cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20066128
title: Global dissemination of H5N1 influenza viruses bearing the clade 2.3.4.4b HA gene and biologic analysis of the ones detected in China

description: H5N1 avian influenza viruses bearing the clade 2.3.4.4b hemagglutinin gene have been widely circulating in wild birds and are responsible for the loss of over 70 million domestic poultry in Europe, Africa, Asia, and North America since October 2020. During our routine surveillance, 13 H5N1 viruses were isolated from 26,767 wild bird and poultry samples that were collected between September 2021 and March 2022 in China. To investigate the origin of these Chinese isolates and understand their genetic relationship with the globally circulating H5N1 viruses, we performed a detailed phylogenic analysis of 233 representative H5N1 strains that were isolated from 28 countries. We found that, after they emerged in the Netherlands, the H5N1 viruses encountered complicated gene exchange with different viruses circulating in wild birds and formed 16 genotypes. Genotype one (G1) was predominant, being detected in 22 countries, whereas all other genotypes were only detected in one or two continents. H5N1 viruses of four genotypes (G1, G7, G9, and G10) were detected in China; three of these genotypes have been previously reported in other countries. The H5N1 viruses detected in China replicated in mice, with pathogenicity varying among strains; the G1 virus was highly lethal in mice. Moreover, we found that these viruses were antigenically similar to and well matched with the H5-Re14 vaccine strain currently used in China. Our study reveals the overall picture of H5N1 virus evolution and provides insights for the control of these viruses.
DOI: 10.6084/m9.figshare.20066128.v2
title: Global dissemination of H5N1 influenza viruses bearing the clade 2.3.4.4b HA gene and biologic analysis of the ones detected in China

description: H5N1 avian influenza viruses bearing the clade 2.3.4.4b hemagglutinin gene have been widely circulating in wild birds and are responsible for the loss of over 70 million domestic poultry in Europe, Africa, Asia, and North America since October 2020. During our routine surveillance, 13 H5N1 viruses were isolated from 26,767 wild bird and poultry samples that were collected between September 2021 and March 2022 in China. To investigate the origin of these Chinese isolates and understand their genetic relationship with the globally circulating H5N1 viruses, we performed a detailed phylogenic analysis of 233 representative H5N1 strains that were isolated from 28 countries. We found that, after they emerged in the Netherlands, the H5N1 viruses encountered complicated gene exchange with different viruses circulating in wild birds and formed 16 genotypes. Genotype one (G1) was predominant, being detected in 22 countries, whereas all other genotypes were only detected in one or two continents. H5N1 viruses of four genotypes (G1, G7, G9, and G10) were detected in China; three of these genotypes have been previously reported in other countries. The H5N1 viruses detected in China replicated in mice, with pathogenicity varying among strains; the G1 virus was highly lethal in mice. Moreover, we found that these viruses were antigenically similar to and well matched with the H5-Re14 vaccine strain currently used in China. Our study reveals the overall picture of H5N1 virus evolution and provides insights for the control of these viruses.
DOI: 10.6084/m9.figshare.20440564
title: Evolutionary and genomic insights into the long-term colonization of <i>Shigella flexneri</i> in animals

description: The enteroinvasive bacterium <i>Shigella flexneri</i> is known as a highly host-adapted human pathogen. There had been no known other reservoirs reported until recently. Here 34 isolates obtained from animals (yaks, dairy cows and beef cattle) from 2016 to 2017 and 268 human <i>S. flexneri</i> isolates from China were sequenced to determine the relationships between animal and human isolates and infer the evolutionary history of animal-associated <i>S. flexneri</i>. The 18 animal isolates (15 yak and 3 beef cattle isolates) in PG1 were separated into 4 lineages, and the 16 animal isolates (1 yak, 5 beef cattle and 10 dairy cow isolates) in PG3 were clustered in 8 lineages. The most recent human isolates from China belonged to PG3 whereas Chinese isolates from the 1950s–1960s belonged to PG1. PG1 <i>S. flexneri</i> may has been transmitted to the yaks during PG1 circulation in the human population in China and has remained in the yak population since, while PG3 <i>S. flexneri</i> in animals were likely recent transmissions from the human population. Increased stability of the large virulence plasmid and acquisition of abundant antimicrobial resistance determinants may have enabled PG3 to expand globally and replaced PG1 in China. Our study confirms that animals may act as a reservoir for <i>S. flexneri</i>. Genomic analysis revealed the evolutionary history of multiple <i>S. flexneri</i> lineages in animals and humans in China. However, further studies are required to determine the public health threat of <i>S. flexneri</i> from animals.
DOI: 10.6084/m9.figshare.20440564.v2
title: Evolutionary and genomic insights into the long-term colonization of <i>Shigella flexneri</i> in animals

description: The enteroinvasive bacterium <i>Shigella flexneri</i> is known as a highly host-adapted human pathogen. There had been no known other reservoirs reported until recently. Here 34 isolates obtained from animals (yaks, dairy cows and beef cattle) from 2016 to 2017 and 268 human <i>S. flexneri</i> isolates from China were sequenced to determine the relationships between animal and human isolates and infer the evolutionary history of animal-associated <i>S. flexneri</i>. The 18 animal isolates (15 yak and 3 beef cattle isolates) in PG1 were separated into 4 lineages, and the 16 animal isolates (1 yak, 5 beef cattle and 10 dairy cow isolates) in PG3 were clustered in 8 lineages. The most recent human isolates from China belonged to PG3 whereas Chinese isolates from the 1950s–1960s belonged to PG1. PG1 <i>S. flexneri</i> may has been transmitted to the yaks during PG1 circulation in the human population in China and has remained in the yak population since, while PG3 <i>S. flexneri</i> in animals were likely recent transmissions from the human population. Increased stability of the large virulence plasmid and acquisition of abundant antimicrobial resistance determinants may have enabled PG3 to expand globally and replaced PG1 in China. Our study confirms that animals may act as a reservoir for <i>S. flexneri</i>. Genomic analysis revealed the evolutionary history of multiple <i>S. flexneri</i> lineages in animals and humans in China. However, further studies are required to determine the public health threat of <i>S. flexneri</i> from animals.
DOI: 10.34740/kaggle/dsv/13773592
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.6084/m9.figshare.18007457
title: Genomic epidemiology and characterisation of penicillin-sensitive <i>Staphylococcus aureus</i> isolates from invasive bloodstream infections in China: an increasing prevalence and higher diversity in genetic typing be revealed

description: Many countries have reported increasing rates of penicillin-susceptible methicillin-sensitive <i>Staphylococcus aureus</i> (MSSA-PEN<sup>S</sup>). To date, there is relatively little known about the current situation and molecular characteristics of MSSA-PEN<sup>S</sup> in China. In this study, we carried out a laboratory-based multi-region retrospective study to investigate the genomic epidemiology and characterisation of MSSA-PEN<sup>S</sup> isolated from invasive bloodstream infections (BSIs) across 17 provinces. The prevalence of MSSA-PEN<sup>S</sup> isolates increased significantly over the 6-year period, with the proportion increasing from 3.51% in 2014–8.80% in 2019, an average relative increase of 22.14% per year (95% confidence interval 9.67%-34.61%, P for trend &lt;0.001), suggesting that China is experiencing a resurgence of MSSA-PEN<sup>S</sup>. Phylogenetic analysis showed a higher strain diversity occurred; the most frequent clonal complexes (CCs) identified were CC188 (17.14%), CC398 (15.71%) and CC5 (15.71%). Over half of MSSA-PEN<sup>S</sup> strains were pan-susceptible, with erythromycin the most frequent resistance observed. Moreover, 25 isolates were identified as immune evasion cluster negative, including CC15, CC188 and CC1, and 6 strains encoded the Panton-Valentine leucocidin gene. Importantly, virulence assays showed that MSSA-PEN<sup>S</sup> exhibited a level of virulence comparable to that of penicillin-resistant MSSA (MSSA-PEN<sup>R</sup>), indicating that more-sensitive strains should not be mistaken for lacking aggressiveness in <i>vivo</i>. Furthermore, 11 of these isolates were confirmed as <i>blaZ</i> positive but phenotype sensitive, with different amino acid changes in <i>blaZ</i>. Our data support the recommendation to clinicians regarding the usage of penicillin in invasive BSIs caused by MSSA-PEN<sup>S</sup>, which might create a novel opportunity for better antimicrobial stewardship in the future.
DOI: 10.6084/m9.figshare.18007457.v2
title: Genomic epidemiology and characterisation of penicillin-sensitive <i>Staphylococcus aureus</i> isolates from invasive bloodstream infections in China: an increasing prevalence and higher diversity in genetic typing be revealed

description: Many countries have reported increasing rates of penicillin-susceptible methicillin-sensitive <i>Staphylococcus aureus</i> (MSSA-PEN<sup>S</sup>). To date, there is relatively little known about the current situation and molecular characteristics of MSSA-PEN<sup>S</sup> in China. In this study, we carried out a laboratory-based multi-region retrospective study to investigate the genomic epidemiology and characterisation of MSSA-PEN<sup>S</sup> isolated from invasive bloodstream infections (BSIs) across 17 provinces. The prevalence of MSSA-PEN<sup>S</sup> isolates increased significantly over the 6-year period, with the proportion increasing from 3.51% in 2014–8.80% in 2019, an average relative increase of 22.14% per year (95% confidence interval 9.67%-34.61%, P for trend &lt;0.001), suggesting that China is experiencing a resurgence of MSSA-PEN<sup>S</sup>. Phylogenetic analysis showed a higher strain diversity occurred; the most frequent clonal complexes (CCs) identified were CC188 (17.14%), CC398 (15.71%) and CC5 (15.71%). Over half of MSSA-PEN<sup>S</sup> strains were pan-susceptible, with erythromycin the most frequent resistance observed. Moreover, 25 isolates were identified as immune evasion cluster negative, including CC15, CC188 and CC1, and 6 strains encoded the Panton-Valentine leucocidin gene. Importantly, virulence assays showed that MSSA-PEN<sup>S</sup> exhibited a level of virulence comparable to that of penicillin-resistant MSSA (MSSA-PEN<sup>R</sup>), indicating that more-sensitive strains should not be mistaken for lacking aggressiveness in <i>vivo</i>. Furthermore, 11 of these isolates were confirmed as <i>blaZ</i> positive but phenotype sensitive, with different amino acid changes in <i>blaZ</i>. Our data support the recommendation to clinicians regarding the usage of penicillin in invasive BSIs caused by MSSA-PEN<sup>S</sup>, which might create a novel opportunity for better antimicrobial stewardship in the future.
DOI: 10.6084/m9.figshare.19830334
title: Evidence of pediatric sepsis caused by a drug resistant <i>Lactococcus garvieae</i> contaminated platelet concentrate

description: Owing to an increasing number of infections in adults, <i>Lactococcus (L.) garvieae</i> has gained recognition as an emerging human pathogen, causing bacteraemia and septicaemia. In September 2020, four paediatric onco-hematologic patients received a platelet concentrate from the same adult donor at Bambino Gesù Children’s Hospital IRCCS, Rome. Three of four patients experienced <i>L. garvieae</i> sepsis one day after transfusion. The <i>L. garvieae</i> pediatric isolates and the donor’s platelet concentrates were retrospectively collected for whole-genome sequencing and shot-gun metagenomics, respectively (Illumina HiSeq). By de novo assembly of the <i>L. garvieae</i> genomes, we found that all three pediatric isolates shared a 99.9% identity and were characterized by 440 common SNPs. Plasmid pUC11C (conferring virulence properties) and the temperate prophage Plg-Tb25 were detected in all three strains. Core SNP genome-based maximum likelihood and Bayesian trees confirmed their phylogenetic common origin and revealed their relationship with <i>L. garvieae</i> strains affecting cows and humans (bootstrap values &gt;100 and posterior probabilities = 1.00). Bacterial reads obtained by the donor’s platelet concentrate have been profiled with MetaPhlAn2 (v.2.7.5); among these, 29.9% belonged to Firmicutes, and 5.16% to Streptococcaceae (&gt;97% identity with <i>L. garvieae</i>), confirming the presence of <i>L. garvieae</i> in the platelet concentrate transfusion. These data showed three episodes of sepsis for the first time due to a transfusion-associated transmission of <i>L. garvieae</i> in three pediatric hospitalized hematology patients. This highlights the importance to implement the screening of platelet components with new human-defined pathogens for ensuring the safety of blood supply, and more broadly, for the surveillance of emerging pathogens.
DOI: 10.6084/m9.figshare.19830334.v1
title: Evidence of pediatric sepsis caused by a drug resistant <i>Lactococcus garvieae</i> contaminated platelet concentrate

description: Owing to an increasing number of infections in adults, <i>Lactococcus (L.) garvieae</i> has gained recognition as an emerging human pathogen, causing bacteraemia and septicaemia. In September 2020, four paediatric onco-hematologic patients received a platelet concentrate from the same adult donor at Bambino Gesù Children’s Hospital IRCCS, Rome. Three of four patients experienced <i>L. garvieae</i> sepsis one day after transfusion. The <i>L. garvieae</i> pediatric isolates and the donor’s platelet concentrates were retrospectively collected for whole-genome sequencing and shot-gun metagenomics, respectively (Illumina HiSeq). By de novo assembly of the <i>L. garvieae</i> genomes, we found that all three pediatric isolates shared a 99.9% identity and were characterized by 440 common SNPs. Plasmid pUC11C (conferring virulence properties) and the temperate prophage Plg-Tb25 were detected in all three strains. Core SNP genome-based maximum likelihood and Bayesian trees confirmed their phylogenetic common origin and revealed their relationship with <i>L. garvieae</i> strains affecting cows and humans (bootstrap values &gt;100 and posterior probabilities = 1.00). Bacterial reads obtained by the donor’s platelet concentrate have been profiled with MetaPhlAn2 (v.2.7.5); among these, 29.9% belonged to Firmicutes, and 5.16% to Streptococcaceae (&gt;97% identity with <i>L. garvieae</i>), confirming the presence of <i>L. garvieae</i> in the platelet concentrate transfusion. These data showed three episodes of sepsis for the first time due to a transfusion-associated transmission of <i>L. garvieae</i> in three pediatric hospitalized hematology patients. This highlights the importance to implement the screening of platelet components with new human-defined pathogens for ensuring the safety of blood supply, and more broadly, for the surveillance of emerging pathogens.
DOI: 10.6084/m9.figshare.17698270
title: Direct neuronal infection of SARS-CoV-2 reveals cellular and molecular pathology of chemosensory impairment of COVID-19 patients

description: Patients with recent pandemic coronavirus disease 19 (COVID-19) complain of neurological abnormalities in sensory functions such as smell and taste in the early stages of infection. Determining the cellular and molecular mechanism of sensory impairment is critical to understand the pathogenesis of clinical manifestations, as well as in setting therapeutic targets for sequelae and recurrence. The absence of studies utilizing proper models of human peripheral nerve hampers an understanding of COVID-19 pathogenesis. Here, we report that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly infects human peripheral sensory neurons, leading to molecular pathogenesis for chemosensory impairments. An in vitro system utilizing human embryonic stem cell (hESC)-derived peripheral neurons was used to model the cellular and molecular pathologies responsible for symptoms that most COVID-19 patients experience early in infection or may develop as sequelae. Peripheral neurons differentiated from hESCs expressed viral entry factor ACE2, and were directly infected with SARS-CoV-2 via ACE2. Human peripheral neurons infected with SARS-CoV-2 exhibited impaired molecular features of chemosensory function associated with abnormalities in sensory neurons of the olfactory or gustatory organs. Our results provide new insights into the pathogenesis of chemosensory dysfunction in patients with COVID-19.
DOI: 10.6084/m9.figshare.17698270.v2
title: Direct neuronal infection of SARS-CoV-2 reveals cellular and molecular pathology of chemosensory impairment of COVID-19 patients

description: Patients with recent pandemic coronavirus disease 19 (COVID-19) complain of neurological abnormalities in sensory functions such as smell and taste in the early stages of infection. Determining the cellular and molecular mechanism of sensory impairment is critical to understand the pathogenesis of clinical manifestations, as well as in setting therapeutic targets for sequelae and recurrence. The absence of studies utilizing proper models of human peripheral nerve hampers an understanding of COVID-19 pathogenesis. Here, we report that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly infects human peripheral sensory neurons, leading to molecular pathogenesis for chemosensory impairments. An in vitro system utilizing human embryonic stem cell (hESC)-derived peripheral neurons was used to model the cellular and molecular pathologies responsible for symptoms that most COVID-19 patients experience early in infection or may develop as sequelae. Peripheral neurons differentiated from hESCs expressed viral entry factor ACE2, and were directly infected with SARS-CoV-2 via ACE2. Human peripheral neurons infected with SARS-CoV-2 exhibited impaired molecular features of chemosensory function associated with abnormalities in sensory neurons of the olfactory or gustatory organs. Our results provide new insights into the pathogenesis of chemosensory dysfunction in patients with COVID-19.
DOI: 10.6084/m9.figshare.19742134
title: Pathogenesis and transmission of human seasonal and swine-origin A(H1) influenza viruses in the ferret model

description: Influenza A viruses (IAVs) in the swine reservoir constantly evolve, resulting in expanding genetic and antigenic diversity of strains that occasionally cause infections in humans and pose a threat of emerging as a strain capable of human-to-human transmission. For these reasons, there is an ongoing need for surveillance and characterization of newly emerging strains to aid pandemic preparedness efforts, particularly for the selection of candidate vaccine viruses and conducting risk assessments. Here, we performed a parallel comparison of the pathogenesis and transmission of genetically and antigenically diverse swine-origin A(H1N1) variant (v) and A(H1N2)v, and human seasonal A(H1N1)pdm09 IAVs using the ferret model. Both groups of viruses were capable of replication in the ferret upper respiratory tract; however, variant viruses were more frequently isolated from the lower respiratory tract as compared to the human-adapted viruses. Regardless of virus origin, observed clinical signs of infection differed greatly between strains, with some viruses causing nasal discharge, sneezing and, in some instances, diarrhea in ferrets. The most striking difference between the viruses was the ability to transmit through the air. Human-adapted viruses were capable of airborne transmission between all ferret pairs. In contrast, only one out of the four tested variant viruses was able to transmit via the air as efficiently as the human-adapted viruses. Overall, this work highlights the need for sustained monitoring of emerging swine IAVs to identify strains of concern such as those that are antigenically different from vaccine strains and that possess adaptations required for efficient respiratory droplet transmission in mammals.
DOI: 10.6084/m9.figshare.19742134.v2
title: Pathogenesis and transmission of human seasonal and swine-origin A(H1) influenza viruses in the ferret model

description: Influenza A viruses (IAVs) in the swine reservoir constantly evolve, resulting in expanding genetic and antigenic diversity of strains that occasionally cause infections in humans and pose a threat of emerging as a strain capable of human-to-human transmission. For these reasons, there is an ongoing need for surveillance and characterization of newly emerging strains to aid pandemic preparedness efforts, particularly for the selection of candidate vaccine viruses and conducting risk assessments. Here, we performed a parallel comparison of the pathogenesis and transmission of genetically and antigenically diverse swine-origin A(H1N1) variant (v) and A(H1N2)v, and human seasonal A(H1N1)pdm09 IAVs using the ferret model. Both groups of viruses were capable of replication in the ferret upper respiratory tract; however, variant viruses were more frequently isolated from the lower respiratory tract as compared to the human-adapted viruses. Regardless of virus origin, observed clinical signs of infection differed greatly between strains, with some viruses causing nasal discharge, sneezing and, in some instances, diarrhea in ferrets. The most striking difference between the viruses was the ability to transmit through the air. Human-adapted viruses were capable of airborne transmission between all ferret pairs. In contrast, only one out of the four tested variant viruses was able to transmit via the air as efficiently as the human-adapted viruses. Overall, this work highlights the need for sustained monitoring of emerging swine IAVs to identify strains of concern such as those that are antigenically different from vaccine strains and that possess adaptations required for efficient respiratory droplet transmission in mammals.