Osteomyelitis infection caused by Arcanobacterium haemolyticum in a diabetic patient: A first case report.

Arcanobacterium haemolyticum can cause deep infections, including osteomyelitis. In this study, an automated system misidentified this causal agent as Cellulomonas species but 16 s rRNA sequencing correctly identified it as A. haemolyticum. Recognizing the capability of A. haemolyticum to establish the disease is of great importance to enable accurate diagnosis and begin the suitable antibiotic therapy. Here we present the first case of successfully treated A. haemolyticum infective osteomyelitis in a 64-year-old Saudi patient with diabetes mellitus type 2 and review the characteristics of this seldom pathogenic agent.

Relative reduction of biological and phylogenetic diversity of the oral microbiota of diabetes and pre-diabetes patients.

BACKGROUND: A reciprocal relationship between oral health and systemic disease, such as type 2 diabetes, has been suggested, whereby a systemic disease is a predisposing factor for oral infection. If the infection occurs, it in turn aggravates the progression of the systemic disease. According to several studies, certain constituents of the oral microbiota are linked to diabetes, metabolic syndrome, and obesity. In the current study, we aimed to compare the microbial diversity and population structure of the oral microbiota of normoglycemic, impaired glucose tolerance (IGT), and diabetes patients. METHODOLOGY: The study followed a case-control design, with 15 type 2 diabetes patients, 10 IGT subjects, and 19 control subjects. All subjects underwent assessment of periodontitis and oral health. Saliva samples were collected, and DNA was isolated from these samples. Hypervariable regions of the 16Sr RNA gene were amplified and sequenced, and the generated sequences underwent bioinformatics analysis. Statistical analysis and diversity index calculations were made using the statistical software R, vegan R-package, and Past3.20 software. RESULTS: Overall, 551 operational taxonomic units (OTUs) were identified. Based on OTU analysis, a clear reduction of the number of species was observed in both IGT (412) and diabetes groups (372) compared with that in the normoglycemic group (502). This was associated with a similar pattern of reduction of biological diversity among the three groups. The phylogenetic diversity (PD-SBL) value in the normoglycemic group was higher than that in the diabetes group. The diabetes group exhibited the highest evenness value and the highest microbiota bacterial pathogenic content. CONCLUSION: A clear reduction of the biological and phylogenetic diversity was apparent in the diabetes and pre-diabetes oral microbiota in comparison with that in the normoglycemic oral microbiota. However, this was associated with an increase in the pathogenic content of the hyperglycemic microbiota. The results of this study may aid to better understanding of the directionality of the mysterious reciprocal relationship.

Design of Arab Diabetes Gene-Centric Array (ADGCA) in population with an epidemic of Type 2 Diabetes: A population specific SNP evaluation.

In the case of diabetes and other complex diseases, the challenge has always been to find genetic markers that explain the excess risk associated with development of the disease. In the last 12 years, advances in genotyping technology provided substantial development in the discovery of loci contributing to Type 2 diabetes (T2D) susceptibility. Therefore, the aim of this study is to custom design, for the first time in Arab world, an "Arab Diabetes Gene Centric Array" (ADGCA) that assays 643, 745 SNP markers including 50,617 diabetes associated SNPs. The array content was designed after comprehensive literature search prioritizing Diabetes associated SNPs. PCA was performed to evaluate the relationship between world populations and the Saudi population in building the backbone for the array. A genotype data matrix for PCA analysis was produced by including the genotypes of the 270 HapMap samples including JPT, CHB, YRI and CEU to genotypes of the 1457 Saudi samples. Imputation was executed using IMPUTE2 software and the 1000GP Phase III reference panel. All markers incorporated to ADGCA were validated. Quality checks and evaluation of its capacity and performance as a platform for genetic screening for T2D was performed using the latest stastical tools available. We were successful in designing ADGCA as a custom made chip array designed with a motive to capture genetic variation in loci known or reported to be associated with the development of T2D. However, implementation of ADGCA is currently being performed by our research group using 2000 DNA samples respectively from diabetic and non diabetic individuals which could further validate the use of ADGSA in genetic screening of T2D.

Current Bioinformatics resources in combating infectious diseases.

Bioinformatics tools and techniques analyzing next-generation sequencing (NGS) data are increasingly used for the diagnosis and monitoring of infectious diseases. It is of interest to review the application of bioinformatics tools, commonly used databases and NGS data in clinical microbiology, focusing on molecular identification, genotypic, microbiome research, antimicrobial resistance analysis and detection of unknown disease-associated pathogens in clinical specimens. This review documents available bioinformatics resources and databases that are used by medical microbiology scientists and physicians to control emerging infectious pathogens.

Genome sequencing and analysis of the first spontaneous Nanosilver resistant bacterium Proteus mirabilis strain SCDR1.

Background: P. mirabilis is a common uropathogenic bacterium that can cause major complications in patients with long-standing indwelling catheters or patients with urinary tract anomalies. In addition, P. mirabilis is a common cause of chronic osteomyelitis in Diabetic foot ulcer (DFU) patients. We isolated P. mirabilis SCDR1 from a Diabetic ulcer patient. We examined P. mirabilis SCDR1 levels of resistance against Nanosilver colloids, the commercial Nanosilver and silver containing bandages and commonly used antibiotics. We utilized next generation sequencing techniques (NGS), bioinformatics, phylogenetic analysis and pathogenomics in the characterization of the infectious pathogen. Results: P. mirabilis SCDR1 was the first Nanosilver resistant isolate collected from a diabetic patient polyclonal infection. P. mirabilis SCDR1 showed high levels of resistance against Nanosilver colloids, Nanosilver chitosan composite and the commercially available Nanosilver and silver bandages. The P. mirabilis -SCDR1 genome size is 3,815,621 bp. with G + C content of 38.44%. P. mirabilis-SCDR1 genome contains a total of 3533 genes, 3414 coding DNA sequence genes, 11, 10, 18 rRNAs (5S, 16S, and 23S), and 76 tRNAs. Our isolate contains all the required pathogenicity and virulence factors to establish a successful infection. P. mirabilis SCDR1 isolate is a potential virulent pathogen that despite its original isolation site, the wound, can establish kidney infection and its associated complications. P. mirabilis SCDR1 contains several mechanisms for antibiotics and metals resistance, including, biofilm formation, swarming mobility, efflux systems, and enzymatic detoxification. Conclusion: P. mirabilis SCDR1 is the first reported spontaneous Nanosilver resistant bacterial strain. P. mirabilis SCDR1 possesses several mechanisms that may lead to the observed Nanosilver resistance.

The bacterial contamination rate of glucose meter test strips in the hospital setting.

OBJECTIVES: To assess the rate of bacterial contamination of the multi-use vial and single-use packed glucose meter strips, and to identify the type and frequency of various bacterial contamination in different hospital wards. METHODS: This prospective observational study was conducted by a team from the Strategic Center for Diabetes Research in 7 general hospitals in the Central region of Saudi Arabia during the period from August to September 2014 to assess the bacterial contamination rate of the unused strips. A total of 10,447 strips were cultured using proper agar media and incubated both aerobically and anaerobically.  RESULTS: The total bacterial contamination rate for the multi-use vials glucose strips was 31.7%, while single-use packed strips were not contaminated at all. Ministry of Health hospitals had the highest contamination rates compared with other hospitals. Critical, obstetric, and surgical wards had the highest bacterial isolates number, where most were in the risk group 3 according to the National Institute of Health guidelines. Staphylococcus species were the most common bacteria found. CONCLUSION: Glucose meter strips should be recognized as a source of bacterial contamination that could be behind serious hospital acquired infections. The hospital infection control team should adopt proper measures to implement protocols for glucose meter cleaning and glucose strips handling.

The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach.

Investigating the molecular evolution of human genome has paved the way to understand genetic adaptation of humans to the environmental changes and corresponding complex diseases. In this review, we discussed the historical origin of genetic diversity among human populations, the evolutionary driving forces that can affect genetic diversity among populations, and the effects of human movement into new environments and gene flow on population genetic diversity. Furthermore, we presented the role of natural selection on genetic diversity and complex diseases. Then we reviewed the disadvantageous consequences of historical selection events in modern time and their relation to the development of complex diseases. In addition, we discussed the effect of consanguinity on the incidence of complex diseases in human populations. Finally, we presented the latest information about the role of ancient genes acquired from interbreeding with ancient hominids in the development of complex diseases.

Presence of Bacterial Virulence Gene Homologues in the dibenzo-p-dioxins degrading bacterium Sphingomonas wittichii.

Sphingomonas wittichii, a close relative of the human pathogen Sphingomonas paucimobilis, is a microorganism of great interest to the bioremediation community for its ability of biodegradation to a large number of toxic polychlorinated dioxins. In the present study we investigated the presence of different virulence factors and genes in S. wittichii. We utilized phylogenetic, comparative genomics and bioinformatics analysis to investigate the potentiality of S. wittichii as a potential virulent pathogen. The 16SrDNA phylogenetic tree showed that the closest bacterial taxon to S. wittichii is Brucella followed by Helicobacter, Campylobacter, Pseudomonas then Legionella. Despite their close phylogenetic relationship, S. wittichii did not share any virulence factors with Helicobacter or Campylobacter. On the contrary, in spite of the phylogenetic divergence between S. wittichii and Pseudomonas spp., they shared many major virulence factors, such as, adherence, antiphagocytosis, Iron uptake, proteases and quorum sensing. S. wittichii contains several major virulence factors resembling Pseudomonas sp., Legionella sp., Brucella sp. and Bordetella sp. virulence factors. Similarity of virulence factors did not match phylogenetic relationships. These findings suggest horizontal gene transfer of virulence factors rather than sharing a common pathogenic ancestor. S. wittichii is a potential virulent bacterium. Another possibility is that reductive evolution process attenuated S. wittichii pathogenic capabilities. Thus plenty of care must be taken when using this bacterium in soil remediation purposes.

Production of silver nanoparticles with strong and stable antimicrobial activity against highly pathogenic and multidrug resistant bacteria.

AIMS: To synthesize, characterize, and analyze antimicrobial activity of AgNPs of Escherichia hermannii (SHE), Citrobacter sedlakii (S11P), and Pseudomonas putida (S5). METHODS: The synthesized AgNPs were examined using ultraviolet-visible spectroscopy (UV-vis) and, zeta potential, and the size and the morphology obtained from the three different isolates were also confirmed by TEM. RESULTS: Among the three isolates tested, SHE showed the best antimicrobial activity due to the presence of small (4-12 nm) and stable (-22 mV) AgNPs. Stability of AgNPs was also investigated and found to be dependent on the nature of isolates. CONCLUSION: Produced AgNPs showed particle stability and antimicrobial efficacy up to 90 days of production. Our AgNPs exhibited greater antimicrobial activity compared with gentamicin against P. aeruginosa isolates and vancomycin against S. aureus and MRSA isolates at very low concentration (0.0002 mg per Microliters).

ACE I/D and MTHFR C677T polymorphisms are significantly associated with type 2 diabetes in Arab ethnicity: a meta-analysis.

In this meta-analysis study, SNPs were investigated for their association with type 2 diabetes (T2D) in both Arab and Caucasian ethnicities. A total of 55 SNPs were analyzed, of which 11 fulfilled the selection criteria, and were used for analysis. It was found that TCF7L2 rs7903146 was significantly associated with a pooled OR of 1.155 (95%C.I.=1.059-1.259), p<0.0001 and I(2)=78.30% among the Arab population, whereas among Caucasians, the pooled OR was 1.45 (95%C.I.=1.386-1.516), p<0.0001 and I(2)=77.20%. KCNJ11 rs5219 was significantly associated in both the populations with a pooled OR of 1.176(1.092-1.268), p<0.0001 and I(2)=32.40% in Caucasians and a pooled OR of 1.28(1.111-1.475), p=0.001 among Arabs. The ACE I/D polymorphism was found to be significantly associated with a pooled OR of 1.992 (95%C.I.=1.774-2.236), p<0.0001 and I(2)=83.20% among the Arab population, whereas among Caucasians, the pooled OR was 1.078 (95%C.I.=0.993-1.17), p=0.073 and I(2)=0%. Similarly, MTHFR C677T polymorphism was also found to be significantly associated among Arabs with a pooled OR of 1.924 (95%C.I.=1.606-2.304), p<0.0001 and I(2)=27.20%, whereas among Caucasians, the pooled OR was 0.986 (95%C.I.=0.868-1.122), p=0.835 and I(2)=0%. Meanwhile PPARG-2 Pro12Ala, CDKN2A/2B rs10811661, IGF2BP2 rs4402960, HHEX rs7923837, CDKAL1 rs7754840, EXT2 rs1113132 and SLC30A8 rs13266634 were found to have no significant association with T2D among Arabs. In conclusion, it seems from this study that both Arabs and Caucasians have different SNPs associated with T2D. Moreover, this study sheds light on the profound necessity for further investigations addressing the question of the genetic components of T2D in Arabs.

Isolation and characterization of microsatellite loci in the entomopathogenic nematode Heterorhabditis bacteriophora.

Twenty microsatellite loci were identified from genomic DNA enrichment and expressed sequence tags of entomopathogenic nematode Heterorhabditis bacteriophora. Eight loci were found to be polymorphic in a Northeast Ohio H. bacteriophora population. Levels of polymorphism were evaluated in 31-56 individuals and the number of alleles ranged from two to three. The values of observed and expected heterozygosities ranged from 0 to 0.536 and from 0.223 to 0.616, respectively. All eight loci showed heterozygote deficiencies, but three conformed to Hardy-Weinberg equilibrium at the subpopulation level. This is the first set of microsatellite markers in entomopathogenic nematodes.

Genetic variation and relationships between isolates and species of the entomopathogenic nematode genus Heterorhabditis deciphered through isozyme profiles.

We studied variation in isozyme patterns of 8 metabolic enzymes in 5 species of Heterorhabditis (H. bacteriophora, H. indica, H. marelata, H. megidis, and H. zealandica) comprising 18 isolates. Isozyme banding patterns of all the 8 enzymes were species specific; however, 3 enzymes, i.e., arginine kinase, fumarate hydratase, and malate dehydrogenase, displayed distinct patterns among all the 18 isolates. Phylogenetic analysis of the isozyme patterns produced dendrograms depicting a high degree of genetic variation among Heterorhabditis species, with the average pairwise distance of 0.2000. Trees constructed using different phylogenetic methods showed a relatively close genetic relationship between H. megidis and H. zealandica and between H. bacteriophora and H. indica. Also, H. bacteriophora HP88 was the most distant species from H. megidis (UK isolate), H. marelatus (Oregon isolate), and H. zealandica (X1 isolate) with pairwise distance of 0.1957, 0.2228, and 0.2120, respectively. Phylogenetic analysis also revealed genetic variation among H. bacteriophora isolates with the average pairwise distance of 0.1507. GPS2 and GPS3 were the most closely related isolates with the average distance of only 0.0870, followed by GPS1 and GPS2 with average distance of 0.1087. In contrast, KMD19 and HP88, OH25, and HP88, and OH25 and Acows isolates were the most divergent populations with a pairwise distance of 0.2011 and 37 character differences. Pairwise distance analysis also revealed that genetic divergence among populations of H. bacteriophora is relatively independent of geographic distance. Overall, these results demonstrate strong subspecies structuring in H. bacteriophora.