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Artikel: Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.

Lu, Dan / Kalantar, Katrina L / Chu, Victoria T / Glascock, Abigail L / Guerrero, Estella S / Bernick, Nina / Butcher, Xochitl / Ewing, Kirsty / Fahsbender, Elizabeth / Holmes, Olivia / Hoops, Erin / Jones, Ann E / Lim, Ryan / McCanny, Suzette / Reynoso, Lucia / Rosario, Karyna / Tang, Jennifer / Valenzuela, Omar / Mourani, Peter M /

Pickering, Amy J / Raphenya, Amogelang R / Alcock, Brian P / McArthur, Andrew G / Langelier, Charles R

bioRxiv : the preprint server for biology

2024

Abstract: Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of ...

Abstract	Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.
Sprache	Englisch
Erscheinungsdatum	2024-04-18
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2024.04.12.589250
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Unique roles of vaginal

Glascock, Abigail L / Jimenez, Nicole R / Boundy, Sam / Koparde, Vishal N / Brooks, J Paul / Edwards, David J / Strauss Iii, Jerome F / Jefferson, Kimberly K / Serrano, Myrna G / Buck, Gregory A / Fettweis, Jennifer M

Microbial genomics

2022 Band 7, Heft 12

Abstract: The composition of the human vaginal microbiome has been extensively studied and is known to influence reproductive health. However, the functional roles of individual taxa and their contributions to negative health outcomes have yet to be well ... ...

Abstract	The composition of the human vaginal microbiome has been extensively studied and is known to influence reproductive health. However, the functional roles of individual taxa and their contributions to negative health outcomes have yet to be well characterized. Here, we examine two vaginal bacterial taxa grouped within the genus
Mesh-Begriff(e)	Bacterial Proteins/genetics ; Base Composition ; Case-Control Studies ; Evolution, Molecular ; Female ; Gene Expression Regulation, Bacterial ; Genome Size ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Megasphaera/classification ; Megasphaera/genetics ; Megasphaera/isolation & purification ; Megasphaera/metabolism ; Phylogeny ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Reproductive Health ; Sequence Analysis, DNA/methods ; Vagina/microbiology ; Vaginosis, Bacterial/epidemiology ; Vaginosis, Bacterial/microbiology
Chemische Substanzen	Bacterial Proteins ; RNA, Ribosomal, 16S
Sprache	Englisch
Erscheinungsdatum	2022-01-28
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000526
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Considerations for the Safe Operation of Schools During the Coronavirus Pandemic.

Lordan, Ronan / Prior, Samantha / Hennessy, Elizabeth / Naik, Amruta / Ghosh, Soumita / Paschos, Georgios K / Skarke, Carsten / Barekat, Kayla / Hollingsworth, Taylor / Juska, Sydney / Mazaleuskaya, Liudmila L / Teegarden, Sarah / Glascock, Abigail L / Anderson, Sean / Meng, Hu / Tang, Soon-Yew / Weljie, Aalim / Bottalico, Lisa / Ricciotti, Emanuela /

Cherfane, Perla / Mrcela, Antonijo / Grant, Gregory / Poole, Kristen / Mayer, Natalie / Waring, Michael / Adang, Laura / Becker, Julie / Fries, Susanne / FitzGerald, Garret A / Grosser, Tilo

Frontiers in public health

2021 Band 9, Seite(n) 751451

Abstract: During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, providing safe in-person schooling has been a dynamic process balancing evolving community disease burden, scientific information, and local regulatory requirements with ... ...

Abstract	During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, providing safe in-person schooling has been a dynamic process balancing evolving community disease burden, scientific information, and local regulatory requirements with the mandate for education. Considerations include the health risks of SARS-CoV-2 infection and its post-acute sequelae, the impact of remote learning or periods of quarantine on education and well-being of children, and the contribution of schools to viral circulation in the community. The risk for infections that may occur within schools is related to the incidence of SARS-CoV-2 infections within the local community. Thus, persistent suppression of viral circulation in the community through effective public health measures including vaccination is critical to in-person schooling. Evidence suggests that the likelihood of transmission of SARS-CoV-2 within schools can be minimized if mitigation strategies are rationally combined. This article reviews evidence-based approaches and practices for the continual operation of in-person schooling.
Mesh-Begriff(e)	COVID-19 ; Child ; Humans ; Pandemics/prevention & control ; Quarantine ; SARS-CoV-2 ; Schools
Sprache	Englisch
Erscheinungsdatum	2021-12-16
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2021.751451
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria.

Abdelmaksoud, Abdallah A / Koparde, Vishal N / Sheth, Nihar U / Serrano, Myrna G / Glascock, Abigail L / Fettweis, Jennifer M / Strauss, Jerome F / Buck, Gregory A / Jefferson, Kimberly K

Microbiology (Reading, England)

2016 Band 162, Heft 3, Seite(n) 466–475

Abstract: Vaginal lactobacilli can inhibit colonization by and growth of other bacteria, thereby preventing development of bacterial vaginosis (BV). Amongst the lactobacilli, Lactobacillus crispatus appears to be particularly effective at inhibiting growth of BV- ... ...

Abstract	Vaginal lactobacilli can inhibit colonization by and growth of other bacteria, thereby preventing development of bacterial vaginosis (BV). Amongst the lactobacilli, Lactobacillus crispatus appears to be particularly effective at inhibiting growth of BV-associated bacteria. Nonetheless, some women who are colonized with this species can still develop clinical BV. Therefore, we sought to determine whether strains of L. crispatus that colonize women with lactobacilli-dominated vaginal microbiomes are distinct from strains that colonize women who develop BV. The genomes of L. crispatus isolates from four women with lactobacilli-dominated vaginal microbiomes ( <1% 16S rRNA reads above threshold from genera other than Lactobacillus) and four women with microbiomes containing BV-associated bacteria (>12% 16S rRNA reads from bacterial taxa associated with BV) were sequenced and compared. Lactic acid production by the different strains was quantified. Phage induction in the strains was also analysed. There was considerable genetic diversity between strains, and several genes were exclusive to either the strains from Lactobacillus-dominated microbiomes or those containing BV-associated bacteria. Overall, strains from microbiomes dominated by lactobacilli did not differ from strains from microbiomes containing BV-associated bacteria with respect to lactic acid production. All of the strains contained multiple phage, but there was no clear distinction between the presence or absence of BV-associated bacteria with respect to phage-induced lysis. Genes found to be exclusive to the Lactobacillus-dominated versus BV-associated bacteria-containing microbiomes could play a role in the maintenance of vaginal health and the development of BV, respectively.
Mesh-Begriff(e)	Bacteriophages/isolation & purification ; DNA, Bacterial/chemistry ; DNA, Bacterial/genetics ; Female ; Genetic Variation ; Genome, Bacterial ; Humans ; Lactic Acid/metabolism ; Lactobacillus/genetics ; Lactobacillus/isolation & purification ; Lactobacillus/metabolism ; Microbiota ; Sequence Analysis, DNA ; Vagina/microbiology ; Vaginosis, Bacterial/microbiology
Chemische Substanzen	DNA, Bacterial ; Lactic Acid (33X04XA5AT)
Sprache	Englisch
Erscheinungsdatum	2016-01-08
Erscheinungsland	England
Dokumenttyp	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1180712-x
ISSN	1465-2080 ; 1350-0872
ISSN (online)	1465-2080
ISSN	1350-0872
DOI	10.1099/mic.0.000238
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Femtomolar SARS-CoV-2 Antigen Detection Using the Microbubbling Digital Assay with Smartphone Readout Enables Antigen Burden Quantitation and Dynamics Tracking

Chen, Hui / Li, Zhao / Feng, Sheng / Wang, Anni / Richard-Greenblatt, Melissa / Hutson, Emily / Andrianus, Stefen / Glaser, Laurel / Rodino, Kyle G / Qian, Jianing / Jayaraman, Dinesh / Collman, Ronald / Glascock, Abigail L / Bushman, Frederic / Lee, Jae Seung / Cherry, Sara / Fausto, Alejandra / Weiss, Susan R / Koo, Hyun /

Corby, Patricia M / ODoherty, Una / Garfall, Alfred L / Vogl, Dan T / Stadtmauer, Edward A / Wang, Ping

medRxiv

Abstract: Background: Little is known about the dynamics of SARS-CoV-2 antigen burden in respiratory samples in different patient populations at different stages of infection. Current rapid antigen tests cannot quantitate and track antigen dynamics with high ... ...

Abstract	Background: Little is known about the dynamics of SARS-CoV-2 antigen burden in respiratory samples in different patient populations at different stages of infection. Current rapid antigen tests cannot quantitate and track antigen dynamics with high sensitivity and specificity in respiratory samples. Methods: We developed and validated an ultra-sensitive SARS-CoV-2 antigen assay with smartphone readout using the Microbubbling Digital Assay previously developed by our group, which is a platform that enables highly sensitive detection and quantitation of protein biomarkers. A computer vision-based algorithm was developed for microbubble smartphone image recognition and quantitation. A machine learning-based classifier was developed to classify the smartphone images based on detected microbubbles. Using this assay, we tracked antigen dynamics in serial swab samples from COVID patients hospitalized in ICU and immunocompromised COVID patients. Results: The limit of detection (LOD) of the Microbubbling SARS-CoV-2 Antigen Assay was 0.5 pg/mL (10.6 fM) recombinant nucleocapsid (N) antigen or 4000 copies/mL inactivated SARS-CoV-2 virus in nasopharyngeal (NP) swabs, comparable to many rRT-PCR methods. The assay had high analytical specificity towards SARS-CoV-2. Compared to EUA-approved rRT-PCR methods, the Microbubbling Antigen Assay demonstrated a positive percent agreement (PPA) of 97% (95% confidence interval (CI), 92-99%) in symptomatic individuals within 7 days of symptom onset and positive SARS-CoV-2 nucleic acid results, and a negative percent agreement (NPA) of 97% (95% CI, 94-100%) in symptomatic and asymptomatic individuals with negative nucleic acid results. Antigen positivity rate in NP swabs gradually decreased as days-after-symptom-onset increased, despite persistent nucleic acid positivity of the same samples. The computer vision and machine learning-based automatic microbubble image classifier could accurately identify positives and negatives, based on microbubble counts and sizes. Total microbubble volume, a potential marker of antigen burden, correlated inversely with Ct values and days-after-symptom-onset. Antigen was detected for longer periods of time in immunocompromised patients with hematologic malignancies, compared to immunocompetent individuals. Simultaneous detectable antigens and nucleic acids may indicate the presence of replicating viruses in patients with persistent infections. Conclusions: The Microbubbling SARS-CoV-2 Antigen Assay enables sensitive and specific detection of acute infections, and quantitation and tracking of antigen dynamics in different patient populations at various stages of infection. With smartphone compatibility and automated image processing, the assay is well-positioned to be adapted for point-of-care diagnosis and to explore the clinical implications of antigen dynamics in future studies.
Schlagwörter	covid19
Sprache	Englisch
Erscheinungsdatum	2021-03-26
Verlag	Cold Spring Harbor Laboratory Press
Dokumenttyp	Artikel ; Online
DOI	10.1101/2021.03.17.21253847
Datenquelle	COVID19

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Artikel ; Online: Species-level classification of the vaginal microbiome.

Fettweis, Jennifer M / Serrano, Myrna G / Sheth, Nihar U / Mayer, Carly M / Glascock, Abigail L / Brooks, J Paul / Jefferson, Kimberly K / Buck, Gregory A

BMC genomics

2012 Band 13 Suppl 8, Seite(n) S17

Abstract: Background: The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species ...

Abstract	Background: The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species level, is necessary to fully understand the association of the vaginal microbiome with bacterial vaginosis, sexually transmitted infections, pregnancy complications, menopause, and other physiological and infectious conditions. However, most current taxonomic assignment strategies based on metagenomic 16S rDNA sequence analysis provide at best a genus-level resolution. While surveys of 16S rRNA gene sequences are common in microbiome studies, few well-curated, body-site-specific reference databases of 16S rRNA gene sequences are available, and no such resource is available for vaginal microbiome studies. Results: We constructed the Vaginal 16S rDNA Reference Database, a comprehensive and non-redundant database of 16S rDNA reference sequences for bacterial taxa likely to be associated with vaginal health, and we developed STIRRUPS, a new method that employs the USEARCH algorithm with a curated reference database for rapid species-level classification of 16S rDNA partial sequences. The method was applied to two datasets of V1-V3 16S rDNA reads: one generated from a mock community containing DNA from six bacterial strains associated with vaginal health, and a second generated from over 1,000 mid-vaginal samples collected as part of the Vaginal Human Microbiome Project at Virginia Commonwealth University. In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment. Conclusions: This database and method provide accurate species-level classifications of metagenomic 16S rDNA sequence reads that will be useful for analysis and comparison of microbiome profiles from vaginal samples. STIRRUPS can be used to classify 16S rDNA sequence reads from other ecological niches if an appropriate reference database of 16S rDNA sequences is available.
Mesh-Begriff(e)	Algorithms ; Bacteria/classification ; Bacteria/genetics ; Databases, Genetic ; Female ; Humans ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Vagina/microbiology
Chemische Substanzen	RNA, Ribosomal, 16S
Sprache	Englisch
Erscheinungsdatum	2012-12-17
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/1471-2164-13-S8-S17
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post-COVID-19 syndrome.

Jia, Xiaolin / Cao, Shu / Lee, Alexandra S / Manohar, Monali / Sindher, Sayantani B / Ahuja, Neera / Artandi, Maja / Blish, Catherine A / Blomkalns, Andra L / Chang, Iris / Collins, William J / Desai, Manisha / Din, Hena Naz / Do, Evan / Fernandes, Andrea / Geng, Linda N / Rosenberg-Hasson, Yael / Mahoney, Megan Ruth / Glascock, Abigail L /

JCI insight

2022 Band 7, Heft 13

Abstract: BACKGROUNDProlonged symptoms after SARS-CoV-2 infection are well documented. However, which factors influence development of long-term symptoms, how symptoms vary across ethnic groups, and whether long-term symptoms correlate with biomarkers are points ... ...

Abstract	BACKGROUNDProlonged symptoms after SARS-CoV-2 infection are well documented. However, which factors influence development of long-term symptoms, how symptoms vary across ethnic groups, and whether long-term symptoms correlate with biomarkers are points that remain elusive.METHODSAdult SARS-CoV-2 reverse transcription PCR-positive (RT-PCR-positive) patients were recruited at Stanford from March 2020 to February 2021. Study participants were seen for in-person visits at diagnosis and every 1-3 months for up to 1 year after diagnosis; they completed symptom surveys and underwent blood draws and nasal swab collections at each visit.RESULTSOur cohort (n = 617) ranged from asymptomatic to critical COVID-19 infections. In total, 40% of participants reported at least 1 symptom associated with COVID-19 six months after diagnosis. Median time from diagnosis to first resolution of all symptoms was 44 days; median time from diagnosis to sustained symptom resolution with no recurring symptoms for 1 month or longer was 214 days. Anti-nucleocapsid IgG level in the first week after positive RT-PCR test and history of lung disease were associated with time to sustained symptom resolution. COVID-19 disease severity, ethnicity, age, sex, and remdesivir use did not affect time to sustained symptom resolution.CONCLUSIONWe found that all disease severities had a similar risk of developing post-COVID-19 syndrome in an ethnically diverse population. Comorbid lung disease and lower levels of initial IgG response to SARS-CoV-2 nucleocapsid antigen were associated with longer symptom duration.TRIAL REGISTRATIONClinicalTrials.gov, NCT04373148.FUNDINGNIH UL1TR003142 CTSA grant, NIH U54CA260517 grant, NIEHS R21 ES03304901, Sean N Parker Center for Allergy and Asthma Research at Stanford University, Chan Zuckerberg Biohub, Chan Zuckerberg Initiative, Sunshine Foundation, Crown Foundation, and Parker Foundation.
Mesh-Begriff(e)	COVID-19/complications ; Humans ; Immunoglobulin G ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome
Chemische Substanzen	Immunoglobulin G
Sprache	Englisch
Erscheinungsdatum	2022-07-08
Erscheinungsland	United States
Dokumenttyp	Journal Article
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.156713
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Species-level classification of the vaginal microbiome

Fettweis Jennifer M / Serrano Myrna G / Sheth Nihar U / Mayer Carly M / Glascock Abigail L / Brooks J Paul / Jefferson Kimberly K / Buck Gregory A

BMC Genomics, Vol 13, Iss Suppl 8, p S

2012 Band 17

Abstract: Abstract Background The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the ... ...

Abstract	Abstract Background The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species level, is necessary to fully understand the association of the vaginal microbiome with bacterial vaginosis, sexually transmitted infections, pregnancy complications, menopause, and other physiological and infectious conditions. However, most current taxonomic assignment strategies based on metagenomic 16S rDNA sequence analysis provide at best a genus-level resolution. While surveys of 16S rRNA gene sequences are common in microbiome studies, few well-curated, body-site-specific reference databases of 16S rRNA gene sequences are available, and no such resource is available for vaginal microbiome studies. Results We constructed the Vaginal 16S rDNA Reference Database, a comprehensive and non-redundant database of 16S rDNA reference sequences for bacterial taxa likely to be associated with vaginal health, and we developed STIRRUPS, a new method that employs the USEARCH algorithm with a curated reference database for rapid species-level classification of 16S rDNA partial sequences. The method was applied to two datasets of V1-V3 16S rDNA reads: one generated from a mock community containing DNA from six bacterial strains associated with vaginal health, and a second generated from over 1,000 mid-vaginal samples collected as part of the Vaginal Human Microbiome Project at Virginia Commonwealth University. In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment. Conclusions This database and method provide accurate species-level classifications of metagenomic 16S rDNA sequence reads that will be useful for analysis and comparison of microbiome profiles from vaginal samples. STIRRUPS can be used to classify 16S rDNA sequence reads from other ecological niches if an appropriate reference database of 16S rDNA sequences is available.
Schlagwörter	Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Sprache	Englisch
Erscheinungsdatum	2012-12-01T00:00:00Z
Verlag	BioMed Central
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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Artikel ; Online: An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease.

Fettweis, Jennifer M / Serrano, Myrna G / Huang, Bernice / Brooks, J Paul / Glascock, Abigail L / Sheth, Nihar U / Strauss, Jerome F / Jefferson, Kimberly K / Buck, Gregory A

PloS one

2014 Band 9, Heft 10, Seite(n) e110943

Abstract: Humans are colonized by thousands of bacterial species, but it is difficult to assess the metabolic and pathogenic potential of the majority of these because they have yet to be cultured. Here, we characterize an uncultivated vaginal mycoplasma tightly ... ...

Abstract	Humans are colonized by thousands of bacterial species, but it is difficult to assess the metabolic and pathogenic potential of the majority of these because they have yet to be cultured. Here, we characterize an uncultivated vaginal mycoplasma tightly associated with trichomoniasis that was previously known by its 16S rRNA sequence as "Mnola." In this study, the mycoplasma was found almost exclusively in women infected with the sexually transmitted pathogen Trichomonas vaginalis, but rarely observed in women with no diagnosed disease. The genomes of four strains of this species were reconstructed using metagenome sequencing and assembly of DNA from four discrete mid-vaginal samples, one of which was obtained from a pregnant woman with trichomoniasis who delivered prematurely. These bacteria harbor several putative virulence factors and display unique metabolic strategies. Genes encoding proteins with high similarity to potential virulence factors include two collagenases, a hemolysin, an O-sialoglycoprotein endopeptidase and a feoB-type ferrous iron transport system. We propose the name "Candidatus Mycoplasma girerdii" for this potential new pathogen.
Mesh-Begriff(e)	Amino Acid Sequence ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Coinfection/microbiology ; Communicable Diseases, Emerging/microbiology ; Female ; Humans ; Hydrogen-Ion Concentration ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Molecular Sequence Data ; Molecular Typing ; Mycoplasma/classification ; Mycoplasma/genetics ; Mycoplasma/isolation & purification ; Mycoplasma Infections/microbiology ; Phylogeny ; Pregnancy ; Pregnancy Complications, Infectious/microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Trichomonas Vaginitis/microbiology ; Trichomonas vaginalis/physiology ; Vagina/metabolism ; Vagina/microbiology
Chemische Substanzen	Bacterial Proteins ; BspA protein, bacteria ; Membrane Proteins ; RNA, Bacterial ; RNA, Ribosomal, 16S
Sprache	Englisch
Erscheinungsdatum	2014-10-22
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0110943
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy.

Serrano, Myrna G / Parikh, Hardik I / Brooks, J Paul / Edwards, David J / Arodz, Tom J / Edupuganti, Laahirie / Huang, Bernice / Girerd, Philippe H / Bokhari, Yahya A / Bradley, Steven P / Brooks, Jamie L / Dickinson, Molly R / Drake, Jennifer I / Duckworth, Robert A / Fong, Stephen S / Glascock, Abigail L / Jean, Sophonie / Jimenez, Nicole R / Khoury, Joseph /

Nature medicine

2019 Band 25, Heft 6, Seite(n) 1001–1011

Abstract: The microbiome of the female reproductive tract has implications for women's reproductive health. We examined the vaginal microbiome in two cohorts of women who experienced normal term births: a cross-sectionally sampled cohort of 613 pregnant and 1,969 ... ...

Abstract	The microbiome of the female reproductive tract has implications for women's reproductive health. We examined the vaginal microbiome in two cohorts of women who experienced normal term births: a cross-sectionally sampled cohort of 613 pregnant and 1,969 non-pregnant women, focusing on 300 pregnant and 300 non-pregnant women of African, Hispanic or European ancestry case-matched for race, gestational age and household income; and a longitudinally sampled cohort of 90 pregnant women of African or non-African ancestry. In these women, the vaginal microbiome shifted during pregnancy toward Lactobacillus-dominated profiles at the expense of taxa often associated with vaginal dysbiosis. The shifts occurred early in pregnancy, followed predictable patterns, were associated with simplification of the metabolic capacity of the microbiome and were significant only in women of African or Hispanic ancestry. Both genomic and environmental factors are likely contributors to these trends, with socioeconomic status as a likely environmental influence.
Mesh-Begriff(e)	Adult ; African Americans ; Biodiversity ; Cohort Studies ; Cross-Sectional Studies ; Female ; Hispanic or Latino ; Host Microbial Interactions/genetics ; Host Microbial Interactions/physiology ; Humans ; Microbiota/genetics ; Microbiota/physiology ; Pregnancy/physiology ; Social Class ; Vagina/microbiology ; Whites
Sprache	Englisch
Erscheinungsdatum	2019-05-29
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-019-0465-8
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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