Elucidating the factors determining reproductive success has challenged scientists since Darwin, ... more Elucidating the factors determining reproductive success has challenged scientists since Darwin, but the exact pathways that shape the evolution of life history traits by connecting extrinsic (e.g., landscape structure) and intrinsic (e.g., female's age and endosymbionts) factors and reproductive success have rarely been studied. Here we collected female fleas from wild rodents in plots differing in their densities and proportions of the most dominant rodent species. We then combined path analysis and model selection approaches to explore the network of effects, ranging from micro to macroscales, determining the reproductive success of these fleas. Our results suggest that female reproductive success is directly and positively associated with their infection by Mycoplasma bacteria and their own body mass, and with the rodent species size and total density. In addition, we found evidence for indirect effects of rodent sex and rodent community diversity on female reproductive success. These results highlight the importance of exploring interrelated factors across organization scales while studying the reproductive success of wild organisms, and they have implications for the control of vector-borne diseases.
Diabetes mellitus is a major risk factor for chronic periodontitis. We investigated the effects o... more Diabetes mellitus is a major risk factor for chronic periodontitis. We investigated the effects of type 2 diabetes on the subgingival plaque bacterial composition by applying culture-independent 16S rDNA sequencing to periodontal bacteria isolated from four groups of volunteers: non-diabetic subjects without periodontitis, non-diabetic subjects with periodontitis, type 2 diabetic patients without periodontitis, and type 2 diabetic patients with periodontitis. A total of 71,373 high-quality sequences were produced from the V1-V3 region of 16S rDNA genes by 454 pyrosequencing. Those 16S rDNA sequences were classified into 16 phyla, 27 classes, 48 orders, 85 families, 126 genera, and 1141 species-level OTUs. Comparing periodontally healthy samples with periodontitis samples identified 20 health-associated and 15 periodontitisassociated OTUs. In the subjects with healthy periodontium, the abundances of three genera (Prevotella, Pseudomonas, and Tannerella) and nine OTUs were significantly different between diabetic patients and their non-diabetic counterparts. In the subjects carrying periodontitis, the abundances of three phyla (Actinobacteria, Proteobacteria, and Bacteriodetes), two genera (Actinomyces and Aggregatibacter), and six OTUs were also significantly different between diabetics and non-diabetics. Our results show that type 2 diabetes mellitus could alter the bacterial composition in the subgingival plaque.
Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have ... more Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have used metagenomic (DNA-dependent) and metaculturomic (culture-dependent) methods to debunk this longstanding dogma. In fact, resident microbial communities (urobiome) have been detected in both adult females and males. Although the field is young, several observations have been made. For example, the urobiome differs between men and women, likely due to anatomical and hormonal differences. Importantly, the urobiome has been associated with a variety of lower urinary tract disorders, including overactive bladder and post-operative urinary tract infection, raising the possibility that clinicians might one day treat symptoms by modifying the urobiome instead of killing the suspected uropathogen. Little is known concerning the relationship between the urobiome and host genetics; so far, only a single paper has reported such a study. However, major efforts have gone into understanding the genomics of the urobiome itself, a process facilitated by the fact that many urobiome studies have used metaculturomic methods to detect and identify microbes. In this narrative review, we will introduce the urobiome with separate sections on the female and male urobiomes, discuss challenges specific to the urobiome, describe newly discovered associations between the urobiome and lower urinary tract symptoms, and highlight the one study that has attempted to relate host genetics and the urobiome. We will finish with a section on how metagenomic surveys and whole genome sequencing of bacterial isolates are improving our understanding of the urobiome and its relationship to lower urinary tract health and disorders.
medRxiv (Cold Spring Harbor Laboratory), Mar 10, 2020
Corporation. The remaining authors (Price, Wolff, Halverson, Limeira, Dong) report no disclosures... more Corporation. The remaining authors (Price, Wolff, Halverson, Limeira, Dong) report no disclosures. ACKNOWLEDGMENTS: We thank Mary Tulke RN for her assistance with participant recruitment. We also acknowledge funding from NIH (R01 DK104718 awarded to AJW and LB). The funders did not play a part in the design or conduct of the study. TKP, BW, LB, ERM, and AJW designed the study. TKP and BW recruited participants. TKP processed the specimens. TH prepared them for DNA sequencing. RL sequenced the specimens. TKP, BW, QD and AJW analyzed the data. TKP and AJW wrote the manuscript. TKP, BW, TH, RL, LB, QD, ERM, and AJW reviewed and edited the manuscript.
Background In yaws-endemic areas, two-thirds of exudative cutaneous ulcers (CU) are associated wi... more Background In yaws-endemic areas, two-thirds of exudative cutaneous ulcers (CU) are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD); one-third are classified as idiopathic ulcers (IU). A yaws eradication campaign on Lihir Island in Papua New Guinea utilizing mass drug administration (MDA) of azithromycin initially reduced but failed to eradicate yaws; IU rates remained constant throughout the study. Using 16S rRNA gene sequencing, we previously determined that Streptococcus pyogenes was associated with some cases of IU. Here, we applied shotgun metagenomics to the same samples we analyzed previously by 16S rRNA sequencing to verify this result, identify additional IU-associated microorganisms, and determine why S. pyogenes-associated IU might have persisted after MDA of azithromycin. Methodology/Principal findings We sequenced DNA extracted from 244 CU specimens separated into four groups based upon microorganism-specific PCR results (HD+, TP+, T...
American Journal of Obstetrics and Gynecology, 2020
BACKGROUND: Since the discovery of the bladder microbiome (urobiome), interest has grown in learn... more BACKGROUND: Since the discovery of the bladder microbiome (urobiome), interest has grown in learning whether urobiome characteristics have a role in clinical phenotyping and/or provide opportunities for novel therapeutic approaches for women with common forms of urinary incontinence (UI).
Introduction and hypothesis Presence of microbial communities (microbiota) in an organ system dep... more Introduction and hypothesis Presence of microbial communities (microbiota) in an organ system depends on environmental factors, such as oxygen availability. We describe a novel technique to measure bladder urine oxygen tension (BUOT) in ambulatory women and use that technique to compare BUOT values to female urinary microbiota and participant urinary signs and symptoms. Methods Ambulatory female urogynecology patients presenting for clinical care who were willing to undergo transurethral catheterization underwent BUOT determination with a non-invasive flow-through oxygen sensor. To detect urinary microbiota in the bladder, 16S rRNA gene sequencing was performed on catheterized urine. Multivariate statistical analyses were performed to examine potential correlations among BUOT, urinary microbiota compositions and clinical variables. Results Significant variation in BUOT existed between individuals (range: 0.47-51.5 mmHg; median: 23.1 ± 13.5). Microbiota compositions were associated with BUOT (p = 0.03). BUOT was significantly lower in urines that were nitrite negative on dipstick analysis (p = 0.0001) and in participants who answered yes to having urinary leakage on the validated Urinary Distress Inventory (p = 0.01). Conclusions BUOTs can be measured in ambulatory women. For urogynecology patients, a wide range of values exist. BUOT may be associated with the presence of urinary microbiota and resultant signs and symptoms.
OBJECTIVES: Women have a 20% risk of developing a urinary tract infection (UTI) following urogyne... more OBJECTIVES: Women have a 20% risk of developing a urinary tract infection (UTI) following urogynecologic surgery. This study assessed the association of post-operative UTI with bacteria in pre-operative samples of catheterized urine. METHODS: Immediately before surgery, vaginal swabs, perineal swabs and catheterized urine samples were collected and the V4 region of the 16S rRNA gene was sequenced. The cohort was
With the continued spread of SARS-CoV-2 virus around the world, researchers often need to quickly... more With the continued spread of SARS-CoV-2 virus around the world, researchers often need to quickly identify novel mutations in newly sequenced SARS-CoV-2 genomes for studying the molecular evolution and epidemiology of the virus. We have developed a Python package, MicroGMT, which takes either raw sequence reads or assembled genome sequences as input and compares against database sequences to identify and characterize indels and point mutations. Although our default setting is optimized for SARS-CoV-2 virus, the package can be also applied to any other microbial genomes. The software is freely available at Github URL https://github.com/ qunfengdong/MicroGMT.
The furin cleavage site in the spike glycoprotein of the SARS-CoV-2 coronavirus is considered imp... more The furin cleavage site in the spike glycoprotein of the SARS-CoV-2 coronavirus is considered important for the virus to enter the host cells. By analyzing 45828 SARS-CoV-2 genome sequences, we identified 103 strains of SARS-CoV-2 with various DNA mutations including 18 unique non-synonymous point mutations, one deletion, and six gains of premature stop codon that may affect the furin cleavage site. Our results revealed that the furin cleavage site might not be required for SARS-CoV-2 to enter human cells in vivo. The identified mutants may represent a new subgroup of SARS-CoV-2 coronavirus with reduced tropism and transmissibility as potential live-attenuated vaccine candidates.
Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-t... more Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-thirds of CU are caused by Treponema pallidum subspecies pertenue and Haemophilus ducreyi , the cause(s) of the remaining one-third is unknown.
Haemophilus ducreyi causes chancroid and is a major cause of cutaneous ulcers in children. Due to... more Haemophilus ducreyi causes chancroid and is a major cause of cutaneous ulcers in children. Due to environmental reservoirs, both class I and class II H. ducreyi strains persist in cutaneous ulcer-endemic regions following mass drug administration of azithromycin, suggesting the need for a vaccine. The hemoglobin receptor (HgbA) is a leading vaccine candidate, but its efficacy in animal models is class-specific. Controlled human infection models can be used to evaluate vaccines, but only a class I strain (35000HP) has been characterized in this model. As a prelude to evaluating HgbA vaccines in the human model, here we tested whether a derivative of 35000HP containing a class II hgbA allele (FX548) is as virulent as 35000HP in humans. In 8 volunteers infected at 3 sites with each strain, the papule formation rate was 95.8% for 35000HP vs. 62.5% for FX548 (P = 0.021). Excluding doses of FX548 that were ≥ 2-fold higher than those of 35000HP, the pustule formation rate was 25% for 35000...
Characterization of urinary bacterial microbiome and antimicrobial peptides after burn injury to ... more Characterization of urinary bacterial microbiome and antimicrobial peptides after burn injury to identify potential mechanisms leading to urinary tract infections and associated morbidities in burn patients. Retrospective cohort study using human urine from control and burn subjects. University research laboratory. Burn patients. None. Urine samples from catheterized burn patients were collected hourly for up to 40 hours. Control urine was collected from "healthy" volunteers. The urinary bacterial microbiome and antimicrobial peptide levels and activity were compared with patient outcomes. We observed a significant increase in urinary microbial diversity in burn patients versus controls, which positively correlated with a larger percent burn and with the development of urinary tract infection and sepsis postadmission, regardless of age or gender. Urinary psoriasin and β-defensin antimicrobial peptide levels were significantly reduced in burn patients at 1 and 40 hours post...
The cutaneous microbiome maintains skin barrier function, regulates inflammation, and stimulates ... more The cutaneous microbiome maintains skin barrier function, regulates inflammation, and stimulates wound healing responses. Burn injury promotes an excessive activation of the cutaneous and systemic immune response directed against commensal and invading pathogens. Skin grafting is the primary method of reconstructing full-thickness burns, and wound infection continues to be a significant complication. In this study, the cutaneous bacterial microbiome was evaluated and subsequently compared to patient outcomes. Three different full-thickness skin specimens were assessed: 1.)control skin from non-burned subjects; 2.)burn margin from burn patients; and 3.)autologous donor skin from the same cohort of burn patients. We observed that skin bacterial community structure of burn patients was significantly altered compared to control patients. We determined that the unburned autologous donor skin from burn patients exhibits a microbiome similar to that of the burn margin, rather than unburned...
BACKGROUND: Since the discovery of the bladder microbiome (urobiome), interest has grown in learn... more BACKGROUND: Since the discovery of the bladder microbiome (urobiome), interest has grown in learning whether urobiome characteristics have a role in clinical phenotyping and/or provide opportunities for novel therapeutic approaches for women with common forms of urinary incontinence (UI).
Urobiome research has the potential to advance the understanding of a wide range of diseases, inc... more Urobiome research has the potential to advance the understanding of a wide range of diseases, including lower urinary tract symptoms and kidney disease. Many scientific areas have benefited from early research method consensus to facilitate the greater, common good.
Historically, the role of bacteria in urinary stone disease (USD) has been limited to urease-prod... more Historically, the role of bacteria in urinary stone disease (USD) has been limited to urease-producing bacteria associated with struvite stone formation. However, growing evidence has revealed bacteria associated with stones of non-struvite composition. These bacteria may be derived from either urine or from the stones themselves. Using 16S rRNA gene sequencing and an enhanced culture technique (EQUC), we identified the urine and stone microbiota of USD patients and then determined if bacteria were statistically enriched in the stones relative to the urine. From 52 patients, bladder urine and urinary stones were collected intraoperatively during ureteroscopy. Stone homogenate and urine specimens were subjected to 16S rRNA gene sequencing and EQUC. Standard Chi-squared tests were applied to determine if the relative abundance of any bacterial taxon was significantly enriched in urinary stones compared to urine. Stones were primarily calcium-based. 29/52 (55.8%) stones had bacteria detected by 16S rRNA gene sequencing. Of these, dominant bacterial taxa were enriched from 12 stones. Bacterial taxa isolated by EQUC include members of the genera Staphylococcus, Enterobacter, Escherichia, Corynebacterium, and Lactobacillus. Dominant bacterial genera were enriched compared to paired bladder urine. Differences between the stone and urine microbiota may indicate that certain bacteria contribute to USD pathophysiology. Further investigation is warranted.
Accurate estimations of the seroprevalence of antibodies to severe acute respiratory syndrome cor... more Accurate estimations of the seroprevalence of antibodies to severe acute respiratory syndrome coronavirus 2 need to properly consider the specificity and sensitivity of the antibody tests. In addition, prior knowledge of the extent of viral infection in a population may also be important for adjusting the estimation of seroprevalence. For this purpose, we have developed a Bayesian approach that can incorporate the variabilities of specificity and sensitivity of the antibody tests, as well as the prior probability distribution of seroprevalence. We have demonstrated the utility of our approach by applying it to a recently published large-scale dataset from the US CDC, with our results providing entire probability distributions of seroprevalence instead of single-point estimates. Our Bayesian code is freely available at https://github.com/qunfengdong/AntibodyTest.
Elucidating the factors determining reproductive success has challenged scientists since Darwin, ... more Elucidating the factors determining reproductive success has challenged scientists since Darwin, but the exact pathways that shape the evolution of life history traits by connecting extrinsic (e.g., landscape structure) and intrinsic (e.g., female's age and endosymbionts) factors and reproductive success have rarely been studied. Here we collected female fleas from wild rodents in plots differing in their densities and proportions of the most dominant rodent species. We then combined path analysis and model selection approaches to explore the network of effects, ranging from micro to macroscales, determining the reproductive success of these fleas. Our results suggest that female reproductive success is directly and positively associated with their infection by Mycoplasma bacteria and their own body mass, and with the rodent species size and total density. In addition, we found evidence for indirect effects of rodent sex and rodent community diversity on female reproductive success. These results highlight the importance of exploring interrelated factors across organization scales while studying the reproductive success of wild organisms, and they have implications for the control of vector-borne diseases.
Diabetes mellitus is a major risk factor for chronic periodontitis. We investigated the effects o... more Diabetes mellitus is a major risk factor for chronic periodontitis. We investigated the effects of type 2 diabetes on the subgingival plaque bacterial composition by applying culture-independent 16S rDNA sequencing to periodontal bacteria isolated from four groups of volunteers: non-diabetic subjects without periodontitis, non-diabetic subjects with periodontitis, type 2 diabetic patients without periodontitis, and type 2 diabetic patients with periodontitis. A total of 71,373 high-quality sequences were produced from the V1-V3 region of 16S rDNA genes by 454 pyrosequencing. Those 16S rDNA sequences were classified into 16 phyla, 27 classes, 48 orders, 85 families, 126 genera, and 1141 species-level OTUs. Comparing periodontally healthy samples with periodontitis samples identified 20 health-associated and 15 periodontitisassociated OTUs. In the subjects with healthy periodontium, the abundances of three genera (Prevotella, Pseudomonas, and Tannerella) and nine OTUs were significantly different between diabetic patients and their non-diabetic counterparts. In the subjects carrying periodontitis, the abundances of three phyla (Actinobacteria, Proteobacteria, and Bacteriodetes), two genera (Actinomyces and Aggregatibacter), and six OTUs were also significantly different between diabetics and non-diabetics. Our results show that type 2 diabetes mellitus could alter the bacterial composition in the subgingival plaque.
Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have ... more Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have used metagenomic (DNA-dependent) and metaculturomic (culture-dependent) methods to debunk this longstanding dogma. In fact, resident microbial communities (urobiome) have been detected in both adult females and males. Although the field is young, several observations have been made. For example, the urobiome differs between men and women, likely due to anatomical and hormonal differences. Importantly, the urobiome has been associated with a variety of lower urinary tract disorders, including overactive bladder and post-operative urinary tract infection, raising the possibility that clinicians might one day treat symptoms by modifying the urobiome instead of killing the suspected uropathogen. Little is known concerning the relationship between the urobiome and host genetics; so far, only a single paper has reported such a study. However, major efforts have gone into understanding the genomics of the urobiome itself, a process facilitated by the fact that many urobiome studies have used metaculturomic methods to detect and identify microbes. In this narrative review, we will introduce the urobiome with separate sections on the female and male urobiomes, discuss challenges specific to the urobiome, describe newly discovered associations between the urobiome and lower urinary tract symptoms, and highlight the one study that has attempted to relate host genetics and the urobiome. We will finish with a section on how metagenomic surveys and whole genome sequencing of bacterial isolates are improving our understanding of the urobiome and its relationship to lower urinary tract health and disorders.
medRxiv (Cold Spring Harbor Laboratory), Mar 10, 2020
Corporation. The remaining authors (Price, Wolff, Halverson, Limeira, Dong) report no disclosures... more Corporation. The remaining authors (Price, Wolff, Halverson, Limeira, Dong) report no disclosures. ACKNOWLEDGMENTS: We thank Mary Tulke RN for her assistance with participant recruitment. We also acknowledge funding from NIH (R01 DK104718 awarded to AJW and LB). The funders did not play a part in the design or conduct of the study. TKP, BW, LB, ERM, and AJW designed the study. TKP and BW recruited participants. TKP processed the specimens. TH prepared them for DNA sequencing. RL sequenced the specimens. TKP, BW, QD and AJW analyzed the data. TKP and AJW wrote the manuscript. TKP, BW, TH, RL, LB, QD, ERM, and AJW reviewed and edited the manuscript.
Background In yaws-endemic areas, two-thirds of exudative cutaneous ulcers (CU) are associated wi... more Background In yaws-endemic areas, two-thirds of exudative cutaneous ulcers (CU) are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD); one-third are classified as idiopathic ulcers (IU). A yaws eradication campaign on Lihir Island in Papua New Guinea utilizing mass drug administration (MDA) of azithromycin initially reduced but failed to eradicate yaws; IU rates remained constant throughout the study. Using 16S rRNA gene sequencing, we previously determined that Streptococcus pyogenes was associated with some cases of IU. Here, we applied shotgun metagenomics to the same samples we analyzed previously by 16S rRNA sequencing to verify this result, identify additional IU-associated microorganisms, and determine why S. pyogenes-associated IU might have persisted after MDA of azithromycin. Methodology/Principal findings We sequenced DNA extracted from 244 CU specimens separated into four groups based upon microorganism-specific PCR results (HD+, TP+, T...
American Journal of Obstetrics and Gynecology, 2020
BACKGROUND: Since the discovery of the bladder microbiome (urobiome), interest has grown in learn... more BACKGROUND: Since the discovery of the bladder microbiome (urobiome), interest has grown in learning whether urobiome characteristics have a role in clinical phenotyping and/or provide opportunities for novel therapeutic approaches for women with common forms of urinary incontinence (UI).
Introduction and hypothesis Presence of microbial communities (microbiota) in an organ system dep... more Introduction and hypothesis Presence of microbial communities (microbiota) in an organ system depends on environmental factors, such as oxygen availability. We describe a novel technique to measure bladder urine oxygen tension (BUOT) in ambulatory women and use that technique to compare BUOT values to female urinary microbiota and participant urinary signs and symptoms. Methods Ambulatory female urogynecology patients presenting for clinical care who were willing to undergo transurethral catheterization underwent BUOT determination with a non-invasive flow-through oxygen sensor. To detect urinary microbiota in the bladder, 16S rRNA gene sequencing was performed on catheterized urine. Multivariate statistical analyses were performed to examine potential correlations among BUOT, urinary microbiota compositions and clinical variables. Results Significant variation in BUOT existed between individuals (range: 0.47-51.5 mmHg; median: 23.1 ± 13.5). Microbiota compositions were associated with BUOT (p = 0.03). BUOT was significantly lower in urines that were nitrite negative on dipstick analysis (p = 0.0001) and in participants who answered yes to having urinary leakage on the validated Urinary Distress Inventory (p = 0.01). Conclusions BUOTs can be measured in ambulatory women. For urogynecology patients, a wide range of values exist. BUOT may be associated with the presence of urinary microbiota and resultant signs and symptoms.
OBJECTIVES: Women have a 20% risk of developing a urinary tract infection (UTI) following urogyne... more OBJECTIVES: Women have a 20% risk of developing a urinary tract infection (UTI) following urogynecologic surgery. This study assessed the association of post-operative UTI with bacteria in pre-operative samples of catheterized urine. METHODS: Immediately before surgery, vaginal swabs, perineal swabs and catheterized urine samples were collected and the V4 region of the 16S rRNA gene was sequenced. The cohort was
With the continued spread of SARS-CoV-2 virus around the world, researchers often need to quickly... more With the continued spread of SARS-CoV-2 virus around the world, researchers often need to quickly identify novel mutations in newly sequenced SARS-CoV-2 genomes for studying the molecular evolution and epidemiology of the virus. We have developed a Python package, MicroGMT, which takes either raw sequence reads or assembled genome sequences as input and compares against database sequences to identify and characterize indels and point mutations. Although our default setting is optimized for SARS-CoV-2 virus, the package can be also applied to any other microbial genomes. The software is freely available at Github URL https://github.com/ qunfengdong/MicroGMT.
The furin cleavage site in the spike glycoprotein of the SARS-CoV-2 coronavirus is considered imp... more The furin cleavage site in the spike glycoprotein of the SARS-CoV-2 coronavirus is considered important for the virus to enter the host cells. By analyzing 45828 SARS-CoV-2 genome sequences, we identified 103 strains of SARS-CoV-2 with various DNA mutations including 18 unique non-synonymous point mutations, one deletion, and six gains of premature stop codon that may affect the furin cleavage site. Our results revealed that the furin cleavage site might not be required for SARS-CoV-2 to enter human cells in vivo. The identified mutants may represent a new subgroup of SARS-CoV-2 coronavirus with reduced tropism and transmissibility as potential live-attenuated vaccine candidates.
Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-t... more Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-thirds of CU are caused by Treponema pallidum subspecies pertenue and Haemophilus ducreyi , the cause(s) of the remaining one-third is unknown.
Haemophilus ducreyi causes chancroid and is a major cause of cutaneous ulcers in children. Due to... more Haemophilus ducreyi causes chancroid and is a major cause of cutaneous ulcers in children. Due to environmental reservoirs, both class I and class II H. ducreyi strains persist in cutaneous ulcer-endemic regions following mass drug administration of azithromycin, suggesting the need for a vaccine. The hemoglobin receptor (HgbA) is a leading vaccine candidate, but its efficacy in animal models is class-specific. Controlled human infection models can be used to evaluate vaccines, but only a class I strain (35000HP) has been characterized in this model. As a prelude to evaluating HgbA vaccines in the human model, here we tested whether a derivative of 35000HP containing a class II hgbA allele (FX548) is as virulent as 35000HP in humans. In 8 volunteers infected at 3 sites with each strain, the papule formation rate was 95.8% for 35000HP vs. 62.5% for FX548 (P = 0.021). Excluding doses of FX548 that were ≥ 2-fold higher than those of 35000HP, the pustule formation rate was 25% for 35000...
Characterization of urinary bacterial microbiome and antimicrobial peptides after burn injury to ... more Characterization of urinary bacterial microbiome and antimicrobial peptides after burn injury to identify potential mechanisms leading to urinary tract infections and associated morbidities in burn patients. Retrospective cohort study using human urine from control and burn subjects. University research laboratory. Burn patients. None. Urine samples from catheterized burn patients were collected hourly for up to 40 hours. Control urine was collected from "healthy" volunteers. The urinary bacterial microbiome and antimicrobial peptide levels and activity were compared with patient outcomes. We observed a significant increase in urinary microbial diversity in burn patients versus controls, which positively correlated with a larger percent burn and with the development of urinary tract infection and sepsis postadmission, regardless of age or gender. Urinary psoriasin and β-defensin antimicrobial peptide levels were significantly reduced in burn patients at 1 and 40 hours post...
The cutaneous microbiome maintains skin barrier function, regulates inflammation, and stimulates ... more The cutaneous microbiome maintains skin barrier function, regulates inflammation, and stimulates wound healing responses. Burn injury promotes an excessive activation of the cutaneous and systemic immune response directed against commensal and invading pathogens. Skin grafting is the primary method of reconstructing full-thickness burns, and wound infection continues to be a significant complication. In this study, the cutaneous bacterial microbiome was evaluated and subsequently compared to patient outcomes. Three different full-thickness skin specimens were assessed: 1.)control skin from non-burned subjects; 2.)burn margin from burn patients; and 3.)autologous donor skin from the same cohort of burn patients. We observed that skin bacterial community structure of burn patients was significantly altered compared to control patients. We determined that the unburned autologous donor skin from burn patients exhibits a microbiome similar to that of the burn margin, rather than unburned...
BACKGROUND: Since the discovery of the bladder microbiome (urobiome), interest has grown in learn... more BACKGROUND: Since the discovery of the bladder microbiome (urobiome), interest has grown in learning whether urobiome characteristics have a role in clinical phenotyping and/or provide opportunities for novel therapeutic approaches for women with common forms of urinary incontinence (UI).
Urobiome research has the potential to advance the understanding of a wide range of diseases, inc... more Urobiome research has the potential to advance the understanding of a wide range of diseases, including lower urinary tract symptoms and kidney disease. Many scientific areas have benefited from early research method consensus to facilitate the greater, common good.
Historically, the role of bacteria in urinary stone disease (USD) has been limited to urease-prod... more Historically, the role of bacteria in urinary stone disease (USD) has been limited to urease-producing bacteria associated with struvite stone formation. However, growing evidence has revealed bacteria associated with stones of non-struvite composition. These bacteria may be derived from either urine or from the stones themselves. Using 16S rRNA gene sequencing and an enhanced culture technique (EQUC), we identified the urine and stone microbiota of USD patients and then determined if bacteria were statistically enriched in the stones relative to the urine. From 52 patients, bladder urine and urinary stones were collected intraoperatively during ureteroscopy. Stone homogenate and urine specimens were subjected to 16S rRNA gene sequencing and EQUC. Standard Chi-squared tests were applied to determine if the relative abundance of any bacterial taxon was significantly enriched in urinary stones compared to urine. Stones were primarily calcium-based. 29/52 (55.8%) stones had bacteria detected by 16S rRNA gene sequencing. Of these, dominant bacterial taxa were enriched from 12 stones. Bacterial taxa isolated by EQUC include members of the genera Staphylococcus, Enterobacter, Escherichia, Corynebacterium, and Lactobacillus. Dominant bacterial genera were enriched compared to paired bladder urine. Differences between the stone and urine microbiota may indicate that certain bacteria contribute to USD pathophysiology. Further investigation is warranted.
Accurate estimations of the seroprevalence of antibodies to severe acute respiratory syndrome cor... more Accurate estimations of the seroprevalence of antibodies to severe acute respiratory syndrome coronavirus 2 need to properly consider the specificity and sensitivity of the antibody tests. In addition, prior knowledge of the extent of viral infection in a population may also be important for adjusting the estimation of seroprevalence. For this purpose, we have developed a Bayesian approach that can incorporate the variabilities of specificity and sensitivity of the antibody tests, as well as the prior probability distribution of seroprevalence. We have demonstrated the utility of our approach by applying it to a recently published large-scale dataset from the US CDC, with our results providing entire probability distributions of seroprevalence instead of single-point estimates. Our Bayesian code is freely available at https://github.com/qunfengdong/AntibodyTest.
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