Additional file 1: Fig. S1. Study protocol for Phase II clinical trial NCT01925417 adapted from r... more Additional file 1: Fig. S1. Study protocol for Phase II clinical trial NCT01925417 adapted from reference [25]. Samples specifically used for this study depicted in Fig. 1. Fig. S2. The relative abundance of bacterial phyla in all patients are shown at day 0 (panel A) and in all donor samples from the 4 donors (panel B). The patient IDs are marked in gray if symptoms resolved in a single dose of the study drug and in red if they required repeat intervention. A) Patient ID is listed after the letter A on the x axis with relative abundance of each phylum in stacked bar chart format on the y-axis. B) Donor samples are named as donor number.samplenumber followed by DS for donor substance. Fig. S3. linear discriminant analysis compares functional pathway abundance, as annotated by HUMAnN2 and visualized with LEfSe, at day 7 between the two outcome groups. In red are pathways more enriched in the reintervention (RI) group, while those patients who recovered after a single treatment had a ...
The capacity of subinhibitory levels of antibiotics to modulate bacterial virulence in vitro has ... more The capacity of subinhibitory levels of antibiotics to modulate bacterial virulence in vitro has recently been brought to light, raising concerns over the appropriateness of low-dose therapies, including antibiotic prophylaxis for recurrent urinary tract infection management. However, the mechanisms involved and their relevance in influencing pathogenesis have not been investigated. We characterized the ability of antibiotics to modulate virulence in the uropathogens Staphylococcus saprophyticus and Escherichia coli. Several antibiotics were able to induce the expression of adhesins critical to urothelial colonization, resulting in increased biofilm formation, colonization of murine bladders and kidneys, and promotion of intracellular niche formation. Mice receiving subinhibitory ciprofloxacin treatment were also more susceptible to severe infections and frequent recurrences. A ciprofloxacin prophylaxis model revealed this strategy to be ineffective in reducing recurrences and worse...
ABSTRACTUrinary tract infections (UTIs) have complex dynamics, with uropathogenicEscherichia coli... more ABSTRACTUrinary tract infections (UTIs) have complex dynamics, with uropathogenicEscherichia coli(UPEC), the major causative agent, capable of colonization from the urethra to the kidneys in both extracellular and intracellular niches while also producing chronic persistent infections and frequent recurrent disease. In mouse and human bladders, UPEC invades the superficial epithelium, and some bacteria enter the cytoplasm to rapidly replicate into intracellular bacterial communities (IBCs) comprised of ∼104bacteria each. Through IBC formation, UPEC expands in numbers while subverting aspects of the innate immune response. Within 12 h of murine bladder infection, half of the bacteria are intracellular, with 3 to 700 IBCs formed. Using mixed infections with green fluorescent protein (GFP) and wild-type (WT) UPEC, we discovered that each IBC is clonally derived from a single bacterium. Genetically tagged UPEC and a multiplex PCR assay were employed to investigate the distribution of UP...
Additional file 3. All genomic resistance gene annotations from Resfinder for all MDRO isolates a... more Additional file 3. All genomic resistance gene annotations from Resfinder for all MDRO isolates are listed here, with their specific genomic location, predicted phenotype, and % identity to reference genes.
Additional file 2. This table shows cultured isolates, their associated ASVs, their taxonomy assi... more Additional file 2. This table shows cultured isolates, their associated ASVs, their taxonomy assignments according to DADA2 and MALDI-TOF, and antibiotic sensitivity results in terms of their clearance zone sizes and the interpretations of sensitive, intermediate, or resistant. Final taxonomy assignments were confirmed by genomic alignments with type strains.
Additional file 6. The two tables show the total ARG hits in RPKM for donors and patients at each... more Additional file 6. The two tables show the total ARG hits in RPKM for donors and patients at each sample collection timepoint, as well as the standard deviation and variance over time.
PURPOSE To describe an unusual case of unilateral, endogenous endophthalmitis in an otherwise hea... more PURPOSE To describe an unusual case of unilateral, endogenous endophthalmitis in an otherwise healthy, term neonate. METHODS A 3-week-old otherwise healthy, term male infant was referred to St. Louis Children's Hospital for a second opinion of presumed panuveitis of the right eye. PATIENTS Single male infant. RESULTS Diffusion weighted magnetic resonance imaging (MRI) demonstrating purulent intraocular contents facilitated the diagnosis of endophthalmitis. Examination of surgical vitreous samples by staining and cytology demonstrated Gram-positive bacterial cocci in short chains, thereby confirming endophthalmitis. Polymerase chain reaction testing of vitreous fluid identified Streptococcus agalactiae, despite an unremarkable systemic workup and a negative pre-partum maternal Group B streptococcal screen. CONCLUSIONS Endogenous endophthalmitis is a rare but devastating cause of vision loss in otherwise healthy, term neonates. Prompt diagnosis may be facilitated by MRI imaging and diagnostic vitreous biopsy.
Recurrent bacterial infections are a significant burden worldwide, and prior history of infection... more Recurrent bacterial infections are a significant burden worldwide, and prior history of infection is often a significant risk factor for developing new infections. For urinary tract infection (UTI), a history of two or more episodes is an independent risk factor for acute infection. However, mechanistic knowledge of UTI pathogenesis has come almost exclusively from studies in naive mice. Here we show that, in mice, an initial Escherichia coli UTI, whether chronic or self-limiting, Reprints and permissions information is available at www.nature.com/reprints.
Host-pathogen interactions are often mediated by extracellular fibers known as pili. The best cha... more Host-pathogen interactions are often mediated by extracellular fibers known as pili. The best characterized Gram negative pili are assembled by the Chaperone Usher Pathway (CUP). CUP pili are often tipped with an adhesin that binds to receptors with stereochemical specificity allowing microbes to colonize and adapt to dynamically changing environments. Type 1 and P pili are prototype CUP pili that mediate colonization of tissues in the urinary tract during infection by uropathogenic Escherichia coli (UPEC). During a urinary tract infection (UTI), UPEC occupy and flux between multiple niches within the bladder and kidneys. In the acute stages of cystitis, UPEC invade superficial bladder epithelial cells, replicate within the cytoplasm, and form large biofilm aggregates termed intracellular bacterial communities (IBCs). Appropriate expression of pili and other virulence factors in the urinary tract is essential for pathogenesis. Type 1 pili, critical for bladder infection, are regulated by cis-encoded recombinases within the fim operon that reversibly invert the fim promoter, regulating expression. Recombinases and many other regulatory proteins serve to cross-regulate CUPs and fine-tune pilus expression. Understanding the structure, regulation, assembly, and function of these pili has lead to the development of novel anti-virulence compounds that prevent bacterial attachment to host tissues.
Urinary tract infections (UTIs) afflict over 9 million women in America every year, often necessi... more Urinary tract infections (UTIs) afflict over 9 million women in America every year, often necessitating long-term prophylactic antibiotics. One risk factor for UTI is frequent sexual intercourse, which dramatically increases the risk of UTI. The mechanism behind this increased risk is unknown; however, bacteriuria increases immediately after sexual intercourse episodes, suggesting that physical manipulation introduces periurethral flora into the urinary tract. In this paper, we investigated whether superinfection (repeat introduction of bacteria) resulted in increased risk of severe UTI, manifesting as persistent bacteriuria, high titer bladder bacterial burdens and chronic inflammation, an outcome referred to as chronic cystitis. Chronic cystitis represents unchecked luminal bacterial replication and is defined histologically by urothelial hyperplasia and submucosal lymphoid aggregates, a histological pattern similar to that seen in humans suffering chronic UTI. C57BL/6J mice are resistant to chronic cystitis after a single infection; however, they developed persistent bacteriuria and chronic cystitis when superinfected 24 hours apart. Elevated levels of interleukin-6 (IL-6), keratinocyte cytokine (KC/CXCL1), and granulocyte colony-stimulating factor (G-CSF) in the serum of C57BL/6J mice prior to the second infection predicted the development of chronic cystitis. These same cytokines have been found to precede chronic cystitis in singly infected C3H/ HeN mice. Furthermore, inoculating C3H/HeN mice twice within a six-hour period doubled the proportion of mice that developed chronic cystitis. Intracellular bacterial replication, regulated hemolysin (HlyA) expression, and caspase 1/11 activation were essential for this increase. Microarrays conducted at four weeks post inoculation in both mouse strains revealed upregulation of IL-1 and antimicrobial peptides during chronic cystitis. These data suggest a mechanism by which caspase-1/11 activation and IL-1 secretion could predispose certain women to recurrent UTI after frequent intercourse, a predisposition predictable by several serum biomarkers in two murine models.
Additional file 1: Fig. S1. Study protocol for Phase II clinical trial NCT01925417 adapted from r... more Additional file 1: Fig. S1. Study protocol for Phase II clinical trial NCT01925417 adapted from reference [25]. Samples specifically used for this study depicted in Fig. 1. Fig. S2. The relative abundance of bacterial phyla in all patients are shown at day 0 (panel A) and in all donor samples from the 4 donors (panel B). The patient IDs are marked in gray if symptoms resolved in a single dose of the study drug and in red if they required repeat intervention. A) Patient ID is listed after the letter A on the x axis with relative abundance of each phylum in stacked bar chart format on the y-axis. B) Donor samples are named as donor number.samplenumber followed by DS for donor substance. Fig. S3. linear discriminant analysis compares functional pathway abundance, as annotated by HUMAnN2 and visualized with LEfSe, at day 7 between the two outcome groups. In red are pathways more enriched in the reintervention (RI) group, while those patients who recovered after a single treatment had a ...
The capacity of subinhibitory levels of antibiotics to modulate bacterial virulence in vitro has ... more The capacity of subinhibitory levels of antibiotics to modulate bacterial virulence in vitro has recently been brought to light, raising concerns over the appropriateness of low-dose therapies, including antibiotic prophylaxis for recurrent urinary tract infection management. However, the mechanisms involved and their relevance in influencing pathogenesis have not been investigated. We characterized the ability of antibiotics to modulate virulence in the uropathogens Staphylococcus saprophyticus and Escherichia coli. Several antibiotics were able to induce the expression of adhesins critical to urothelial colonization, resulting in increased biofilm formation, colonization of murine bladders and kidneys, and promotion of intracellular niche formation. Mice receiving subinhibitory ciprofloxacin treatment were also more susceptible to severe infections and frequent recurrences. A ciprofloxacin prophylaxis model revealed this strategy to be ineffective in reducing recurrences and worse...
ABSTRACTUrinary tract infections (UTIs) have complex dynamics, with uropathogenicEscherichia coli... more ABSTRACTUrinary tract infections (UTIs) have complex dynamics, with uropathogenicEscherichia coli(UPEC), the major causative agent, capable of colonization from the urethra to the kidneys in both extracellular and intracellular niches while also producing chronic persistent infections and frequent recurrent disease. In mouse and human bladders, UPEC invades the superficial epithelium, and some bacteria enter the cytoplasm to rapidly replicate into intracellular bacterial communities (IBCs) comprised of ∼104bacteria each. Through IBC formation, UPEC expands in numbers while subverting aspects of the innate immune response. Within 12 h of murine bladder infection, half of the bacteria are intracellular, with 3 to 700 IBCs formed. Using mixed infections with green fluorescent protein (GFP) and wild-type (WT) UPEC, we discovered that each IBC is clonally derived from a single bacterium. Genetically tagged UPEC and a multiplex PCR assay were employed to investigate the distribution of UP...
Additional file 3. All genomic resistance gene annotations from Resfinder for all MDRO isolates a... more Additional file 3. All genomic resistance gene annotations from Resfinder for all MDRO isolates are listed here, with their specific genomic location, predicted phenotype, and % identity to reference genes.
Additional file 2. This table shows cultured isolates, their associated ASVs, their taxonomy assi... more Additional file 2. This table shows cultured isolates, their associated ASVs, their taxonomy assignments according to DADA2 and MALDI-TOF, and antibiotic sensitivity results in terms of their clearance zone sizes and the interpretations of sensitive, intermediate, or resistant. Final taxonomy assignments were confirmed by genomic alignments with type strains.
Additional file 6. The two tables show the total ARG hits in RPKM for donors and patients at each... more Additional file 6. The two tables show the total ARG hits in RPKM for donors and patients at each sample collection timepoint, as well as the standard deviation and variance over time.
PURPOSE To describe an unusual case of unilateral, endogenous endophthalmitis in an otherwise hea... more PURPOSE To describe an unusual case of unilateral, endogenous endophthalmitis in an otherwise healthy, term neonate. METHODS A 3-week-old otherwise healthy, term male infant was referred to St. Louis Children's Hospital for a second opinion of presumed panuveitis of the right eye. PATIENTS Single male infant. RESULTS Diffusion weighted magnetic resonance imaging (MRI) demonstrating purulent intraocular contents facilitated the diagnosis of endophthalmitis. Examination of surgical vitreous samples by staining and cytology demonstrated Gram-positive bacterial cocci in short chains, thereby confirming endophthalmitis. Polymerase chain reaction testing of vitreous fluid identified Streptococcus agalactiae, despite an unremarkable systemic workup and a negative pre-partum maternal Group B streptococcal screen. CONCLUSIONS Endogenous endophthalmitis is a rare but devastating cause of vision loss in otherwise healthy, term neonates. Prompt diagnosis may be facilitated by MRI imaging and diagnostic vitreous biopsy.
Recurrent bacterial infections are a significant burden worldwide, and prior history of infection... more Recurrent bacterial infections are a significant burden worldwide, and prior history of infection is often a significant risk factor for developing new infections. For urinary tract infection (UTI), a history of two or more episodes is an independent risk factor for acute infection. However, mechanistic knowledge of UTI pathogenesis has come almost exclusively from studies in naive mice. Here we show that, in mice, an initial Escherichia coli UTI, whether chronic or self-limiting, Reprints and permissions information is available at www.nature.com/reprints.
Host-pathogen interactions are often mediated by extracellular fibers known as pili. The best cha... more Host-pathogen interactions are often mediated by extracellular fibers known as pili. The best characterized Gram negative pili are assembled by the Chaperone Usher Pathway (CUP). CUP pili are often tipped with an adhesin that binds to receptors with stereochemical specificity allowing microbes to colonize and adapt to dynamically changing environments. Type 1 and P pili are prototype CUP pili that mediate colonization of tissues in the urinary tract during infection by uropathogenic Escherichia coli (UPEC). During a urinary tract infection (UTI), UPEC occupy and flux between multiple niches within the bladder and kidneys. In the acute stages of cystitis, UPEC invade superficial bladder epithelial cells, replicate within the cytoplasm, and form large biofilm aggregates termed intracellular bacterial communities (IBCs). Appropriate expression of pili and other virulence factors in the urinary tract is essential for pathogenesis. Type 1 pili, critical for bladder infection, are regulated by cis-encoded recombinases within the fim operon that reversibly invert the fim promoter, regulating expression. Recombinases and many other regulatory proteins serve to cross-regulate CUPs and fine-tune pilus expression. Understanding the structure, regulation, assembly, and function of these pili has lead to the development of novel anti-virulence compounds that prevent bacterial attachment to host tissues.
Urinary tract infections (UTIs) afflict over 9 million women in America every year, often necessi... more Urinary tract infections (UTIs) afflict over 9 million women in America every year, often necessitating long-term prophylactic antibiotics. One risk factor for UTI is frequent sexual intercourse, which dramatically increases the risk of UTI. The mechanism behind this increased risk is unknown; however, bacteriuria increases immediately after sexual intercourse episodes, suggesting that physical manipulation introduces periurethral flora into the urinary tract. In this paper, we investigated whether superinfection (repeat introduction of bacteria) resulted in increased risk of severe UTI, manifesting as persistent bacteriuria, high titer bladder bacterial burdens and chronic inflammation, an outcome referred to as chronic cystitis. Chronic cystitis represents unchecked luminal bacterial replication and is defined histologically by urothelial hyperplasia and submucosal lymphoid aggregates, a histological pattern similar to that seen in humans suffering chronic UTI. C57BL/6J mice are resistant to chronic cystitis after a single infection; however, they developed persistent bacteriuria and chronic cystitis when superinfected 24 hours apart. Elevated levels of interleukin-6 (IL-6), keratinocyte cytokine (KC/CXCL1), and granulocyte colony-stimulating factor (G-CSF) in the serum of C57BL/6J mice prior to the second infection predicted the development of chronic cystitis. These same cytokines have been found to precede chronic cystitis in singly infected C3H/ HeN mice. Furthermore, inoculating C3H/HeN mice twice within a six-hour period doubled the proportion of mice that developed chronic cystitis. Intracellular bacterial replication, regulated hemolysin (HlyA) expression, and caspase 1/11 activation were essential for this increase. Microarrays conducted at four weeks post inoculation in both mouse strains revealed upregulation of IL-1 and antimicrobial peptides during chronic cystitis. These data suggest a mechanism by which caspase-1/11 activation and IL-1 secretion could predispose certain women to recurrent UTI after frequent intercourse, a predisposition predictable by several serum biomarkers in two murine models.
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