16S rRNA sequencing reveals microbiota differences in orthopedic implants between aseptic loosening and prosthetic joint infection cases

Prosthetic joint infection (PJI) and aseptic loosening (AL) are common complications of total joint arthroplasty. An accumulation of evidence indicates the presence of microbial communities on prosthetic implants, but the overall microbial profile is unclear. In this study, we aimed to investigate the differences in the microbial composition of prosthetic implants obtained from PJI and AL patients using the 16S rRNA sequencing method. Patients who underwent revision hip, knee, or shoulder arthroplasty caused by PJI (n = 20) or AL (n = 10) were enrolled in the study. 16S rRNA sequencing targeting the V3-V4 region was performed on the microbial specimens collected from synovial fluid, periprosthetic deep-tissue, and biofilm during the revision surgery. The sequenced raw data were analysed for microbial composition and ecological and differential abundance analyses using bioinformatics tools. The AL group had relatively balanced and higher diversity, with Staphylococcus, Streptococcus, and Veillonella being prominent. In the PJI group, Staphylococcus and Pseudomonas were predominant, especially in deep-tissue samples and biofilm samples, respectively. The differential abundance analysis identified 15 and 2 distinctive taxa in the AL and PJI groups, respectively. Our findings provided preliminary insights supporting the existence of periprosthetic microbiota in orthopedic implants and explaining the differences in microbial composition between the AL and PJI groups.

The role of the Mediterranean diet in modulating the gut microbiome: A review of current evidence

The Mediterranean diet (MedDiet) is recognized as one of the United Nations Educational, Scientific and Cultural Organization Intangible Cultural Heritage assets associated with lower rates of cardiometabolic diseases; lower prevalence of cancer, Alzheimer's disease, depression, and onset of inflammatory bowel disease; and more generally low-grade inflammation and mortality risks. Beyond being an input source of beneficial micronutrients, it recently has been discovered that the MedDiet plays a role in a more complex human microbiome-mediated mechanism. An interesting hypothesis suggests a bidirectional relationship between the MedDiet and the gut microbiome, where gut microbiota assembly and biosynthetic capacity are responsive to the diet; in return, the microbiome-reachable nutrients shape and modulate the microbiome toward a characteristic probiotic state. It can be speculated that that primary health benefits of the MedDiet exerted via the gut microbiome are mediated by the bioactive compounds transformed by the microbiome. Furthermore, it is possible that additional probiotic properties of the organisms promoted by diet adherence have secondary benefits. As more detailed omic-based studies take place, more evidence on the MedDiet as a core generic probiotic microbiome modulation strategy surface. However, individual-specific microbiome compositions might impose personal variations on the diet outcome. Therefore, a prospective strategy of a fine-tuned precision nutrition approach might deliver optimized benefits of the MedDiet.

Artificial intelligence-based personalized diet: A pilot clinical study for irritable bowel syndrome

We enrolled consecutive IBS-M patients (n = 25) according to Rome IV criteria. Fecal samples were obtained from all patients twice (pre-and post-intervention) and high-throughput 16S rRNA sequencing was performed. Six weeks of personalized nutrition diet (n = 14) for group 1 and a standard IBS diet (n = 11) for group 2 were followed. AI-based diet was designed based on optimizing a personalized nutritional strategy by an algorithm regarding individual gut microbiome features. The IBS-SSS evaluation for pre- and post-intervention exhibited significant improvement (p < .02 and p < .001 for the standard IBS diet and personalized nutrition groups, respectively). While the IBS-SSS evaluation changed to moderate from severe in 78% (11 out of 14) of the personalized nutrition group, no such change was observed in the standard IBS diet group. A statistically significant increase in the Faecalibacterium genus was observed in the personalized nutrition group (p = .04). Bacteroides and putatively probiotic genus Propionibacterium were increased in the personalized nutrition group. The change (delta) values in IBS-SSS scores (before-after) in personalized nutrition and standard IBS diet groups are significantly higher in the personalized nutrition group. AI-based personalized microbiome modulation through diet significantly improves IBS-related symptoms in patients with IBS-M. Further large-scale, randomized placebo-controlled trials with long-term follow-up (durability) are needed.

A comparative study of the clonal diversity and virulence characteristics of uropathogenic Escherichia coli isolated from Australian and Turkish (Turkey) children and adults with urinary tract infections

Introduction

The virulence-associated gene (VAG) repertoire and clonal organization of uropathogenic Escherichia coli (UPEC) strains is influenced by host demographic, geographic locale, and the setting of urinary tract infection (UTI). Nevertheless, a direct comparison of these features among Australian and Turkish UPEC remains unexplored. Accordingly, this study investigated the clonal composition and virulence characteristics of a collection of UPEC isolated from Australian and Turkish UTI patients.

Methods

A total of 715 UPEC strains isolated from Australian (n=361) and Turkish (n=354) children and adults with hospital (HA)- and community-acquired (CA)-UTIs were included in this study. Typing of the strains using RAPD-PCR and PhPlate fingerprinting grouped all strains into 25 clonal groups (CGs). CG representatives were phylogrouped and screened for the presence of 18 VAGs associated with extraintestinal pathogenic E. coli.

Results

Turkish UPEC strains were characterized by high clonal diversity and predominance of the phylogroup D, while few distinct clonal groups with phylogenetic group B2 backgrounds dominated among the Australian strains. Twelve identical CGs were shared between ≥1 patient group from either country. Australian strains, particularly those isolated from children with HA-UTI, showed higher virulence potential than their Turkish counterparts, carrying significantly more genes associated with adhesion, iron acquisition and capsule biosynthesis.

Conclusions

This study identified identical CGs of UPEC causing HA- and CA-UTIs among Australian and Turkish UTI patients. These CGs frequently carried VAGs associated with adhesion, iron acquisition, immune evasion, and toxin production, which may contribute to their ability to disseminate internationally and to cause UTI.

Acromegaly is associated with a distinct oral and gut microbiota

PURPOSE

Our aim was to investigate the changes in the composition of oral and gut microbiota in patients with newly diagnosed acromegaly and their relationship with IGF-1 levels.

METHODS

Oral and fecal samples were collected from patients with newly diagnosed acromegaly without comorbidities and from healthy controls. The composition of the microbiota was analyzed. The general characteristics, oral and stool samples of the patients and healthy control subjects were compared. The changes in microbiota composition in both habitats, their correlations and associations with IGF-1 were statistically observed using machine learning models.

RESULTS

Fifteen patients with newly diagnosed acromegaly without comorbidities and 15 healthy controls were included in the study. There was good agreement between fecal and oral microbiota in patients with acromegaly (p = 0.03). Oral microbiota diversity was significantly increased in patients with acromegaly (p < 0.01). In the fecal microbiota, the Firmicutes/Bacteroidetes ratio was lower in patients with acromegaly than in healthy controls (p = 0.011). Application of the transfer learned model to the pattern of microbiota allowed us to identify the patients with acromegaly with perfect accuracy.

CONCLUSIONS

Patients with acromegaly have their own oral and gut microbiota even if they do not have acromegaly-related complications. Moreover, the excess IGF-1 levels could be correctly predicted based on the pattern of the microbiome.

Temporal overexpression of IL-22 and Reg3γ differentially impacts the severity of experimental autoimmune encephalomyelitis

IL-22 is an alpha-helical cytokine which belongs to the IL-10 family of cytokines. IL-22 is produced by RORγt+ innate and adaptive lymphocytes, including ILC3, γδ T, iNKT, Th17 and Th22 cells and some granulocytes. IL-22 receptor is expressed primarily by non-haematopoietic cells. IL-22 is critical for barrier immunity at the mucosal surfaces in the steady state and during infection. Although IL-22 knockout mice were previously shown to develop experimental autoimmune encephalomyelitis (EAE), a murine model of multiple sclerosis (MS), how temporal IL-22 manipulation in adult mice would affect EAE course has not been studied previously. In this study, we overexpressed IL-22 via hydrodynamic gene delivery or blocked it via neutralizing antibodies in C57BL/6 mice to explore the therapeutic impact of IL-22 modulation on the EAE course. IL-22 overexpression significantly decreased EAE scores and demyelination, and reduced infiltration of IFN-γ+IL-17A+Th17 cells into the central nervous system (CNS). The neutralization of IL-22 did not alter the EAE pathology significantly. We show that IL-22-mediated protection is independent of Reg3γ, an epithelial cell-derived antimicrobial peptide induced by IL-22. Thus, overexpression of Reg3γ significantly exacerbated EAE scores, demyelination and infiltration of IFN-γ+IL-17A+ and IL-17A+GM-CSF+Th17 cells to CNS. We also show that Reg3γ may inhibit IL-2-mediated STAT5 signalling and impair expansion of Treg cells in vivo and in vitro. Finally, Reg3γ overexpression dramatically impacted intestinal microbiota during EAE. Our results provide novel insight into the role of IL-22 and IL-22-induced antimicrobial peptide Reg3γ in the pathogenesis of CNS inflammation in a murine model of MS.

Gut microbiota in patients with newly diagnosed acromegaly: a pilot cross-sectional study

PURPOSE

Microbiota has crucial biological importance for human well-being. Bidirectional interaction exists between microbiota and the host, and there have been no studies investigating this interaction in patients with acromegaly. We aimed to analyze the composition of microbiota in patients with newly diagnosed acromegaly.

METHOD

Stool samples were obtained from the patients with newly diagnosed acromegaly in the Endocrinology Clinic of Erciyes University Medical School. The composition of microbiota was analyzed, and the results were compared to healthy volunteers matched to the patients in terms of age, gender and body mass index.

RESULTS

Seven patients (three male, four female) with a mean age of 48 ± 17.6 years were included in the study. The stool analysis revealed a significantly lower bacterial diversity in the patients with acromegaly. Bacteroidetes phylum was predominating in the patient group, and Firmicutes/Bacteroidetes ratio was altered significantly. Bifidobacterium, Collinsella, Bacteroides, Butyricimonas, Clostridium, Oscillospira, and Dialister were predominating in the control group.

CONCLUSION

The gut microbiota is significantly altered in patients with newly diagnosed acromegaly. Further prospective studies are needed to elucidate the causative relationship between acromegaly, colorectal pathologies, and microbial alterations.

Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 "ML4Microbiome" that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies.

An outbreak of bloodstream infection due to extensively resistant Acinetobacter baumannii among neonates

BACKGROUND

Extensively resistant Acinetobacter baumannii has emerged and spread worldwide as a significant cause of health care-associated infections and outbreaks. It also causes life-threatening infections among neonates, including bacteremia. The aim of this study was to investigate an outbreak of A baumannii bacteremia (ABB) among neonates.

MATERIALS AND METHODS

A retrospective, case-control study was conducted from July 2014 to July 2015 in a neonatal intensive care unit (NICU). Risk factors associated with ABB in univariate and multivariate analysis with logistic regression was performed. Molecular typing by pulsed field gel electrophoresis was used to confirm relatedness of bacteremic A baumannii strains.

RESULTS

During the 5-year period (2011-2016), 68 patients in our NICU were diagnosed with BSI due to A baumannii. The case-control study included 41 case patients within the outbreak caused by a major epidemic clone and 108 control patients. Risk factors (by univariate analysis) associated with ABB were intubation, 14-day mortality, and use of peritoneal dialysis and an umbilical catheter. Multivariate analysis identified 14-day mortality (odds ratio, 5.75; 95% confidence interval, 2.58-12.79) and umbilical catheter use (odds ratio, 2.44; 95% confidence interval, 1.1-5.4) as independent risk factors for ABB.

CONCLUSIONS

This outbreak of bacteremia due to resistant A baumannii affected 41 infants and was associated with 58% mortality. Control of the outbreak was achieved by implementing long-term sustained infection control measures within the unit.

Could Frequent Carbapenem Use Be a Risk Factor for Colistin Resistance?

AIMS

The antibiotic colistin, which had been previously abandoned, is being brought back as a last line of defense against bacterial infection. However, colistin resistance was reported shortly after its reintroduction. This study evaluated the risk factors for colonization/infections due to colistin-resistant Acinetobacter baumannii (ColR-Ab) and Klebsiella pneumoniae (ColR-Kp) strains and characterized the molecular epidemiology of these two strains.

RESULTS

Age, previous hospitalization duration, and previous use of carbapenem and colistin were risk factors for ColR-Kp, whereas previous use of carbapenem and colistin was a risk factor for ColR-Ab. According to pulsed-field gel electrophoresis analysis, most ColR-Kp strains could be grouped into two major pulsotypes. This appears to be an indicator of cross contamination of ColR-Kp strain, since different isolates appeared to be belonging to the same clones. The existence of colistin-susceptible (ColS) and colistin-resistant (ColR) strains in the same pulsotypes might also be an indicator of the recent emergence of resistance mechanisms.

CONCLUSIONS

The results highlight the emergence of ColR pathogens in Turkey, which is considered to be developing country, and that carbapenem use coupled with insufficient infection control measures might increase the risk of ColR outbreaks.

Insufficient decontamination in Sewage treatment plants induce the risk of artificial selection of extended-spectrum β-lactamase producing Escherichia coli

Quantitative data about extended-spectrum beta-lactamase producing E. coli (ESBLEC) in the wastewaters are scarce, especially in developing countries. These data could be useful to raise awareness about the potential risk of spreading ESBLEC strains in the community. Water samples were collected weekly over a 10-week period, from one urban sewage treatment plant (STP), one rural STP and one hospital complex's wastewater (HWW) in Turkey. Mean E. coli and ESBLEC loads were determined for each sampling point. For the 580 ESBLEC isolated, antimicrobial resistance profiles, phylogenetic grouping, presence of common beta-lactamese-typesand integrons were studied using PCR. The mean ESBLEC ratio was accounted for 0.58%, 0,12%, 1.53% of the total E. coli in urban, rural untreated wastewater and HWW, respectively. These values were higher for the outlets. The mean number of different antimicrobial classes to which the strains were resistant was highest in urban STP (4.0± 1.6). The antimicrobial resistance ratios of ESBLEC strains isolated from HWW were observed to be in between those of urban and rural STPs. The most common phylogenetic group was C composing (29.7%) and the most susceptible strains belonged to phylogroup B1. Wastewater treatments without sufficient decontamination, resulting in artificial selection of ESBLEC might lead to public health risk as these strains reach communities through environment. To avoid such risks and protect the human health as well as the environment, well-established decontamination measures imposing barriers against this artificial selection should be implemented.

Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases

A short while ago, the human genome and microbiome were analysed simultaneously for the first time as a multi-omic approach. The analyses of heterogeneous population cohorts showed that microbiome components were associated with human genome variations. In-depth analysis of these results reveals that the majority of those relationships are between immune pathways and autoimmune disease-associated microbiome components. Thus, it can be hypothesized that autoimmunity may be associated with homeostatic disequilibrium of the human-microbiome interactome. Further analysis of human genome–human microbiome relationships in disease contexts with tailored systems biology approaches may yield insights into disease pathogenesis and prognosis.

In vitro Effectiveness of Commercial Bacteriophage Cocktails on Diverse Extended-Spectrum Beta-Lactamase Producing Escherichia coli Strains

The objective of this study is to determine the in vitro susceptibility of Georgian bacteriophage cocktails on multidrug resistant (MDR) extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC) isolated from patients’ blood and urine cultures. A total of 615 E. coli isolates were included in this study. Phene Plate (PhP)-typing and phylogenetic grouping were used for the typing. Antimicrobial resistance profiles and ESBL production of all isolates were confirmed according to Clinical and Laboratory Standards Institute (CLSI) criteria. The activities of four bacteriophage cocktails (Enko-phage, SES-bacteriophage, Pyo-bacteriophage, and Intesti-bacteriophage) were determined against 142 ESBL-EC using in vitro spot tests. According to this, Enko-phage were active against 87.3% of the tested strains while that ratio was 81.7% for Intesti-bacteriophage, 81.7% for Pyo-bacteriophage, and 59.2% for SES-bacteriophage cocktails. Based on the contingency tests, the phage cocktails were observed to be statistically significantly (p < 0.001) more effective on ESBL-EC strains belonging to phylogenetic groups D and B2. The employed phage cocktails were found to be affective against all tested resistant types. These results are promising especially for the infections that are caused by MDR pathogens that are difficult to treat. As this is a preliminary step to the potential clinical trials to be designed for the country, in vitro confirmation of their success on a MDR ESBL-EC collection should be accepted as an initial action, which is encouraging to consider clinical trials of phage therapy especially in countries which are not introduce phage therapy.

Hypokalemic paralysis due to thyrotoxicosis accompanied by Gitelman's syndrome

A 35-year-old male patient was admitted with fatigue and muscle weakness. He had been on methimazole due to thyrotoxicosis for 2 weeks. Laboratory tests showed overt hyperthyroidism and hypokalemia. Potassium replacement was started with an initial diagnosis of thyrotoxic hypokalemic periodic paralysis. Later on, despite the euthyroid condition and potassium chloride treatment, hypokalemia persisted. Further investigations revealed hyperreninemic hyperaldosteronism. The patient was considered to have Gitelman's syndrome (GS) and all genetic analysis was done. A c. 1145C>T, p. Thr382Met homozygote missense mutation located on solute carrier family 12, member gene 3, exon 9 was detected and GS was confirmed.

Analysis of mosses along Sarp-Samsun highway in Turkey

The elemental analysis of mosses along Sarp-Samsun highway in Turkey was determined using energy dispersive X-ray fluorescence method. A radioisotope excited X-ray fluorescence analysis using the method of multiple standard additions is applied for the elemental analysis of mosses. An annular 50 mCi (241)Am radioactive source and annular 50 mCi (55)Fe radioactive source were used for excitation of characteristic K X-rays. An Si(Li) detector which has a 147 eV full width at half maximum for 5.9 keV photons was used for intensity measurements. A qualitative analysis of spectral peaks showed that the samples contained phosphates, potassium, calcium, titanium, iron, strontium, tin and barium. Since this study is the elemental analysis along the highway, one can expect to detect Pb. Due to the detection limit of EDXRF, elements were analyzed with Atomic Absorption Spectroscopy (AAS) for Pb. Evaluation of these elements with their potential hazards for ecology and human is briefly discussed.

Removal of cadmium from aqueous solution by Nordmann fir (Abies nordmanniana (Stev.) Spach. Subsp. nordmanniana) leaves

The utility of Nordmann fir (Abies nordmanniana (Stev.) Spach. Subsp. nordmanniana) leaves from Eastern Black Sea region for the removal (sorption) of metal ions from aqueous solutions was investigated. For this, the optimum values of pH, time, metal concentration, leaf concentration, leaf particle size and adsorption capacity were determined. Also the recovery conditions of the metals from leaves were studied. Cd metal was selected because of its toxic properties. Freundlich isotherm model was used to describe the adsorption behaviour and the experimental results obtained for Cd(2+) adsorption, followed this model well. The utility of Nordmann fir leaves to remove toxic metals from aqueous solutions was proved. Hence, this study showed that the leaves of Nordmann fir can provide cheap source as biosorbents for toxic metal removal from natural or wastewaters.