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

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

Molecular epidemiology of diarrhoeal virus infection in children in Saudi Arabia.

The etiology of viral diarrhoea in children in the Kingdom of Saudi Arabia (KSA) is incompletely characterized. Available data suggest that the causative agents are found at approximately similar frequencies here as elsewhere. However KSA is not a typical country; the lack of rivers and lakes may affect the paths open for virus spread in the Kingdom and the relatively high year-round temperature may limit virus survival in the environment. Sewage is disposed of to sea after treatment, and although virus is found in seawater, exposure via recreational use is limited those living along the coast. Virus is also found in seafood which may aid transmission inland but drinking water is supplied by desalination, a process that would effectively inactivate most viruses. Thus the bulk of viral transmission must be presumably via person to person or food-borne spread inland. Secondly, KSA plays host to many millions of visitors each year who flock to the country from all over the world in a short time period; the Hajj or annual pilgrimage to Makkah. This influx of persons offers opportunity both for the introduction of new strains of viruses and also for person to person transmission in these crowded venues. Consequently, there may be subtle differences in the manner of circulation of these viruses in KSA. This project 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. Viruses were sought in faecal specimens and characterized for genotype using molecular methods 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 six years or less) presenting with diarrhoea and thus representing community acquired rather than nosocomial infections. Human rotavirus (HRV) group A was detected in 6% (60/ 1000). By RT-PCRG1 was the predominant VP7 genotype (36/58, 62%), followed by the unique G9 (19/58, 33%). The other HRV genotypes found, 02 and 03, were less common at 1.2% (1/58) and 3.4% (2/58), respectively. P-type determination was also performed by RT-PCR and P[8] was clearly the most common (45/56, 80.3%). Overall 01P[8] was the most common, accounting for 60.7% of total samples positive for both genotypes. Rarer types 09P[4] (2/56, 3.57%) and 09P[6] (6/56, 10.7%) were identified for the first time in KSA. Enteric adenovirus (EAdV) was evident in 14/1000 pediatric stool samples (1.4%) by ELISA and all were also positive by RT- PCR. Enteric types 40 and 41 were distinguished using RT- PCR and RFLP; five samples were positive for EAdV-40 and 7 for EAdV-41. One sample showed a mixed infection of both 40 and 41. A single sample was eventually typed as type 31 by Sequencing. Human astrovirus (HAstV) was found in 1.9% (19/1000 samples). All but one was identified as type 8. This was a surprising finding since these infections were not nosocomial but independent, community-acquired cases. The remaining sample could not be amplified. Human caliciviruses are among the most common causes of gastrointestinal and there are no data for these viruses in Saudi Arabia. A smaller panel of 253 stool samples was tested for norovirus by ELISA and 9/253 were found positive (3.5%). Overall, most infections with rotavirus were detected in children of 1 year of age or less (P=0.047), and in children of 3 year of age or less with astrovirus likewise, in adenovirus most of the infections were detected in children of 2 year of age or less with P-Value of= 0.05, and 0.01 respectively. All viruses were distributed equally between males and females. HRV was the most common diarrhoeal virus detected followed by norovirus, although the rotavirus incidence found here was lower than that reported in previous studies. Infections showed a peak shortly after the Hajj during the study period. Novel HRV were found, with the first detection of the emergent G9 serotype and some combinations of G and P types new in KSA. Adenovirus 31 was reported for the first time and we found an unexpectedly high incidence of astrovirus serotype 8

Molecular epidemiology of diarrhoeal virus infection in children in Saudi Arabia.

The etiology of viral diarrhoea in children in the Kingdom of Saudi Arabia (KSA) is incompletely characterized. Available data suggest that the causative agents are found at approximately similar frequencies here as elsewhere. However KSA is not a typical country; the lack of rivers and lakes may affect the paths open for virus spread in the Kingdom and the relatively high year-round temperature may limit virus survival in the environment. Sewage is disposed of to sea after treatment, and although virus is found in seawater, exposure via recreational use is limited those living along the coast. Virus is also found in seafood which may aid transmission inland but drinking water is supplied by desalination, a process that would effectively inactivate most viruses. Thus the bulk of viral transmission must be presumably via person to person or food-borne spread inland. Secondly, KSA plays host to many millions of visitors each year who flock to the country from all over the world in a short time period; the Hajj or annual pilgrimage to Makkah. This influx of persons offers opportunity both for the introduction of new strains of viruses and also for person to person transmission in these crowded venues. Consequently, there may be subtle differences in the manner of circulation of these viruses in KSA. This project 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. Viruses were sought in faecal specimens and characterized for genotype using molecular methods 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 six years or less) presenting with diarrhoea and thus representing community acquired rather than nosocomial infections. Human rotavirus (HRV) group A was detected in 6% (60/ 1000). By RT-PCRG1 was the predominant VP7 genotype (36/58, 62%), followed by the unique G9 (19/58, 33%). The other HRV genotypes found, 02 and 03, were less common at 1.2% (1/58) and 3.4% (2/58), respectively. P-type determination was also performed by RT-PCR and P[8] was clearly the most common (45/56, 80.3%). Overall 01P[8] was the most common, accounting for 60.7% of total samples positive for both genotypes. Rarer types 09P[4] (2/56, 3.57%) and 09P[6] (6/56, 10.7%) were identified for the first time in KSA. Enteric adenovirus (EAdV) was evident in 14/1000 pediatric stool samples (1.4%) by ELISA and all were also positive by RT- PCR. Enteric types 40 and 41 were distinguished using RT- PCR and RFLP; five samples were positive for EAdV-40 and 7 for EAdV-41. One sample showed a mixed infection of both 40 and 41. A single sample was eventually typed as type 31 by Sequencing. Human astrovirus (HAstV) was found in 1.9% (19/1000 samples). All but one was identified as type 8. This was a surprising finding since these infections were not nosocomial but independent, community-acquired cases. The remaining sample could not be amplified. Human caliciviruses are among the most common causes of gastrointestinal and there are no data for these viruses in Saudi Arabia. A smaller panel of 253 stool samples was tested for norovirus by ELISA and 9/253 were found positive (3.5%). Overall, most infections with rotavirus were detected in children of 1 year of age or less (P=0.047), and in children of 3 year of age or less with astrovirus likewise, in adenovirus most of the infections were detected in children of 2 year of age or less with P-Value of= 0.05, and 0.01 respectively. All viruses were distributed equally between males and females. HRV was the most common diarrhoeal virus detected followed by norovirus, although the rotavirus incidence found here was lower than that reported in previous studies. Infections showed a peak shortly after the Hajj during the study period. Novel HRV were found, with the first detection of the emergent G9 serotype and some combinations of G and P types new in KSA. Adenovirus 31 was reported for the first time and we found an unexpectedly high incidence of astrovirus serotype 8

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

Abstract 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

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

Abstract 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

S4_Table_Stress_tolerance – Supplemental material for The Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup

<p>Supplemental material, S4_Table_Stress_tolerance for The Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup by Amr TM Saeb, Mohamed Abouelhoda, Manojkumar Selvaraju, Sahar I Althawadi, Maysoon Mutabagani, Mohammad Adil, Abdullah Al Hokail and Hamsa T Tayeb in Evolutionary Bioinformatics</p

S9_Table_Phage_associated_proteins – Supplemental material for The Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup

<p>Supplemental material, S9_Table_Phage_associated_proteins for The Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup by Amr TM Saeb, Mohamed Abouelhoda, Manojkumar Selvaraju, Sahar I Althawadi, Maysoon Mutabagani, Mohammad Adil, Abdullah Al Hokail and Hamsa T Tayeb in Evolutionary Bioinformatics</p

S7_Table_phospholipases,_lipoproteins,_integrons_and_transposons_elements – Supplemental material for The Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup

<p>Supplemental material, S7_Table_phospholipases,_lipoproteins,_integrons_and_transposons_elements for The Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup by Amr TM Saeb, Mohamed Abouelhoda, Manojkumar Selvaraju, Sahar I Althawadi, Maysoon Mutabagani, Mohammad Adil, Abdullah Al Hokail and Hamsa T Tayeb in Evolutionary Bioinformatics</p