Identification of Burkholderia fungorum in the urine of an individual with spinal cord injury and augmentation cystoplasty using 16S sequencing: copathogen or innocent bystander?

Abstract

Introduction People with neuropathic bladder (NB) secondary to spinal cord injury (SCI) are at risk for multiple genitourinary complications, the most frequent of which is urinary tract infection (UTI). Despite the high frequency with which UTI occurs, our understanding of the role of urinary microbes in health and disease is limited. In this paper, we present the first prospective case study integrating symptom reporting, urinalysis, urine cultivation, and 16S ribosomal ribonucleic acid (rRNA) sequencing of the urine microbiome. Case presentation A 55-year-old male with NB secondary to SCI contributed 12 urine samples over an 8-month period during asymptomatic, symptomatic, and postantibiotic periods. All bacteria identified on culture were present on 16S rRNA sequencing, however, 16S rRNA sequencing revealed the presence of bacteria not isolated on culture. In particular, Burkholderia fungorum was present in three samples during both asymptomatic and symptomatic periods. White blood cells of ≥5-10/high power field and leukocyte esterase ≥2 on urinalysis was associated with the presence of symptoms. Discussion In this patient, there was a predominance of pathogenic bacteria and a lack of putative probiotic bacteria during both symptomatic and asymptomatic states. Urinalysis-defined inflammatory markers were present to a greater extent during symptomatic periods compared to the asymptomatic state, which may underscore a role for urinalysis or other inflammatory markers in differentiating asymptomatic bacteriuria from UTI in patients with NB. The finding of potentially pathogenic bacteria identified by sequencing but not cultivation, suggests a need for greater understanding of the relationships amongst bacterial species in the bacteriuric neuropathic bladder.

Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans

“…As a first hypothesis, these strains could have survived in a clinical environment solely as commensal bacteria, causing no harm to their host. The previous isolation of Burkholderia strains from CF patients or patients suffering from another infectious pathology, without being the apparent causative agent supports this hypothesis [79–81]. Although strain AU1054 was shown to cause high mortality rates in diverse plant and animal models [50, 82], this is not sufficient to assess its pathogenesis against humans.…”

Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.

“…The genus Paraburkholderia comprises over 70 species that appear mostly restricted to environmental samples. They are isolated from different types of soil and, occasionally, aquatic environments, plant nodules and rhizosphere samples [2][3][4][5][6][7]; yet some Paraburkholderia species, including Paraburkholderia fungorum, Paraburkholderia tropica and Paraburkholderia ginsengisoli, have been isolated from a range of infections in humans and animals [8][9][10][11][12][13].…”

Draft genome of Paraburkholderia fungorum sequence type 868 recovered from human synovial tissues

“…These are molecular signatures unique to the genus Paraburkholderia [1]. P. fungorum is the only member of this environment-associated bacterial genus capable of causing human infections [1], [2], [3], albeit rarely. A novel sequence type 868 (ST868) was obtained upon sequencing and analyses of the seven housekeeping genes according to the multi locus sequence typing scheme for Burkholderia cepacia complex (https://pubmlst.org/bcc).…”