Whole genome sequencing is becoming a leading technology in typing and epidemiology of microbial pathogens, but the increase in genomics information necessitates significant investment in bioinformatic resources and expertise, and currently used methodologies struggle with genetically heterogeneous bacteria such as the human gastric pathogen Helicobacter pylori. Here we demonstrate that the alignment-free analysis method Feature Frequency Profiling (FFP) can be used to rapidly construct phylogenetic trees of draft bacterial genome sequences on a standard desktop computer, and that the coupling with in silico genotyping methods gives useful information for comparative and clinical genomics and molecular epidemiology applications. FFP-phylogenetic trees of seven gastric Helicobacter species matched those obtained by analysis of 16S rDNA and ribosomal proteins, and FFP- and core genome single nucleotide polymorphism-based analysis of 63 H. pylori genomes showed again comparable phylogenetic clustering, consistent with genomotypes assigned using multi-locus sequence typing (MLST). Analysis of 377 H. pylori genomes highlighted conservation of genomotypes and linkage with phylogeographic characteristics, and predicted the presence of an incomplete or non-functional cag pathogenicity island in 18/276 genomes. In silico analysis of antibiotic susceptibility markers suggests that most H. pylori hspAmerind and hspEAsia isolates are predicted to carry the T2812C mutation conferring low level clarithromycin-resistance, while levels of metronidazole resistance were similar in all MLST-types. In conclusion, the use of FFP phylogenetic clustering and in silico genotyping allows determination of genome evolution and phylogeographic clustering, and can contribute to clinical microbiology by genomotyping for outbreak management, and the prediction of pathogenic potential and antibiotic susceptibility.
This research output has an Altmetric Attention Score of 9. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 22 February 2026.
All research outputs
#5,760,550
of 34,185,767 outputs
Outputs from Journal of Clinical Microbiology
#5,408
of 19,281 outputs
Outputs of similar age
#54,581
of 303,629 outputs
Outputs of similar age from Journal of Clinical Microbiology
#23
of 133 outputs
Altmetric has tracked 34,185,767 research outputs across all sources so far. Compared to these this one has done well and is in the 83rd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 19,281 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 8.7. This one has gotten more attention than average, scoring higher than 71% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 303,629 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 82% of its contemporaries.
We're also able to compare this research output to 133 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 82% of its contemporaries.
