viruses Review The Potential of Phage Therapy against the Emerging Opportunistic Pathogen Stenotrophomonas maltophilia Jaclyn G. McCutcheon and Jonathan J. Dennis * Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; [email protected] * Correspondence: [email protected] Abstract: The isolation and characterization of bacteriophages for the treatment of infections caused by the multidrug resistant pathogen Stenotrophomonas maltophilia is imperative as nosocomial and community-acquired infections are rapidly increasing in prevalence. This increase is largely due to the numerous virulence factors and antimicrobial resistance genes encoded by this bacterium. Research on S. maltophilia phages to date has focused on the isolation and in vitro characterization of novel phages, often including genomic characterization, from the environment or by induction from bacterial strains. This review summarizes the clinical significance, virulence factors, and antimicrobial resistance mechanisms of S. maltophilia, as well as all phages isolated and characterized to date and strategies for their use. We further address the limited in vivo phage therapy studies conducted against this bacterium and discuss the future research needed to spearhead phages as an alternative treatment option against multidrug resistant S. maltophilia. Keywords: Stenotrophomonas maltophilia; bacteriophage; phage therapy; antibiotic resistance Citation: McCutcheon, J.G.; Dennis, 1. Introduction J.J. The Potential of Phage Therapy against the Emerging Opportunistic The increasing prevalence of broad-spectrum antimicrobial resistance in bacterial Pathogen Stenotrophomonas maltophilia. infections worldwide is a global health concern. Use and misuse of antimicrobials have Viruses 2021, 13, 1057. https:// driven the evolution of resistant bacteria and the effectiveness of current antibiotics against doi.org/10.3390/v13061057 bacterial pathogens is rapidly declining, created the risk of a post-antibiotic era in the near future; reports estimate that antimicrobial resistant bacterial infections will cause 10 million Academic Editor: Mikael Skurnik deaths annually worldwide by the year 2050 with significant socio-economic impacts if alternative treatment options are not discovered [1,2]. Received: 12 May 2021 Stenotrophomonas maltophilia is one bacterium of concern that is emerging as a mul- Accepted: 31 May 2021 tidrug resistant opportunistic nosocomial pathogen. S. maltophilia infections are difficult to Published: 3 June 2021 treat with conventional antibiotics due to numerous chromosomally encoded antimicrobial resistance mechanisms [3]. The use of bacterial viruses, or bacteriophages, as an alternative Publisher’s Note: MDPI stays neutral treatment is an attractive option due to the specificity of these viruses to their host. In with regard to jurisdictional claims in this review, we will first briefly summarize the currently existing research on S maltophilia published maps and institutional affil- pathogenicity mechanisms and then examine the potential of phage therapy as an alter- iations. native treatment option to antibiotics in light of the extreme antibiotic resistance of this bacterial pathogen. 2. Stenotrophomonas maltophilia Copyright: © 2021 by the authors. S. maltophilia is a Gram-negative obligate aerobe that is motile due to the presence of po- Licensee MDPI, Basel, Switzerland. lar flagella, as well as type IV pili that aid in twitching motility and biofilm formation [3–5] This article is an open access article (Figure1). This bacteria is ubiquitous in the environment, often having beneficial in- distributed under the terms and teractions with plants, both on their surface and in the rhizosphere [6]. First isolated conditions of the Creative Commons as Bacterium bookeri in 1943 by J. L. Edwards, this species was originally named Pseu- Attribution (CC BY) license (https:// domonas maltophilia by Hugh and Ryschenko in 1961 [7], followed by controversial reclassi- creativecommons.org/licenses/by/ fication into the genus Xanthomonas in 1983 [8] before finally being given its own genus 4.0/). Viruses 2021, 13, 1057. https://doi.org/10.3390/v13061057 https://www.mdpi.com/journal/viruses Viruses 2021, 13, x FOR PEER REVIEW 2 of 29 Viruses 2021, 13, 1057 2 of 32 maltophilia by Hugh and Ryschenko in 1961 [7], followed by controversial reclassification into the genus Xanthomonas in 1983 [8] before finally being given its own genus in 1993 in[9] 1993. S. maltophilia [9]. S. maltophilia is now oneis now of 20 one species of 20 speciesin the genus in the Stenotrophomonas genus Stenotrophomonas currentlycurrently listed in listedthe NCBI in the taxonomy NCBI taxonomy browser. browser. Strains with Strains 16S with rRNA 16S gene rRNA sequence gene sequence similarities similarities greater greaterthan 99.0% than have 99.0% been have grouped been grouped into the into ‘S. the maltophilia ‘S. maltophilia complexcomplex’’ (Smc (Smc)) to encompass to encompass the thegenetic genetic heterogeneity heterogeneity and and diversity diversity of these of these bacteria bacteria [10] [10. ]. FigureFigure 1.1. TransmissionTransmission electronelectron micrographmicrograph of S. maltophilia cell attacked by phages phages.. S.S. maltophilia maltophilia strainstrain D1585D1585 with with numerous numerous DLP1 DLP1 bacteriophage bacteriophage [11 [11]] virions virions binding binding to to type type IV IV pili pili that that are are protrud- pro- ingtruding from from the cell. the cell. Cells Cells and and phages phage weres were stained stained with with 2% phosphotungstic2% phosphotungstic acid acid and and visualized visualized at at 18,000-fold magnification by transmission electron microscopy (McCutcheon, J. G. and Oatway, 18,000-fold magnification by transmission electron microscopy (McCutcheon, J. G. and Oatway, A.; A.; University of Alberta). University of Alberta). TheThe genusgenus namenameStenotrophomonas Stenotrophomonas,, translating translating as as “narrow “narrow one one who who feeds”feeds” was was meantmeant toto reflectreflect thethe perceivedperceived limitedlimited nutritionalnutritional spectrumspectrum ofof thesethese bacteria,bacteria, howeverhowever furtherfurther researchresearch hashas demonstrateddemonstrated thethe vastvast metabolicmetabolic diversitydiversity andand intraspecificintraspecific heterogeneityheterogeneity withinwithin thisthis genusgenus [[6,12]6,12].. WeWenow nowknow knowthat thatS. S. maltophiliamaltophiliabacteria bacteriaare are capablecapable ofof utilizingutilizing aa widewide rangerange ofof carboncarbon sources,sources, havehave anan intrinsicintrinsic resistanceresistance toto heavyheavy metals,metals,and andtolerate tolerate nutrient-poornutrient-poor environments,environments, allowingallowing themthem toto survivesurvive andand persistpersist inin manymany undesirableundesirable conditionsconditions [ [3,6,13]3,6,13].. InIn additionaddition toto thethe abilityability toto metabolizemetabolize aa varietyvariety ofof organic compounds,compounds, suchsuch as as phenolics phenolics and and xenobiotics, xenobiotics,Stenotrophomonas Stenotrophomonasspecies species are are not not phytopathogenic, phytopathogenic unlike, un- thelike closely the closely related related genera generaXanthomonas Xanthomonasand Xylella and Xylella, and can, and promote can promote plant productivityplant productiv- via theity expressionvia the expression of the plant of the growth plant hormone growth indole-3-acetichormone indole acid-3-acetic (IAA) acid [6]. These(IAA) properties [6]. These makepropertiesS. maltophilia make S. amaltophilia desirable candidatea desirable for candidate the bioremediation for the bioremediation of soil contaminated of soil contam- with heavyinated metals with heavy or pesticides metals andor pesticides for biotechnical and for applications biotechnical in applications agriculture to in promote agriculture plant to productivitypromote plant [6 productivity,13–15], however, [6,13– the15], ability however of ,S. the maltophilia ability of S.to maltophilia cause disease to cause in humans disease discouragesin humans discourages their use in agriculturetheir use in [agriculture6,13]. [6,13]. 2.1.2.1. ClinicalClinical PrevalencePrevalence andand SignificanceSignificance S.S. maltophiliamaltophiliais is thethe mostmost prominentprominent speciesspecies within within this this genus genus and and is is of of risingrising concern concern duedue toto its ability to to cause cause human human disease disease [3,6] [3,6. ].The The significant significant genetic genetic and and phenotypic phenotypic het- heterogeneityerogeneity within within S. S.maltophilia maltophilia populationspopulations allow allowss these these bacteria bacteria to adapt rapidlyrapidly underunder changingchanging selective selective pressures pressures in in both both a clinical a clinical and and environmental environmental setting setting [3,5,10 [3,5,10,,13,16].13,16] This. highThis genetichigh genetic diversity diversity can be can observed be observed even betweeneven between isolates isolates from from the same the same hospital hospital [17], with[17], higherwith higher mutation mutation frequencies frequencies observed observed in clinical in clinical isolates isolates compared compared to those to fromthose environmental sources [18]. Global surveillance programs began tracking the prevalence and clinical significance of S. maltophilia in the late 1990s; the frequency of S. maltophilia Viruses 2021, 13, 1057 3 of 32 occurrence