Genomic insights of Pannonibacter phragmitetus strain 31801 isolated from a patient with a liver abscess

Abstract

Pannonibacter phragmitetus is a bioremediation reagent for the detoxification of heavy metals and polycyclic aromatic compounds (PAHs) while it rarely infects healthy populations. However, infection by the opportunistic pathogen P. phragmitetus complicates diagnosis and treatments, and poses a serious threat to immunocompromised patients owing to its multidrug resistance. Unfortunately, genome features, antimicrobial resistance, and virulence potentials in P. phragmitetus have not been reported before. A predominant colony (31801) was isolated from a liver abscess patient, indicating that it accounted for the infection. To investigate its infection mechanism(s) in depth, we sequenced this bacterial genome and tested its antimicrobial resistance. Average nucleotide identity (ANI) analysis assigned the bacterium to the species P. phragmitetus (ANI, >95%). Comparative genomics analyses among Pannonibacter spp. representing the different living niches were used to describe the Pannonibacter pan‐genomes and to examine virulence factors, prophages, CRISPR arrays, and genomic islands. Pannonibacter phragmitetus 31801 consisted of one chromosome and one plasmid, while the plasmid was absent in other Pannonibacter isolates. Pannonibacter phragmitetus 31801 may have a great infection potential because a lot of genes encoding toxins, flagellum formation, iron uptake, and virulence factor secretion systems in its genome. Moreover, the genome has 24 genomic islands and 2 prophages. A combination of antimicrobial susceptibility tests and the detailed antibiotic resistance gene analysis provide useful information about the drug resistance mechanisms and therefore can be used to guide the treatment strategy for the bacterial infection.

Identification and denitrification characteristics of a salt-tolerant denitrifying bacterium Pannonibacter phragmitetus F1

“…A few similar strains of Pannonibacter phragmitetus were isolated and most of the related studies were conducted regarding their ability to reduce Cr(VI) in soil with high Cr(VI) concentrations, to detoxify polycyclic aromatic hydrocarbons under extreme conditions and their drug resistance to elucidate antibiotic resistance and infectivity mechanisms etc. (Zhou et al 2017; Chai et al 2019). To the best of our knowledge, only one study was conducted to evaluate the denitrification capacity of similar strains of Pannonibacter phragmitetus .…”

Comparison of petroleum biodegradation efficiencies of three different bacterial consortia determined in petroleum-contaminated waste mud pit

“…Klebsiella pneumoniae and P. phragmitetus isolated from petroleum-contaminated waste mud pit were known to be effective in the bioremediation process. Previous studies indicated that K. pneumoniae plays an active role in the biodegradation of petroleum [24] and P. phragmitetus is effective in the detoxification of heavy metals and PAHs [30].…”

“…However, You et al [28] clearly showed that K. pneumoniae only biodegraded hydrocarbons in the range of C 10 -C 14 in diesel. Zhou et al [30] reported that Pannonibacter phragmitetus was resistant to extreme environmental conditions such as hot springs, high alkaline conditions and high salt concentration and plays a role in the detoxification of PAHs and heavy metal chrome reduction in these environmental conditions. Acinetobacter sp.…”

The Composition and Assembly of Soil Microbial Communities Differ across Vegetation Cover Types of Urban Green Spaces

“…For instance, Pannonibacter was one of the most abundant animal putative pathogens among the grasslands, shrublands, and woodlands (Figure 5a), which could be used as a bioremediation agent for the detoxification of heavy metals and polycyclic aromatic compounds (PAHs), while rarely infect healthy populations. However, the infection caused by the opportunistic pathogen Pannonibacter can complicate diagnosis and treatment and pose a serious threat to immunocompromised patients due to its multidrug resistance [64]. In addition to animal pathogens, there were a variety of plant pathogens in the urban green spaces (Figure 5a).…”