Spontaneous sequence duplication within an open reading frame of the pneumococcal type 3 capsule locus causes high-frequency phase variation

The molecular genetic basis of high-frequency serotype 3 capsule phase variation in Streptococcus pneumoniae (the pneumococcus) was investigated. Pneumococci were grown in sorbarod biofilms at 34 degrees C to mimic nasopharyngeal carriage. Different type 3 pneumococci commonly associated with invasive disease generated apparently random tandem duplications of 11-239 bp segments within the cap3A gene of the type 3 capsule locus. These duplications alone were found to be responsible for high-frequency capsule phase variation, in which (phase off) acapsular variants possessed duplications within cap3A, and (phase on) capsular revertants possessed wild-type cap3A genes, indicating the precise excision of the duplication. Additionally, the frequency of phase reversion (off to on) was found to exhibit a linear relationship between (log) frequency of reversion and (log) length of duplication. This apparently random duplication giving rise to phase variation is in stark contrast to the 'preprogrammed' contingency genes in many Gram-negative organisms that possess homopolymeric sequence repeats or motifs for site-specific recombination.     

A Cross Sectional Analysis of Gonococcal and Chlamydial Infections among Men-Who-Have-Sex-with-Men in Cape Town,South Africa

Background

Men-who-have-sex-with-men (MSM) are at high risk of HIV and sexually transmitted infection (STI) transmission. Asymptomatic STIs are common in MSM and remain undiagnosed and untreated where syndromic management is advocated. Untreated STIs could be contributing to high HIV rates. This study investigated symptomatic (SSTI) and asymptomatic STIs (ASTIs) in MSM in Cape Town.

Methods

MSM, 18 years and above, were enrolled into this study. Participants underwent clinical and microbiological screening for STIs. Urine, oro-pharyngeal and anal swab specimens were collected for STI analysis, and blood for HIV and syphilis screening. A psychosocial and sexual questionnaire was completed. STI specimens were analysed for Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) infection.

Results

200 MSM were recruited with a median age of 32 years (IQR 26–39.5). Their median number of sex partners within the last year was 5 (IQR 2–20). 155/200 (78%) reported only male sex partners while 45/200 (23%) reported sex with men and women. 77/200 (39%) reported transactional sex. At enrolment, 88/200 (44%) were HIV positive and 8/112 (7%) initially HIV-negative participants seroconverted during the study. Overall, 47/200 (24%) screened positive for either NG or CT. There were 32 MSM (16%) infected with NG and 7 (3.5%) of these men had NG infections at two anatomical sites (39 NG positive results in total). Likewise, there were 23 MSM (12%) infected with CT and all these men had infections at only one site. Eight of the 47 men (17%) were infected with both NG and CT. ASTI was more common than SSTI irrespective of anatomical site, 38 /200 (19%) versus 9/200 (5%) respectively (p<0.001). The anus was most commonly affected, followed by the oro-pharynx and then urethra. Asymptomatic infection was associated with transgender identity (OR 4.09 CI 1.60–5.62), ≥5 male sex partners in the last year (OR 2.50 CI 1.16–5.62) and transactional sex (OR 2.33 CI 1.13–4.79) but not with HIV infection.

Conclusions

Asymptomatic STI was common and would not have been detected using a syndromic management approach. Although molecular screening for NG/CT is costly, in our study only four MSM needed to be screened to detect one case. This supports dual NG/CT molecular screening for MSM, which, in the case of confirmed NG infections, may trigger further culture-based investigations to determine gonococcal antimicrobial susceptibility in the current era of multi-drug resistant gonorrhoea.     

Validity of <Emphasis Type="Italic">Scorpaena jacksoniensis</Emphasis> and a redescription of <Emphasis Type="Italic">S. cardinalis</Emphasis>, a senior synonym of <Emphasis Type="Italic">S. cookii</Emphasis> (Scorpaeniformes: Scorpaenidae)

The Scorpaena cardinalis complex, including S. cardinalis, S. jacksoniensis and S. orgila, is defined. The genus Ruboralga (type species: S. jacksoniensis) is regarded as a junior synonym of Scorpaena. Scorpaena jacksoniensis Steindachner 1866, previously treated as a junior synonym of Scorpaena cardinalis Solander and Richardson 1842, is regarded here as a valid species. Scorpaena cookii Günther 1874, previously treated as a valid species, is regarded here as a junior synonym of S. cardinalis. Thus, recent recognition of the two Australasian scorpionfishes, i.e., S. cardinalis and S. cookii, are re-identified in this study as S. jacksoniensis and S. cardinalis, respectively. Scorpaena plebeia Solander 1842 is regarded as a junior synonym of S. cardinalis. Scorpaena jacksoniensis is distributed along the east coast of Australia from southern Queensland to eastern Victoria, whereas S. cardinalis occurs around northern New Zealand, the Kermadec Islands and offshore islands of the Tasman Sea. A neotype is designated for S. cardinalis. Morphological changes with growth in the two species are described in detail.     

A particular diffusion model for incomplete longitudinal data: application to the multicenter AIDS cohort study

Longitudinal studies, in which individuals are measured repeatedly in time, are often incomplete. We model continuous-time longitudinal data from the Multicenter AIDS Cohort Study using a diffusion model in which the diffusion parameters are functions of the covariates. These data are jointly modeled with the process of time-to-death due to AIDS. We show that, even for large data sets with a large number of missing variables, a Bayesian analysis is feasible using Gibbs sampling and compare a complete case analysis with a Bayesian treatment of missing values.