PCR can help to increase detection rates of bacterial etiology. Healthy sinuses are not sterile. A. otitidis may be one of the pathogens causing sinusitis.

Effects of laparoscopic models on anaerobic bacterial growth with bacteroides fragilis in experimentally induced peritonitis.

BACKGROUND: Previous reports of recurrent intra-abdominal abcess formation after the laparoscopic treatment of perforated acute appendicitis led us to investigate the possible effects of gas insufflation on the spread of infection. We previously showed that Escherichia coli counts were significantly higher in a laparoscopy group that underwent carbon dioxide (CO2) insufflation than in control and laparotomy groups. The aim of this study is to investigate the effects of intra-abdominal CO2 and nitrous oxide (N2O) insufflation on anaerobic bacterial growth in a rat model. METHODS: A standard strain of Bacteroides fragilis (ATCC 25285) was injected intraperitoneally (1 x 10(6) cfu/mL per kilogram) in 40 Wistar rats under sterile conditions. Forty rats with induced peritonitis were randomly divided into five groups: control, laparotomy, CO2 insufflation, N2O insufflation, and one group without pneumoperitoneum. Eight hours after the intraperitoneal injection of B. fragilis, peritoneal aspirates were obtained and inoculated onto Brucella agar. At the sixteenth hour of induced peritoneal infection (corresponding to hour 8 in the laparoscopy groups) all animals underwent laparotomy; peritoneal aspirates were obtained and inoculated into Brucella agar for bacterial counts. The colonies of B. fragilis were counted manually, and the results were expressed as the mean number of colony-forming units per milliliter. RESULTS: No significant differences in microorganism counts were noted between the study groups before the procedure (p>.05 for all comparisons). We observed a significant increase in the number of bacteria (mean +/- SD) in the CO2 insufflation group between hour 8 and hour 16 of peritoneal contamination. CONCLUSION: The results suggest that CO2 insufflation may promote the growth of intra-abdominal anaerobic bacteria. Such bacterial growth may lead to intra-abdominal abcess formation or cause localized peritonitis to develop into generalized peritonitis. We suggest that laparoscopy without pneumoperitoneum may be preferred in patients with peritonitis.

Primary drug resistance and molecular epidemiology of Mycobacterium tuberculosis isolates from patients in a population with high tuberculosis incidence in Turkey.

To determine the rate of primary drug resistance and compare the fingerprint pattern diversity of the resistant and sensitive Mycobacterium tuberculosis isolates, antituberculosis susceptibility testing and restriction fragment length polymorphism (RFLP) analysis were performed on 88 M. tuberculosis isolates of the patients who were diagnosed as new tuberculosis cases in 2000. Primary resistance to isoniazid, rifampicin, ethambutol, and streptomycin were determined by the BACTEC method. IS6110 and pTBN12 were used as molecular markers. The frequency of resistance to at least one drug was 32.95%, whereas 10.23% of the isolates were resistant to more than one drug. Single-drug resistance to isoniazid, streptomycin, ethambutol, and rifampicin was found in 9 (10.22%), 7 (7.95%), 4 (4.54%), and 0 (0.0%) strains, respectively. Two M. tuberculosis strains (2.26%) showed multiple drug resistance. The combination of two fingerprinting procedures on a total of 88 isolates identified 58 (65.9%) strains as unique and clustered 30 strains in 11 clusters (clustering = 34.1%). The clustering rate for resistant and sensitive isolates was 13.8% and 40.1%, respectively. In conclusion; drug susceptibility testing showed that the majority of the drug-resistant infections involved either isoniazid or streptomycin alone. In addition to the high tuberculosis incidence, elevated primary drug resistance and high clustering rate indicate problems in the present control programs. New control strategies supported by molecular typing might be more effective to reduce tuberculosis.

[Use of transcription-based amplification and enzyme immunoassay methods to investigate possible Chlamydia trachomatis infections in women with genital complaints]. / Genital yakinmasi olan kadinlarda Chlamydia trachomatis enfeksiyonunun, transkripsiyon esasli amplifikasyon ve enzim immünoassay yöntemleri ile arastirilmasi.

This study was performed to determine the prevalence of Chlamydia trachomatis infections in the female patients with genital complaints, and to compare the transcription mediated amplification assay and enzyme immunoassay methods for the diagnosis of genital C. trachomatis infections. C. trachomatis (Ct) antigens and ribosomal RNAs were researched by enzyme immunoassay (EIA) and transcription-mediated amplification (TMA) assay, respectively in the endocervical swab samples of 90 patients. C. trachomatis IgG and IgM antibodies were also screened in the sera of these subjects, by EIA method. Of 90 patients, 18 (20%) were found to be positive for Ct-rRNA, 12 (13%) for Ct-antigen, 20 (22%) for IgG, 12 (13%) for IgM and 14 (16%) for both IgG and IgM. Among the patients 11 (12%) were found positive for Ct-antigen, Ct-rRNA and Ct-IgM antibodies. According to the TMA results, the sensitivity and specificity of EIA-Ct antigen method were estimated as 67% and 100%, respectively. There was statistically significant difference between TMA positivity and those of two EIA methods. In conclusion, the positive results obtained with EIA are reliable for the diagnosis of genital C. trachomatis infections, however the negative results should be confirmed by TMA.

[Enterotoxigenic Bacteroides fragilis as a factor in diarrhea]. / Ishal etkeni olarak enterotoksijenik Bacteroides fragilis.

The etiology of almost half of the diarrheal diseases has not been cleared yet, in spite of modern diagnostic methods. Bacteroides fragilis strains which secrete an enterotoxin are termed as enterotoxigenic B.fragilis (ETBF). These strains are associated with diarrheal diseases in children above 1 year of age and in adults. B. fragilis toxin (BFT) stimulates intestinal secretion and in-vitro cytotoxic response in HT29/C1 cells. Recent studies suggest that BFT is related to inflammatory bowel disease and colon cancer by triggering nuclear activation with potential oncogene expression. In this review, the molecular pathogenesis, epidemiology and laboratory diagnosis of ETBF have been reviewed to focus on ETBF as a diarrheal agent.