Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera

The family Streptomycetaceae is a large and diverse family within the phylum Actinomycetota . The members of the family are known for their ability to produce medically important secondary metabolites, notably antibiotics. In this study, 19 type strains showing low 16S rRNA gene similarity (<97.3 %) to other members of the family Streptomycetaceae were identified and their high genetic diversity was reflected in a phylogenomic analysis using conserved universal proteins. This analysis resulted in the identification of six distinct genus-level clades, with two separated from the genus Streptacidiphilus and four separated from the genus Streptomyces . Compared with members of the genera Streptacidiphilus and Streptomyces , average amino acid identity (AAI) analysis of the novel genera identified gave values within the range of 63.9–71.3 %, as has been previously observed for comparisons of related but distinct bacterial genera. The whole-genome phylogeny was reconstructed using PhyloPhlAn 3.0 based on an optimized subset of conserved universal proteins, the results of AAI and percentage of conserved proteins (POCP) analyses indicated that these phylogenetically distinct taxa may be assigned to six novel genera, namely Actinacidiphila gen. nov., Mangrovactinospora gen. nov., Peterkaempfera gen. nov., Phaeacidiphilus gen. nov., Streptantibioticus gen. nov. and Wenjunlia gen. nov

Incipient parallel evolution of SARS-CoV-2 Deltacron variant in South Brazil

With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. These processes could result in genetic introgression and the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of the Spike gene. The 5′ genome portion (circa 22 kb) resembles the AY.101 (Delta), and the 3′ genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 (Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, AYBA-RS, is one of the dozens of recombinants described in 2022. The submission of only four sequences in the GISAID database suggests that this lineage had a minor epidemiological impact. However, the recent emergence of this and other Deltacron recombinant lineages (XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that supports this assertion, concluding that this stresses the need for continued genomic surveillance. This monitoring is vital for countries where multiple variants are present, as well as for countries that receive significant inbound international travel

Serotypes and Genotypes of Invasive <i>Streptococcus pneumoniae</i> Before and After PCV10 Implementation in Southern Brazil

<div><p>To reduce the burden of pneumococcal diseases, different formulations of pneumococcal conjugate vaccines (PCV) have been introduced in many countries. In Brazil, PCV10 has been available since 2010. We aimed to analyze the serotype and genetic composition of invasive pneumococci from Brazil in pre- and post- vaccination periods (2007–2012). Antibiotic susceptibility was determined and genotypes of macrolide and fluoroquinolone resistance were characterized. The genotypes of isolates of the most frequent serotypes were determined by multilocus sequence typing. The study included 325 isolates, which were primarily recovered from blood. The most common serotypes recovered were 14, 3, 4, 23F, 7F, 9V, 12F, 20, 19F, 8, 19A, and 5. Thirty-eight pneumococci (11.7%) were from children ≤5 years old. Considering the overall population, PCV10 and PCV13 serotype coverage was 50.1% and 64.9%, respectively. During the pre-vaccine period, isolates with serotypes belonging to the PVC10 represented 51.5% (100/194), whereas in the post vaccine they represented 48.0% (63/131). PCV13 serotypes represented 67.5% (131/194) and 59.2% (77/131) of total for pre- and post-vaccination periods, respectively. Seventy different sequence types [STs] were found, accounting for 9 clonal complexes [CCs] and 45 singletons. Eight STs (156, 180, 218, 8889, 53, 191, 770, and 4967) represented the majority (51.5%) of isolates. Fifty STs were associated with the pre-vaccination period (27 exclusive) and 43 (20 exclusive) with the post-vaccination period; 23 STs were identified in both periods. Some serotypes were particularly clonal (7F, 8, 12F, 20). Non-susceptibility to penicillin was associated with serotype 19A, CC320. Erythromycin resistance was heterogeneous when considering serotype and ST. A single serotype 23F (ST4967) isolate was resistant to levofloxacin. Continued surveillance is required to determine vaccine impact and to monitor changes in pneumococcal population biology post-PCV10 introduction in Brazil.</p></div

Distribution of serotypes in pre- and post-vaccination period among pneumococci recovered from IPD, during 2007–2012.

<p>Black bars represent pre-PCV10 and gray bars post-PCV10.</p

Population structure of invasive <i>S. pneumoniae</i> collected from 2007 to 2012.

<p>Black circles: pre-vaccine isolates; Green circles: post-vaccine isolates; pink circles: isolates present in both pre and post vaccine years; Blue circles: the ancestor of the CC.</p

New STs and their relationship with serotypes and STs in the database at MLST website (MLST database – accessed 19^th October, 2013).

<p>*Pre: pre-vaccination; Post: post-vaccination;</p><p>**More frequent ST and/or the ones isolated in Brazil;</p>#<p>8897 is DLV of STs 2781 (serotype 6B) and 8248 (serotype 6A/B), isolated previously in Brazil;</p>##<p>8881 is DLV of STs 9 (serotype 14) and 15 (serotype 14). The first ST was previously isolated in many countries, as the second one, which was also related to Brazilian isolates.</p><p>New STs and their relationship with serotypes and STs in the database at MLST website (MLST database – accessed 19^th October, 2013).</p

Distribution of serotypes belonging to PCV10 among invasive pneumococci recovered from 2007 to 2012 (the distribution of all serotypes is demonstrated on the Table S1).

<p>*Pre-vaccination period;</p><p>**post-vaccination period;</p>#<p>OR: odds ratio.</p><p>Distribution of serotypes belonging to PCV10 among invasive pneumococci recovered from 2007 to 2012 (the distribution of all serotypes is demonstrated on the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111129#pone.0111129.s001" target="_blank">Table S1</a>).</p

Serotypes and STs observed among 231 pneumococci recovered from IPD (2007–2012).

<p>Serotypes and STs observed among 231 pneumococci recovered from IPD (2007–2012).</p