OBJECTIVE: Streptococcus pneumoniae (Spn) is a major cause of child death. We investigated the epidemiology of S. pneumoniae in a pediatric fever clinic and explored the genomics basis of the limited vaccine response of serotype 14 strains worldwide.
METHODS: Febrile disease and pneumonia were diagnosed following criteria from the WHO at the end of 2019 at a tertiary children\'s hospital. Spn was isolated by culture from nasopharyngeal (NP) swabs. The density was determined by lytA-base qPCR. Isolates were serotyped by Quellung and underwent antimicrobial susceptibility testing. Whole-genome sequencing was employed for molecular serotyping, MLST, antibiotic gene determination, SNP calling, recombination prediction, and phylogenetic analysis.
RESULTS: The presence of pneumococcus in the nasopharynx (87.5%, 7/8, p = 0.0227) and a high carriage (100%, 7/7, p = 0.0123) were significantly associated with pneumonia development. Living with siblings (73.7%, 14/19, p = 0.0125) and non-vaccination (56.0%, 28/50, p = 0.0377) contributed significantly to the Spn carriage. Serotype 14 was the most prevalent strain (16.67%, 5/30). The genome analysis of 1497 serotype 14 strains indicated S14/ST876 strains were only prevalent in China, presented limited vaccine responses with higher recombination activities within its cps locus, and unique variation patterns in the genes wzg and lrp.
CONCLUSIONS: With the lifting of the one-child policy, it will be crucial for families with multiple children to get PCV vaccinations in China. Due to the highly variant cps locus and distinctive variation patterns in capsule shedding and binding proteins genes, the prevalent S14/ST876 strains have shown poor response to current vaccines. It is necessary to continue monitoring the molecular epidemiology of this vaccine escape clone.

Streptococcus pneumoniae is a notorious pathogen that affects ∼450 million people worldwide and causes up to four million deaths per annum. Despite availability of antibiotics (i.e., penicillin, doxycycline, or clarithromycin) and conjugate vaccines (e.g., PCVs), it is still challenging to treat because of its drug resistance ability. The rise of antibiotic resistance in S. pneumoniae is a major source of concern across the world. Computational subtractive genomics is one of the most applied techniques in which the whole proteome of the bacterial pathogen is gradually reduced to a limited number of potential therapeutic targets. Whole-genome sequencing has greatly reduced the time required and provides more opportunities for drug target identification. The goal of this work is to evaluate and analyze metabolic pathways in serotype 14 of S. pneumonia to identify potential drug targets. In the present study, 47 potent drug targets were identified against S. pneumonia by employing the computational subtractive genomics approach. Among these, two proteins are prioritized (i.e., 4-oxalocrotonate tautomerase and Sensor histidine kinase uniquely present in S. pneumonia) as novel drug targets and selected for further structure-based studies. The identified proteins may provide a platform for the discovery of a lead drug candidate that may be capable of inhibiting these proteins and, therefore, could be helpful in minimizing the associated risk related to the drug-resistant S. pneumoniae. Finally, these enzymatic proteins could be of prime interest against S. pneumoniae to design rational targeted therapy.

Streptococcus suis is an emerging zoonotic bacterium causing septicemia and meningitis in humans. Due to rapid disease progression, high mortality rate, and many underdiagnosed cases by time-consuming routine identification methods, alternative diagnostic testing is essential. Among 29 broadly accepted S. suis serotypes, serotypes 2 and 14 are high prevalent; however, many PCR assays showed an inability to differentiate serotype 2 from 1/2, and 1 from 14. In this study, we developed and validated a new multiplex PCR assay that facilitates the identification of only the 29 true serotypes of S. suis and simultaneously differentiates serotypes 1, 1/2, 2, and 14 within a single reaction. Importantly, the multiplex PCR could detect S. suis directly from positive hemocultures and CSF. The results revealed high sensitivity, specificity, and 100% accuracy with almost perfect agreement (κ = 1.0) compared to culture and serotyping methods. Direct detection enables a decrease in overall diagnosis time, rapid and efficient treatment, reduced fatality rates, and proficient disease control. This multiplex PCR offers a rapid, easy, and cost-effective method that can be applied in a routine laboratory. Furthermore, it is promising for developing point-of-care testing (POCT) for S. suis detection in the future.

This paper reports a case of bluetongue virus (BTV) infection in the Smolensk and Kaluga regions of Russia in 2011-2012. The virus was initially detected in heifers transferred in Russia from Germany through Poland and Belarus in 2011. On day 27 of quarantine, RNA and infectious viruses of BTV were detected in four heifers, but five were serologically positive. However, on day 3 before shipment, all heifers were seronegative and PCR-negative for BTV. Thus, a few animals from this consignment were viremic without any evident subclinical infection. Based on Seg-2 (VP2 gene) and Seg-5 (NS1 gene) sequencing, the recovered virus had 99.86-100% nucleotide identity with BTV-14-like viruses such as the vaccine BTV-14 strain RSArrrr/BTV 14 and the BTV-14 isolates detected in Lithuania and Poland in 2012. Subsequently, BTV-14 was also reported in local animals in two regions of Russia. During the monitoring survey, 1623 local animals within a 300-km radius were tested, of which 471 tested positive by ELISA and 183 by PCR for BTV-14 RNA. No other serotypes were identified in either imported or aboriginal animals within that radius. The Culicoides midges trapped at the site of the outbreak in May 2012 tested positive for the BTV-14 genome, indicating that the possible mechanism of spread most likely occurs via vector bites. However, further investigation is required to confirm this hypothesis, which would provide an improved understanding of the circulation and overwintering of BTV in northern latitudes.

Streptococcus suis is an important zoonotic pathogen. Serotype 2 and sequence type (ST) 1 are the most frequently reported strains in both infected humans and pigs. ST7 is only endemic to China, and it was responsible for outbreaks in 1998 and 2005 in China. In the present study, 38 sporadic ST7 S. suis strains, which mostly caused sepsis, were collected from patients in the Guangxi Zhuang Autonomous Region (GX) between 2007 and 2018. Of 38 sporadic ST7 strains, serotype 14 was the most frequent (27 strains, 71.1%), followed by serotype 2 (11 strains, 28.9%). The phylogenetic structure of the ST7 population, including epidemic and sporadic ST7 strains, was constructed using mutational single-nucleotide polymorphisms (SNPs). High diversity within the ST7 population was revealed and divided into five lineages. Only one sporadic ST7 strain, GX14, from a Streptococcal toxic-shock-like syndrome (STSLS) patient was clustered into the same lineage as the epidemic strains. GX14 and the epidemic strains diverged in 1974. The sporadic ST7 strains of GX were mainly clustered into lineage 5, which emerged in 1980. Comparing to genome of epidemic strain, the major differences in genome of sporadic ST7 strains of GX was the absence of 89 kb pathogenicity island (PAI) specific to epidemic strain and insertion of 128 kb ICE_phage tandem MGE or ICE portion of the MGE. These mobile elements play a significant role in the horizontal transfer of antibiotic resistance genes in sporadic ST7 strains. Our results enhanced the understanding of the evolution of the ST7 strains and their ability to cause life-threatening infections in humans.

During the 2014-15 influenza season, 13/168 respiratory samples from students with influenza-like illness (ILI) at a college in New York, USA, were positive for human adenovirus (HAdV); 4/13 samples were positive for HAdV-B14p1. During influenza season, HAdV should be included in the differential diagnostic panel used to determine the etiology of ILI.