ABSTRACT
Primary apical periodontitis occurs due to various insults to the dental pulp including microbial infections, physical and iatrogenic trauma, whereas inadequate elimination of intraradicular infection during root canal treatment may lead to secondary apical periodontitis. We explored the complex intra-radicular microbial communities and their functional potential through genome reconstruction. We applied shotgun metagenomic sequencing, binning and functional profiling to identify the significant contributors to infection at the acute and chronic apical periodontal lesions. Our analysis revealed the five classified clusters representing Enterobacter, Enterococcus, Lacticaseibacillus, Pseudomonas, Streptococcus and one unclassified cluster of contigs at the genus level. Of them, the major contributors were Pseudomonas, with 90.61% abundance in acute conditions, whereas Enterobacter followed by Enterococcus with 69.88% and 15.42% abundance, respectively, in chronic conditions. Enterobacter actively participated in antibiotic target alteration following multidrug efflux-mediated resistance mechanisms, predominant in the chronic stage. The prediction of pathways involved in the destruction of the supportive tissues of the tooth in Enterobacter and Pseudomonas support their crucial role in the manifestation of respective disease conditions. This study provides information about the differential composition of the microbiome in chronic and acute apical periodontitis. It takes a step to interpret the role of a single pathogen, solely or predominantly, in establishing endodontic infection types through genome reconstruction following high throughput metagenomic DNA analysis. The resistome prediction sheds a new light on the therapeutic treatment guidelines for endodontists. However, it needs further conclusive research to support this outcome using a larger number of samples with similar etiological conditions, but different demographic origin.
ABSTRACT
The emergence of colistin-carbapenem-resistant Klebsiella pneumoniae (CCR-Kp) in bloodstream infection results in high mortality, and virulence factor contributes further to the difficulty of treatment. A total of 158 carbapenem-resistant K. pneumoniae (CRKP) isolates causing bloodstream infection were collected from three Indian tertiary care hospitals during the 9-month study period, of which 27 isolates exhibited resistance to both colistin and carbapenem antibiotics. In this study, all the strains were characterized for antimicrobial resistance, virulence factors and capsular serotypes that facilitate the development of colistin and carbapenem-resistant K.pneumoniae (CCR-Kp) in bloodstream infection. Fourteen isolates displayed extremely drug resistance (XDR), susceptible only to tigecycline, and the remaining 13 isolates displayed multidrug resistance (MDR). The gene prevalence analysis for CCR-Kp isolates showed the predominance of bla KPC (81.48%) followed by bla NDM (62.96%), bla VIM (37.03%) and bla IMP (18.51%) genes. The distribution of virulence genes was found to be fimH (81.48%), wabG (59.25%), mrkD (55.56%), entB (48.15%), irp1 (33.33%), and rmpA (18.52%). The capsular serotypes K1, K2, K5 and K54 have been identified in 16 isolates. The absence of plasmid-mediated colistin resistance (mcr) genes implies the involvement of other mechanisms. The ERIC and (GTG)5 molecular typing methods detected 18 and 22 distinct clustering patterns among the CCR-Kp isolates, respectively. A strong correlation between ERIC and (GTG)5 genotyping method was established with antimicrobial resistance patterns and virulence determinants at P < 0.05, while no correlation was found with capsular serotyping. Similar virulence and resistance typing among the isolates suggest hospital-acquired infection in a health care setup. These outcomes will advance our awareness of CCR-Kp outbreaks associated with tertiary care hospitals and help forecast their occurrence in the near future. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-03056-4.
