Genome-wide patterns of population structure and admixture in West Africans and African Americans

Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th–75th percentiles: 11.6–27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.     

免疫途径和佐剂对NTHiP6蛋白疫苗免疫效果的影响

目的观察不同免疫途径和佐剂对NTHiP6蛋白疫苗免疫效果的影响。方法将原核表达质粒PGEX-6P2/P6转入E.coli XL1-Blue,IPTG诱导P6蛋白的表达并进行纯化。以不同免疫途径(皮下,腹腔,滴鼻)用P6蛋白免疫小鼠,每组12只。然后另取小鼠分为PBS组和不同佐剂组(MDC、IL-2、弗氏佐剂),每组15只,采用皮下注射途径免疫。共免疫3次,间隔2周,用ELISA检测小鼠血清特异性IgG抗体,用CCK-8法检测脾淋巴细胞增殖活性,用ELISA检测IL-4和IFN-γ水平。结果在大肠埃希菌中成功表达P6蛋白。3种免疫途径相比,皮下途径免疫诱导的IgG抗体滴度为1 279.97±3.87,腹腔免疫组为427.16±3.08,滴鼻免疫组为253.98±3.30,差异有统计学意义(F=5.43,P<0.05)。采用皮下免疫途径时,MDC组诱导的IgG抗体滴度、IL-4水平分别为7 421.02±3.30和79.64±2.75,与其他组比较差异有统计学意义(P<0.05)。IFN-γ水平和脾淋巴细胞增殖指数与IL-2组相比差异无统计学意义(P>0.05)。结论使用MDC佐剂并采用皮下途径注射可使NTHiP6蛋白疫苗获得较好的免疫效果。     

Role of nontypeable Haemophilus influenzae in exacerbations and progression of chronic obstructive pulmonary disease

PURPOSE OF REVIEW: Nontypeable Haemophilus influenzae is the most common bacterial pathogen associated with airway infection in chronic obstructive pulmonary disease, both in stable disease and during exacerbations. Past attempts to elucidate its role as a pathogen in this disease yielded confusing and contradictory results, leading to its designation as an 'innocent bystander' with little if any pathogenic role in exacerbations and stable disease. Application of modern understanding of bacterial pathogenesis and of innovative research methodologies, however, has considerably clarified its role. RECENT FINDINGS: Acquisition of antigenically diverse strains of nontypeable H. influenzae which engender a neutrophilic inflammatory response and strain-specific immunity appears to be the mechanism underlying recurrent exacerbations of chronic obstructive pulmonary disease. In the stable phase of the disease, this pathogen appears to be an inflammatory stimulus in the lower airways with the potential to contribute to progressive airway obstruction that is characteristic of the condition. Several mechanisms may allow the infection to persist in the lower airways of patients with chronic obstructive pulmonary disease, including tissue invasion, antigenic alteration and biofilm formation. SUMMARY: Though much has been learnt about nontypeable H. influenzae in chronic obstructive pulmonary disease, new therapeutic and preventive approaches require an even greater understanding of this host-pathogen interaction.     

Impaired phagocytosis of nontypeable Haemophilus influenzae by human alveolar macrophages in chronic obstructive pulmonary disease

BACKGROUND: Interactions of nontypeable Haemophilus influenzae (NTHI) with human alveolar macrophages are implicated in the persistence of NTHI in chronic obstructive pulmonary disease (COPD). However, the immunologic mechanisms that mediate NTHI-induced macrophage responses are poorly understood. We hypothesized that immunologic responses of alveolar macrophages to NTHI are impaired in COPD. METHODS: Blood and alveolar macrophages--obtained from ex-smokers with COPD (n = 14), ex-smokers without COPD (n = 15), and nonsmokers (n = 9)--were incubated with 3 distinct NTHI strains obtained from patients with COPD. Phagocytosis of 3H-NTHI, expressed as a percentage of the mean total radioactivity, and of intracellular viability, assessed as a percentage of viable cell-associated NTHI, were measured. RESULTS: Alveolar macrophages from donors with COPD, compared with those from donors without COPD, had impaired phagocytosis (median [interquartile range]) for each NTHI strain: 14P13H5, 0.26 (0.08-0.61) versus 1.36 (0.69-1.95); 6P5H1, 0.92 (0.32-1.82) versus 1.90 (1.32-2.68); and 14P14H1, 0.79 (0.23-1.32) versus 2.13 (1.13-2.40) (P < or = .01 for each). However, phagocytosis of all NTHI strains by blood macrophages from donors with COPD was indistinguishable from that of blood macrophages from donors without COPD and from nonsmokers. The intracellular killing of NTHI was not impaired in alveolar macrophages from donors with COPD. CONCLUSIONS: These results support a paradigm of impaired phagocytosis by alveolar macrophages, but not blood macrophages, in COPD and provide an immunologic basis for persistence of NTHI in the airways of adults with COPD.     

临床分离流感嗜血杆菌和副流感嗜血杆菌的耐药性研究

目的 了解上海部分医院分离的流感和副流感嗜血杆菌对常用抗菌药物的敏感性、对β内酰胺类和喹诺酮类药物的耐药机制以及耐药菌株的克隆传播情况.方法 以琼脂稀释法测定氨苄西林等13种抗菌药物对2006年上海5所医院临床分离的156株嗜血杆菌属细菌的体外抗菌活性,头孢硝噻吩纸片法检测β-内酰胺酶,PCR扩增检测TEM和ROB型β-内酰胺酶基因和喹诺酮类耐药株的喹诺酮耐药决定区,以肠杆菌科基因间重复序列聚合酶链反应(ERIC-PCR)比较细菌的同源性.药物敏感性试验结果采用χ2检验,ERIC-PCR条带模型转换数据进行聚类分析.结果 109株流感嗜血杆菌对氨苄西林敏感率为74.3%,而对氨苄西林舒巴坦、头孢菌素类、氟喹诺酮类等敏感率为100.0%.109株流感嗜血杆菌和47株副流感嗜血杆菌β-内酰胺酶产酶率分别为25.7%和19.1%(χ2=0.776,P=0.378),产酶株均检测到TEM基因.109株流感嗜血杆菌中仅1株对环丙沙星耐药,其gyrA基因存在84位丝氨酸突变为亮氨酸,parC基因存在206位甘氨酸突变为精氨酸.ERIC-PCR结果显示,106株流感嗜血杆菌在85%相似度水平可被分为73型.结论 上海地区流感嗜血杆菌临床菌株对除氨苄西林外的其他常用抗菌药物仍保持很高的敏感率.受试流感嗜血杆菌对氨苄西林耐药的主要机制均为产TEM型β-内酰胺酶.在包括氨苄西林耐药株在内的流感嗜血杆菌中,克隆传播尚不普遍.     

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice, hotspots are largely defined by binding sites of the positive-regulatory domain zinc finger protein 9. To investigate the detailed recombination pattern in a flowering plant, we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in positive-regulatory domain zinc finger protein 9–knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms.Meiotic recombination is a highly regulated process that enables pairing of homologous chromosomes and, by the formation of crossovers, ensures proper segregation (1). Along with mutation, drift, and selection, recombination is a critical factor in shaping genome-wide sequence variation. Recombination rates vary substantially across eukaryote genomes (2) in a manner that we are only beginning to understand. In humans and mice, the location of regions of strong recombination (“hotspots”) is largely determined by positive-regulatory domain zinc finger protein 9 (PRDM9) binding sites (3), whereas in yeast such regions are associated with nucleosome-depleted open chromatin often associated with gene promoters (4). When PRDM9 is disabled in mice, hotspots tend to relocalize to promoter regions (5). In flowering plants, at least one example of a promoter-associated hotspot has been reported (6), but it remains an open question whether this is a general tendency in plants.The positions of crossovers and the boundaries of gene conversion tracts resulting from meiotic recombination are often imprecisely known, because they can only be identified based on the location of nearby segregating markers. Within a species, genome-wide variation in recombination rates can be determined by following the inheritance of such genetic markers in crosses or pedigrees (7–10) or by examining patterns of linkage disequilibrium within a population (11–15). Population-based approaches have the advantage that in diverse populations, hundreds of thousands of historical recombination events can be sampled, compared with only hundreds in the largest pedigrees.The monkeyflower Mimulus guttatus has an exceptionally high nucleotide diversity, which makes it a particularly appealing system for characterizing the boundaries of recombination events. We observed an average pairwise nucleotide difference of π = 2.9% in a sample of 98 wild plants (196 haploid genomes) from four locations within a 16-km radius in the Sierra Nevada foothills in Northern California. At such high diversity, pairs of adjacent SNPs defining local haplotypes are often found on the same Illumina sequencing read (e.g., within 50 bases). Thus, short-range haplotypes can be determined cost-effectively by shotgun sequencing pooled samples rather than by sequencing each plant individually.For a pair of nearby segregating biallelic SNPs we expect to observe only three of the four possible haplotypes unless recombination and/or parallel mutation has occurred since the originating mutations. This is the essence of Hudson’s four-gamete test (16) and allows us to identify putative boundaries of historical crossovers and gene conversion tracts (Fig. 1) to within a fraction of a read length. If this information is combined with population genetic models, local recombination rates can then be inferred (17).Open in a separate windowFig. 1.Appearance of four haplotypes at a pair of SNP loci by recombination. From a single ancestral sequence (Top) a single mutation produces a second haplotype. A second mutation at a nearby site (Middle) generates a third haplotype In the population. Finally, a recombination boundary between the two SNP loci (Bottom) generates a fourth haplotype. Note that the recombination boundary can be due to a crossover event or a gene conversion tract. A fourth haplotype can also appear due to a parallel mutation (not shown), but this scenario can be distinguished from recombination because parallel mutation at a site should not depend on the distance to the nearest SNP.     

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.The oldest Gaelic literature describes the origins of the Irish people as a series of ancient invasions, and the archaeological record in Ireland, as elsewhere in Europe, exhibits several horizons where major cultural shifts are apparent (1). The two most transformative are the arrival of agriculture (∼3750 BC) followed by the onset of metallurgy (∼2300 BC). The Neolithic package characterized by animal husbandry, cereal crops, ceramics, and timber houses reached the shores of Ireland some 5,000 years after its beginnings in the Near East. The second great wave of change starts with the appearance of copper mines, associated with Bell Beaker pottery, which are quickly followed by Bronze tool-making, weaponry, and gold-working, with distinct Food Vessel pottery succeeding from the earlier beakers (2). This period coincides with the end of the large passage graves of Neolithic Ireland in favor of single burials and smaller wedge tombs.Twentieth-century archaeology was dominated by two non-mutually-exclusive paradigms for how such large scale social change occurs (3). The first, demic diffusion, linked archaeological change with the displacement and disruption of local populations by inward migrations. However, from the 1960s onwards, this assertion was challenged by a paradigm of cultural diffusion whereby social change happened largely through indigenous processes.High-throughput sequencing has opened the possibility for genome-wide comparisons of genetic variation in ancient populations, which may be informatively set in the context of extensive modern data (4–10). In Europe, these clearly show population replacement by migrating farmers from southwest Asia at the onset of the Neolithic with some retrenchment of the earlier Mesolithic genome at later stages (5–9, 11, 12). Three longitudinal genome studies have also shown later genome-wide shifts around the beginnings of the Bronze Age in central Europe with substantial introgression originating with the Yamnaya steppe herders (7, 9, 10). However, replacement coupled to archaeological horizons is unlikely to be a universal phenomenon, and whether the islands of Britain and Ireland, residing at the temporal and geographical edges of both the Neolithic and steppe migrations, were subject to successive substantial population influxes remains an open and debated question. For example, a recent survey of archaeological opinion on the origins of agriculture in Ireland showed an even split between adoption and colonization as explanatory processes (13). Recent archaeological literature is also divided on the origins of the insular Bronze Age, with most opinion favoring incursion of only small numbers of technical specialists (1, 2, 14, 15).To address this controversy, we present here the first, to our knowledge, genome-wide data from four ancient Irish individuals, a Neolithic woman (3343–3020 cal BC) from Ballynahatty, Co. Down, found in the context of an early megalithic passage-like grave, and three Early Bronze Age men from a cist burial in Rathlin Island, Co. Antrim (2026–1534 cal BC) with associated Food Vessel pottery (16) (SI Appendix, Section S1).     

Protein D of Haemophilus influenzae: a protective nontypeable H. influenzae antigen and a carrier for pneumococcal conjugate vaccines.

Protein D (PD) is a highly conserved 42 kDa surface lipoprotein found in all Haemophilus influenzae, including nontypeable (NT) H. influenzae. PD is involved in the pathogenesis of respiratory tract infections, in the context of which it has been shown to impair ciliary function in a human nasopharyngeal tissue culture model and to augment the capacity to cause otitis media in rats. A likely mechanism indicating that PD is a virulence factor is its glycerophosphodiesterase activity, which leads to the release of phosphorylcholine from host epithelial cells. PD has been demonstrated to be a promising vaccine candidate against experimental NT H. influenzae infection. Rats vaccinated with PD cleared NT H. influenzae better after middle ear and pulmonary bacterial challenge, and chinchillas vaccinated with PD showed significant protection against NT H. influenzae-dependent acute otitis media. In a clinical trial involving children, PD was used as an antigenically active carrier protein in an 11-valent pneumococcal conjugate investigational vaccine; significant protection was achieved against acute otitis media not only caused by pneumococci but also caused by NT H. influenzae. This may have great clinical implications, because PD is the first NT H. influenzae antigen that has induced protective responses in humans.     

High nasopharyngeal carriage of drug resistant Streptococcus pneumoniae and Haemophilus influenzae in North Indian schoolchildren

OBJECTIVES: To determine the carriage rate of Streptococcus pneumoniae and Haemophilus influenzae in healthy Indian schoolchildren. The prevalence of antibiotic resistant strains in the community may be used to assess the trends of antibiotic resistance in invasive strains. Prevalence of resistance to various antimicrobial drugs among S. pneumoniae and H. influenzae was estimated. METHODS: Two thousand four hundred subjects, aged 5-10 years, were enrolled from 45 rural and 45 urban schools. A nasopharyngeal swab was collected from each child, after taking informed written consent. Swabs were processed to isolate S. pneumoniae and H. influenzae. All isolates were tested for resistance to chloramphenicol, erythromycin and co-trimoxazole. Streptococcus pneumoniae isolates were also tested against tetracycline and oxacillin while H. influenzae isolates were tested against ampicillin. RESULTS: Nasopharyngeal carriage of S. pneumoniae and H. influenzae was high in healthy schoolchildren. Stratified analysis showed that nasal carriage of pneumococci in urban children was significantly lower than in rural children [46.8% vs. 53.2%, P<0.001]. Carriage rates of H. influenzae in male and female populations were significantly different (47.8% vs. 52.3%, P<0.04). Penicillin resistance in S. pneumoniae was found low (3.3%), but 22.9% of H. influenzae isolates were ampicillin resistant. Resistance to co-trimoxazole was very high in both S. pneumoniae (81.8%) and H. influenzae (67.3%). CONCLUSION: There is high nasopharyngeal carriage of drug resistant S. pneumoniae and H. influenzae in schoolchildren of north India. Currently, in India, co-trimoxazole for 5 days is recommended for treatment of non-severe pneumonia and third generation cephalosporins are drug of choice for management of severe pneumococcal/H. influenzae diseases. We found high co-trimoxazole resistance and low penicillin resistance in pneumococcal isolates. This justifies empirical use of penicillin in management of invasive pneumococcal infections in India.     

Global genetic structure and molecular epidemiology of encapsulated Haemophilus influenzae

A collection of 2,209 isolates of six polysaccharide capsule types of Haemophilus influenzae, including 1,975 serotype b isolates recovered in 30 countries was characterized for electrophoretically demonstrable allele profiles at 17 metabolic enzyme loci. Two hundred eighty distinct multilocus genotypes were distinguished, and cluster analysis revealed two primary phylogenetic divisions. The population structure of encapsulated H. influenzae is clonal. Currently, most of the invasive disease worldwide is caused by serotype b strains of nine clones. Strains producing serotype c, e, and f capsules belong to single divisions and have no close genetic relationships to strains of other serotypes. Serotype a and b strains occur in both primary phylogenetic divisions, probably as a result of transfer and recombination of serotype-specific sequences of the cap region between clonal lineages. A close genetic relatedness between serotype d isolates and some strains of serotypes a and b was identified. There are strong patterns of geographic variation, on an intercontinental scale, in both the extent of genetic diversity and the clonal composition of populations of encapsulated strains. The analysis suggests that the present distribution of clones is, in part, related to patterns of racial or ethnic differentiation and historical demographic movements of the human host populations.     

Immunization with HMW1 and HMW2 adhesins protects against colonization by heterologous strains of nontypeable Haemophilus influenzae

Nontypeable Haemophilus influenzae (NTHi) is a common cause of localized respiratory tract disease and results in significant morbidity. The pathogenesis of NTHi disease begins with nasopharyngeal colonization, and therefore, the prevention of colonization represents a strategy to prevent disease. The NTHi HMW1 and HMW2 proteins are a family of conserved adhesins that are present in 75 to 80% of strains and have been demonstrated to play a critical role in colonization of the upper respiratory tract in rhesus macaques. In this study, we examined the vaccine potential of HMW1 and HMW2 using a mouse model of nasopharyngeal colonization. Immunization with HMW1 and HMW2 by either the subcutaneous or the intranasal route resulted in a strain-specific antibody response associated with agglutination of bacteria and restriction of bacterial adherence. Despite the specificity of the antibody response, immunization resulted in protection against colonization by both the parent NTHi strain and heterologous strains expressing distinct HMW1 and HMW2 proteins. Pretreatment with antibody against IL-17A eliminated protection against heterologous strains, indicating that heterologous protection is IL-17A dependent. This work demonstrates the vaccine potential of the HMW1 and HMW2 proteins and highlights the importance of IL-17A in protection against diverse NTHi strains.

Nontypeable (nonencapsulated) Haemophilus influenzae (NTHi) is a common cause of acute otitis media (AOM), otitis media with effusion, sinusitis, and exacerbations of underlying lung disease in children (1). NTHi is also frequently associated with community-acquired pneumonia and exacerbations of chronic obstructive pulmonary disease in adults (2).The pathogenesis of NTHi disease begins with colonization of the nasopharynx. Colonization occurs early in life and is common throughout childhood and into adulthood (3). NTHi spreads contiguously within the respiratory tract to cause localized disease, typically in the setting of a viral respiratory infection or allergic disease (4–6). Recent evidence indicates that colonization in early infancy may predispose to the development of neutrophilic asthma and allergic airway disease (7). Given the burden of NTHi disease and the association between early life NTHi colonization and asthma, there is interest in developing a vaccine against NTHi.Currently, vaccines against H. influenzae are limited to polysaccharide conjugate vaccines targeting the capsule of type b strains (Hib). While these vaccines have been largely successful in eliminating Hib invasive disease, there has been no effect on strains of NTHi, which lack a capsule. Efforts to identify highly conserved antigens in NTHi and develop a vaccine against NTHi have been significantly more difficult. While Hib and other encapsulated strains of H. influenzae are clonal, NTHi strains exhibit much greater genetic diversity and heterogeneity (8). Across NTHi strains, common surface antigens exhibit high degrees of antigenic variation, resulting in variable and strain-specific antibody responses. In studies of mice, antibodies acquired during NTHi infection, including IgG in nasal washes directed against outer membrane proteins, are associated with reduced nasopharyngeal colonization density following subsequent challenge by NTHi (9). This suggests a protective role for antibodies at the mucosal surface. However, evidence in children indicates that despite the presence of antibody against an infecting strain, children remain susceptible to subsequent infections by new strains, suggesting that the antibody response may only protect against infection by the same strain.In combination with antibody responses, cell-mediated immunity has been increasingly recognized as a key driver of protection against airway infection by respiratory pathogens. The production of IL-17A by host cells mediates many effector functions at mucosal surfaces, including the production of antimicrobial peptides, proinflammatory cytokines, chemotactic factors, and granulopoietic factors. These effector functions result in increased recruitment of macrophages and neutrophils and enhanced cytotoxicity and phagocytosis (10–12). There is also evidence that IL-17–producing cells drive humoral immunity, including the generation of antibody in mucosal secretions (13, 14). IL-17 production is known to be essential for defense against various mucosal pathogens, including Mycoplasma pneumoniae, Streptococcus pneumoniae, Klebsiella pneumoniae, and Bordetella pertussis (15–17). In studies of Staphylococcus aureus, clearance of bacteria colonizing the nasopharynx is driven by IL-17–mediated neutrophil influx and antimicrobial peptide production (16, 18). Thus far, it is unclear whether IL-17 production directly contributes to host defense against nasopharyngeal colonization by NTHi.NTHi colonization of the nasopharynx begins with bacterial adherence to respiratory epithelial cells, which is dependent on NTHi adhesive proteins. The HMW1 and HMW2 high-molecular weight proteins are surface-exposed glycoproteins and are the predominant adhesins in ∼75 to 80% of NTHi strains (19–23). HMW1 and HMW2 also facilitate upper respiratory tract colonization in rhesus macaques as highlighted in studies comparing a wild-type strain and an isogenic mutant lacking both of these proteins (24). HMW1 and HMW2 are highly homologous to each other, sharing ∼70% identity and 80% similarity. HMW1 and HMW2 are also highly homologous among diverse NTHi strains (25, 26).In children recovering from AOM, HMW1 and HMW2 are the major targets of the serum antibody response to infection. Similarly, rhesus macaques colonized with HMW1/HMW2-expressing strains develop serum antibody responses against HMW1 and HMW2, and serum antibodies against HMW1 and HMW2 are present in adults, suggesting that these adhesins are highly immunogenic. The development of HMW1/HMW2-specific antibodies in humans also coincides with increased serum bactericidal activity (27). However, antibody-mediated killing appears to be directed primarily against the homologous infecting strain rather than broadly acting against heterologous strains (28). The conservation of HMW1 and HMW2 among diverse strains, the immunogenicity of HMW1 and HMW2, the surface localization of HMW1 and HMW2, and the role of HMW1 and HMW2 in adherence to respiratory epithelial cells and in colonization make these adhesins promising antigens for a vaccine.In this study, we evaluated whether immunization with HMW1 and HMW2 protects against nasopharyngeal colonization. Using a mouse model of immunization and nasopharyngeal challenge, we found that immunization with the HMW1 and HMW2 proteins results in protection against colonization by homologous and heterologous strains, despite a highly strain-specific antibody response. Protection against nasopharyngeal colonization is mediated by both antibody and T cell responses.     

Haemophilus influenzae disease in Alaskan Eskimos: characteristics of a population with an unusual incidence of invasive disease

During 1971-77 the incidence of bacterial meningitis among Alaskan Eskimos was 84.4 cases per 100 000 population per year, which is more than 10 times that for most other U.S. populations. Haemophilus influenzae (HI) accounted for 68% of meningitis cases. The average annual incidence of HI disease per 100 000 children below 5 years of age was 409 for patients with meningitis only and 491 for patients with all systemic HI disease. Children with HI meningitis in Alaska tended to be younger than those in other U.S. populations, 98% of the children affected being less than 18 months of age. The risk for all HI disease was 2.4% during the first year of life. The spectrum of HI disease in Alaska differs from that in other populations in that no patient had epiglottitis and 5% of children had recurrent HI disease. Alaskan newborns and children over 4 years old had HI anticapsular antibody titres that were nearly thrice those for children of similar ages in other U.S. populations (p less than 0.005). The pharyngeal carriage of HI type b (5%) and the rectal carriage of Escherichia coli K100 (2%), an organism with a capsule antigenically similar to HI type b, did not differ from those in other populations. The high incidence of disease almost exclusively in the very young and the early development of antibody in this population suggest that the high rate of disease is due to early exposure to HI type b rather than to an unusual susceptibility to HI type b.     

The genetic structure of the Turkish population reveals high levels of variation and admixture

The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 50% of TR individuals had high inbreeding coefficients (≥0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28% of exome and 49% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.

Even in the Paleolithic period, Anatolia (or Asia Minor as it was once called) served as a bridge for migrations between Africa, Asia, and Europe. Long before the establishment of nation states, intermixing between human populations occurred in Anatolia. Indeed, Anatolia has been home to many civilizations including Hattians, Hurrians, Assyrians, Hittites, Greeks, Thracians, Phrygians, Urartians, Armenians, and Turks. Gene flow between Anatolian, Caucasus, and northern Levantine populations occurred during the Late Neolithic and Chalcolithic to the Early Bronze age, including long-distance migration from Central Asia to Anatolia (1). The Turkic peoples, a collection of ethnolinguistically related populations originating from Central Asia, were first documented in western Eurasia in the fourth/fifth century BCE and currently live in Central, Eastern, Northern, and Western Asia as well as in parts of Europe and in North Africa. The expansion of Turkic tribes into Western Asia and Eastern Europe occurred between the sixth and 11th centuries, beginning with the Seljuk Turks followed by the Ottomans (2). The sphere of Ottoman influence started to increase greatly, beginning in the 14th century; following the conquest of Constantinople in 1453, the Ottoman Empire controlled a vast region including all of southeastern Europe south of Vienna, parts of Central Europe, Western Asia, the Caucasus, North Africa, and the Horn of Africa. The modern Republic of Turkey was founded in 1923 after the fall of the Ottoman Empire at the end of World War I and is currently home to more than 80 million people. Turkish-speaking people constitute the major ethnolinguistic group in Turkey. There are also more than 70 million people who live in the five independent Turkic countries in Central Asia, namely Azerbaijan, Turkmenistan, Uzbekistan, Kazakhstan, and Kyrgyzstan. A study investigating the Y haplogroups of Turkish (TR) males revealed that the proportion of recent paternal gene flow from Central Asia was ∼9%, thereby raising the possibility that modern-day Anatolia is an admixture of preexisting Anatolian and Turkic peoples (3).The practice of consanguineous marriage is frequent in Turkey, especially in the eastern provinces (4). This should, in principle, help to facilitate disease gene discovery, as the increased frequency of homozygosity among members of inbred populations has led to the identification of many disease genes (5–8). The genetic admixture and consanguinity have had a significant effect on the genetic diversity of Middle Eastern populations (9, 10). The characterization of the Greater Middle East (GME) Variome, comprising the most comprehensive genomic database for Middle Eastern populations, has shown that knowledge of the genomic architecture of these populations facilitates disease gene identification in family studies and in genome-wide association studies (GWAS) of populations (11). Until now, the GME has been the largest resource representing the genetic variation in Turkey, albeit with only 140 out of a total of 1,111 samples coming from the TR Peninsula. Thus, based on the larger population of Turkey relative to its immediate neighbors, the TR population is underrepresented in current genomic databases. Furthermore, gnomAD, as one of the most comprehensive genetic variation resources, does not contain TR whole-exome sequencing (WES) or whole-genome sequencing (WGS) data (12). Therefore, a comprehensive database of alleles in the TR population should facilitate disease gene identification in consanguineous families and the assessment of the clinical phenotypes of individuals who are homozygous for mutations in specific genes.Finally, most GWAS to date have analyzed DNA from European ancestry–derived populations, and it will be important to extend the GWAS of complex traits to underrepresented populations. One of the key steps in GWAS is to “predict” or “impute” the missing genotypes by using a reference haplotype panel. It is becoming increasingly common for researchers to generate such panels for imputation from population-specific WGS data. Population-specific reference panels increase imputation accuracy, especially when they are combined with existing reference panels such as the 1000 Genomes Project (1000GP) (13–15). In this study, we have described the high-resolution genetic structure of the TR population, generated a TR Variome, and imputed a TR reference panel for future genetics studies.     

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences for reliable diagnosis of infectious disease agents and regulations for transport and possession of organisms of economic importance. E. coli traditionally is thought to live within the gastrointestinal tract of humans and other warm-blooded animals and not to survive for extended periods outside its host; this understanding is the basis for its widespread use as a fecal contamination indicator. Here, we report the genome sequences of nine environmentally adapted strains that are phenotypically and taxonomically indistinguishable from typical E. coli (commensal or pathogenic). We find, however, that the commensal genomes encode for more functions that are important for fitness in the human gut, do not exchange genetic material with their environmental counterparts, and hence do not evolve according to the recently proposed fragmented speciation model. These findings are consistent with a more stringent and ecologic definition for bacterial species than the current definition and provide means to start replacing traditional approaches of defining distinctive phenotypes for new species with omics-based procedures. They also have important implications for reliable diagnosis and regulation of pathogenic E. coli and for the coliform cell-counting test.     

Horizontal transfer of the gene encoding outer membrane protein P2 of nontypeable Haemophilus influenzae,in a patient with chronic obstructive pulmonary disease

An adult with chronic obstructive pulmonary disease was monitored prospectively for 2 years. Nontypeable Haemophilus influenzae was isolated from sputum cultures at 22 of 23 monthly clinic visits. Analysis of the isolates, by pulsed-field gel electrophoresis (PFGE), revealed that the patient was colonized by 3 different strains during the 2-year period. The gene encoding outer-membrane protein (OMP) P2, ompP2, was amplified from sputum samples and selected strains obtained from this patient. Analysis of the ompP2 sequences, in combination with the PFGE patterns, indicated that ompP2 horizontal transfer between 2 strains occurred in the respiratory tract, between clinic visits 13 and 14. Observation of ompP2 horizontal transfer in the human respiratory tract has important implications for both the understanding of ompP2 diversity among strains and the future design of OMP P2-based vaccines.     

Genetic population structure of coagulase-negative staphylococci associated with carriage and disease in preterm infants.

Coagulase-negative staphylococci (CoNS) are a leading cause of sepsis in the neonatal intensive care unit (NICU) setting. To evaluate the hypothesis that isolates of CoNS associated with disease belong to hypervirulent clones, as opposed to being drawn randomly from the neonatal unit carriage flora, we conducted a prospective, case-controlled study in a busy NICU. Using pulsed-field gel electrophoresis (PFGE), we compared the population structures of CoNS isolates associated with bacteremia with isolates from the skin of healthy and infected neonates and with blood culture contaminants. Endemic clones of CoNS were identified, but there was no difference in the distribution of the 6 species or 73 PFGE types between the carriage and disease isolate groups; this suggests that hypervirulent clones with an enhanced ability to cause disease were not present in this NICU setting.     

Antibiotic susceptibility of invasive Haemophilus influenzae type b isolates in Denmark in 1988 and 1989

A system for surveillance of invasive Haemophilus influenzae type b infections in Denmark yielded 135 strains isolated from blood or cerebrospinal fluid from August 1988 through December 1989. The susceptibility of the strains to 7 antibiotics was investigated by an agar dilution method. Ceftriaxone was found to be the most active drug followed by cefotaxime, ceftazidime, rifampicin, ampicillin, cefuroxime, and chloramphenicol. Except for ampicillin the MICs for the individual antibiotics were similar. Seven strains (5.2%), which all produced beta-lactamase, were resistant to ampicillin. Since H. influenzae type b meningitis in otherwise healthy individuals almost exclusively occurs in children aged 2 months to 4 years, a third generation cephalosporin such as ceftriaxone or cefotaxime may be considered the drug of choice for initial therapy of meningitis in this age group.     

Network analysis identifies weak and strong links in a metapopulation system

The identification of key populations shaping the structure and connectivity of metapopulation systems is a major challenge in population ecology. The use of molecular markers in the theoretical framework of population genetics has allowed great advances in this field, but the prime question of quantifying the role of each population in the system remains unresolved. Furthermore, the use and interpretation of classical methods are still bounded by the need for a priori information and underlying assumptions that are seldom respected in natural systems. Network theory was applied to map the genetic structure in a metapopulation system by using microsatellite data from populations of a threatened seagrass, Posidonia oceanica, across its whole geographical range. The network approach, free from a priori assumptions and from the usual underlying hypotheses required for the interpretation of classical analyses, allows both the straightforward characterization of hierarchical population structure and the detection of populations acting as hubs critical for relaying gene flow or sustaining the metapopulation system. This development opens perspectives in ecology and evolution in general, particularly in areas such as conservation biology and epidemiology, where targeting specific populations is crucial.