Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy

Abstract

In 2016, a 68-year-old patient with a disseminated multidrug-resistant Acinetobacter baumannii infection was successfully treated using lytic bacteriophages. Here we report the genomes of the nine phages used for treatment and three strains of A. baumannii isolated prior to and during treatment. The phages used in the initial treatment are related, T4-like myophages. Analysis of 19 A. baumannii isolates collected before and during phage treatment shows that resistance to the T4-like phages appeared two days following the start of treatment. We generate complete genomic sequences for three A. baumannii strains (TP1, TP2 and TP3) collected before and during treatment, supporting a clonal relationship. Furthermore, we use strain TP1 to select for increased resistance to five of the phages in vitro, and identify mutations that are also found in phage-insensitive isolates TP2 and TP3 (which evolved in vivo during phage treatment). These results support that in vitro investigations can produce results that are relevant to the in vivo environment.

Genome-wide phage susceptibility analysis inAcinetobacter baumanniireveals capsule modulation strategies that determine phage infectivity

“…Phage with broadened specificity for both Gtr6 + and Gtr6capsules may allow targeting of K3/K22 A. baumannii while blocking the rise of undesired mutants. In sum, these observations support the notion that prior research into resistance mechanisms can enhance the predictability of bacterial evolution during phage exposure and may allow improvements to the therapeutic uses of phage [18,23,62]. Controlling the abundance of capsule is also tightly connected to modulation of virulence, and we show here that this control has the additional effect of modulating phage susceptibility, with implications for developing phage-drug synergies [62][63][64] and for understanding variable capsule production in the pathogen.…”

“…Mutational capsule loss is an additional, well-described phage escape mechanism usually associated with lowered in vivo fitness and other trade-offs, making this form of resistance an appealing target of sequential or combination therapies exploiting the trade-offs [18,62]. Our data, and potentially those of [23], argue that capsule-loss mutations should not be considered a universally predictable path of phage resistance and that capsule-altered mutants with maintained or enhanced virulence should also be considered. This may be especially relevant when targeting particular capsules, such as K3/K22.…”

“…Our findings thus suggest that phage, in the environment or during therapy, may impose selective pressures that could facilitate the evolution of altered capsules with the undesired collateral effect of increased pathogenicity. Notably, a repeat region within another predicted side-chain glycosyltransferase, gtr76, was a site of mutations in phage-resistant K116 A. baumannii isolated from a patient receiving phage [23], although effects on capsule structure were not determined.…”

“…Our findings thus suggest that phage, in the environment or during therapy, may impose selective pressures that could facilitate the evolution of altered capsules with the undesired collateral effect of increased pathogenicity. Notably, a repeat region within another predicted side-chain glycosyltransferase, gtr76 , was a site of mutations in phage-resistant K116 A. baumannii isolated from a patient receiving phage [23], although effects on capsule structure were not determined. Mutational capsule loss is an additional, well-described phage escape mechanism usually associated with lowered in vivo fitness and other trade-offs, making this form of resistance an appealing target of sequential or combination therapies exploiting the trade-offs [18, 62].…”

“…In the case of A. baumannii phages, this drawback may be mitigated by tradeoffs associated with phage resistance, such as lowered in vivo fitness/virulence, enhanced collateral antibiotic sensitivity, or both [12,[17][18][19]. These costs likely emerge due to A. baumannii phages exploiting the bacterial capsule as a requisite receptor for initiating infection [20][21][22][23].…”