Draft Genome Sequence of Actinomyces neuii UMB1295, Isolated from the Female Urinary Tract

Markovic, Tijana; Miller-Ensminger, Taylor; Voukadinova, Adelina; Wolfe, Alan J.; Putonti, Catherine

doi:10.1128/mra.00402-20

Cited by 5 publications

(4 citation statements)

References 13 publications

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“…We selected seven bacterial strains ( Table 1 ) isolated from a single urine sample and thus members of a single community, for our in silico tests. Five of these strains were sequenced as part of our prior work [ 42 , 43 , 44 , 45 , 46 ], and two strains were sequenced as part of this study. Prophage sequences were predicted for the seven genomes using PHASTER.…”

Section: Resultsmentioning

confidence: 99%

“…Bacteria from freezer stocks were streaked onto CNA Blood agar plates and incubated at 35 °C and 5% CO 2 for 18–36 h. A single colony from each plate was grown in 1 mL of the bacterium’s respective medium ( Table 1 ) for 18–36 h at 35 °C and 5% CO 2 . DNA extraction and sequencing of some of these strains has been previously described: E. coli UMB1284 [ 42 ], A. neuii UMB1295 [ 43 ], L. jensenii UMB1303 [ 44 ], E. faecalis UMB1309 [ 45 ], and P. mirabilis UMB1310 [ 46 ]. For E. coli UMB1284, DNA was extracted using the Qiagen DNeasy UltraClean Microbial Kit following the manufacturer’s protocol, and libraries were constructed using the Nextera XT DNA Library preparation kit and sequenced on the Illumina MiSeq platform (MiSeq Reagent Kit v2 (500-cycles)) at Loyola University Chicago’s Genomics Facility (Maywood, IL, USA) [ 42 ].…”

Section: Methodsmentioning

confidence: 99%

“…For the remaining strains, including the two strains sequenced as part of this study ( S. hominus UMB1296-1T and C. amycolatum UMB1310-1E), bacterial cultures were extracted using a modified version of the Qiagen Blood and Tissue Kit Protocol. (For details regarding modifications, see [ 43 , 45 , 46 ].) DNA concentrations were quantified using a Qubit fluorometer following the manufacturer’s protocol.…”

Section: Methodsmentioning

confidence: 99%

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When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages

Miller-Ensminger

Johnson

Banerjee

et al. 2023

Viruses

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High-throughput sequencing of microbial communities has uncovered a large, diverse population of phages. Frequently, phages found are integrated into their bacterial host genome. Distinguishing between phages in their integrated (lysogenic) and unintegrated (lytic) stage can provide insight into how phages shape bacterial communities. Here we present the Prophage Induction Estimator (PIE) to identify induced phages in genomic and metagenomic sequences. PIE takes raw sequencing reads and phage sequence predictions, performs read quality control, read assembly, and calculation of phage and non-phage sequence abundance and completeness. The distribution of abundances for non-phage sequences is used to predict induced phages with statistical confidence. In silico tests were conducted to benchmark this tool finding that PIE can detect induction events as well as phages with a relatively small burst size (10×). We then examined isolate genome sequencing data as well as a mock community and urinary metagenome data sets and found instances of induced phages in all three data sets. The flexibility of this software enables users to easily include phage predictions from their preferred tool of choice or phage sequences of interest. Thus, genomic and metagenomic sequencing now not only provides a means for discovering and identifying phage sequences but also the detection of induced prophages.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages

Miller-Ensminger

Johnson

Banerjee

et al. 2023

Viruses

Self Cite

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“…A. neuii is the only species of Actinomyces spp. so far associated with urinary pathology, especially in patients with urolithiasis or urinary catheterization [3,8,9].…”

Section: Introductionmentioning

confidence: 99%

Let's Talk About a New Urogenital Pathogen: Actinomyces Neuii

2023

IJPMC

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In traditional bacterial cultures of clinical samples, the presence of coryneform has often been considered as local flora, but it is well known that in patients with predisposing factors, these micro-organisms may have a pathogenic implication that would be underestimated. Among other causes, this is due to the difficulty in making an adequate identification to species level. The advent of mass spectrometry in clinical laboratories has greatly facilitated this task. We describe a clinical case of Actinomyces naoi urinary tract infection in an elderly multipath logical patient with urinary catheterization. For this purpose, a descriptive clinical-microbiological study of A. naoi as a pathogen was performed. It was identified by Maldi-TOF mass spectrometry. The clinical course was satisfactory after antibiotic treatment with amoxicillin/clavulanic acid. In urine cultures, if there is a significant monomicrobial count of choryneform micro-organisms, we should rule out microorganisms potentially involved in infection before reporting the result as local microbiota.

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A case of Winkia neuii (Actinomyces neuii) vertebral osteomyelitis and review of the literature

Richwagen,

Morris,

Paulis

et al. 2024

The American Journal of the Medical Sciences

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Draft Genome Sequence of Actinomyces neuii UMB1295, Isolated from the Female Urinary Tract

Cited by 5 publications

References 13 publications

When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages

When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages

Let's Talk About a New Urogenital Pathogen: Actinomyces Neuii

A case of Winkia neuii (Actinomyces neuii) vertebral osteomyelitis and review of the literature

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