Camelid genomes reveal evolution and adaptation to desert environments.

Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

Genome-wide analysis of the emerging infection with Mycobacterium avium subspecies paratuberculosis in the Arabian camels (Camelus dromedarius).

Mycobacterium avium subspecies paratuberculosis (M. ap) is the causative agent of paratuberculosis or Johne's disease (JD) in herbivores with potential involvement in cases of Crohn's disease in humans. JD is spread worldwide and is economically important for both beef and dairy industries. Generally, pathogenic ovine strains (M. ap-S) are mainly found in sheep while bovine strains (M. ap-C) infect other ruminants (e.g. cattle, goat, deer), as well as sheep. In an effort to characterize this emerging infection in dromedary/Arabian camels, we successfully cultured M. ap from several samples collected from infected camels suffering from chronic, intermittent diarrhea suggestive of JD. Gene-based typing of isolates indicated that all isolates belong to sheep lineage of strains of M. ap (M. ap-S), suggesting a putative transmission from infected sheep herds. Screening sheep and goat herds associated with camels identified the circulation of this type in sheep but not goats. The current genome-wide analysis recognizes these camel isolates as a sub-lineage of the sheep strain with a significant number of single nucleotide polymorphisms (SNPs) between sheep and camel isolates (∼1000 SNPs). Such polymorphism could represent geographical differences among isolates or host adaptation of M. ap during camel infection. To our knowledge, this is the first attempt to examine the genomic basis of this emerging infection in camels with implications on the evolution of this important pathogen. The sequenced genomes of M. ap isolates from camels will further assist our efforts to understand JD pathogenesis and the dynamic of disease transmission across animal species.

Pathology and molecular diagnosis of paratuberculosis of camels.

Camels are the prime source of meat and milk in many desert regions of the world including Saudi Arabia. Paratuberculosis of camels, locally called Silag, is a serious and invariably fatal disease in the Arabian camel. Six camels were used in this study. Five camels with clinical paratuberculosis were used to study the pathology of the disease and confirm its aetiology. The sixth camel was clinically healthy and used as a control. The camels were examined clinically and bled for haematological and blood chemistry analysis. They were then humanely killed with a high intravenous dose of thiopental sodium (10 mg/kg) for pathological studies as well as obtaining tissues for microbiological and molecular studies. The clinical signs of the disease were emaciation, diarrhoea, alopecia, wry neck and pale mucous membranes. Laboratory diagnosis showed reduced haemoglobin concentration, low haematocrit and high activity of the serum enzyme alanine aminotransferase. Serum creatinine concentration was normal. These results indicated the infected camels were anaemic and the function of their livers was affected. Postmortem examination showed thickened and corrugated intestinal mucosa, enlarged granulomatous mesenteric lymph nodes, miliary and diffuse granulomas in the liver (in four camels), generalized lymph node granulomas (in one camel), splenic granuloma (in one camel) and mediastinal lymph node granuloma (in two camels). Histopathological examination showed diffuse infiltration of macrophages in all organs showing lesions. Ziehl-Neelsen staining of tissue scraping and tissue sections showed masses of acid fast bacilli, except for the spleen. Infection with Mycobacterium avium subsp. paratuberculosis was confirmed by PCR by targeting the IS900 gene.

Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedarius.

Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF) analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF>300 bp and approximately 40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes. Similarity analyses are done separately for different organisms including human, mouse, bovine, and rat. Accompanying web portal, CAGBASE (http://camel.kacst.edu.sa/), hosts a relational database containing annotated EST sequences and analysis tools with possibility to add sequences from public domain. We anticipate our results to provide a home base for genomic studies of camel and other comparative studies enabling a starting point for whole genome sequencing of the organism.

Phenotypic and genotypic characterization of invasive Streptococcus pneumoniae clinical isolates.

BACKGROUND: The emergence of infection caused by invasive penicillinnonsusceptible (PNS) and multidrug-resistant strains of Streptococcus pneumoniae has become a worldwide concern, necessitating the epidemiologic surveillance of such strains. OBJECTIVES: One aim of this study was to identify clones of invasive PNS S pneumoniae among isolates in Riyadh, Saudi Arabia. The second aim was to compare these clones with international clones to track their spread in Saudi Arabia. METHODS: The phenotypes of invasive isolates characterized as S pneumoniae were determined using susceptibility testing and serotyping (capsular test and E-test). The genotypes of PNS isolates were determined using random amplified polymorphic DNA analysis. The genetic relatedness of these local strains to the international widespread clones was investigated. RESULTS: Of 296 S pneumoniae isolates identified using biochemical and culture characteristics, 89 (30.1%) were invasive. Susceptibility testing using the E-test revealed that 17 of the 89 invasive isolates (19.1%) were PNS. Most of the 89 isolates (89.9%) were resistant to sulfamethoxazole-trimethoprim; 32.6% and 23.6% of isolates were resistant to chloramphenicol and tetracycline, respectively. All of the isolates (100.0%) were fully susceptible to ceftriaxone and vancomycin. Capsular serotyping of the 89 isolates showed that 19A (18.0%), 613 (14.6%), 23F (13.5%), 9V (11.2%), 14 (6.7%), 19F (5.6%), and 18C (4.5%) were the most predominant serogroups/serotypes. The 17 PNS strains were confirmed on polymerase chain reaction to have penicillin resistance genes. Of these 17 strains, international clone 19A-a was the most predominant (41.2%), followed by 6B-a (17.6%), and 23F-a and 9V-a (each, 11.8%). CONCLUSIONS: The present study identified the spread of the 4 most commonPNS S pneumoniae isolates (clones)-19A, 613, 23F, and 9V-to Riyadh, but identified no new clones among patients having invasive infection with S pneumoniae in Riyadh. This study emphasizes that international PNS clones have contributed to the prevalence and spread of PNS pneumococci among the clinical isolates in Saudi Arabia.