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Table 3 Evidence for bacteria in qPCR-positive ureteral stent encrustation samples by cultivation, NGS and SEM

From: Encrustations on ureteral stents from patients without urinary tract infection reveal distinct urotypes and a low bacterial load

UT

Sample

Dominant OTUs

Cultivation of encrustations

Urine culture (pre-surgery)

SEM

H’

2a

ST13

Escherichia

n.d.

E. coli

n.d.

0.56

2b

ST15*

Corynebacterium

Corynebacterium

coagulase negative Staphylococci, alpha haemolytic Streptococci, Lactobacilli

n.d.

2.14

ST51

Corynebacterium

n.d.

n.d.

Coccoid

2.38

2c

ST85

Staphylococcus

S. epidermidis

coagulase negative Staphylococci , Enterococci

Coccoid

0.61

ST45

Staphylococcus

n.d.

n.d.

Coccoid

1.1

2d

ST64*

Streptococcus, Klebsiella,

Staphylococcus

n.d.

n.d.

Coccoid

2.81

ST14

Streptococcus, Facklamia,

A. tetradius, Escherichia

E.coli

E. coli

n.d.

1.03

2e

ST30

Corynebacteria, Lactobacillus

n.d.

Corynebacteriaceae, non-haemolytic Streptococci

Coryne -shaped

0.71

3

ST08

Ureaplasma parvum, A. tetradius, G. vaginalis, minor amounts of Escherichia, S. anginosus

E.coli

S. anginosus

E.coli

S. anginosus

Coccoid

1.83

ST05

A. tetradius, S. anginosus

Prevotella, Escherichia

n.d.

E. coli

Coccoid

1.39

4

ST22

Actinobaculum, G. vaginalis

Lactobacillus iners

G. vaginalis

Rods

0.56

ST52

G. vaginalis

G. vaginalis

n.d.

Coccoid

0.40

ST65

G. vaginalis

n.d.

S. epidermidis

Coccoid

1.13

5

ST56

Veillonella

n.d.

K. pneumoniae

Coccoid

2.59

6

ST55

L. jensenii

L. jensenii

L. jensenii

Rods

0.03

ST80

L. crispatus

n.d.

Streptococcus gallolyticus

n.d.

0.32

ST73

L. iners

n.d.

Corynbacterium amycolatum, S. epidermidis

Coccoid

0.96

ST39

L. iners

n.d.

Aerococcus urinae, Aerococcus sanguinicola, S. epidermidis, S. aureus

n.d.

1.50

ST68

L jensenii

n.d.

Corynebacteriaceae, coagulase negative Staphylococci, alpha haemolytic Streptococci, Lactobacilli

n.d.

0.19

  1. Boldface data denote concordant results of NGS and cultivation of the encrustations, urine culture or SEM.
  2. *samples very close to the LOD of the qPCR assay
  3. n.d. not detected, H’ Shannon index