Corynebacterium phoceense, resident member of the urogenital microbiota?

Microbiology ◽  
2021 ◽  
Vol 167 (7) ◽  
Author(s):  
Silvia Giannattasio-Ferraz ◽  
Adriana Ene ◽  
Laura Maskeri ◽  
Andre Penido Oliveira ◽  
Edel F. Barbosa-Stancioli ◽  
...  
Keyword(s):  
Urinary Tract ◽  
Genomic Analysis ◽  
Urogenital Tract ◽  
The Other ◽  
Content Type ◽  
Link Type ◽  
Healthy Cattle ◽  
Vaginal Tract ◽  
Tract Infections ◽  
Genome Assemblies

Corynebacterium phoceense is a Gram-positive species previously isolated from human urine. Although other species from the same genus have been associated with urinary tract infections, C. phoceense is currently believed to be a non-pathogenic member of the urogenital microbiota. Prior to our study, only two isolates were described in the literature, and very little is known about the species. Here, we describe C. phoceense UFMG-H7, the first strain of this species isolated from the urine of healthy cattle. The genome for this isolate was produced and compared to the two other publicly available C. phoceense as well as other Corynebacterium genome assemblies. Our in-depth genomic analysis identified four additional publicly available genome assemblies that are representatives of the species, also isolated from the human urogenital tract. Although none of the strains have been associated with symptoms or disease, numerous genes associated with virulence factors are encoded. In contrast to related Corynebacterium species and Corynebacterium species from the bovine vaginal tract, all C. phoceense strains examined code for the SpaD-type pili suggesting adherence is essential for its persistence within the urinary tract. As the other C. phoceense strains analysed were isolated from the human urogenital tract, our results suggest that this species may be specific to this niche.

scholarly journals Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction forKlebsiellaGenomes

2018 ◽  
Vol 56 (6) ◽  
Author(s):  
Ryan R. Wick ◽  
Eva Heinz ◽  
Kathryn E. Holt ◽  
Kelly L. Wyres
Keyword(s):  
Control Strategies ◽  
Genomic Analysis ◽  
Relevant Information ◽  
Multidrug Resistant ◽  
Content Type ◽  
Link Type ◽  
Antimicrobial Resistance Genes ◽  
Typing Methods ◽  
Genome Assemblies ◽  
User Friendly

ABSTRACTAs whole-genome sequencing becomes an established component of the microbiologist's toolbox, it is imperative that researchers, clinical microbiologists, and public health professionals have access to genomic analysis tools for the rapid extraction of epidemiologically and clinically relevant information. For the Gram-negative hospital pathogens such asKlebsiella pneumoniae, initial efforts have focused on the detection and surveillance of antimicrobial resistance genes and clones. However, with the resurgence of interest in alternative infection control strategies targetingKlebsiellasurface polysaccharides, the ability to extract information about these antigens is increasingly important. Here we present Kaptive Web, an online tool for the rapid typing ofKlebsiellaK and O loci, which encode the polysaccharide capsule and lipopolysaccharide O antigen, respectively. Kaptive Web enables users to upload and analyze genome assemblies in a web browser. The results can be downloaded in tabular format or explored in detail via the graphical interface, making it accessible for users at all levels of computational expertise. We demonstrate Kaptive Web's utility by analyzing >500K. pneumoniaegenomes. We identify extensive K and O locus diversity among 201 genomes belonging to the carbapenemase-associated clonal group 258 (25 K and 6 O loci). The characterization of a further 309 genomes indicated that such diversity is common among the multidrug-resistant clones and that these loci represent useful epidemiological markers for strain subtyping. These findings reinforce the need for rapid, reliable, and accessible typing methods such as Kaptive Web. Kaptive Web is available for use athttp://kaptive.holtlab.net/, and the source code is available athttps://github.com/kelwyres/Kaptive-Web.

Capnocytophaga periodontitidis sp. nov., isolated from subgingival plaque of periodontitis patient

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Yifei Zhang ◽  
Dan Qiao ◽  
Wenyu Shi ◽  
Danni Wu ◽  
Man Cai
Keyword(s):  
Genomic Analysis ◽  
Gene Families ◽  
Core Gene ◽  
The Other ◽  
Specific Gene ◽  
Rrna Gene ◽  
Subgingival Plaque ◽  
Content Type ◽  
Periodontitis Patient ◽  
Link Type

Two carbon dioxide-requiring, gliding, Gram-stain-negative strains, designated p1a2T and 051621, were isolated from subgingival plaque in association with severe periodontitis. The 16S rRNA gene sequence analysis revealed that they represented members of the genus Capnocytophaga and had less than 96.4 % pairwise similarity with species with validly published names in this genus. The whole-genome sequences of those strains had less than 91.9 % average nucleotide identity and 48.4 % digital DNA–DNA hybridization values with the other type strains of species of the genus Capnocytophaga , both below the species delineation threshold. The results of pan-genomic analysis indicated that p1a2T and 051621 shared 765 core gene families with the other ten species in this genus, and the numbers of strain-specific gene families were 493 and 455, respectively. The major fatty acids were iso-C15 : 0 and C16 : 0. A combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicate that p1a2T and 051621 should be considered to represent a novel species of the genus Capnocytophaga , for which the name Capnocytophaga periodontitidis sp. nov. is proposed. The type strain is p1a2T (=CGMCC 1.17337T=JCM 34126T).

scholarly journals Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Dmitriy Li ◽  
Cameron J. Reid ◽  
Timothy Kudinha ◽  
Veronica M. Jarocki ◽  
Steven P. Djordjevic
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Resistance Genes ◽  
Type Species ◽  
Medical Attention ◽  
Snp Analysis ◽  
Content Type ◽  
Link Type ◽  
Tract Infections

Urinary tract infections (UTIs) are the most common bacterial infections requiring medical attention and a leading justification for antibiotic prescription. Trimethoprim is prescribed empirically for uncomplicated cases. UTIs are primarily caused by extraintestinal pathogenic Escherichia coli (ExPEC) and ExPEC strains play a central role in disseminating antimicrobial-resistance genes worldwide. Here, we describe the whole-genome sequences of trimethoprim-resistant ExPEC and/or ExPEC from recurrent UTIs (67 in total) from patients attending a regional Australian hospital from 2006 to 2008. Twenty-three sequence types (STs) were observed, with ST131 predominating (28 %), then ST69 and ST73 (both 7 %). Co-occurrence of trimethoprim-resistance genes with genes conferring resistance to extended-spectrum β-lactams, heavy metals and quaternary ammonium ions was a feature of the ExPEC described here. Seven trimethoprim-resistance genes were identified, most commonly dfrA17 (38 %) and dfrA12 (18 %). An uncommon dfrB4 variant was also observed. Two blaCTX-M variants were identified – blaCTX-M-15 (16 %) and blaCTX-M-14 (10 %). The former was always associated with dfrA12, the latter with dfrA17, and all blaCTX-M genes co-occurred with chromate-resistance gene chrA. Eighteen class 1 integron structures were characterized, and chrA featured in eight structures; dfrA genes featured in seventeen. ST131 H30Rx isolates possessed distinct antimicrobial gene profiles comprising aac(3)-IIa, aac(6)-Ib-cr, aph(3′)-Ia, aadA2, blaCTX-M-15 , blaOXA-1 and dfrA12. The most common virulence-associated genes (VAGs) were fimH, fyuA, irp2 and sitA (all 91 %). Virulence profile clustering showed ST131 H30 isolates carried similar VAGs to ST73, ST405, ST550 and ST1193 isolates. The sole ST131 H27 isolate carried molecular predictors of enteroaggregative E. coli /ExPEC hybrid strains (aatA, aggR, fyuA). Seven isolates (10 %) carried VAGs suggesting ColV plasmid carriage. Finally, SNP analysis of serial UTI patients experiencing worsening sequelae demonstrated a high proportion of point mutations in virulence factors.

scholarly journals Draft Genome Sequence of Streptococcus anginosus UMB7768, Isolated from a Woman with Recurrent UTI Symptoms

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Sarah Miller ◽  
Taylor Miller-Ensminger ◽  
Adelina Voukadinova ◽  
Alan J. Wolfe ◽  
Catherine Putonti
Keyword(s):  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Genome Sequence ◽  
Draft Genome ◽  
Urogenital Tract ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Streptococcus Anginosus ◽  
Recurrent Uti ◽  
Tract Infections

ABSTRACT Streptococcus anginosus recently was implicated as a pathogen involved in urinary tract infections. A strain of S. anginosus was isolated from the female urogenital tract. Here, we present the draft genome sequence of S. anginosus strain UMB7768.

scholarly journals Genomic relatedness and clinical significance of Streptococcus mitis strains isolated from the urogenital tract of sexual partners

2021 ◽  
Vol 7 (3) ◽  
Author(s):  
Carine R. Mores ◽  
Travis K. Price ◽  
Birte Wolff ◽  
Thomas Halverson ◽  
Roberto Limeira ◽  
...  
Keyword(s):  
Urinary Tract ◽  
Type Species ◽  
Temporal Dynamics ◽  
Sexual Partners ◽  
Urogenital Tract ◽  
Female Participant ◽  
Vaginal Intercourse ◽  
Streptococcus Mitis ◽  
Content Type ◽  
Link Type

Research into the lower urinary tract (LUT) microbiota has primarily focused on its relationship to LUT symptoms (LUTS), taking snapshots of these communities in individuals with and without LUTS. While certain bacterial taxa have been associated with LUTS, or the lack thereof, the temporal dynamics of this community were largely unknown. Recently, we conducted a longitudinal study and found that vaginal intercourse resulted in a shift in species richness and diversity within the LUT microbiota. This is particularly relevant as frequent vaginal intercourse is a major risk factor for urinary tract infection (UTI) in premenopausal women (Aydin et al. Int Urogynecol J 2015;26:795–804). To further investigate the relationship between vaginal intercourse and LUT microbiota, here we present the results of a 3 week study in which daily urogenital specimens were collected from a female participant and her male sexual partner. Consistent with our previous findings, the LUT microbiota changed after vaginal intercourse, most notably a high abundance of Streptococcus mitis was observed post-coitus. We isolated and sequenced S. mitis from both sexual partners finding that: (i) the S. mitis isolates from the female partner’s urogenital tract were genomically similar throughout the duration of the study, and (ii) they were related to one isolate from the male partner’s oral cavity collected at the end of the study, suggesting transmission between the two individuals. We hypothesize that blooms in S. mitis after vaginal intercourse may play a role in coitus-related UTI. We found that a S. mitis isolate, in contrast to a Lactobacillus jensenii isolate displaced after vaginal intercourse, cannot inhibit the growth of uropathogenic Escherichia coli . Thus, this bloom in S. mitis may provide a window of opportunity for a uropathogen to colonize the LUT.

scholarly journals Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant In Situ Populations

mBio ◽  
2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Dana Willner ◽  
Serene Low ◽  
Jason A. Steen ◽  
Narelle George ◽  
Graeme R. Nimmo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Clinical Isolates ◽  
Content Type ◽  
E Coli ◽  
Strain Diversity ◽  
Amplicon Pyrosequencing ◽  
Culture Independent ◽  
Tract Infections

ABSTRACTUrinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenicEscherichia colistrains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and characterization is phenotypic in nature. Here, we explored the genotypic identity of communities in acute uncomplicated UTIs from 50 individuals by using culture-independent amplicon pyrosequencing and whole-genome and metagenomic shotgun sequencing. Genus-level characterization of the UTI communities was achieved using the 16S rRNA gene (V8 region). Overall UTI community richness was very low in comparison to other human microbiomes. We strain-typedEscherichia-dominated UTIs using amplicon pyrosequencing of the fimbrial adhesin gene,fimH. There were nine highly abundantfimHtypes, and each UTI sample was dominated by a single type. Molecular analysis of the corresponding clinical isolates revealed that in the majority of cases the isolate was representative of the dominant taxon in the community at both the genus and the strain level. Shotgun sequencing was performed on a subset of eightE. coliurine UTI and isolate pairs. The majority of UTI microbial metagenomic sequences mapped to isolate genomes, confirming the results obtained using phylogenetic markers. We conclude that for the majority of acute uncomplicatedE. coli-mediated UTIs, single cultured isolates are diagnostic of the infection.IMPORTANCEIn clinical practice, the diagnosis and treatment of acute uncomplicated urinary tract infection (UTI) are based on analysis of a single bacterial isolate cultured from urine, and it is assumed that this isolate represents the dominant UTI pathogen. However, these methods detect only culturable bacteria, and the existence of multiple pathogens as well as strain diversity within a single infection is not examined. Here, we explored bacteria present in acute uncomplicated UTIs using culture-independent sequence-based methods.Escherichia coliwas the most common organism identified, and analysis ofE. colidominant UTI samples and their paired clinical isolates revealed that in the majority of infections the cultured isolate was representative of the dominant taxon at both the genus and the strain level. Our data demonstrate that in most cases single cultured isolates are diagnostic of UTI and are consistent with the notion of bottlenecks that limit strain diversity during UTI pathogenesis.

scholarly journals New Aspects of RpoE in Uropathogenic Proteus mirabilis

2014 ◽  
Vol 83 (3) ◽  
pp. 966-977 ◽  
Author(s):  
Ming-Che Liu ◽  
Kuan-Ting Kuo ◽  
Hsiung-Fei Chien ◽  
Yi-Lin Tsai ◽  
Shwu-Jen Liaw
Keyword(s):  
Urinary Tract ◽  
Virulence Factors ◽  
Stress Responses ◽  
Proteus Mirabilis ◽  
Immune Cell ◽  
Polymyxin B ◽  
Urothelial Cells ◽  
Cationic Antimicrobial Peptide ◽  
Content Type ◽  
Tract Infections

Proteus mirabilisis a common human pathogen causing recurrent or persistent urinary tract infections (UTIs). The underlying mechanisms forP. mirabilisto establish UTIs are not fully elucidated. In this study, we showed that loss of the sigma factor E (RpoE), mediating extracytoplasmic stress responses, decreased fimbria expression, survival in macrophages, cell invasion, and colonization in mice but increased the interleukin-8 (IL-8) expression of urothelial cells and swarming motility. This is the first study to demonstrate that RpoE modulated expression of MR/P fimbriae by regulatingmrpI, a gene encoding a recombinase controlling the orientation of MR/P fimbria promoter. By real-time reverse transcription-PCR, we found that the IL-8 mRNA amount of urothelial cells was induced significantly by lipopolysaccharides extracted fromrpoEmutant but not from the wild type. These RpoE-associated virulence factors should be coordinately expressed to enhance the fitness ofP. mirabilisin the host, including the avoidance of immune attacks. Accordingly,rpoEmutant-infected mice displayed more immune cell infiltration in bladders and kidneys during early stages of infection, and therpoEmutant had a dramatically impaired ability of colonization. Moreover, it is noteworthy that urea (the major component in urine) and polymyxin B (a cationic antimicrobial peptide) can induce expression ofrpoEby the reporter assay, suggesting that RpoE might be activated in the urinary tract. Altogether, our results indicate that RpoE is important in sensing environmental cues of the urinary tract and subsequently triggering the expression of virulence factors, which are associated with the fitness ofP. mirabilis, to build up a UTI.

scholarly journals Synchrotron X-Ray Fluorescence Microscopy of Gallium in Bladder Tissue following Gallium Maltolate Administration during Urinary Tract Infection

2013 ◽  
Vol 57 (11) ◽  
pp. 5197-5201 ◽  
Author(s):  
Katherine R. Ball ◽  
Francesca Sampieri ◽  
Manuel Chirino ◽  
Don L. Hamilton ◽  
Robert I. R. Blyth ◽  
...  
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Tract Infection ◽  
Transitional Epithelium ◽  
Bladder Tissue ◽  
Content Type ◽  
X Ray ◽  
E Coli ◽  
Tract Infections ◽  
X Ray Absorption

ABSTRACTA mouse model of cystitis caused by uropathogenicEscherichia coliwas used to study the distribution of gallium in bladder tissue following oral administration of gallium maltolate during urinary tract infection. The median concentration of gallium in homogenized bladder tissue from infected mice was 1.93 μg/g after daily administration of gallium maltolate for 5 days. Synchrotron X-ray fluorescence imaging and X-ray absorption spectroscopy of bladder sections confirmed that gallium arrived at the transitional epithelium, a potential site of uropathogenicE. coliinfection. Gallium and iron were similarly but not identically distributed in the tissues, suggesting that at least some distribution mechanisms are not common between the two elements. The results of this study indicate that gallium maltolate may be a suitable candidate for further development as a novel antimicrobial therapy for urinary tract infections caused by uropathogenicE. coli.

scholarly journals The Extracellular Domain of the β2Integrin β Subunit (CD18) Is Sufficient forEscherichia coliHemolysin andAggregatibacter actinomycetemcomitansLeukotoxin Cytotoxic Activity

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Laura C. Ristow ◽  
Vy Tran ◽  
Kevin J. Schwartz ◽  
Lillie Pankratz ◽  
Andrew Mehle ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Integrin Signaling ◽  
Β Subunit ◽  
Wild Type ◽  
Α Subunit ◽  
Content Type ◽  
Animal Pathogens ◽  
Tract Infections

ABSTRACTTheEscherichia colihemolysin (HlyA) is a pore-forming exotoxin associated with severe complications of human urinary tract infections. HlyA is the prototype of the repeats-in-toxin (RTX) family, which includes LtxA fromAggregatibacter actinomycetemcomitans, a periodontal pathogen. The existence and requirement for a host cell receptor for these toxins are controversial. We performed an unbiased forward genetic selection in a mutant library of human monocytic cells, U-937, for host factors involved in HlyA cytotoxicity. The top candidate was the β2integrin β subunit. Δβ2cell lines are approximately 100-fold more resistant than wild-type U-937 cells to HlyA, but remain sensitive to HlyA at high concentrations. Similarly, Δβ2cells are more resistant than wild-type U-937 cells to LtxA, as Δβ2cells remain LtxA resistant even at >1,000-fold-higher concentrations of the toxin. Loss of any single β2integrin α subunit, or even all four α subunits together, does not confer resistance to HlyA. HlyA and LtxA bind to the β2subunit, but not to αL, αM, or αXin far-Western blots. Genetic complementation of Δβ2cells with either β2or β2with a cytoplasmic tail deletion restores HlyA and LtxA sensitivity, suggesting that β2integrin signaling is not required for cytotoxicity. Finally, β2mutations do not alter sensitivity to unrelated pore-forming toxins, as wild-type or Δβ2cells are equally sensitive toStaphylococcus aureusα-toxin andProteus mirabilisHpmA. Our studies show two RTX toxins use the β2integrin β subunit alone to facilitate cytotoxicity, but downstream integrin signaling is dispensable.IMPORTANCEUrinary tract infections are one of the most common bacterial infections worldwide. UropathogenicEscherichia colistrains are responsible for more than 80% of community-acquired urinary tract infections. Although we have known for nearly a century that severe infections stemming from urinary tract infections, including kidney or bloodstream infections are associated with expression of a toxin, hemolysin, from uropathogenicEscherichia coli, how hemolysin functions to enhance virulence is unknown. Our research defines the interaction of hemolysin with the β2integrin, a human white cell adhesion molecule, as a potential therapeutic target during urinary tract infections. TheE. colihemolysin is the prototype for a toxin family (RTX family) produced by a wide array of human and animal pathogens. Our work extends to the identification and characterization of the receptor for an additional member of the RTX family, suggesting that this interaction may be broadly conserved throughout the RTX toxin family.

scholarly journals Ceftolozane-Tazobactam Activity against Phylogenetically Diverse Clostridium difficile Strains

2015 ◽  
Vol 59 (11) ◽  
pp. 7084-7085 ◽  
Author(s):  
Mark D. Gonzalez ◽  
Meghan A. Wallace ◽  
Tiffany Hink ◽  
Erik R. Dubberke ◽  
Carey-Ann D. Burnham
Keyword(s):  
Urinary Tract ◽  
Clostridium Difficile ◽  
Urinary Tract Infections ◽  
Anaerobic Bacteria ◽  
Content Type ◽  
Tract Infections ◽  
High Mics

ABSTRACTCeftolozane-tazobactam (C/T) is approved for the treatment of complicated intra-abdominal and urinary tract infections and has varied activity against anaerobic bacteria. Here, we evaluate the activity of C/T against a phylogenetically diverse collection ofClostridium difficileisolates and report uniformly high MICs (≥256 μg/ml) to C/T.

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