Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha).

Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.

Behavioral transcriptomic effects of triploidy and probiotic therapy (Bifidobacterium, Lactobacillus, and Lactococcus mixture) on juvenile Chinook salmon (Oncorhynchus tshawytscha).

Aquaculturists use polyploid fish to maximize production albeit with some unintended consequences including compromised behaviors and physiological function. Given benefits of probiotic therapies (e.g., improved immune response, growth, and metabolism), we explored probiotic supplementation (mixture of Bifidobacterium, Lactobacillus, and Lactococcus), to overcome drawbacks. We first examined fish gut bacterial community composition using 16S metabarcoding (via principal coordinate analyses and PERMANOVA) and determined probiotics significantly impacted gut bacteria composition (p = 0.001). Secondly, we examined how a genomic disruptor (triploidy) and diet supplements (probiotics) impact gene transcription and behavioral profiles of hatchery-reared Chinook salmon (Oncorhynchus tshawytscha). Juveniles from four treatment groups (diploid-regular feed, diploid-probiotic feed, triploid-regular feed, and triploid-probiotic feed; n = 360) underwent behavioral assays to test activity, exploration, neophobia, predator evasion, aggression/sociality, behavioral sensitivity, and flexibility. In these fish, transcriptional profiles for genes associated with neural functions (neurogenesis/synaptic plasticity) and biomarkers for stress response and development (growth/appetite) were (i) examined across treatments and (ii) used to describe behavioral phenotypes via principal component analyses and general linear mixed models. Triploids exhibited a more active behavioral profile (p = 0.002), and those on a regular diet had greater Neuropeptide Y transcription (p = 0.02). A growth gene (early growth response protein 1, p = 0.02) and long-term neural development genes (neurogenic differentiation factor, p = 0.003 and synaptysomal-associated protein 25-a, p = 0.005) impacted activity and reactionary profiles, respectively. Overall, our probiotic treatment did not compensate for triploidy. Our research highlights novel applications of behavioral transcriptomics for identifying candidate genes and dynamic, mechanistic associations with complex behavioral repertoires.

Fecal microbiota transplantation: current challenges and future landscapes.

SUMMARYGiven the importance of gut microbial homeostasis in maintaining health, there has been considerable interest in developing innovative therapeutic strategies for restoring gut microbiota. One such approach, fecal microbiota transplantation (FMT), is the main "whole gut microbiome replacement" strategy and has been integrated into clinical practice guidelines for treating recurrent Clostridioides difficile infection (rCDI). Furthermore, the potential application of FMT in other indications such as inflammatory bowel disease (IBD), metabolic syndrome, and solid tumor malignancies is an area of intense interest and active research. However, the complex and variable nature of FMT makes it challenging to address its precise functionality and to assess clinical efficacy and safety in different disease contexts. In this review, we outline clinical applications, efficacy, durability, and safety of FMT and provide a comprehensive assessment of its procedural and administration aspects. The clinical applications of FMT in children and cancer immunotherapy are also described. We focus on data from human studies in IBD in contrast with rCDI to delineate the putative mechanisms of this treatment in IBD as a model, including colonization resistance and functional restoration through bacterial engraftment, modulating effects of virome/phageome, gut metabolome and host interactions, and immunoregulatory actions of FMT. Furthermore, we comprehensively review omics technologies, metagenomic approaches, and bioinformatics pipelines to characterize complex microbial communities and discuss their limitations. FMT regulatory challenges, ethical considerations, and pharmacomicrobiomics are also highlighted to shed light on future development of tailored microbiome-based therapeutics.

Fecal-adherent mucus is a non-invasive source of primary human MUC2 for structural and functional characterization in health and disease.

The O-glycoprotein Mucin-2 (MUC2) forms the protective colon mucus layer. While animal models have demonstrated the importance of Muc2, few studies have explored human MUC2 in similar depth. Recent studies have revealed that secreted MUC2 is bound to human feces. We hypothesized human fecal MUC2 (HF-MUC2) was accessible for purification and downstream structural and functional characterization. We tested this via histologic and quantitative imaging on human fecal sections; extraction from feces for proteomic and O-glycomic characterization; and functional studies via growth and metabolic assays in vitro. Quantitative imaging of solid fecal sections showed a continuous mucus layer of varying thickness along human fecal sections with barrier functions intact. Lectin profiling showed HF-MUC2 bound several lectins but was weak to absent for Ulex europaeus 1 (α1,2 fucose-binding) and Sambucus nigra agglutinin (α2,6 sialic acid-binding), and did not have obvious b1/b2 barrier layers. HF-MUC2 separated by electrophoresis showed high molecular weight glycoprotein bands (∼1-2 MDa). Proteomics and Western analysis confirmed the enrichment of MUC2 and potential MUC2-associated proteins in HF-MUC2 extracts. MUC2 O-glycomics revealed diverse fucosylation, moderate sialylation, and little sulfation versus porcine colonic MUC2 and murine fecal Muc2. O-glycans were functional and supported the growth of Bacteroides thetaiotaomicron (B. theta) and short-chain fatty acid (SCFA) production in vitro. MUC2 could be similarly analyzed from inflammatory bowel disease stools, which displayed an altered glycomic profile and differential growth and SCFA production by B. theta versus healthy samples. These studies describe a new non-invasive platform for human MUC2 characterization in health and disease.

Impact of a 50bp insertion/deletion polymorphism of the superoxide dismutase-1 on oxidative stress status and risk of keratoconus.

Keratoconus (KC) is characterized by the predominant primary ectatic disease, affecting the cornea, necessitating corneal transplants in some cases. While some loci associated with KC risk have been identified, the understanding of the disease remains limited. Superoxide dismutase (SOD) enzymes play a crucial role in countering the reactive oxygen species and providing protection against oxidative stress (OS). Accordingly, the objective of this study was to investigate a potential association of a 50 nucleotide base pairs (bp) insertion/deletion (I/D) within the SOD1 promoter, and the located 1684 bp upstream of the SOD1 ATG, with KC in the Iranian population. Additionally, an assessment was conducted on SOD activity and the total antioxidant capacity (TAC), as determined by the ferric reducing-antioxidant power assay, along with malondialdehyde (MDA) levels. In this case-control study, genomic DNA was extracted from the blood cells of KC (n = 402) and healthy (n = 331) individuals. The genotype of this gene was determined using the PCR technique. Furthermore, the amount of SOD enzyme activity and the MDA and TAC levels were measured in the serum of the study groups. The (I/I) genotype was present in 84.23%, the (I/D) genotype in 15.06%, and the (D/D) genotype in 0.69% of both groups. A statistically significant relationship was seen between different genotypes and TAC, MDA, and SOD1 activity indices (P < 0.05). Individuals with the D/D genotype exhibited a decrease in total antioxidant capacity, an increase in the amount of MDA, and a decrease in SOD1 enzyme activity (P < 0.05). Moreover, the logistic regression analysis of KC development indicated that elevated levels of MDA increased the risk of KC incidence in the patient group compared to the healthy group, while a higher activity of SOD1 and greater values of TAC decreased the KC risk. The removal of the 50 bp fragment reduced SOD1 activity and elevated OS levels, thereby impacting the oxidant-antioxidant balance. This could potentially play a significant role in individuals afflicted by KC.

The bidirectional relationship between opioids and the gut microbiome: Implications for opioid tolerance and clinical interventions.

Opioids are widely used in treating patients with acute and chronic pain; however, this class of drugs is also commonly abused. Opioid use disorder and associated overdoses are becoming more prevalent as the opioid crisis continues. Chronic opioid use is associated with tolerance, which decreases the efficacy of opioids over time, but also puts individuals at risk of fatal overdoses. Therefore, it is essential to identify strategies to reduce opioid tolerance in those that use these agents. The gut microbiome has been found to play a critical role in opioid tolerance, with opioids causing dysbiosis of the gut, and changes in the gut microbiome impacting opioid tolerance. These changes in turn have a detrimental effect on the gut microbiome, creating a positive feedback cycle. We review the bidirectional relationship between the gut microbiome and opioid tolerance, discuss the role of modulation of the gut microbiome as a potential therapeutic option in opioid-induced gut dysbiosis, and suggest opportunities for further research and clinical interventions.

Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome.

BACKGROUND: While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation. RESULTS: We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes. CONCLUSIONS: Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.

Comparing morphologic features and complications of main clear corneal incision between junior and senior residents observed using anterior segment optical coherence tomography.

Background: Wound construction is a critical step in phacoemulsification. Using anterior segment optical coherence tomography (AS-OCT), we compared the morphological features and complications of main incisions made by junior or senior residents during phacoemulsification. Methods: This cross-sectional comparative study included eyes with senile cataracts that underwent uneventful phacoemulsification with a clear corneal incision made by seven senior and eight junior ophthalmology residents. All eyes underwent postoperative image acquisition using AS-OCT on day one and at three months, examining for morphological features and potential complications of the main incision. Results: We included 50 eyes of 50 patients with a male-to-female ratio of 22 (44%) to 28 (56%); 26 (52%) were operated on by junior residents and 24 (48%) by seniors. The mean geometric features of the main incisions and the frequency of early and late wound complications were comparable between the two groups (all P > 0.05). A significant correlation was found between the incision length and angle with the superior (r = + 0.80; P < 0.001 and r = - 0.63; P < 0.001, respectively) and inferior (r = + 0.84; P < 0.001 and r = - 0.68; P < 0.001, respectively) areas of the incision, as well as between the length and angle of incision (r = - 0.74; P < 0.001). The number of planes in the wound architecture was not significantly different according to senior or junior resident status (P > 0.05). Although the number of eyes with stromal hydration was significantly greater for junior residents than for seniors (P < 0.001), the corneal thickness at the entrance to the cornea or the anterior chamber, presence of endothelial wound gaping, and Descemet's membrane detachment were comparable between eyes with and without stromal hydration (all P > 0.05). At three months, 29 (58%) patients returned for examination, in whom seven (24%) had late wound complications. Conclusions: This study found no significant differences in the performances of junior and senior residents in terms of wound construction or its associated complications. However, considering the overall rate of some observed wound-related complications, we recommended revision of the resident educational curriculum concerning the structure and complications of the main incision.

Development and validation of a clinical model for predicting the severity of carpal tunnel syndrome.

OBJECTIVES: Pain, discomfort, and cost may result in incomplete or inconclusive electrodiagnostic studies to assess the severity of carpal tunnel syndrome. We aimed to develop a clinical instrument for stratifying patients based on easy-to-measure variables to assess carpal tunnel syndrome severity. METHODS: We performed a secondary analysis of data from patients diagnosed with a diagnosis of carpal tunnel syndrome using a factor analysis of mixed data. In total, 1037 patients (405; 39.1% male) with a mean (SD) age of 58.0 (10.8) years were included. For each patient, demographic information, physical examination findings, ultrasonographic findings, and the severity of the syndrome based on electrodiagnostic studies were recorded. RESULTS: We devised a composite index incorporating a pain numeric rating scale (NRS) rated from 0 (no pain at all) to 10 (the worst pain ever possible), presence of thenar muscle weakness or atrophy (TW), cross-sectional area (CSA) of the median nerve (mm2), and occurrence of nocturnal pain (NP). The composite index was calculated as [scale(NRS)+scale(CSA)+NP+TW]/4, where both NP and TW are binary features (0 or 1). The overall accuracy and area under the curve of the index for stratifying the syndrome severity were 0.85 and 0.71, respectively (Cohen's Kappa = 0.51, McNemar's test P = 0.249). The composite index increased pretest probability by 1.6, 1.8, and 3.3 times with positive likelihood ratios of 3.3, 2.5, and 13.5, and false-positive rates of 26.6, 17.6, and 4.8% for mild, moderate, and severe syndrome, respectively. The index thresholds for mild, moderate, and severe carpal tunnel syndrome were <0.8, ≥0.8 to <1.1, and ≥1.1, respectively. CONCLUSION: Using a composite index, patients with carpal tunnel syndrome can be categorized for the severity of the syndrome before carrying out electrodiagnostic studies.

Functional gene transcription variation in bacterial metatranscriptomes in large freshwater Lake Ecosystems: Implications for ecosystem and human health.

Little is known regarding the temporal and spatial functional variation of freshwater bacterial community (BC) under non-bloom conditions, especially in winter. To address this, we used metatranscriptomics to assess bacterial gene transcription variation among three sites across three seasons. Our metatranscriptome data for freshwater BCs at three public beaches (Ontario, Canada) sampled in the winter (no ice), summer and fall (2019) showed relatively little spatial, but a strong temporal variation. Our data showed high transcriptional activity in summer and fall but surprisingly, 89% of the KEGG pathway genes and 60% of the selected candidate genes (52 genes) associated with physiological and ecological activity were still active in freezing temperatures (winter). Our data also supported the possibility of an adaptively flexible gene expression response of the freshwater BC to low temperature conditions (winter). Only 32% of the bacterial genera detected in the samples were active, indicating that the majority of detected taxa were non-active (dormant). We also identified high seasonal variation in the abundance and activity of taxa associated with health risks (i.e., Cyanobacteria and waterborne bacterial pathogens). This study provides a baseline for further characterization of freshwater BCs, health-related microbial activity/dormancy and the main drivers of their functional variation (such as rapid human-induced environmental change and climate change).

Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha).

Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship are not well characterized. Here, we modified the fish gut microbiota using antibiotic and probiotic feed treatments to address the effect of host microbiome on gene expression patterns. Chinook salmon (Oncorhynchus tshawytscha) gut gene expression was evaluated using whole transcriptome sequencing (RNA-Seq) on hindgut mucosa samples from individuals treated with antibiotic, probiotic and control diets to determine differentially expressed (DE) host genes. Fifty DE host genes were selected for further characterization using nanofluidic qPCR chips. We used 16S rRNA gene metabarcoding to characterize the rearing water and host gut microbiome (bacterial) communities. Daily administration of antibiotics and probiotics resulted in significant changes in fish gut and aquatic microbiota as well as more than 100 DE genes in the antibiotic and probiotic treatment fish, relative to healthy controls. Normal microbiota depletion by antibiotics mostly led to downregulation of different aspects of immunity and upregulation of apoptotic process. In the probiotic treatment, genes related to post-translation modification and inflammatory responses were up-regulated relative to controls. Our qPCR results revealed significant effects of treatment (antibiotic and probiotic) on rabep2, aifm3, manf, prmt3 gene transcription. Moreover, we found significant associations between members of Lactobacillaceae and Bifidobacteriaceae with host gene expression patterns. Overall, our analysis showed that the microbiota had significant impacts on many host signalling pathways, specifically targeting immune, developmental and metabolic processes. Our characterization of some of the molecular mechanisms involved in microbiome-host interactions will help develop new strategies for preventing/ treating microbiome disruption-related diseases.

Microbial community and abiotic effects on aquatic bacterial communities in north temperate lakes.

The aquatic bacterial community (BC) plays a vital role in determining the nature and rate of ecosystem function. However, the biotic and abiotic factors influencing BC structure and function are largely unknown. Hence, the current study characterizes the impact of biotic and abiotic factors on aquatic bacterial biodiversity to determine whether the dominant effects are biotic or abiotic by partitioning their relative effects across temperate Canadian lakes. We collected water samples from sixty southern Ontario lakes and characterized their BC and microbial eukaryotic community (MEC) compositions using high throughput metabarcode sequencing of 16S and 18S rRNA gene fragments. The diversity and richness of aquatic BCs differed considerably among our study lakes, and those differences were explained by environmental, spatial, and biotic (MEC) factors (31%, 23%, and 23% of variance explained, respectively). The relatively large contribution from biotic and abiotic factors (54%), relative to spatial effects, shows deterministic processes prevail in shaping BC assembly in freshwater lakes. However, spatial effects also contributed significantly, highlighting the role of stochastic processes (ecological drift and coupled with limited dispersal) in shaping BC structure. Furthermore, our co-occurrence network analysis showed strong positive and negative interactions within and between the BCs and MECs, indicating mutualistic or antagonistic co-occurrence patterns relationships play important roles in driving the variation in BC composition among our sampled lakes. Considered together, our community analyses show that deterministic and stochastic processes combined contribute to determining the aquatic BC composition, and hence likely function as well, across a broad array of temperate freshwater lakes.

High Rate of Serotype Switching and Genetic Variations Indicates Widespread Recombination Between Clinical and Commensal Penicillin-Nonsusceptible Streptococcus pneumoniae in Tehran.

A total of 161 Streptococcus pneumoniae were collected between 2013 and 2015 in Tehran, Iran. The strains were tested for antimicrobial susceptibility and minimum inhibitory concentrations, serotyped, and genotyped by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Penicillin-binding proteins (PBPs) were also typed by restriction fragment length polymorphism (PBP-RFLP). Out of 161 strains, 32 isolates (20%) were highly resistant to penicillin. The most frequent serotypes among the penicillin-nonsusceptible S. pneumoniae (PNSP) were 14 (24%), 23F (18%), and 19F (17%). RFLP of pbp2b, pbp2x, and pbp1a genes revealed 8, 6, and 7 different patterns, respectively. Analysis of 93 PNSP isolates displayed 80 PFGE types with 8 common types constituting 21 (23%) isolates. The remaining 72 isolates (77%) were single types. MLST indicated a high degree of genetic diversity among the 93 PNSP with 36 different sequence types. Six internationally known penicillin resistant clones were identified in our isolates among which Spain23F-1 (ST81), Spain6B-2 (ST90), and Spain9V-3 (ST156) were the predominant clones. The results indicated international identifiable clones of S. pneumoniae, especially Spain23F-1 with high penicillin resistance could play a major role in spread of antimicrobial resistance in Iran. The extensive sequence variation in PBP2x, PBP2b, and PBP1a in resistant strains of clinical and commensal S. pneumoniae was suggestive of a widespread homologous recombination within S. pneumoniae populations.

Long-term Evaluation of Corneal Biomechanical Properties After Corneal Cross-linking for Keratoconus: A 4-Year Longitudinal Study.

PURPOSE: To compare the long-term changes in corneal biomechanics, topography, and tomography before and 4 years after corneal cross-linking (CXL) with the Dresden protocol and correlate these changes with visual acuity. METHODS: In this longitudinal study, 18 eyes of 18 patients with progressive keratoconus who were treated with CXL were included. All patients received a standard ophthalmological examination and were examined by Placido disc-based topography, Scheimpflug tomography, and biomechanical assessments with the Corvis ST (OCULUS Optikgeräte GmbH, Wetzlar, Germany) and Ocular Response Analyzer (ORA; Reichert Ophthalmic Instruments, Buffalo, NY) before and 4 years after CXL. The main outcome measures were dynamic corneal response (DCR) parameters obtained from the Corvis ST, corneal hysteresis (CH), corneal resistance factor (CRF), visual acuity, refraction, corneal curvature, and corneal thickness. RESULTS: There were no significant differences in mean visual acuity, refraction, intraocular pressure, corneal topography, corneal astigmatism in both corneal surfaces, maximum keratometry, corneal thickness at apical and thinnest points, thickness profile indices, corneal volume, and specular microscopy before and 4 years after CXL (P > .05). Significant changes were observed in many DCR parameters, including radius at highest concavity and integrated inverse radius, both of which were consistent with stiffening. The CH and CRF values after CXL were not statistically significant. The new parameters using the Corvis ST include integrated inverse concave radius, which showed a significant decrease 1.07 ± 0.93 mm-1, consistent with stiffening. The corneal stiffness parameter at the first applanation, Ambrósio's Relational Thickness to the horizontal profile, deformation amplitude ratio, and Corvis Biomechanical Index as a combined biomechanical screening parameter did not show significant changes. CONCLUSIONS: CXL is a minimally invasive treatment option to prevent keratoconus progression over 4 years. Pressure-derived biomechanical parameters obtained from the ORA did not show any change following CXL at 4 years of follow-up, whereas the Corvis ST DCR parameters detected changes in corneal biomechanical properties. [J Refract Surg. 2018;34(12):849-856.].

Determination of Characteristics of Erythromycin Resistant Streptococcus pneumoniae with Preferred PCV Usage in Iran.

Amongst 100 Streptococcus pneumoniae isolated from clinical cases and nasopharynx of healthy individuals, 60 erythromycin resistant strains were isolated and characterized using MLST, PFGE, transposon analysis and Quellung reaction. Most of the S. pneumoniae erythromycin resistant (80%) were found to be attributable to the ermB-edncoded ribosome methylase activity which differs from the dominant mechanism of macrolide resistance seen in North America. The most predominant transposons were; Tn1545/6003 (27%), Tn6002 (22%), Tn2009 (20%), Tn2010 (17%). Number of the clinical isolates carrying Tn2010 was more significant than the normal flora. The serotypes found were; 14 (33%), 3 (22%), 23F (15%), 19F (15%), 19A (7%), 6A (3%), 9V (3%) and 6B (2%). The most prevalent serotypes among the clinical (n = 28) and normal flora (n = 32) isolates were serotypes 14 (46%) and 3 (31%), respectively. The most prevalent vaccine serotypes amongst the clinical isolates and the healthy individuals were pneumococcal conjugate vaccines (PCV) 13 and PCV10, respectively. PFGE revealed 34 pulsotypes with 9 common and 25 single types. Significant number of the normal isolates belonged to CT5 and CT6. On the other hand, significant number of clinical isolates belonged to CT8 as compared to the normal flora isolates. MLST showed 2 dominant sequence types. ST3130 (23%) and ST180 (22%) were the most predominant sequence types in the clinical and normal isolates, respectively. There was no significant difference in other sequence types between clinical and normal flora isolates. Three polyclonal complexes including Sweden15A -25, Spain23F-1 and Spain9V-3 constituted 58% of the isolates. Our results suggest that the genetic diversity and transposon distribution were high among S. pneumoniae, particularly in the isolates containing erm(B) and double antibiotic resistant genes (erm/mef). The results presented here could influence the change in the current vaccination practices in Iran which currently calls for vaccination with PCV7 or PCV10.

Clinical Evaluation of Percutaneous Caudal Epidural Adhesiolysis With the Racz Technique for Low Back Pain Due to Contained Disc Herniation.

OBJECTIVES: The authors evaluated the effectiveness of percutaneous epidural adhesiolysis (PEA) in patients with low back pain due to contained disc herniation. PATIENTS AND METHODS: Twenty patients with low back pain due to contained disc herniation underwent PEA treatment with the Racz technique. The patients were evaluated for pain score, medication intake, significant pain relief, and complications. RESULTS: At three days, one month, three months, and six months after PEA compared to pre-PEA evaluations, the pain scores and medication intake were significantly decreased. Significant pain relief declined from 95% at three days to 75% at six months. CONCLUSIONS: PEA for low back pain due to contained disc herniation is a safe and effective procedure. Therefore, it may be considered as an option for treatment before invasive operations are performed.

Antibacterial potential and genetic profile of Enterococcus faecium strains isolated from human normal flora.

Enterococci have a widespread attendance in the circumference and belongs to the enteric commensal microbiota. Most of them produce the antimicrobial compounds and have an inhibition effect on pathogenic microorganisms. The objective of this study was to characterize the enterococcal strains isolated from human normal flora and assess their antibacterial activity. Enterococcal isolates were obtained from the feces of eighteen healthy humans. All enterococcal species were identified by biochemical and species-specific polymerase chain reaction (PCR). These isolates were investigated further to examine their ability to inhibit growth of Salmonella typhi, Shigella flexneri and Escherichia coli by well diffusion assay. Furthermore, antibiotic susceptibility test was performed and genetic relatedness of all isolates was evaluated by Pulse Field Gel Electrophoresis (PFGE). In all, 432 isolates were obtained from fecal samples. All of the isolates identified as Enterococcus faecium by biochemical and molecular (PCR) methods. Using repetitive element palindromic (REP)-PCR method 54 patterns have been obtained and were selected for further evaluation. The results indicated that 66%, 38% and 24% of our isolates had antimicrobial effect against S. typhi, S flexneri and enteroaggregative Escherichia coli (EAEC), respectively. On the other hand, there was no significant inhibition effect against enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC). All isolates were sensitive to vancomycin, teicoplanin, linezolid, ampicillin, chloramphenicol and gentamicin. On the other hand, the resistance rates for erythromycin, tetracycline and ciprofloxacin were 20%, 22%, and 1.8% respectively. In addition, the analysis of PFGE showed forty patterns with eight (40.7%) common types (CT) and thirty two (59.2%) single types (ST). Among eight common types, only one common type (CT5) had similar antimicrobial effect. These results suggested that enterococcal isolates obtained from human normal flora have potential antibacterial effect against S. typhi, S. flexneri and E. coli.

Genotypic Diversity of Methicillin-Resistant Coagulase-Negative Staphylococci Isolated from Inpatients and Outpatients.

We investigated the prevalence of methicillin-resistant coagulase-negative staphylococci (MRCoNS) isolated from hospitalized patients and outpatients (OP). Out of 350 staphylococcal isolates collected from three hospitals, 190 were coagulase-negative staphylococci (CoNS). These isolates were subjected to antimicrobial susceptibility tests, detection of mecA, and pulsed-field gel electrophoresis (PFGE) typing. Among the 190 isolated CoNS, Staphylococcus epidermidis (47.3%) and Staphylococcus haemolyticus (44.2%) were the most prevalent species. Other CoNS species that were isolated were Staphylococcus saprophyticus (2.1%), Staphylococcus warneri (2.1%), Staphylococcus simulans (1.6%), Staphylococcus capitis (1.1%), Staphylococcus schleiferi (1.1%), and Staphylococcus hominis (0.5%). The rate of resistance to methicillin was 60% with 58 (50%) S. epidermidis and 55 (49%) S. haemolyticus. The rate of resistance to 13 antibiotics tested with the lowest and highest to chloramphenicol and penicillin, respectively. High clonal diversity with different PFGE patterns was obtained for methicillin-resistant S. epidermidis and S. haemolyticus by 32 and 31 types, respectively. Our results indicated that the dissemination of MRCoNS is widespread in Tehran. The majority of these isolates showed distinct genotyping patterns. At the same time, the common patterns were found among the MRCoNS obtained from outpatient and inpatient isolates, suggestive of an epidemiological link.

Isolation and Biochemical Fingerprinting of Vancomycin-Resistant Enterococcus faecium From Meat, Chicken and Cheese.

BACKGROUND: Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens and food chain has been considered as an assumed source for dissemination of VRE to human. OBJECTIVES: The presence of VRE isolates from food samples and typing of these isolates with Phene plate, a biochemical fingerprinting method, were investigated. MATERIALS AND METHODS: Thirty samples of meat, chicken and cheese were analyzed for VRE during 2010. Antibiotic susceptibility tests and minimum inhibitory concentration (MIC) were also examined. VRE isolates were typed with the Phene plate system (PhPlate), a biochemical fingerprinting method. RESULTS: A total of 70 VRE isolates were obtained and identified as Enterococcus faecium by species-specific PCR. All the isolates carried vanA, while none of them harbored vanB. The VRE isolates included 35, 27, and 8 isolates from meat, chicken and cheese, respectively. Typing with the PhPlate revealed a diversity index of 0.78 for E. faecium, containing 10 common and four single types. The results of antibiotic susceptibility and MIC tests showed an increased resistance to ciprofloxacin, erythromycin, ampicillin and gentamicin, to which, 100%, 100%, 100%, and 95% of VRE isolates were resistant, respectively. Only 5% of the isolates were resistant to chloramphenicol and the MIC of the isolates for vancomycin and teicoplanin was ≥ 256 µg/mL and for gentamicin-resistant isolates it was 1024 µg/mL. Conventional and molecular identification tests exhibited that all the isolates were E. faecium carrying vanA. None of the isolates harbored vanB. CONCLUSIONS: The results showed that enterococci are common contaminants in food. Indeed, this study indicates a high prevalence of multidrug-resistant enterococci in food of animal origin in Iran. Isolating some persisting enterococcal isolates revealed that continuous surveillance of antimicrobial resistance in enterococci from food is essential.

Clonal Diversity in Multi Drug Resistant (MDR) Enterococci Isolated from Fecal Normal Flora.

Enterococci are Gram positive and catalase- negative cocci that are found in the gastrointestinal tract of mammals and birds, and are readily isolated from soil, surface and waters. The aim of this study was to discriminate between Enterococcus isolates based on repetitive element sequence based -PCR (Rep-PCR) with the BOXA2R primer and their antibiotics profile. Enterococci isolates were obtained from 180 fecal samples. The isolates were identified by biochemical reaction and specific identification was confirmed by PCR with species specific primers. All isolates were subjected to Rep typing and antimicrobial susceptibility tests. Rep-PCR analysis of 180 isolates revealed 93 REP types with forty-five single types (ST1 to ST45) and forty-eight common types (CT1 to 48). Antibiotic susceptibility tests exhibited that 53 (29.4%), 43 (23.8%), 11 (6.1%) and 9 (5%) were resistant to erythromycin, tetracycline, gentamicin and ciprofloxacin respectively but among the isolates, sixteen were multi drug resistant (MDR). These MDR isolates showed 11 Rep types with seven single types and four common types. In addition, 81.2% of MDR isolates were from male subjects and the average age of these persons was more than fifty years. This study showed that 56.2% of MDR isolates were homogeneous with 95 % similarity, and high rate of resistance to tetracycline and erythromycin (81.2%) were observed in these isolates. The concern about these normal flora isolates are the pathogenic potential of these bacteria through the horizontal transfer of antibiotic resistance and virulence genes.