A first insight into the genetic diversity and population structure of Mycobacterium tuberculosis in Zonguldak, Turkey.

This study evaluated the molecular epidemiology and biodiversity of Mycobacterium tuberculosis isolates in Zonguldak, Turkey, and investigated the presence and significance of the LAM7-TUR clone by spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) analysis. In total, 128 isolates were tested by spoligotyping; 25 selected isolates representative of the LAM7-TUR clone and similar types were also tested by MIRU-VNTR analysis. In total, 47 distinct patterns were revealed by spoligotyping, represented by 13 clusters containing between two and 28 isolates (94 isolates in total), and 34 unique patterns (a clustering rate of 73%). Using MIRU-VNTR analysis, the clustering relationships revealed by spoligotyping were confirmed. The most common spoligotyping profile was SIT53, followed by SIT41 (LAM7-TUR) and SIT50. The SIT284 clone was another phylogeographically specific clonal complex whose presence in Turkey may be endemic. The LAM7-TUR genotype was highly prevalent in Zonguldak.     

Microbial pathogenesis: an insight into Mycobacterium tuberculosis

Tuberculosis, as yet, is far from being controlled. Several reasons can be attributed to this, a major contributing factor being the development of resistance to the currently available drugs due to the successful adaptation of the pathogen. Most of the inferences about the pathogen are based on the observation of mycobacteria grown in synthetic media in vitro and of the mycobacteria maintained in macrophages simulating the in vivo conditions. Molecular studies in mycobacteria had been slow to come due to the difficulty in the generation of mutants. However, new technologies that have now been developed for studying in vivo expressed molecules in other bacterial systems are being successfully applied to mycobacteria, especially the pathogenic M. tuberculosis. Additionally, an equally important factor in the study of the disease is the genetic predisposition of population to the infection. New findings link the Nramp1 and Toll receptor polymorphisms to susceptibility to infectious diseases.     

First Insight into Mycobacterium tuberculosis Epidemiology and Genetic Diversity in Trinidad and Tobago

This report is based on a 1-year recruitment of all of the culture-positive Mycobacterium tuberculosis cases in Trinidad and Tobago (n = 132). The study population was characterized by a high male-to-female sex ratio of 4 and a human immunodeficiency virus-tuberculosis (TB) coinfection rate of 30%. It mainly occurred among African descendants, who represent 37.5% of the total population but 69.7% of all TB cases (P < 0.001). Spoligotyping resulted in 25 different patterns and 12 clusters (2 to 74 strains per cluster), with the predominance of a highly conserved spoligotype international type clone, SIT566.Referred to as the business capital of the Caribbean, Trinidad and Tobago (T&T) had an annual tuberculosis (TB) incidence rate of 17 cases/100,000 population in 2006, and control of TB remains a priority in T&T (6). The number of reported cases has remained stable over the last decade, with an average of 196 cases per year (range, 159 to 253) and in 2006, the majority of the cases were seen in the County of St. George, with more than one-half of the reported cases. Although Mycobacterium tuberculosis genetic biodiversity was recently studied in the French departments of the Americas and Haiti (3, 5), the present study conducted in T&T is the first among all English-speaking Caribbean islands to study the genetic diversity of circulating M. tuberculosis clones.All of the 132 TB patients presenting a positive M. tuberculosis culture from October 2006 to September 2007 were included in the present study, and basic demographic data were collected by using a standard questionnaire from the files provided at the hospital. Spoligotyping was carried out as previously described (7) on bacterial DNA samples shipped to the Pasteur Institute of Guadeloupe, and the patterns obtained were compared by using the SITVIT2 proprietary database of the Pasteur Institute of Guadeloupe, which is an updated version of the previously released SpolDB4 database (2). In this database, SIT (spoligotype international type) designates spoligotyping shared by two or more patient isolates, whereas MIT (mycobacterial interspersed repetitive unit [MIRU] international type) designates 12-locus MIRU patterns shared by two or more patient isolates, as opposed to “orphan,” which designates patterns reported for a single isolate. Major phylogenetic clades were assigned according to the signatures provided in SpolDB4 (2). Lastly, PCR-based 12-locus MIRU typing was performed on selected DNA samples by using primers described previously (9, 13).Compared to the extremely high annual TB incidence in some hot spots in the Caribbean such as Haiti (299/100,000) and the Dominican Republic (89/100,000) (http://www.who.int/globalatlas/dataQuery/default.asp), the TB incidence in T&T remained moderate at 17/100,000 in 2006 (6). However, the TB patients in T&T were characterized by a very high male-to-female sex ratio of 4.0, which is significantly higher than the sex ratios observed in Martinique (1.0), Haiti (1.2), and Guadeloupe (2.1) (P < 0.001 for Martinique and Haiti, P < 0.02 for Guadeloupe) (3, 6). African descendants represented 37.5% of the total population but 69.7% of all TB cases (P < 0.001). Of the 119 patients whose case statuses were known, 77.3% (92/119) were new cases and 22.7% (27/119) belonged to the category of treatment failure/relapse/defaulter. The study population (mean age, 42.8 years; range, 17 to 78 years; 54/125 cases in the 35-to-54-year age group, P < 0.05) was characterized by a human immunodeficiency virus (HIV)-TB coinfection rate of 30.6% (HIV serology results were available for 121/132 patients). No cases of multidrug-resistant TB (combined resistance to isoniazid and rifampin) were observed, a finding which is in contrast to previous studies in Africa and the Caribbean, where high HIV-TB coinfection rates were often accompanied by the emergence of multidrug-resistant TB (4, 5, 8, 12). Regarding the geographic origin of the patients, 40.5% (15/37) of the HIV-positive patients versus 17.9% (15/84) of the HIV-negative patients lived in central St. George county, which includes the capital city of Port of Spain (P < 0.01).Spoligotyping resulted in 25 patterns corresponding to 13 single isolates and 12 clusters (2 to 74 strains per cluster) (Table ​(Table1).1). A high clustering rate of 90% (119/132 isolates) was due to a single large cluster of 74 strains (SIT566) along with five other major clusters (SIT1, SIT61, SIT2550, and two newly created shared-types, SIT2934, SIT2935; 5 to 8 strains/cluster). The six remaining smaller clusters (SIT42, 50, SIT119, 478, 958, and 1823) contained two or three strains per cluster. Among the 13 unclustered strains, 12 belonged to preexisting SIT designations in the database, while a single isolate corresponded to an orphan pattern. The genotypic lineage determination showed that 43.2% (57/132) of the clinical isolates were correctly classified (Table ​(Table1).1). The predominant clone, SIT566, and Latin American-Mediterranean (LAM) and East African-Indian (EAI) lineage strains were found throughout the country (with the exception of LAM and EAI in the eastern county of St. Andrew/St. David and LAM on Tobago). The patients harboring the SIT566 clone (versus other spoligotypes) were more often HIV positive (62.2% of the HIV-TB-coinfected patients), were significantly younger (mean age, 39.1 years versus 47.7 years, P < 0.0005), and mostly originated from central St. George County (31.4% of all SIT566 patients, P < 0.05).

TABLE 1.

Spoligotyping-based biodiversity in T&T and SITVIT2 database comparison^a

Primary Antibody Deficiency in Arabs: First Report from Eastern Saudi Arabia

Epidemiological studies have shown wide geographical and racial variations in the prevalence and pattern of immunodeficiency diseases. As there is no national registry, very little is known of the prevalence and nature of humoral immunodeficiency in the Arabian peninsula. We report here for the first time the analysis of serum immunoglobulin (Ig) levels in 2000 consecutive patients (age, 1–80 years). They were seen over a period of 6 years and were referred to us from six district hospitals for suspected immunodeficiency, autoimmunity, allergy, or immunoglobulin dyscrasia. Forty-six were found to be immunodeficient, in whom at least one of the Ig class was low; 15 had secondary immunodeficiency. The remaining 31 cases, representing 1.5% of the population studied (giving a prevalence of 1550/100,000 hospital registered patients), were categorized into four primary humoral immunodeficiency groups: these included, in order of frequency, (i) selective IgA deficiency (45%; 700/100,000) (ii) common variable immunodeficiency (CVID) (29%; 450/100,000), (iii) agammaglobulinemia (16%; 250/100,000), and (iv) selective IgG deficiency (10%; 150/100,000). Compared with similar hospital-based surveys in the west the prevalence of humoral immunodeficiency seems to be higher in Arabs; this in part may be related to race and higher rate of consanguinity. Most patients with IgA deficiency had either infection, atopy or autoimmunity. Compared with some other races, agammaglobulinemia (X- and non-X-linked) seems to be more prevalent.     

Cold urticaria in Saudi Arabia

During an 8-year period we have seen two cases of cold-induced urticaria at the King Faisal Specialist Hospital and Research Centre, a major tertiary centre in Saudi Arabia. This indicates a lower prevalence in Saudi Arabia compared with other countries. One of our patients did not respond to cyproheptadine but she had an excellent response to ketotifen.     

Genetic diversity and population structure of Mycobacterium tuberculosis in Casablanca, a Moroccan city with high incidence of tuberculosis

Although lower-resource countries have by far the highest burden of tuberculosis, knowledge of Mycobacterium tuberculosis population structure and genetic diversity in these regions remains almost nonexistent. In this paper, 150 Moroccan M. tuberculosis isolates circulating in Casablanca were genotyped by random amplified polymorphic DNA analysis using 10 different primers and by mycobacterial interspersed repetitive units-variable number of tandem repeats typing at 12 loci. The population genetic tests revealed a basically clonal structure for this population, without excluding rare genetic exchanges. Genetic analysis also showed a notable genetic polymorphism for the species M. tuberculosis, a weak cluster individualization, and an unexpected genetic diversity for a population in such a high-incidence community. Phylogenetic analyses of this Moroccan sample also supported that these isolates are genetically heterogeneous.     

Benign sickle cell disease in Saudi Arabia: survival estimate and population dynamics

A survey of 8,084 adult Saudi male employment applicants yielded 872 with the sickle cell trait (AS) and 51 with sickle cell disease. Based on the known distribution of hemoglobin S genes between oasis and non-oasis populations in Saudi Arabia, and on calculation of the expected number of abnormal homozygotes within the non-oasis and oasis subgroups as well as the entire employment applicant group, it appears that virtually 100% of Saudis with SS disease survive to adult life. Saudi Arabs and other Caucasian populations in the Middle East exhibit a benign type of SS disease as compared with Blacks in Africa and the Americas. In the Middle East, gene contributions from SS individuals will shift equilibrium frequencies to higher levels than encountered in Black populations under sustained selective pressures, and the polymorphism will tend to be stable with decline in selective pressure. There are some indications that the hemoglobin S gene may have been a recent import into the Middle East.     

First molecular epidemiology study of Mycobacterium tuberculosis in Burkina Faso

We conducted a molecular epidemiology study on 120 Mycobacterium tuberculosis isolates from patients presenting pulmonary tuberculosis (TB) in Burkina Faso. Classical antibiogram studies and genetic characterization, using mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing and spoligotyping, were applied after culture. Molecular analysis of specific signatures showed that all TB cases reported in this study were caused by M. tuberculosis and identified no Mycobacterium bovis or Mycobacterium africanum isolates. This result is unexpected, as M. africanum strains were reportedly the etiologic agent in 20% of TB cases 2 decades ago. The comparison of spoligotypes from Burkina Faso with an international spoligotype database (SpolDB4) showed that the majority of isolates belong to major clades of M. tuberculosis (Haarlem, 9%; Latin American-Mediterranean, 30%; and T, 20%). The predominant group of isolates (30%) corresponds to spoligotype 61, described in Cameroon as the "Cameroon family." In Burkina Faso, as in Cameroon, this family could be associated with recent transmission of TB, suggesting a recent expansion in West Africa. Our data suggest a low level of primary drug resistance that may be a positive result of the Directly Observed Therapy Shortcourse program. Besides, based on spoligotyping plus MIRU-VNTR, data showed a high number of clusters in our sample, suggesting a high level of recent TB transmission in Burkina Faso. Nevertheless, an important genetic polymorphism was observed in this country, reflecting an endemicity situation where the control of TB would have less impact in the main towns.     

Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti

Djibouti is an East African country with a high tuberculosis incidence. This study was conducted over a 2-month period in Djibouti, during which 62 consecutive patients with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using mycobacterial interspersed repetitive-unit variable-number tandem-repeat typing and spoligotyping, was performed. The genetic and phylogenetic analysis revealed only three major families (Central Asian, East African Indian and T). The high diversity and linkage disequilibrium within each family suggest a long period of clonal evolution. A Bayesian approach shows that the phylogenetic structure observed in our sample of 62 isolates is very likely to be representative of the phylogenetic structure of the M. tuberculosis population in the total number of TB cases.     

A new insight into PMM2 mutations in the French population

Congenital disorder of Glycosylation type Ia is an autosomal recessive disorder, characterized by a central nervous system dysfunction and multiorgan failure associated with defective N-glycosylation and phosphomannomutase (PMM) deficiency related to mutations in the PMM2 gene (mRNA U85773.1, gene ID 5373). More than 75 different mutations have been previously described. In our study, 38 different mutations were found in 52 French families with CDG-Ia. Eleven mutations had not been previously published in CDG-Ia patients: eight missense and three splice mutations. We studied the PMM activity of eight novel recombinant mutant proteins in an E. coli expression system, comparing them with the wild type protein, c.422 G>A (R141H), and c.415 G>A (E139K) mutant proteins. We also studied the previously described c.590 C>A (E197A) found on the same allele as c.394 A>T (I132F). All mutant proteins studied except E197A had decreased activity and/or were thermolabile, and were pathogenic mutations. Haplotype studies revealed a founder effect for E139K mutation, only described in France and found in seven CDG-Ia families (7.6%). In contrast, at least two different haplotypes were observed for the R141H mutation in France, studied in 23 families. The R141H seems to be a combination of the "old" R141H mutation found all over Europe and a second "French" R141H, and could be substantially older than E139K.     

Increased prevalence of asthma in Saudi Arabia.

BACKGROUND: Bronchial asthma is among the most common chronic illnesses of childhood. A number of reports in the recent past suggest that the prevalence of asthma is increasing globally. OBJECTIVE: To investigate the changing prevalence of asthma in the Kingdom of Saudi Arabia. SUBJECTS AND METHODS: Two populations of schoolchildren between the ages of 8 and 16 years were studied using an internationally designed protocol in 1986 and 1995. The questionnaire used in these studies was very similar to the one used in the International Study of Allergy and Asthma in Childhood. A total of 2,123 school-children in 1986 (Jeddah and Riyadh) and 1,008 schoolchildren in 1995 (Hail and Gizan) were enrolled in the surveys. These cross-sectional studies of randomly selected schoolchildren were statistically analyzed using ANOVA and a Z test. RESULTS: The comparison of data between Riyadh versus Hail (inland desert dry environment) and Jeddah versus Gizan (coastal humid environment) revealed that the prevalence of asthma in the similar populations increased significantly from 8% in 1986 to 23% in 1995 (P < .0001). Likewise, the prevalence of allergic rhinitis also increased from 20% to 25% (P < .003) since 1986. However, no significant change in the prevalence of eczema (from 12% to 13%) was noted between 1986 and 1995. CONCLUSIONS: The study indicates that there was a significant increase in the prevalence of bronchial asthma and, to a lesser extent, in the prevalence of allergic rhinitis in the Kingdom of Saudi Arabia during this 9-year period. The study also revealed increased exposure to environmental factors such as tobacco smoke and indoor animals in Saudi houses. It seems that the continuing changes in contemporary life may well have contributed to the increased prevalence of asthma in the country.     

The occurrence of indoor allergens in Saudi Arabia

Investigations on indoor airborne allergens in Saudi Arabia were performed by mold cultures and dust analyses by counter-current immunoelectrophoresis. Twenty fungal genera were isolated, with Aspergillus as the most often encountered. Most of the dust-bound fungi found are ubiquitous and common. Antibodies against Dermatophagoides pteronyssinus, cat- cow- and rat dander, and Cynodon dactylon pollen were used in the dust analyses. Animal antigens were found in five of the ten dust samples. House dust mites were extraordinarily rare. Pollen of Cynodon dactylon (Bermuda grass) was present in nearly all the samples, and in a concurrent clinical study this antigen was found to be the most common cause of perennial rhinitis.     

Molecular characterization of Joubert syndrome in Saudi Arabia

Joubert syndrome (JS) is a ciliopathy that is defined primarily by typical cerebellar structural and ocular motility defects. The genetic heterogeneity of this condition is significant with 16 genes identified to date. We have used a combination of autozygome‐guided candidate gene mutation analysis and exome sequencing to identify the causative mutation in a series of 12 families. The autozygome approach identified mutations in RPGRIP1L, AHI1, TMEM237, and CEP290, while exome sequencing revealed families with truncating mutations in TCTN1 and C5ORF42. Our study, the largest comprehensive molecular series on JS, provides independent confirmation of the recently reported TCTN1, TMEM237, and C5ORF42 as bona fide JS disease genes, and expands the allelic heterogeneity of this disease. Hum Mutat 33:1423–1428, 2012. © 2012 Wiley Periodicals, Inc.     

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.     

New insight into the Rh system: structure and function

Since the inception of the molecular era of Rh biology in the early 1990s with the cloning of Rh CcEe [ 1 , 2 ], D [ 3 , 4 ] and RhAG [ 5 ] cDNAs, there has been a large degree of speculation concerning the function and molecular assembly of the Rh protein complex. This is for two important reasons: the Rh antigens are of considerable importance in transfusion medicine and are of functional and structural significance to the red cell membrane, as Rh_null erythrocytes that lack all proteins of the Rh complex have key structural and biochemical anomalies. In this review I will consider recent advances in our understanding of Rh structure, and indicate how this relates to function. As has been historical since the discovery of the Rh system in 1939, there is some controversy surrounding current ideas of both structure and function(s) and I will attempt to provide a balanced viewpoint on this debate. The reader is referred to several comprehensive reviews on the molecular biology and genetics of the Rh blood group system which deal in much greater depth with the clinical significance and molecular basis of Rh alleles [ 6 - 9 ].