cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27079095
title: Genomic epidemiology of <i>Clostridioides difficile</i> sequence type 35 reveals intraspecies and interspecies clonal transmission

description: <i>Clostridioides difficile</i> sequence type (ST) 35 has been found in humans and animals worldwide. However, its genomic epidemiology and clonal transmission have not been explored in detail. In this study, 176 <i>C. difficile</i> ST35 isolates from six countries were sequenced. Genomic diversity, clonal transmission and epidemiological data were analyzed. Sporulation and virulence capacities were measured. Four ribotypes (RT) were identified including RT046 (97.2%), RT656 (1.1%), RT427 (0.6%), and RT AI-78 (1.1%). Phylogenetic analysis of 176 ST35 genomes, along with 50 publicly available genomes, revealed two distinctive lineages without time-, region-, or source-dependent distribution. However, the distribution of antimicrobial resistance genes differed significantly between the two lineages. Nosocomial and communal transmission occurred in humans with the isolates differed by ≤ two core-genome single-nucleotide polymorphism (cgSNPs) and clonal circulation was found in pigs with the isolates differed by ≤ four cgSNPs. Notably, interspecies clonal transmission was identified among three patients with community acquired <i>C. difficile</i> infection and pigs with epidemiological links, differed by ≤ nine cgSNPs. Toxin B (TcdB) concentrations were significantly higher in human isolates compared to pig isolates, and ST35 isolates exhibited stronger sporulation capacities than other STs. Our study provided new genomic insights and epidemiological evidence of <i>C. difficile</i> ST35 intraspecies and interspecies clonal transmission, which can also be facilitated by its strong sporulation capacity.
DOI: 10.6084/m9.figshare.27079095.v2
title: Genomic epidemiology of <i>Clostridioides difficile</i> sequence type 35 reveals intraspecies and interspecies clonal transmission

description: <i>Clostridioides difficile</i> sequence type (ST) 35 has been found in humans and animals worldwide. However, its genomic epidemiology and clonal transmission have not been explored in detail. In this study, 176 <i>C. difficile</i> ST35 isolates from six countries were sequenced. Genomic diversity, clonal transmission and epidemiological data were analyzed. Sporulation and virulence capacities were measured. Four ribotypes (RT) were identified including RT046 (97.2%), RT656 (1.1%), RT427 (0.6%), and RT AI-78 (1.1%). Phylogenetic analysis of 176 ST35 genomes, along with 50 publicly available genomes, revealed two distinctive lineages without time-, region-, or source-dependent distribution. However, the distribution of antimicrobial resistance genes differed significantly between the two lineages. Nosocomial and communal transmission occurred in humans with the isolates differed by ≤ two core-genome single-nucleotide polymorphism (cgSNPs) and clonal circulation was found in pigs with the isolates differed by ≤ four cgSNPs. Notably, interspecies clonal transmission was identified among three patients with community acquired <i>C. difficile</i> infection and pigs with epidemiological links, differed by ≤ nine cgSNPs. Toxin B (TcdB) concentrations were significantly higher in human isolates compared to pig isolates, and ST35 isolates exhibited stronger sporulation capacities than other STs. Our study provided new genomic insights and epidemiological evidence of <i>C. difficile</i> ST35 intraspecies and interspecies clonal transmission, which can also be facilitated by its strong sporulation capacity.
DOI: 10.25549/webster-c100-38530
title: Inter-Agency Team Final Report, Los Angeles County Sheriff's Department, 1992

description: Inter-Agency Team Final Report, Appendix: Los Angeles County Sheriff's Department Miscellaneous materials collected by the Inter-Agency team regarding the role of the Los Angeles County Sheriff's Department in the response to the 1992 riots, 1992. PART OF SERIES: In addition to analyzing the 1992 riots as a whole, the Webster Commission also divided into several smaller task forces and study groups, each of which addressed one specific aspect of the civil disturbance. The series consists of reports and appendices produced by five of these groups: the Chronology Team, the Public Officials and Community Team, the LAPD Team, the Comparisons Study Group, and the Inter-Agency Team. Also included are two copies of Webster Scope, a report that interprets the riots and their cumulative effects primarily through graphs, charts, statistics, and figures, and several research memoranda that discuss the legality of several riot-response tactics. PART OF SUBSERIES: Materials related to a final report issued by the Webster Commission's Inter-Agency Team. which evaluated the collaboration between the LAPD and other law enforcement agencies in the advent of the 1992 riots. Included is a copy of the final report and the report's appendices, which are comprised of interviews, memoranda, statistical analyses, handbooks, and other miscellaneous documents.
DOI: 10.6084/m9.figshare.24884946
title: Genomic analysis of lineage-specific transmission of multidrug resistance tuberculosis in China

description: We investigated the genetic diversities and lineage-specific transmission dynamics of multidrug-resistant tuberculosis (MDR-TB), with the goal of determining the potential factors driving the MDR epidemics in China. We curated a large nationwide <i>Mycobacterium tuberculosis</i> (<i>M. tuberculosis</i>) whole genome sequence data set, including 1313 MDR strains. We reconstructed the phylogeny and mapped the transmission networks of MDR-TB across China using Bayesian inference. To identify drug-resistance variants linked to enhanced transmissibility, we employed ordinary least-squares (OLS) regression analysis. The majority of MDR-TB strains in China belong to lineage 2.2.1. Transmission chain analysis has indicated that the repeated and frequent transmission of L2.2.1 plays a central role in the establishment of MDR epidemic in China, but no occurrence of a large predominant MDR outbreak was detected. Using OLS regression, the most common single nucleotide polymorphisms (SNPs) associated with resistance to isoniazid (<i>katG_p.Ser315Thr</i> and <i>katG_p.Ser315Asn</i>) and rifampicin (<i>rpoB_p.Ser450Leu</i>, <i>rpoB_p.His445Tyr</i>, <i>rpoB_p.His445Arg</i>, <i>rpoB_p.His445Asp</i>, and <i>rpoB_p.His445Asn</i>) were more likely to be found in L2 clustered strains. Several putative compensatory mutations in <i>rpoA</i>, <i>rpoC</i>, and <i>katG</i> were significantly associated with clustering. The eastern, central, and southern regions of China had a high level of connectivity for the migration of L2 MDR strains throughout the country. The skyline plot showed distinct population size expansion dynamics for MDR-TB lineages in China. MDR-TB epidemic in China is predominantly driven by the spread of highly transmissible Beijing strains. A range of drug-resistance mutations of L2 MDR-TB strains displayed minimal fitness costs and may facilitate their transmission.
DOI: 10.6084/m9.figshare.24884946.v2
title: Genomic analysis of lineage-specific transmission of multidrug resistance tuberculosis in China

description: We investigated the genetic diversities and lineage-specific transmission dynamics of multidrug-resistant tuberculosis (MDR-TB), with the goal of determining the potential factors driving the MDR epidemics in China. We curated a large nationwide <i>Mycobacterium tuberculosis</i> (<i>M. tuberculosis</i>) whole genome sequence data set, including 1313 MDR strains. We reconstructed the phylogeny and mapped the transmission networks of MDR-TB across China using Bayesian inference. To identify drug-resistance variants linked to enhanced transmissibility, we employed ordinary least-squares (OLS) regression analysis. The majority of MDR-TB strains in China belong to lineage 2.2.1. Transmission chain analysis has indicated that the repeated and frequent transmission of L2.2.1 plays a central role in the establishment of MDR epidemic in China, but no occurrence of a large predominant MDR outbreak was detected. Using OLS regression, the most common single nucleotide polymorphisms (SNPs) associated with resistance to isoniazid (<i>katG_p.Ser315Thr</i> and <i>katG_p.Ser315Asn</i>) and rifampicin (<i>rpoB_p.Ser450Leu</i>, <i>rpoB_p.His445Tyr</i>, <i>rpoB_p.His445Arg</i>, <i>rpoB_p.His445Asp</i>, and <i>rpoB_p.His445Asn</i>) were more likely to be found in L2 clustered strains. Several putative compensatory mutations in <i>rpoA</i>, <i>rpoC</i>, and <i>katG</i> were significantly associated with clustering. The eastern, central, and southern regions of China had a high level of connectivity for the migration of L2 MDR strains throughout the country. The skyline plot showed distinct population size expansion dynamics for MDR-TB lineages in China. MDR-TB epidemic in China is predominantly driven by the spread of highly transmissible Beijing strains. A range of drug-resistance mutations of L2 MDR-TB strains displayed minimal fitness costs and may facilitate their transmission.
DOI: 10.6084/m9.figshare.27079095.v1
title: Genomic epidemiology of <i>Clostridioides difficile</i> Sequence Type 35 reveals intraspecies and interspecies clonal transmission

description: <i>Clostridioides difficile</i> sequence type (ST) 35 has been found in humans and animals worldwide. However, its genomic epidemiology and clonal transmission have not been explored in detail. In this study, 176 <i>C. difficile</i> ST35 isolates from six countries were sequenced. Genomic diversity, clonal transmission and epidemiological data were analyzed. Sporulation and virulence capacities were measured. Four ribotypes (RT) were identified including RT046 (97.2%), RT656 (1.1%), RT427 (0.6%), and RT AI-78 (1.1%). Phylogenetic analysis of 176 ST35 genomes, along with 50 publicly available genomes, revealed two distinctive lineages without time-, region-, or source-dependent distribution. However, the distribution of antimicrobial resistance genes differed significantly between the two lineages. Nosocomial and communal transmission occurred in humans with the isolates differed by ≤ two core-genome single-nucleotide polymorphism (cgSNPs) and clonal circulation was found in pigs with the isolates differed by ≤ four cgSNPs. Notably, interspecies clonal transmission was identified among three patients with community acquired <i>C. difficile</i> infection and pigs with epidemiological links, differed by ≤ nine cgSNPs. Toxin B (TcdB) concentrations were significantly higher in human isolates compared to pig isolates, and ST35 isolates exhibited stronger sporulation capacities than other STs. Our study provided new genomic insights and epidemiological evidence of <i>C. difficile</i> ST35 intraspecies and interspecies clonal transmission, which can also be facilitated by its strong sporulation capacity.
DOI: 10.6084/m9.figshare.27162299
title: <i>Cryptosporidium</i> species and subtypes in Norway: predominance of <i>C. parvum</i> and emergence of <i>C. mortiferum</i>

description: PCR-based diagnostics has revealed the previously largely unknown <i>Cryptosporidium</i> transmission and infections in high-income countries. This study aimed to determine domestic and imported subtypes of <i>Cryptosporidium</i> species in Norway, evaluate their demographic distribution, and identify potential small outbreaks. <i>Cryptosporidium</i>-positive human faecal samples were obtained from six medical microbiology laboratories between February 2022 and January 2024, together with 22 <i>Cryptosporidium</i>-positive animal samples. Species and subtypes were identified by sequencing PCR products from gp60 and SSU rRNA genes. Most cryptosporidiosis cases occurred during late summer/early autumn, primarily in children and young adults. Of 550 human samples, 359 were successfully characterized molecularly (65%), revealing infection with 10 different <i>Cryptosporidium</i> species. <i>C. parvum</i> occurred in 245 (68%) human isolates with IIa and IId being major allele families, with distinct regional distribution patterns of common subtypes. A kindergarten outbreak with 5 cases was due to <i>C. parvum</i> IIaA14G1R1. <i>C. mortiferum</i> was identified in 33 (9.2%) human cases of which 24 were known to be of domestic origin, making it the second most common species in human autochthonous cases in Norway. All <i>C. mortiferum</i> isolates were of the same genotype; XIVaA20G2T1, including 13 cases from a suspected small outbreak in Trøndelag. <i>C. hominis</i> occurred in 68 typed cases (19%), but mostly in infections acquired abroad, with allele families Ib and If occurring most often. In conclusion, this study of recent <i>Cryptosporidium</i> spp. and subtypes in Norway, highlights the predominance of <i>C. parvum</i> and the emergence of <i>C. mortiferum</i> among autochthonous cases.
DOI: 10.6084/m9.figshare.27162299.v2
title: <i>Cryptosporidium</i> species and subtypes in Norway: predominance of <i>C. parvum</i> and emergence of <i>C. mortiferum</i>

description: PCR-based diagnostics has revealed the previously largely unknown <i>Cryptosporidium</i> transmission and infections in high-income countries. This study aimed to determine domestic and imported subtypes of <i>Cryptosporidium</i> species in Norway, evaluate their demographic distribution, and identify potential small outbreaks. <i>Cryptosporidium</i>-positive human faecal samples were obtained from six medical microbiology laboratories between February 2022 and January 2024, together with 22 <i>Cryptosporidium</i>-positive animal samples. Species and subtypes were identified by sequencing PCR products from gp60 and SSU rRNA genes. Most cryptosporidiosis cases occurred during late summer/early autumn, primarily in children and young adults. Of 550 human samples, 359 were successfully characterized molecularly (65%), revealing infection with 10 different <i>Cryptosporidium</i> species. <i>C. parvum</i> occurred in 245 (68%) human isolates with IIa and IId being major allele families, with distinct regional distribution patterns of common subtypes. A kindergarten outbreak with 5 cases was due to <i>C. parvum</i> IIaA14G1R1. <i>C. mortiferum</i> was identified in 33 (9.2%) human cases of which 24 were known to be of domestic origin, making it the second most common species in human autochthonous cases in Norway. All <i>C. mortiferum</i> isolates were of the same genotype; XIVaA20G2T1, including 13 cases from a suspected small outbreak in Trøndelag. <i>C. hominis</i> occurred in 68 typed cases (19%), but mostly in infections acquired abroad, with allele families Ib and If occurring most often. In conclusion, this study of recent <i>Cryptosporidium</i> spp. and subtypes in Norway, highlights the predominance of <i>C. parvum</i> and the emergence of <i>C. mortiferum</i> among autochthonous cases.
DOI: 10.6084/m9.figshare.27162299.v1
title: <i>Cryptosporidium</i> species and subtypes in Norway: Predominance of <i>C. parvum</i> and emergence of <i>C. mortiferum</i>

description: PCR-based diagnostics has revealed the previously largely unknown <i>Cryptosporidium</i> transmission and infections in high-income countries. This study aimed to determine domestic and imported subtypes of <i>Cryptosporidium</i> species in Norway, evaluate their demographic distribution, and identify potential small outbreaks. <i>Cryptosporidium</i>-positive human faecal samples were obtained from six medical microbiology laboratories between February 2022 and January 2024, together with 22 <i>Cryptosporidium</i>-positive animal samples. Species and subtypes were identified by sequencing PCR products from gp60 and SSU rRNA genes. Most cryptosporidiosis cases occurred during late summer/early autumn, primarily in children and young adults. Of 550 human samples, 359 were successfully characterized molecularly (65%), revealing infection with 10 different <i>Cryptosporidium</i> species. <i>C. parvum</i> occurred in 245 (68%) human isolates with IIa and IId being major allele families, with distinct regional distribution patterns of common subtypes. A kindergarten outbreak with 5 cases was due to <i>C. parvum</i> IIaA14G1R1. <i>C. mortiferum</i> was identified in 33 (9.2%) human cases of which 24 were known to be of domestic origin, making it the second most common species in human autochthonous cases in Norway. All <i>C. mortiferum</i> isolates were of the same genotype; XIVaA20G2T1, including 13 cases from a suspected small outbreak in Trøndelag. <i>C. hominis</i> occurred in 68 typed cases (19%), but mostly in infections acquired abroad, with allele families Ib and If occurring most often. In conclusion, this study of recent <i>Cryptosporidium</i> spp. and subtypes in Norway, highlights the predominance of <i>C. parvum</i> and the emergence of <i>C. mortiferum</i> among autochthonous cases.
DOI: 10.25549/webster-c100-39737
title: Interviews of city of Los Angeles, Emergency Operations Organization, 1992-08/1992-09

description: Summaries of interviews conducted with personnel from the City of Los Angeles's Emergency Operations Organization, 1992 August - September. PART OF SERIES: In addition to analyzing the 1992 riots as a whole, the Webster Commission also divided into several smaller task forces and study groups, each of which addressed one specific aspect of the civil disturbance. The series consists of reports and appendices produced by five of these groups: the Chronology Team, the Public Officials and Community Team, the LAPD Team, the Comparisons Study Group, and the Inter-Agency Team. Also included are two copies of Webster Scope, a report that interprets the riots and their cumulative effects primarily through graphs, charts, statistics, and figures, and several research memoranda that discuss the legality of several riot-response tactics. PART OF SUBSERIES: Materials related to a final report issued by the Webster Commission's Inter-Agency Team. which evaluated the collaboration between the LAPD and other law enforcement agencies in the advent of the 1992 riots. Included is a copy of the final report and the report's appendices, which are comprised of interviews, memoranda, statistical analyses, handbooks, and other miscellaneous documents.
DOI: 10.25549/webster-c100-38495
title: Inter-Agency Team Final Report, Los Angeles County Sheriff's Department, 1992

description: Inter-Agency Team Final Report, Appendix: Los Angeles County Sheriff's Department Miscellaneous materials collected by the Inter-Agency team regarding the role of the Los Angeles County Sheriff's Department in the response to the 1992 riots, 1992. PART OF SERIES: In addition to analyzing the 1992 riots as a whole, the Webster Commission also divided into several smaller task forces and study groups, each of which addressed one specific aspect of the civil disturbance. The series consists of reports and appendices produced by five of these groups: the Chronology Team, the Public Officials and Community Team, the LAPD Team, the Comparisons Study Group, and the Inter-Agency Team. Also included are two copies of Webster Scope, a report that interprets the riots and their cumulative effects primarily through graphs, charts, statistics, and figures, and several research memoranda that discuss the legality of several riot-response tactics. PART OF SUBSERIES: Materials related to a final report issued by the Webster Commission's Inter-Agency Team. which evaluated the collaboration between the LAPD and other law enforcement agencies in the advent of the 1992 riots. Included is a copy of the final report and the report's appendices, which are comprised of interviews, memoranda, statistical analyses, handbooks, and other miscellaneous documents.
DOI: 10.25549/webster-c100-39770
title: Interviews of city of Los Angeles, Emergency Operations Organization, 1992-08/1992-09

description: Summaries of interviews conducted with personnel from the City of Los Angeles's Emergency Operations Organization, 1992 August - September. PART OF SERIES: In addition to analyzing the 1992 riots as a whole, the Webster Commission also divided into several smaller task forces and study groups, each of which addressed one specific aspect of the civil disturbance. The series consists of reports and appendices produced by five of these groups: the Chronology Team, the Public Officials and Community Team, the LAPD Team, the Comparisons Study Group, and the Inter-Agency Team. Also included are two copies of Webster Scope, a report that interprets the riots and their cumulative effects primarily through graphs, charts, statistics, and figures, and several research memoranda that discuss the legality of several riot-response tactics. PART OF SUBSERIES: Materials related to a final report issued by the Webster Commission's Inter-Agency Team. which evaluated the collaboration between the LAPD and other law enforcement agencies in the advent of the 1992 riots. Included is a copy of the final report and the report's appendices, which are comprised of interviews, memoranda, statistical analyses, handbooks, and other miscellaneous documents.
DOI: 10.25549/webster-c100-76722
title: After-action reporting for April/May riots, 1992

description: After-action reporting for April/May riots, Operations - Bureau of Special Investigation, 1992. PART OF SERIES: Included in the series are internal documents produced by the LAPD, which aided the Webster Commission in its assessment of the Department's operations. Materials include copies of the Watch Commander's Daily Reports between October, 1991 and May, 1992; critiques and after-action reports on the riots issued by each LAPD bureau; and correspondence regarding personnel and budget matters, crime statistics, and several Department-initiated programs. Also included are several documents, including schedules, press releases, and memoranda, that were issued by the office of Los Angeles Mayor Tom Bradley regarding the verdicts in the Rodney King case.
DOI: 10.25549/webster-c100-39562
title: Inter-agency team, final report, 1992

description: Inter-Agency Team Final Report, Appendix: Local police departments, materials collected by the Inter-Agency Team regarding the policies, procedures, and operations of several local police departments aside from the Los Angeles Police Department, 1992. PART OF SERIES: In addition to analyzing the 1992 riots as a whole, the Webster Commission also divided into several smaller task forces and study groups, each of which addressed one specific aspect of the civil disturbance. The series consists of reports and appendices produced by five of these groups: the Chronology Team, the Public Officials and Community Team, the LAPD Team, the Comparisons Study Group, and the Inter-Agency Team. Also included are two copies of Webster Scope, a report that interprets the riots and their cumulative effects primarily through graphs, charts, statistics, and figures, and several research memoranda that discuss the legality of several riot-response tactics. PART OF SUBSERIES: Materials related to a final report issued by the Webster Commission's Inter-Agency Team. which evaluated the collaboration between the LAPD and other law enforcement agencies in the advent of the 1992 riots. Included is a copy of the final report and the report's appendices, which are comprised of interviews, memoranda, statistical analyses, handbooks, and other miscellaneous documents.
DOI: 10.25549/webster-c100-32350
title: Roundtable 2, discussion, 1992-06-12

description: Roundtable discussion with Sheriff Sherman Block and several top members of his staff to discuss the Los Angeles Sheriff's Office's involvement in the civil disturbance, 1992 June 12. PART OF SERIES: After the violence had subsided, the Webster Commission met of a variety of public officials, law enforcement personnel, activists, and community leaders to discuss the rioting, its root causes, and the adequacy of the LAPD's response. The series includes summaries of these meetings, including questions and comments along of the interviewers' own mental impressions, conclusions, and opinions. Materials are arranged in alphabetical order, according to the last name of the interviewee.