Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement

Multidrug-resistant organism (MDRO) colonization is a fundamental challenge in antimicrobial resistance. Limited studies have shown that fecal microbiota transplantation (FMT) can reduce MDRO colonization, but its mechanisms are poorly understood. We conducted a randomized, controlled trial of FMT for MDRO decolonization in renal transplant recipients called PREMIX (NCT02922816). Eleven participants were enrolled and randomized 1:1 to FMT or an observation period followed by delayed FMT if stool cultures were MDRO positive at day 36. Participants who were MDRO positive after one FMT were treated with a second FMT. At last visit, eight of nine patients who completed all treatments were MDRO culture negative. FMT-treated participants had longer time to recurrent MDRO infection versus PREMIX-eligible controls who were not treated with FMT. Key taxa (Akkermansia muciniphila, Alistipes putredinis, Phocaeicola dorei, Phascolarctobacterium faecium, Alistipes species, Mesosutterella massiliensis, Barnesiella intestinihominis, and Faecalibacterium prausnitzii) from the single feces donor used in the study that engrafted in recipients and metabolites such as short-chain fatty acids and bile acids in FMT-responding participants uncovered leads for rational microbiome therapeutic and diagnostic development. Metagenomic analyses revealed a previously unobserved mechanism of MDRO eradication by conspecific strain competition in an FMT-treated subset. Susceptible Enterobacterales strains that replaced baseline extended-spectrum β-lactamase-producing strains were not detectable in donor microbiota manufactured as FMT doses but in one case were detectable in the recipient before FMT. These data suggest that FMT may provide a path to exploit strain competition to reduce MDRO colonization.

Parallel deployment of passive and composite samplers for surveillance and variant profiling of SARS-CoV-2 in sewage

Wastewater-based epidemiology during the COVID-19 pandemic has proven useful for public health decision-making but is often hampered by sampling methodology constraints, particularly at the building- or neighborhood-level. Time-weighted composite samples are commonly used; however, autosamplers are expensive and can be affected by intermittent flows in sub-sewershed contexts. In this study, we compared time-weighted composite, grab, and passive sampling via Moore swabs, at four locations across a college campus to understand the utility of passive sampling. After optimizing the methods for sample handling and processing for viral RNA extraction, we quantified SARS-CoV-2 N1 and N2, as well as a fecal strength indicator, PMMoV, by ddRT-PCR and applied tiled amplicon sequencing of the SARS-CoV-2 genome. Passive samples compared favorably with composite samples in our study area: for samples collected concurrently, 42 % of the samples agreed between Moore swab and composite samples and 58 % of the samples were positive for SARS-CoV-2 using Moore swabs while composite samples were below the limit of detection. Variant profiles from Moore swabs showed a shift from variant BA.1 to BA.2, consistent with in-person saliva samples. These data have implications for the broader implementation of sewage surveillance without advanced sampling technologies and for the utilization of passive sampling approaches for other emerging pathogens.

Quinone Moieties Link the Microbial Respiration of Natural Organic Matter to the Chemical Reduction of Diverse Nitroaromatic Compounds

Insensitive munitions compounds (IMCs) are emerging nitroaromatic contaminants developed by the military as safer-to-handle alternatives to conventional explosives. Biotransformation of nitroaromatics via microbial respiration has only been reported for a limited number of substrates. Important soil microorganisms can respire natural organic matter (NOM) by reducing its quinone moieties to hydroquinones. Thus, we investigated the NOM respiration combined with the abiotic reduction of nitroaromatics by the hydroquinones formed. First, we established nitroaromatic concentration ranges that were nontoxic to the quinone respiration. Then, an enrichment culture dominated by Geobacter anodireducens could indirectly reduce a broad array of nitroaromatics by first respiring NOM components or the NOM surrogate anthraquinone-2,6-disulfonate (AQDS). Without quinones, no nitroaromatic tested was reduced except for the IMC 3-nitro-1,2,4-triazol-5-one (NTO). Thus, the quinone respiration expanded the spectrum of nitroaromatics susceptible to transformation. The system functioned with very low quinone concentrations because NOM was recycled by the nitroaromatic reduction. A metatranscriptomic analysis demonstrated that the microorganisms obtained energy from quinone or NTO reduction since respiratory genes were upregulated when AQDS or NTO was the electron acceptor. The results indicated microbial NOM respiration sustained by the nitroaromatic-dependent cycling of quinones. This process can be applied as a nitroaromatic remediation strategy, provided that a quinone pool is available for microorganisms.

Abstract 720: Comparison of the gut microbiome between children with solid tumor receiving chemotherapy and healthy children

Background: Chemotherapy is commonly used for children with cancer. Intensive chemotherapy can disturb the gut microbiome, which may be associated with treatment-related toxicities. This study aimed to compare profiles of the gut microbiome in children with solid tumors pre- and post-chemotherapy with those of healthy children.

Methods: A case-control study was conducted in 44 children (21 with solid tumors and 23 healthy). Children aged 7-18 years with solid tumors receiving chemotherapy were recruited from Children’s Healthcare of Atlanta (CHOA); healthy children were recruited by e-news in CHOA. The gut microbiome was measured using stool specimens that were collected pre cycle 2 chemotherapy and post the completion of all chemotherapy for cancers, and only once for healthy controls. Demographics and clinical variables (e.g., race and use of antibiotics) were reported by parents. Bacterial 16S rRNA gene V4 region was amplified and sequenced. Bacterial taxonomies were assigned using the Silva reference via QIIME 2. Permutational multivariate analysis of variance, analysis of composition of microbiomes, and linear discriminant analysis effect size were used to compare the gut microbiome between cancer and healthy children.

Results: Children with solid tumors and healthy controls showed no differences in age, race, and BMI; more boys were enrolled in the solid tumor group than the healthy group (p=0.009). Both groups were dominated by phyla Firmicutes and Bacteroidetes. Compared to healthy children, children with solid tumors had significantly lower α-diversity metrics: Shannon p=0.042 and Chao1 p=0.015; children pre- (Shannon p=0.021; Chao1 p=0.024) and post-chemotherapy (Shannon p=0.011; Chao1 p=0.025) showed lower α-diversity metrics than healthy children; and difference was not significant between children pre- and post-chemotherapy. The β-diversity analysis (Bray-Curtis distance) showed that study group (p=0.008), gender (p=0.017), race (p=0.009), and cancer type (p=0.001) impacted the gut microbiome dissimilarities. Children with solid tumors had a lower abundance of phylum Verrucomicrobiotaand a higher abundance of genus Acidaminoccous than healthy controls; healthy children had a higher abundance of beneficial genera Prevotella and Akkermansia. Children with solid tumors had enriched in pathogenic oropportunistically pathogenic genera Clostridioides and Enterococcus. Children post all chemotherapy had enriched genera Blautia and CAG-352 associated with gut-brain axis.

Conclusions: Children with solid tumors suggested different diversity profiles of the gut microbiome and a higher abundance of pathogenic taxa than healthy children. These different gut microbial profiles may be associated with treatment toxicities. Additional studies are needed to further corroborate these associations in children with cancer and reveal the underlying mechanisms.

Citation Format: Jinbing Bai, Kumru Kocaman, Julia Slack, Melissa Martin, Christie Powell, Kathryn S. Sutton, Bradley George, Thomas Olson, Konstantinos T. Konstantinidis, Deborah W. Bruner. Comparison of the gut microbiome between children with solid tumor receiving chemotherapy and healthy children [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 720.