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.

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 Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup.

Clostridium haemolyticum is the causal agent of bacillary hemoglobinuria in cattle, goat, sheep, and ruminants. In this study, we report the first recorded human-infecting C. haemolyticum strain collected from an 18-year-old woman diagnosed with acute lymphoblastic leukemia. After failure of traditional techniques, only next-generation sequencing (NGS) technology in combination with bioinformatics, phylogenetic, and pathogenomics analyses revealed that our King Faisal Specialist Hospital and Research Center (KFSHRC) bacterial isolate belongs to C. haemolyticum species. KFSHRC isolate is composed of 1 chromosome and 4 plasmids. The total genome size is estimated to be 2.7 Mbp with a low GC content of 28.02%. Comparative pathogenomics analysis showed that C. haemolyticum KFSHRC isolate is a potential virulent pathogenic bacterium as it possesses the virulence factors necessary to establish an infection, acquire essential nutrients, resist antimicrobial agents, and tolerate hostile conditions both in the human host and in its surrounding environment. These factors are included in the main chromosome in addition to novel recombination of the plasmids, and they could be the reason for the incidence of that human infection. This work demonstrated the importance of using NGS in medical microbiology for pathogen identification. It also demonstrates the importance of sequencing more microbial samples and sharing this information in public databases to facilitate the identification of pathogenic microbes with better accuracy.

Genotyping of CYP2C19 polymorphisms and its clinical validation in the ethnic Arab population.

OBJECTIVES: The drug-metabolizing enzymes and transporters (DMET) Plus microarray and x-Tag assays have recently been developed for genotyping individuals in personalized medicine. Furthermore, the cytochrome 450-2C19 (CYP2C19) is a key metabolic enzyme encoded by a polymorphic gene commonly associated with diminished metabolism and variable clinical responses to several drugs in an ethnicity-dependent fashion. Therefore, validation of these clinical procedures as well as knowledge of the ethnic-specific incidences of these gene variants is prerequisite for determining their clinical relevance in any given population. METHODS: We determined the distribution of familiar CYP2C19 variants by the DMET Plus chip in 600 candidates and replicated the findings by the Affymetrix Axiom Genome-Wide Asian Structure Identification Array in 5413 individuals, all Saudis of ethic Arab origin. We then tested the robustness of employing the Luminex xMAP system clinically by comparing the results of genotyping 500 Saudi individuals visiting the Blood Bank of our institution with the findings of the two platforms. KEY FINDINGS: The DMET Plus genotyping revealed that eight of the CYP2C19 variants showed some changes. Thereby, the CYP2C19*17 exhibited the highest minor allele frequency (MAF) of 0.256, followed by the CYP2C19_801 (frequency = 0.055). Six other variants, including the CYP2C19*3, showed MAF in the range of 0.001-0.002. We replicated the frequencies of the CYP2C19*17 and CYP2C19*3, and additionally established that of the CYP2C19*2 (0.099) using the Axiom platform. The xTag genotyping also indicated that 0.834 of the 500 Saudi individuals were extensive metabolizers (*1/*1), 0.158 carried the *1/*2 genotype, 0.01% carried *2/*2 (poor metabolizers) and one each (0.2%) harboured the *1/*8, *2/*3 (intermediate metabolizers) and *8/*8 (poor metabolizers) genotypes. CONCLUSIONS: The results showed reproducible genotyping of the CYP2C19 variants in the Saudi Arab population using two Affymetrix platforms and phenotyping using the Luminex xTag assay. The prevalence of two clinically relevant genotypes (CYP2C19*2 and CYP2C19*3) were similar to other ethnic groups, while that of the CYP2C19*17 was comparably higher.

Increased prevalence of rotavirus among children associated gastroenteritis in Riyadh Saudi Arabia.

UNLABELLED: The aim of this study is to assess the epidemiology along with the molecular structure of rotavirus causing pediatric diarrhea among Saudi patients. However, in this report we sited the epidemiological reflect coming from our project. METHODS: One thousand and seven diarrheal stool samples had been collected between Jan 1st, 2008 and OCT 31st, 2010 from hospitalized patients below the age of 5 year. Samples were then examined using Enzyme-linked immunosorbent assay (ELISA). Demographic data were collected including age, sex, date of admission and discharge. Finally, the chi-squire test, α level of significance was used to test the variables in the data. RESULTS: Of these 1007 stool samples, rotavirus was detected in 65.5% (660/1007 samples). We observed that children who are 1 year of age or less had more infection with rotavirus 81% (534/660) than those who is over 1 year of age (19%,126/660) (P = 0.000). Infections occur throughout the year with no clear significant seasonal peaks. The difference between males (57.5%, 380/660) and females (42.4%, 280/660) in terms of rotavirus positivity is statistically significant. CONCLUSIONS: The high rate of positivity, are at variance with previously published reports of rotavirus infection in Saudi Arabia since 2005 which reported a major decrease year by year in the incidence of rotavirus over; 2005, 2006 and 2008 with percentage of; 25%, 10%, 6% respectively explained by improvements in public health introduced in recent years. Our increasing rate result (65.5%) may suggest emerging of unusual serotypes, not been represent to our country earlier.

Molecular epidemiology of human astrovirus infections in Saudi Arabia pediatric patients.

Earlier work Tayeb et al. [Tayeb et al. (2008): J Med Virol 80: 1919-1929] set out to study the epidemiology of diarrhea viruses in pediatric populations. The study addressed initially rotavirus, enteric adenovirus, and astrovirus but was later expanded to include norovirus (NoV). Viruses were sought in fecal specimens and characterized for genotype using molecular methods (PCR, RT-PCR, and RFLP) for the first time in KSA. The survey focused on three locations; Jeddah, Makkah, and Riyadh. During the Hajj, the chief population fluxes are via Jeddah to Makkah. One thousand samples were obtained from children (aged 6 years or less) presenting with diarrhea and thus representing community acquired rather than nosocomial infections. Rotavirus was identified in 6% of the samples followed by NoV accounted for 3.5%, astrovirus 1.9%, and adenovirus 1.4%. Rotavirus G9 was characterized for the first time in Saudi Arabia. Adenoviruses were confirmed and further typed using hexon-specific PCR and RFLP. These data were published by Tayeb et al. [Tayeb et al. (2008): J Med Virol 80: 1919-1929]. However, the nature of astrovirus identified was not investigated further. Therefore, more analysis details are appropriate for astrovirus in the Kingdom. As an extension of earlier work carried out on astrovirus serotype distribution in the Kingdom [Tayeb et al. (2008): J Med Virol 80: 1919-1929], a major objective of the project is to use molecular methods to determine the distribution of astrovirus genotype. Such data will help to provide valuable insights into genetic identities and possible sources of virus strains involved not only in pediatric gastroenteritis but also possible outbreaks in the community.

Enteric viruses in pediatric diarrhea in Saudi Arabia.

Between September 1st, 2002 and August 31st, 2003, a panel of 1,000 stool samples was collected from patients presenting with diarrhea in the three major urban centers of Saudi Arabia; Riyadh, Mecca, and Jeddah. Each sample was tested for rotavirus, and astrovirus by ELISA, G and P type was determined for all rotaviruses. Adenoviruses were sought by hexon-specific PCR and identified by RFLP. A subset of 253 samples was also tested for norovirus by ELISA. Data were analyzed for seasonality of infection, patient nationality and likelihood of hospitalization. Although the overall incidence of rotavirus identification in acute diarrheal stool continued to decline, this was still the virus identified most commonly (6%). Norovirus accounted for 3.5%, astrovirus, 1.9% and adenovirus, 1.4%. Type G9 rotavirus was found to be present (and already common) in 2003, predating its first reported identification in the country in 2004. Most of the virus infections (and most of the G9 detections) occurred in April, the month following the occurrence of the Hajj in the study year. Although most viruses were spread equally in the population, rotaviruses were significantly more common in non-Saudis than in Saudi citizens. Overall the data are consistent with an increase in all virus infections following al Hajj and the potential introduction of novel strains (such as the G9 rotaviruses) by pilgrims. Hospitalization was significantly associated only with norovirus infections.