Genomic Identification of Two Phytobacter diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore

Abstract

We report the draft genome sequences of two Phytobacter diazotrophicus isolates recovered from a swab specimen from the water faucet located in the Neonatal Intensive Care Unit (ICU), National University Hospital, Singapore. The isolates were misidentified as Cronobacter sakazakii and Klebsiella oxytoca using biochemical methods. Whole-genome sequencing (WGS) was performed to determine their identity.

Gram-negative sepsis caused by a rare pathogenPhytobacter ursingii

“…Since this clarification, there has been a growing body of primary evidence that species within this genus, mainly P. diazotrophicus, have played a role in multidrug-resistant nosocomial infections. [2][3][4] Despite this emerging understanding of P. diazotrophicus, there are currently no case reports describing P. ursingii infection. This paucity of data may be representative of the difficulties of correct organism identification, more so than a lack of P. ursingii infections.…”

“…4 Misidentification of Phytobacter spp is a known issue, with retrospective genotypical analysis of strains in GenBank having shown Phytobacter misclassified as Metakosakonia, Kluyvera, Enterobacter, Pantoea, Citrobacter and Enterobacteriaceae spp. 3 Commonly employed phenotypical identification methods in clinical laboratories often misrepresent Phytobacter isolates as Pantoea spp, with as many as 100 reported Pantoae cases currently in question of being misidentified Phytobacter. 4 With retrospective correction of a handful of these errant identifications, at present, P. ursingii has been confirmed to be isolated from sputum, gut, pancreatic cyst, hospital wastewater, soil, rectum and intravenous fluid samples, with unpublished results additionally having isolates from urine and blood.…”

“…1 Since the discovery of the Phytobacter genus in 2008, there has been a growing body of evidence that species within this genus, mainly P. diazothrophicus, play a role in opportunistic nosocomial infections. [2][3][4] Currently, there are no published case reports describing P. ursingii infection. However, retrospective genomic analysis has confirmed P. ursingii's presence in a prior sepsis outbreak of contaminated intravenous fluids in 1972 and showed its potential misidentification as Pantoea agglomerans in prior outbreaks.…”