Mycobacterium tuberculosis complex: Detection and patterns of resistance to the first line anti-TB drugs at the King Abdulaziz University Hospital, Saudi Arabia

Tuberculosis (TB) remains a major cause of morbidity and mortality worldwide. Continued surveillance of drug susceptibility help determining treatment regimen by anti-tuberculous drugs. Gene Xpert PCR sensitivity was compared to the liquid culture media by Versa TREK for detecting Mycobacterium tuberculosis complex(MTBC). Rates, patterns and types of anti-tuberculosis drug- resistance atKing Abdulaziz University Hospital (KAUH), Jeddah, KSA were determined from January 2013 to June 2014.A total of 101 tuberculous patients were included, 43 Saudi tuberculous patients and 58 non-Saudi tuberculous patients. All resistances detected were primary resistances. PCR Sensitivities for detection of MTBC were 29.4%, 80%, 87.5%, 77.8% and 100% in AFB-negative samples and AFB +1,+2,+3 and +4 positive samples respectively. MTBC percentage detected by PCR was 88.1% in AFB-positive samples and 29.9% in AFB-negative ones. Versa Trek detection time was 15.01±7.32 days in AFB-positive samples and 26.63±6.7 days in AFB-negative ones. MTBC pyrazinamide resistance was (13.86%), followed by streptomycin (7.9%), rifampicin (3.96%) and isoniazid (3.96%). Mono-resistance percentages to pyrazinamide, rifampicin and isoniazid were 11.88%, 1.98% and 0.99% respectively. MDR-TB were 1.98% and anti-TB resistance percentage was 24.75%. There was no significant difference between Saudi and non-Saudi tuberculous patients regarding anti- tuberculous drugs resistance.Â

A new focus of autochthonous transmission of Cordylobia anthropophaga in Saudi Arabia

AbstractBackgroundCordylobia anthropophaga, is responsible for nodular cutaneous myiasis in sub-Saharan Africa. The fly has long been limited to tropical Africa except for Asir Province, Saudi Arabia. Al Baha Province; north of Asir has an ecological pattern close to that dominant in subtropical Africa. The Southern parts of Saudi Arabia, including Al Baha, are considered part of the Afro-tropical zoogeographical belt where C. anthropophaga is dominant. A case, with cutaneous nodular lesions, was presented to us, where comprehensive investigations were done to establish the diagnosis and to relate it to the known epidemiological background.Materials and methodsA thorough history taking, comprehensive clinical examination and an intensive parasitological examination on a viable larva recovered from the cutaneous lesions, were performed. Taxonomic identification of the larva was done based on various criteria including shape, size, cuticle spine pattern and the posterior spiracles of the recovered larva.ResultsWe report a case of cutaneous myiasis, caused by Cordylobia anthropophaga, indigenously acquired in Al-Baha. The recovered larva was identified as the third instar of C. anthropophaga. With no history of travel to Africa or to Asir, along with a comprehensive epidemiological assessment, an autochthonous pattern of transmission was confirmed.ConclusionWe present a new focus of autochthonous transmission of C. anthropophaga in Saudi Arabia suggesting a need for an epidemiological reassessment. We also propose considering Cordylobia myiasis as a differential diagnosis in furuncular skin lesions, even in individuals with no history of traveling to Africa

Anti-Tuberculous Activity of Treponemycin Produced by a Streptomyces Strain MS-6-6 Isolated from Saudi Arabia

A Streptomyces strain MS-6-6 with promising anti-tuberculous activity was isolated from soil samples in Saudi Arabia. The nucleotide sequence of its 16S rRNA gene (1426 bp) evidenced a 100% similarity to Streptomyces mutabilis. Through an anti-tuberculous activity-guided approach, a polyketide macrolide was isolated and identified as treponemycin (TP). The structure of the isolated compound was determined by comprehensive analyses of its 1D and 2D NMR as well as HRESI-MS. In addition to the promising anti-tuberculous activity (MIC = 13.3 µg/mL), TP showed broad spectrum of activity against the Gram positive, Gram negative strains, and Candida albicans. Improvement of TP productivity (150%) was achieved through modification in liquid starch nitrate medium by replacing KNO3 with corn steep liquor and yeast extract or tryptone, and removing CaCO3 and K2HPO4. The follow up of TP percentage as well as its metabolites profile for each media was assessed by LC/DAD/MS

Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota

This work is dedicated to the memory of Marcel Sy (PhD student died on 15 September 2016); Marcel Sy has made a substantial contribution to this work, especially in fungal culturomics.International audienceHerein, the mycobiota was characterized in fecal samples from sick patients and healthy subjects, collected from different geographical locations and using both culturomics and amplicon-based metagenomics approaches. Using the culturomics approach, a total of 17,800 fungal colonies were isolated from 14 fecal samples, and resulted in the isolation of 41 fungal species, of which 10 species had not been previously reported in the human gut. Deep sequencing of fungal-directed ITS1 and ITS2 amplicons led to the detection of a total of 142 OTUs and 173 OTUs from the ITS1 and ITS2 regions, respectively. Ascomycota composed the largest fraction of the total OTUs analyzed (78.9% and 68.2% of the OTUs from the ITS1 and ITS2 regions, respectively), followed by Basidiomycota (16.9% and 30.1% of the OTUs from the ITS1 and ITS2 regions, respectively). Interestingly, the results demonstrate that the ITS1/ITS2 amplicon sequencing provides different information about gut fungal communities compared to culturomics, though both approaches complete each other in assessing fungal diversity in fecal samples. We also report higher fungal diversity and abundance in patients compared to healthy subjects. In conclusion, combining both culturomic and amplicon-based metagenomic approaches may be a novel strategy towards analyzing fungal compositions in the human gut

Bacterial Community and Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates from the Environment of a Health Care Facility in the Western Region of Saudi Arabia

The escalating transmission of hospital-acquired infections, especially those due to antimicrobial-resistant bacteria, is a major health challenge worldwide. In this study, a culturomic analysis of bacterial community in a tertiary care hospital in the western region of Saudi Arabia is performed using environmental samples. The genome sequencing of four Acinetobacter baumannii was performed on isolates recovered from an intensive care unit (ICU) environment and clinical samples. A total of 361 bacterial isolates from surface and air samples were identified by MALDI-TOF technique or 16S rRNA gene sequencing. The isolates were classified into 70 distinct species, including ESKAPE pathogens. Resistance in Gram-positive isolates was mainly found to be against benzylpenicillin, azithromycin, ampicillin, and trimethoprim/sulfamethoxazole. Carbapenem- and multidrug-resistant isolates of A. baumannii and Klebsiella pneumonia were found on the ICU surfaces. Genome sequencing revealed that the carbapenem-resistant A. baumannii isolate from ICU environment was linked with those of clinical origin. The isolate Ab133-HEnv was classified as a novel sequence type (ST2528) based on a new allele of Oxf_gdhB-286. Three beta-lactam-antibiotic-resistance genes, blaADC-25, blaOXA-23, and blaOXA-66, were found in most of the analyzed genomes. Collectively, the results of this study highlight the spread of antimicrobial-resistant nosocomial pathogens in a health care facility in Saudi Arabia

Gut microbiome and dietary patterns in different Saudi populations and monkeys

International audienceHost genetics, environment, lifestyle and proximity between hosts strongly influence the composition of the gut microbiome. To investigate the association of dietary variables with the gut microbiota, we used 16S rDNA sequencing to test the fecal microbiome of Bedouins and urban Saudis and we compared it to the gut microbiome of baboons living in close contact with Bedouins and eating their leftovers. We also analyzed fermented dairy products commonly consumed by Bedouins in order to investigate their impact on the gut microbiome of this population. We found that the gut microbiomes of westernized urban Saudis had significantly lower richness and biodiversity than the traditional Bedouin population. The gut microbiomes of baboons were more similar to that of Bedouins compared to urban Saudis, probably due the dietary overlap between baboons and Bedouins. Moreover, we found clusters that were compositionally similar to clusters identified in humans and baboons, characterized by differences in Acinetobacter, Turicibacter and Collinsella. The fermented food presented significantly more bacteria genera common to the gut microbiome of Bedouins compared to urban Saudis. These results support the hypothesis that dietary habits influence the composition of the gut microbiome

Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov.

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