03014nas a2200457   4500000000100000008004100001653001100042653001900053653002200072653001200094653001500106100001400121700001300135700002200148700001300170700001400183700001200197700001400209700001700223700001500240700001200255700001200267700001800279700001100297700001600308700001300324700001400337700001300351700002300364700001200387700001500399700001200414700001100426700001200437245010200449856009800551300001300649490000700662520187300669022001402542       2017                            d10aBrazil10aDrug resistane10aGenome sequencing10aleprosy10aRecurrence1 aStefani M1 aAvanzi C1 aBührer-Sékula S1 aBenjak A1 aLoiseau C1 aSingh P1 aPontes MA1 aGonçalves H1 aHungria EM1 aBusso P1 aPiton J1 aSilveira MI S1 aCruz R1 aSchetinni A1 aCosta MB1 aVirmond M1 aDiorio S1 aDias-Baptista IM F1 aRosa PS1 aMatsuoka M1 aPenna M1 aCole S1 aPenna G00aWhole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases.  uhttp://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0005598&type=printable  ae00055980 v113 a<p><strong>BACKGROUND: </strong>Since leprosy is both treated and controlled by multidrug therapy (MDT) it is important to monitor recurrent cases for drug resistance and to distinguish between relapse and reinfection as a means of assessing therapeutic efficacy. All three objectives can be reached with single nucleotide resolution using next generation sequencing and bioinformatics analysis of Mycobacterium leprae DNA present in human skin.</p>

<p><strong>METHODOLOGY: </strong>DNA was isolated by means of optimized extraction and enrichment methods from samples from three recurrent cases in leprosy patients participating in an open-label, randomized, controlled clinical trial of uniform MDT in Brazil (U-MDT/CT-BR). Genome-wide sequencing of M. leprae was performed and the resultant sequence assemblies analyzed in silico.</p>

<p><strong>PRINCIPAL FINDINGS: </strong>In all three cases, no mutations responsible for resistance to rifampicin, dapsone and ofloxacin were found, thus eliminating drug resistance as a possible cause of disease recurrence. However, sequence differences were detected between the strains from the first and second disease episodes in all three patients. In one case, clear evidence was obtained for reinfection with an unrelated strain whereas in the other two cases, relapse appeared more probable.</p>

<p><strong>CONCLUSIONS/SIGNIFICANCE: </strong>This is the first report of using M. leprae whole genome sequencing to reveal that treated and cured leprosy patients who remain in endemic areas can be reinfected by another strain. Next generation sequencing can be applied reliably to M. leprae DNA extracted from biopsies to discriminate between cases of relapse and reinfection, thereby providing a powerful tool for evaluating different outcomes of therapeutic regimens and for following disease transmission.</p>
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