A Laboratory-Based Surveillance Study of Invasive Neisseria meningitidis, Streptococcus pneumoniae, and Haemophilus influenzae Diseases in a Serbian Pediatric Population—Implications for Vaccination

The aim of this study was to present the epidemiology of invasive diseases caused by Neisseria meningitidis and Streptococcus pneumoniae in the pre-vaccine period, and Haemophilus influenzae in the post-vaccine period in a pediatric population from Serbia. Among the meningococci, serogroup B dominated (83%), followed by serogroup C (11.3%). High antigenic diversity was found, with fine type P1.5-1,10-4 being the most frequent. Moderate susceptibility to penicillin was common (55%). Within pneumococci, serotypes 19F, 14, 6B, 6A, 18C, 23F, 3, and 7F prevailed, while 19A was rare (3.6%). The coverages of PCV10 and PCV13 were 68% and 84%, respectively. Major sequence types were ST320, ST15, ST273, ST271, and ST81. Non-susceptibility to penicillin (66.7%), cefotaxime (37%), and macrolides (55%) was predominantly detected in vaccine-related serotypes. Among the 11 invasive H. influenzae isolates collected, there were six Hib, three non-type b, and two non-typeable strains (ntHi) that were antibiotic susceptible. These results imply a potential benefit of future Men-B vaccine implementations. For pneumococci, as PCV10 was recently introduced, a significant reduction of morbidity and antibiotic resistance might be expected. The efficiency of Hib vaccination is evident, but a shift towards non-type b and ntHi strains may be anticipated.

New Insights into the Lake Erie Fault System from the 2019 ML 4.0 Ohio Earthquake Sequence

We present a detailed analysis of the 10 June 2019 ML 4.0 Ohio earthquake sequence, which is the largest earthquake that struck Lake County, northeastern Ohio, since 1986. This sequence is well recorded by local seismic networks, which provides an unprecedented opportunity to understand the local seismotectonics. We utilize a waveform-based cross-correlation method to identify ∼12 times more events than reported by the Advanced National Seismic System (ANSS) Comprehensive Earthquake Catalog: the whole sequence started with several small earthquakes (ML 1–2) beginning 12 March 2019, and the last one occurred ∼1min immediately before the ML 4.0 mainshock; many previously unreported aftershocks (ML 0.3–2.2) are found, which were active for the first week after the mainshock; another major sequence with a 7 December 2019 ML 2.6 mainshock occurred and also started with a few smaller events beginning in mid-November and was followed by its own aftershocks. The relocated seismicity delineates a linear feature, orientation of which is consistent with the resolved focal plane that may correspond to the ruptured fault. Our results highlight that closer monitoring of local seismicity is crucial for understanding the seismotectonics and mitigating future seismic hazard around the southern Great Lakes.

Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae

Satellite repeats are major sequence constituents of centromeres in many plant and animal species. Within a species, a single family of satellite sequences typically occupies centromeres of all chromosomes and is absent from other parts of the genome. Due to their common origin, sequence similarities exist among the centromere-specific satellites in related species. Here, we report a remarkably different pattern of centromere evolution in the plant tribe Fabeae, which includes genera Pisum, Lathyrus, Vicia, and Lens. By immunoprecipitation of centromeric chromatin with CENH3 antibodies, we identified and characterized a large and diverse set of 64 families of centromeric satellites in 14 species. These families differed in their nucleotide sequence, monomer length (33–2,979 bp), and abundance in individual species. Most families were species-specific, and most species possessed multiple (2–12) satellites in their centromeres. Some of the repeats that were shared by several species exhibited promiscuous patterns of centromere association, being located within CENH3 chromatin in some species, but apart from the centromeres in others. Moreover, FISH experiments revealed that the same family could assume centromeric and noncentromeric positions even within a single species. Taken together, these findings suggest that Fabeae centromeres are not shaped by the coevolution of a single centromeric satellite with its interacting CENH3 proteins, as proposed by the centromere drive model. This conclusion is also supported by the absence of pervasive adaptive evolution of CENH3 sequences retrieved from Fabeae species.

Revised stratigraphy of the Eifelian (Middle Devonian) of southern Belgium: sequence stratigraphy, global events, reef development and basin structuration

The Eifelian lithostratigraphic succession of southern Belgium is here revised based on new field investigations and reconsideration of biostratigraphic data. The Couvin Formation is divided into four members: the Villers-la-Tour Member recorded the onset of stromatoporoid biostromes, the Petigny Member is a dark fine-grained limestone that recorded the Choteč event, the Cul d’Efer Member is dominated by stromatoporoid-coral biostromes. These first three members were previously united in the Foulerie Member and correspond to the transgressive and highstand system tracts of the Middle Devonian 3rd-order sequence MD1. The argillaceous and bioclastic successive units of the Abîme Member recorded the sequence MD2. Laterally, this sequence is only composed of siliciclastic deposits of the Vieux Moulin, Station and Cimetière members of the Jemelle Formation. The highstand system tract is the newly introduced carbonate Vierves Member. Large bioherms, newly described as the Wancennes Formation, recorded the first two sequences MD1 and MD2. A major sequence boundary caps the Couvin Formation and is overlaid by the transgressive and diachronous Chavées Member of the Jemelle Formation with a depositional gap increasing eastwards. The highstand system tract of sequence MD3 is recorded in the bioherms of the Tienne Sainte-Anne Member (upper part of the Jemelle Formation), also capped by a sequence boundary. These bioherms probably acted as highs around which the sandy deposits of the Lomme Formation accumulated as lowstand system tract of sequence MD4. The Hanonet Formation and its crinoidal Wellin Member form the transgressive system tracts of sequence MD4 that terminates in the bioclastic and biohermal Trois-Fontaines Formation (Givetian). The Kačák event is identified in the transgressive system tract of this sequence. The geographic distribution of facies and of reefs in particular led to the recognition of at least six sedimentation areas corresponding most probably to synsedimentary faulted blocks here defined as the Eau Blanche, Viroin, Lesse, Ourthe, Condroz and Sambre blocks. These sedimentation areas structured the Namur-Dinant Basin and recorded distinct depositional history and were probably active during the Devonian and Carboniferous interval.

Development and Evaluation of a Duo Chikungunya Virus Real-Time RT-PCR Assay Targeting Two Regions within the Genome

Chikungunya virus (CHIKV) re-emerged as a globalized health threat fifteen years ago. There are dozens of RT-PCR assays published. An inventory of the latter was made, and after in silico analysis, two assays were selected for their ability to detect strains belonging to the five CHIKV genetic lineages. They were combined in order to provide a robust assay not affected by genetic point mutations and the resulting Duo CHIKV real-time RT-PCR assay was compared to the two parental single-plex tests against five strains belonging to the five genetic lineages. The Duo CHIKV assay performed equally, or better, in terms of sensitivity, specificity, linearity and signal intensity. Dual-target assays are better suited for viruses having the propensity to evolve into new variants via point mutations or major sequence deletions/insertions. Here, we demonstrated that combining two single systems into a dual-target assay did not impair sensitivity and specificity, and proved a potent diagnostic tool to face a potential emergence of CHIKV variants by newly evolving mutations.

Integrated bio- and cyclostratigraphy of Middle Triassic (Anisian) ramp deposits, NW Bulgaria

A cyclostratigraphic interpretation of peritidal to shallow-marine ramp deposits of the early Middle Triassic (Anisian) Opletnya Member exposed in outcrops along the Iskar River gorge, NW Bulgaria, is presented. Based on facies trends and bounding surfaces, depositional sequences of several orders can be identified. New biostratigraphic data provide a time frame of the studied succession with placement of the boundaries of the Anisian substages and show that the Aegean (early Anisian) substage lasted about 1.6 Myr. In the corresponding interval in the two studied sections, 80 elementary sequences are counted. Five elementary sequences compose a small-scale sequence. The prominent cyclic pattern of the Opletnya Member can thus be interpreted in terms of Milankovitch cyclicity: elementary sequences represent the precession (20-kyr) cycle and small-scale sequences the short eccentricity (100-kyr) cycle in the Milankovitch frequency band. Medium-scale sequences are defined based on lithology but only in two cases can be attributed to the long eccentricity cycle of 405 kyr. The transgressive-regressive facies trends within the sequences of all scales imply that they were controlled by sea-level changes, and that these were in tune with the climate changes induced by the orbital cycles. However, the complexity of facies and sedimentary structures seen in the Opletnya Member also implies that additional factors such as lateral migration of sediment bodies across the ramp were active. In addition, three major sequence boundaries have been identified in the studied sections, which can be correlated with the boundaries Ol4, An1, and An2 of the Tethyan realm.

Fantastic yeasts and where to find them: the discovery of a predominantly clonal Cryptococcus deneoformans population in Saudi Arabian soils

ABSTRACT Cryptococcus deneoformans is an opportunist yeast pathogen and causative agent of meningoencephalitis in humans. It is known to be mainly distributed in temperate climates. Most of our current understanding of this species has come from clinical isolates, leaving environmental populations largely unexplored. The Middle East remains one such underexplored area with no published study to date investigating cryptococcal diversity in soil. In this study, we identified 76 C. deneoformans isolates from a survey of 562 soil samples collected from six cities in Saudi Arabia. Multilocus sequence typing revealed the presence of two major sequence types (STs), ST160 (n = 63) and ST294 (n = 9), along with four singleton STs, three of which were novel. One novel ST, ST613, was likely a recombinant product between ST160 and ST294. Among the 76 isolates, 75 belonged to mating type (MAT)α while one isolate was MATa. Our analyses suggest that the Saudi Arabian C. deneoformans population likely reproduces both asexually and sexually in nature. Our study is the first to report the occurrence of C. deneoformans in a desert climate, representing a novel expansion to this species’ currently known ecological niche.

Analysis of Genetic Characterization and Clonality of Legionella pneumophila Isolated from Cooling Towers in Japan

We investigated the genetic characteristics of 161 Legionella pneumophila strains isolated over a period of 10 years from cooling towers in Japan. Minimum spanning tree analysis based on the sequence-based typing (SBT) of them identified three clonal complexes (CCs); CC1 (105/161, 65.2%), CC2 (22 /161, 13.7%), and CC3 (20/161, 12.4%). CC1 was formed by serogroup (SG) 1 and SG7, whereas CC2 was mainly formed by SG1. All of the CC3 isolates except two strains were SG13. The major sequence types (STs) in CC1 and CC2 were ST1 (88/105, 83.8%) and ST154 (15/22, 68.2%), respectively. These STs are known as typical types of L. pneumophila SG1 in Japanese cooling tower. Additionally, we identified 15 strains of ST2603 as the major type in CC3. This ST has not been reported in Japanese cooling tower. Whole genome sequencing (WGS) analysis of the representative strains in the three CCs, which were isolated from various cooling towers over the 10 years, elucidated high clonal population of L. pneumophila in Japanese cooling tower. Moreover, it revealed that the strains of CC2 are phylogenetically distant compared to those of CC1 and CC3, and belonged to L. pneumophila subsp. fraseri.

The Early to Middle Triassic continental–marine transition of NW Bulgaria: sedimentology, palynology and sequence stratigraphy

Sedimentary facies and cycles of the Triassic continental–marine transition of NW Bulgaria are documented in detail from reference sections along the Iskar river gorge between the villages of Tserovo and Opletnya. The depositional environments evolved from anastomosing and meandering river systems in the Petrohan Terrigenous Group to mixed fluvial and tidal settings in the Svidol Formation, and to peritidal and shallow-marine conditions in the Opletnya Member of the Mogila Formation. For the first time, the palynostratigraphic data presented here allow for dating the transitional interval and for the precise identification of a major sequence boundary between the Petrohan Terrigenous Group and the Svidol Formation (Iskar Carbonate Group). This boundary most probably corresponds to the major sequence boundary Ol4 occurring in the upper Olenekian of the Tethyan realm and thus enables interregional correlation. The identification of regionally traceable sequence boundaries based on biostratigraphic age control is a first step towards a more accurate stratigraphic correlation and palaeogeographic interpretation of the Early to early Middle Triassic in NW Bulgaria.