According to the so-called upwelling paradigm, development of equatorial plasma bubbles (EPBs) involves (1) appearance of an upwelling (i.e., local uplift with a zonal width of~400 km) in the bottomside of the equatorial F layer, (2) its growth via the F-region interchange instability during the post-sunset rise (PSSR) of the F layer, and (3) launching of EPBs, which starts near the end of PSSR, from within the confines of the upwelling. In this description, the PSSR is presumed to be the primary driver of the paradigm, with upwelling growth dependent on PSSR strength. As constructed, the paradigm describes EPB development when PSSR is strong (i.e., high solar activity), but not when it is weak. We, show, for the first time, that when PSSR is weak (e.g., low solar activity), upwelling growth can still be comparable in strength to what would be considered a strong PSSR, and that this growth drives EPB development. Given that EPBs do not develop outside of upwellings, regardless of solar activity, we are led to conclude, against mainstream thinking, that the controlling driver for EPB development is upwelling growth, not PSSR. For continued progress toward understanding EPB development, a crucial next step is to identify the source mechanism for upwelling growth, especially when PSSR is weak, and to better understand the complexities of the underlying physics.

RSV infection induces a clearly different host response pattern compared with hRV and induced strong innate immune responses both locally and systemically. B cell lymphoma (BCL6) is a hub gene that positively correlates with RSV load and disease severity.

We report 6 cases of bacteremia due to Tsukamurella species, all of which were in immunosuppressed patients with indwelling central venous catheters (CVCs). Fewer than 20 cases of serious illness due to these gram-positive bacilli have been reported in the medical literature; these cases have mostly been ascribed to the species Tsukamurella paurometabola. Tsukamurella species are frequently misidentified as Rhodococcus or Corynebacterium species. We used high-performance liquid chromatography to identify these organisms to the genus level and 16S ribosomal RNA gene sequencing and DNA-DNA dot blots for species identification. Three of our isolates were identified as Tsukamurella pulmonis, 1 was identified as Tsukamurella tyrosinosolvans, and 1 was identified as a unique species. One isolate was not maintained long enough for species identification. All patients were successfully treated with antimicrobial therapy and CVC removal. Infection with this organism should be considered in the immunosuppressed patient with an indwelling CVC and gram-positive bacilli in the blood.

We describe here the characterization of five isolates of Mycobacterium simiae-like organisms representing a novel group based on whole-cell fatty acid analysis and genotypic evaluation. Two of the five isolates in this study, W55 and W58, were previously considered to belong to M. simiae serotype 2. Analysis of cellular fatty acids by gas-liquid chromatography indicated a close clustering of this group, which was well differentiated from the other M. simiae-like species. Molecular characterization was performed by nucleic acid sequencing of the small subunit rRNA gene and the gene encoding the 65-kDa heat shock protein and genomic DNA hybridization. Sequence analysis of the entire 16S rRNA gene showed a unique sequence most closely related to those of M. triplex and M. simiae. The hsp65 partial gene sequence was identical for the five isolates, with 97% identity to the M. simiae type strain. However, qualitative whole genomic DNA hybridization analysis confirmed that this group is genetically distinct from M. simiae and M. triplex. Antimicrobial susceptibilities for this group resemble those of M. simiae and M. lentiflavum. We conclude that this group represents a unique Mycobacterium species for which we propose the name Mycobacterium sherrisii sp. nov.The genus Mycobacterium consists of a diverse group of acidfast bacilli that exist in the environment and cause infections in humans and animals (22). Conventional methods for identification of these organisms are well established and inexpensive, but these methods are also time-consuming and labor-intensive and can provide inconsistent results, leading to species identifications based on a "best-fit" method. The introduction of several molecular tools and improved techniques in the last two decades has not only revolutionized the identification process by reducing the time to identification but also has provided clues to the presence of novel strains. Mycolate analysis has proven to be a powerful phenotypic method for determining the presence of new species based on novel patterns (9, 25). Fatty acid analysis techniques such as high-performance liquid chromatography (HPLC) and gas-liquid chromatography (GLC) were developed to analyze the mycolic acid and whole-cell fatty acid profiles, respectively, to identify characteristic patterns of established mycobacterial species (7,10,12,30).The advent of nucleotide probes designed to hybridize to specific rRNA gene sequences allowed rapid identification of the most common mycobacterial species (16). Lately, genotypic analyses aimed at identifying nucleotide sequences of several chromosomal genes in the Mycobacterium genus coding for 16S rRNA, internal transcribed spacer 1, and 65-kDa heat shock protein (hsp65) have proven to be useful in the molecular characterization of well-established species and in identifying new ones, including previously misidentified groups (8,15,17,26). Analysis of the hypervariable region in the 16S rRNA gene sequence has a high species specificity and also has been useful to assign new spec...

BackgroundDespite a high burden of respiratory syncytial virus (RSV) infections among children, data on demographic and clinical characteristics of RSV are scarce in low and middle income countries. This study aims to describe the viral etiologies, the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a lower respiratory tract infections (LRTI), focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity.MethodsA prospective study among children under two years of age, hospitalized with LRTI was conducted in two referral pediatric hospitals in Ho Chi Minh City, Vietnam, from May 2009 to December 2010. Socio-demographic, clinical data and nasopharyngeal swabs were collected on enrolment and discharge. Multiplex real-time RT-PCR (13 viruses) and quantitative RSV RT-PCR were used to identify viral pathogens, RSV load and subgroups.ResultsAmong 632 cases, 48% were RSV positive. RSV infections occurred at younger age than three other leading viral infections i.e rhinovirus (RV), metapneumovirus (MPV), parainfluenza virus (PIV-3) and were significantly more frequent in the first 6 months of life. Clinical severity score of RSV infection was significantly higher than PIV-3 but not for RV or MPV. In multivariate analysis, RV infection was significantly associated with severity while RSV infection was not. Among RSV infections, neither viral load nor viral co-infections were significantly associated with severity. Young age and having fever at admission were significantly associated with both RSV and LRTI severity. A shift in RSV subgroup predominance was observed during two consecutive rainy seasons but was not associated with severity.ConclusionWe report etiologies, the epidemiological and clinical characteristics of LRTI among hospitalized children under two years of age and risk factors of RSV and LRTI severity.

We have isolated a gram-positive, weakly acid-alcohol-fast, irregular rod-shaped bacterium from cultures of blood from a 5-year-old girl with acute myelogenous leukemia. This isolate was compared with 14 other strains including reference strains of Tsukamurella species by a polyphasic approach based on physiological and biochemical properties, whole-cell short-chain fatty acid and mycolic acid analyses, DNA-DNA hybridization, and sequencing of the 16S rRNA gene. This isolate represents a new taxon within the genus Tsukamurella for which we propose the name Tsukamurella strandjordae sp. nov. Our study also revealed that Tsukamurella paurometabola ATCC 25938 represents a misnamed Tsukamurella inchonensis isolate and confirms that Tsukamurella wratislaviensis belongs to the genus Rhodococcus.Tsukamurellae are members of the mycolic acid-containing aerobic actinomycetes. The genus was created in 1988 to accommodate a group of chemically unique organisms characterized by a series of very long chain (68 to 76 carbons) highly unsaturated (two to six double bonds) mycolic acids, in addition to possessing meso-diaminopimelic acid and arabinogalactan, common to the genus Corynebacterium (6). The type species, Tsukamurella paurometabola, described by Steinhaus as Corynebacterium paurometabolum in 1941, was originally isolated from the mycetomes and ovaries of bed bugs (27). The first human isolate of Tsukamurella was reported in 1971 as Gordona aurantiaca (33). Four additional species were proposed in the 1990s. Tsukamurella wratislaviensis was isolated from soil (10). Strains of Tsukamurella inchonensis, Tsukamurella pulmonis, and Tsukamurella tyrosinosolvens have been isolated only from human specimens, and all were associated with clinical disease (34-36). We have encountered an unusual isolate in multiple cultures of blood from a 5-year-old girl with acute myelogenous leukemia who presented with sepsis. On the basis of physiological and biochemical characteristics, analysis of cell components, DNA-DNA hybridizations, and the 16S rRNA gene sequence, we propose that this strain represents a new taxon within the genus Tsukamurella to which we assign the name Tsukamurella strandjordae sp. nov. Our study compared this isolate to reference and clinical strains of the other Tsukamurella species and found that T. paurometabola ATCC 25938 is a misnamed T. inchonensis isolate. MATERIAL AND METHODSStrains. The study included type strains of all proposed Tsukamurella species. T. paurometabola ATCC 8368 and T. wratislaviensis ATCC 51786 were purchased from the American Type Culture Collection (ATCC). A. F. Yassin generously provided the type strains T. pulmonis ATCC 700081 and T. inchonesis ATCC 700082. Type strain T. tyrosinosolvens DSMZ 44234 was purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ; Braunschweig, Germany). Other purchased reference strains included strains T. paurometabola ATCC 25938 and T. tyrosinosolvens DSMZ 44316. The strain of T. strandjordae, the subject of this study, was is...

Human respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children ,2 years of age. Little is known about RSV intra-host genetic diversity over the course of infection or about the immune pressures that drive RSV molecular evolution. We performed whole-genome deep-sequencing on 53 RSV-positive samples (37 RSV subgroup A and 16 RSV subgroup B) collected from the upper airways of hospitalized children in southern Vietnam over two consecutive seasons. RSV A NA1 and RSV B BA9 were the predominant genotypes found in our samples, consistent with other reports on global RSV circulation during the same period. For both RSV A and B, the M gene was the most conserved, confirming its potential as a target for novel therapeutics. The G gene was the most variable and was the only gene under detectable positive selection. Further, positively selected sites in G were found in close proximity to and in some cases overlapped with predicted glycosylation motifs, suggesting that selection on amino acid glycosylation may drive viral genetic diversity. We further identified hotspots and coldspots of intra-host genetic diversity in the RSV genome, some of which may highlight previously unknown regions of functional importance.

Plasma structure in nighttime equatorial F layer, referred to as equatorial spread F (ESF), displays climatology whose seasonal variation depends on longitude. At longitudes where ESF favors equinoxes, times when maxima occur can be predicted in terms of the day of year, when E region sunset is simultaneous in conjugate hemispheres (i.e., "sunset nodes"). Aside from occurrences around equinoxes, there are only three longitudes where ESF also occurs during a solstice; one is the central Pacific region. Here ESF activity is strong during the June solstice, when solar activity is high. To understand this puzzling behavior, ESF climatology over the Kwajalein Atoll was compared with properties of the postsunset rise (PSSR) of the F layer and seeding activity in the troposphere. The key findings are as follows: (1) Maxima in PSSR velocity (V PSSR ) are better aligned with equinoxes than with sunset nodes; hence, seasonal pattern of V PSSR , not only sunset nodes, should be included in interpretation of ESF climatology. (2) The source of V PSSR during solstice appears to differ from that during equinoxes. (3) Equinoctial maxima in V PSSR could be related to a semiannual variation in equatorial electrojet strength and its contribution to polarization of the F region dynamo current. (4) Enhanced V PSSR during the June solstice is interpreted in terms of tidal forcing with a wave number of 2. (5) Displacements of maxima in ESF climatology from maxima in V PSSR are shown to be consistent with deep convective activity.