Characterizing Plasmids in Bacteria Species Relevant to Urinary Health

Hernandez, Cesar Montelongo; Putonti, Catherine; Wolfe, Alan J.

doi:10.1128/spectrum.00942-21

Cited by 5 publications

(9 citation statements)

References 88 publications

(152 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…No plasmids were identified in L. gasseri 5006-2 using PlasmidFinder 2.1 ( 25 ), possibly due to the poor knowledge of lactobacilli plasmids in general and in urinary isolates in particular ( 26 , 27 ). An examination of assembly graphs using BANDAGE v0.8.1 ( 28 ) and the BLAST search results showed the presence of at least one plasmid approximately 40 kB long with a copy number of ~2.2 to 2.4.…”

Section: Announcementmentioning

confidence: 99%

Draft Genome Sequence of a Lactobacillus gasseri Strain Isolated from the Catheterized Urine of a Healthy Postmenopausal Woman

Johnson

Modliszewski

Siddiqui

et al. 2022

Microbiol Resour Announc

View full text Add to dashboard Cite

show abstract

Section: Announcementmentioning

confidence: 99%

Draft Genome Sequence of a Lactobacillus gasseri Strain Isolated from the Catheterized Urine of a Healthy Postmenopausal Woman

Johnson

Modliszewski

Siddiqui

et al. 2022

Microbiol Resour Announc

View full text Add to dashboard Cite

show abstract

“…coli , Enterococcus faecalis , K. pneumoniae , Staphylococcus epidermidis and Streptococcus anginosus [5].…”

Section: Introductionmentioning

confidence: 99%

“…Recently, we investigated the plasmid population of bacteria within the urinary tract, focusing on representatives of 11 clinically relevant urinary species [ 5 ]. Prior research has found that plasmids can promote pathogenicity in the urinary tract, e.g.…”

Section: Introductionmentioning

confidence: 99%

“… Escherichia coli urinary tract infections (UTIs) [ 6–8 ], Klebsiella pneumoniae UTIs [ 7 ] and Acinetobacter baumannii catheter-associated urinary tract infections [ 9 ]. Our prior bioinformatic analysis of 11 species led to the identification of plasmid sequences in strains of E. coli , Enterococcus faecalis , K. pneumoniae , Staphylococcus epidermidis and Streptococcus anginosus [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

“…Herein, we present an expanded analysis of the plasmidome of the urinary microbiota (urobiome), considering 102 different species that are representative of the phylogenetic diversity of the urobiome. In contrast to our prior work [ 5 ], we employed two different tools for plasmid detection: plasmidSPAdes [ 14 ] and Recycler [ 15 ]. While both tools utilize de Bruijn graphs for predicting plasmid sequences, plasmidSPAdes is tuned to identify contigs with sequencing coverages deviating from the average (e.g.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Plasmids of the urinary microbiota

Johnson

Bataclan

et al. 2022

Access Microbiology

Self Cite

View full text Add to dashboard Cite

Studies of the last decade have identified a phylogenetically diverse community of bacteria within the urinary tract of individuals with and without urinary symptoms. Mobile genetic elements (MGEs), including plasmids and phages, within this niche have only recently begun to be explored. These MGEs can expand metabolic capacity and increase virulence, as well as confer antibiotic resistance. As such, they have the potential to contribute to urinary symptoms. While plasmids for some of the bacterial taxa found within the urinary microbiota (urobiome) have been well characterized, many urinary species are under-studied with few genomes sequenced to date. Using a two-pronged bioinformatic approach, we have conducted a comprehensive investigation of the plasmid content of urinary isolates representative of 102 species. The bioinformatic tools plasmidSPAdes and Recycler were used in tandem to identify plasmid sequences from raw short-read sequence data followed by manual curation. In total, we identified 603 high-confidence plasmid sequences in 20 different genera of the urobiome. In total, 70 % of these high-confidence plasmids exhibit sequence similarity to plasmid sequences from the gut. This observation is primarily driven by plasmids from E. coli , which is found in both anatomical niches. To confirm our bioinformatic predictions, long-read sequencing was performed for 23 of the E. coli isolates in addition to two E. coli strains that were sequenced as part of a prior study. Overall, 66.95 % of these predictions were confirmed highlighting the strengths and weaknesses of current bioinformatic tools. Future studies of the urobiome, especially concerning under-studied species in the urobiome, should employ long-read sequencing to expand the catalogue of plasmids for this niche.

show abstract

Genomic analyses of an Escherichia coli and Klebsiella pneumoniae urinary tract co‐infection using long‐read nanopore sequencing

Fordham,

Barrow,

Mantzouratou

et al. 2024

MicrobiologyOpen

View full text Add to dashboard Cite

Escherichia coli and Klebsiella pneumoniae isolates presenting with the same antimicrobial susceptibility profile were recovered from the same catheter sample of urine (CSU). Both strains were recovered from a patient with a long‐standing indwelling urinary catheter. Each isolate had its DNA extracted following culture. Nanopore long‐read sequencing was used to build the plasmids and chromosomes from each strain to closure to discern the potential horizontal propagation of resistance‐encoding plasmids and the relationship between resistance genes and insertion sequences. Plasmids derived from resistance strains in the urinary microbiota remain poorly characterized. The same 11 antimicrobial resistance (AMR) genes were found in plasmids from each strain. The 185,239‐bp FIB(K) pKBM1, from the K. pneumoniae strain, additionally encoded the five AMR genes: sul2, strA, strB, blaTEM‐1B, and blaCTX‐M‐15. A multimeric array of AMR genes and IS26 insertion sequences were found in the plasmids from both isolates. Both plasmids from each isolate were similar. Horizontal transfer of plasmids, followed by subsequent plasmid rearrangement, is likely to have occurred during infection. Furthermore, the resistance region in the plasmids shared similarity against the internationally prevalent plasmid, pKPN3‐307_typeA, commonly identified in K. pneumoniae ST307. Biofilm formation in catheterized patients may allow close cell contact between strains. Horizontal propagation of resistance genes may occur, leading to polymicrobial infections.

show abstract

Characterizing Plasmids in Bacteria Species Relevant to Urinary Health

Abstract: The microbial community of the urinary tract (urobiota) has been associated with human health. Whole genome sequencing of bacteria permits examination of urobiota genomes, including plasmids.

Cited by 5 publications

References 88 publications

Draft Genome Sequence of a Lactobacillus gasseri Strain Isolated from the Catheterized Urine of a Healthy Postmenopausal Woman

Draft Genome Sequence of a Lactobacillus gasseri Strain Isolated from the Catheterized Urine of a Healthy Postmenopausal Woman

Plasmids of the urinary microbiota

Genomic analyses of an Escherichia coli and Klebsiella pneumoniae urinary tract co‐infection using long‐read nanopore sequencing

Contact Info

Product

Resources

About