T o the E ditor —Evans et al, for the Antibacterial Resistance Leadership Group (ARLG), provide valuable foundational data for determining antibacterial resistance phenotypes from resistance gene content [ 1 ]. Their approach, combined with knowledge of the prevalence of resistance in the community or population, could inform and enhance the ability of high-throughput sequencing pipelines to provide more clinically actionable data. However, their article begs a question and a comment.

The question: Given the decreasing cost, the increasing speed accessibility, and impact of whole-genome sequencing (WGS) [ 2–4 ], along with the growing number of reports of how WGS is poised to revolutionize infectious diseases and microbiology [ 5 , 6 ], why wasn't such an approach included in the study? Although a next-generation sequencing (NGS) platform was included, WGS was not utilized. Rather, their next-generation method was to use the Ion Torrent to sequence polymerase chain reaction amplification products designed against a defined set of β-lactamase genes. In the study, the ARLG infers, and then confirms, the phenotype with gold-standard susceptibility testing. The genotype to phenotype determination/conclusion is based solely on the presence or absence of preselected alleles of a predetermined set of genes. However, the phenotype could have been the result of the presence or absence of novel or unknown genes or alleles, the presence or absence of a different set of well-known genes, or deletions of a gene or gene set. Unlike WGS, none of 4 of the platforms distinguishes between those possibilities.

WGS is more comprehensive than any of the methods mentioned in the article, and would have allowed the ARLG to produce a more useful and comprehensive set of data. WGS can detect all antimicrobial resistance genes, not just the set of genes one is looking for. And the more accurate NGS platforms can reliably detect new alleles of known genes. If turnaround time is critical, laboratories can use rapid NGS protocols such as single-read sequencing or paired short-read sequencing in combination with read mapping to a comprehensive panel of antimicrobial resistance gene sequences. Using such an approach, Evans and coworkers may have been able to identify porin gene mutations in their Klebsiella isolates that were carbapenem resistant, yet lacked carbapenemase genes.

Using 2 × 150 bp sequencing on the Illumina MiSeq and a custom bioinformatics pipeline, our laboratory is able to provide whole genome–based reports to submitting hospitals that include bacterial genus and species, resistance gene content, and core genome single-nucleotide polymorphism–based phylogeny in about 48 hours (including bacterial culturing and DNA extraction) [ 7 ]. The cost is $30–$50 per genome.

The cost and turnaround time of each of the 4 platforms should have been included in the main body, and more quantitatively presented (not relatively indicated with 1–4 plus signs). That would have helped the reader better gauge the performance of those platforms, especially to other commercially available or more popular platforms.

Notes

Disclaimer.  The views expressed are solely those of the authors and are not to be construed as official or representing the US Army or the Department of Defense.

Potential conflict of interest.  Both authors: No reported conflicts. Both authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

References

1
Evans
SR
,
Hujer
AM
,
Jiang
H
et al
.
Rapid molecular diagnostics, antibiotic treatment decisions, and developing approaches to inform empiric therapy: PRIMERS I and II
.
Clin Infect Dis
 
2016
;
62
:
181
9
.
2
Tyson
GH
,
McDermott
PF
,
Li
C
et al
.
WGS accurately predicts antimicrobial resistance in Escherichia coli
.
J Antimicrob Chemother
 
2015
;
70
:
2763
9
.
3
Zhao
S
,
Tyson
GH
,
Chen
Y
et al
.
Whole-genome sequencing analysis accurately predicts antimicrobial resistance phenotypes in Campylobacter spp
.
Appl Environ Microbiol
 
2015
;
82
:
459
66
.
4
Holmes
A
,
Allison
L
,
Ward
M
et al
.
Utility of whole-genome sequencing of Escherichia coli O157 for outbreak detection and epidemiological surveillance
.
J Clin Microbiol
 
2015
;
53
:
3565
73
.
5
Pak
TR
,
Kasarskis
A
.
How next-generation sequencing and multiscale data analysis will transform infectious disease management
.
Clin Infect Dis
 
2015
;
61
:
1695
702
.
6
Ehrlich
GD
,
Post
JC
.
The time is now for gene-and genome-based bacterial diagnostics
.
JAMA Intern Med
 
2013
;
173
:
1405
6
.
7
McGann
P
,
Bunin
JL
,
Snesrud
E
et al
.
Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time
?
Diagn Microbiol Infect Dis
 
2016
; .

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