Inference of Antibiotic Resistance and Virulence among Diverse Group A Streptococcus Strains Using emm Sequencing and Multilocus Genotyping Methods

typing (direct sequencing of the genomic segment coding for the antigenic portion of the M protein) or by multilocus genotyping methods. Phenotype analysis, including critical AbR typing, is generally achieved by much slower and more laborious direct culture-based methods. type and the associated AbR and virulence phenotypes. types

The Prevalence and Risk Factors for Pneumococcal Colonization of the Nasopharynx among Children in Kilifi District, Kenya

BACKGROUND: Pneumococcal conjugate vaccines (PCV) reduce nasopharyngeal carriage of vaccine-serotype pneumococci but increase in the carriage of non-vaccine serotypes. We studied the epidemiology of carriage among children 3-59 months old before vaccine introduction in Kilifi, Kenya. METHODS: In a rolling cross-sectional study from October 2006 to December 2008 we approached 3570 healthy children selected at random from the population register of the Kilifi Health and Demographic Surveillance System and 134 HIV-infected children registered at a specialist clinic. A single nasopharyngeal swab was transported in STGG and cultured on gentamicin blood agar. A single colony of pneumococcus was serotyped by Quellung reaction. RESULTS: Families of 2840 children in the population-based sample and 99 in the HIV-infected sample consented to participate; carriage prevalence was 65.8% (95% CI, 64.0-67.5%) and 76% (95% CI, 66-84%) in the two samples, respectively. Carriage prevalence declined progressively with age from 79% at 6-11 months to 51% at 54-59 months (p<0.0005). Carriage was positively associated with coryza (Odds ratio 2.63, 95%CI 2.12-3.25) and cough (1.55, 95%CI 1.26-1.91) and negatively associated with recent antibiotic use (0.53 95%CI 0.34-0.81). 53 different serotypes were identified and 42% of isolates were of serotypes contained in the 10-valent PCV. Common serotypes declined in prevalence with age while less common serotypes did not. CONCLUSION: Carriage prevalence in children was high, serotypes were diverse, and the majority of strains were of serotypes not represented in the 10-valent PCV. Vaccine introduction in Kenya will provide a natural test of virulence for the many circulating non-vaccine serotypes

Biphonal calls in Atlantic spotted dolphins (<i>Stenella frontalis</i>): bitonal and burst-pulse whistles

<p>Biphonation, the simultaneous production of two sounds by a single animal, is found in the vocalizations of a range of mammalian species. Its prevalence suggests it plays an important role in acoustic communication. Concurrent vocal and behavioural recordings were made of Atlantic spotted dolphins (<i>Stenella frontalis</i>) off Bimini, The Bahamas. The occurrence of two types of biphonal signals is reported: burst-pulse whistles with combined tonal and burst-pulse elements, and bitonal whistles. Biphonal whistles are rarely described in reports of dolphin acoustic repertoires, but were common in these dolphins: of all whistles analysed (<i>n</i> = 1211), 26.84% were burst-pulse whistles and 4.71% were bitonal whistles. A subset of whistles (<i>n</i> = 397) were attributed to dolphins of specific age classes, and used to compare prevalence of biphonation across age. Biphonation occurred in 61.54% of sexually mature and 48.32% of sexually immature dolphins’ whistles. Sexually immature dolphins emitted more burst-pulse whistles than older dolphins: 44.13% of sexually immature dolphins’ whistles were burst-pulse whistles, while 15.38% of adult whistles were burst-pulse whistles. Bitonal whistle production was more prevalent in sexually mature dolphins: 41.03% of adult whistles were bitonal, while only 4.19% of sexually immature dolphins’ whistles were bitonal. The prevalence of a biphonal component in specific repeated, stereotyped whistle contours suggests that these acoustic features could be important components of contact calls, or signature whistles. The biphonal components of spotted dolphin whistles may serve to convey additional information as to identity, age or other factors to conspecifics.</p

Angiotensin II receptor I auto-antibodies following SARS-CoV-2 infection.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is associated with endothelial activation and coagulopathy, which may be related to pre-existing or infection-induced pro-thrombotic autoantibodies such as those targeting angiotensin II type I receptor (AT1R-Ab). METHODS: We compared prevalence and levels of AT1R-Ab in COVID-19 cases with mild or severe disease to age and sex matched negative controls utilizing multivariate logistic and quantile regression adjusted for comorbidities including hypertension, diabetes, and heart disease. RESULTS: There were trends toward increased prevalence (50% vs. 33%, p = 0.1) and level of AT1R-Ab (median 9.8 vs. 6.1 U/mL, p = 0.06) in all cases versus controls. When considered by COVID-19 disease severity, there was a trend toward increased prevalence of AT1R-Ab (55% vs. 31%, p = 0.07), as well as significantly higher AT1R-Ab levels (median 10.7 vs. 5.9 U/mL, p = 0.03) amongst individuals with mild COVID-19 versus matched controls. In contrast, the prevalence (42% vs. 37%, p = 0.9) and level (both medians 6.7 U/mL, p = 0.9) of AT1R-Ab amongst those with severe COVID-19 did not differ from matched controls. CONCLUSIONS: These findings support an association between COVID-19 and AT1R-Ab, emphasizing that vascular pathology may be present in individuals with mild COVID-19 as well as those with severe disease

“Only God Knows” : the emergence of a family movement against state violence in Libya

This study investigates how individuals organize against state violence in the context of an authoritarian state through an examination of the development of the “Association of the Families of the Martyrs of the Abū Salīm Prison Massacre” in Libya. This association of families was formed in 2007 to seek knowledge of the whereabouts of forcibly disappeared and imprisoned relatives who are believed to be victims in a contested massacre at Abū Salīm Prison in 1996. For years, families visited the prison, bringing packages of food and clothing, in the hopes of visiting their disappeared relatives. Their persistence, from inquiring about their relatives’ whereabouts to eventually organizing public demonstrations, constituted an unprecedented public resistance to the regime of Mu‘amar Gaddafi, who ruled one of the world’s most repressive authoritarian systems for over forty years. Through interviews with members of the family association from both eastern and western regions of the country, I trace how the organization emerged through connections between families in Libya. This case illustrates how an important form of collective mobilization rests in the context of the family, for which I develop the term “family movements.” I argue that family movements, which can include mobilizations exclusively among mothers or can more broadly encompass mobilizations that draw on any relation of kinship, represent a significant mode of collective action in authoritarian states cross-nationally. This analysis has implications for many sites, as for example in Latin America, where disappearance has been an integral strategy of state repression. Despite the power of forced disappearance as a mode of effacing political dissidence, the practice produces several unintended consequences. Namely, the absent body prevents families from experiencing closure, the ambiguity of which opens a space for the relatives left behind to mobilize. The uncertainty of death, and the protracted mourning process it induces, as well as the ongoing inquiries of the families sustain mobilization in a way that social movement scholars have not fully recognized. This study therefore contributes to our understandings of forced disappearance as a strategy of repression and explores the central role of the families in contesting this form of state violence.Sociolog

Large-scale association analyses identify host factors influencing human gut microbiome composition

To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 x 10(-8)) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 x 10(-20)), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 x 10(-10) < P < 5 x 10(-8)) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis