Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.
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ABSTRACT:
SUBMITTER: Brooks B
PROVIDER: S-EPMC5703836 | biostudies-literature | 2017 Nov
REPOSITORIES: biostudies-literature
Publications
Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.
Brooks Brandon B Olm Matthew R MR Firek Brian A BA Baker Robyn R Thomas Brian C BC Morowitz Michael J MJ Banfield Jillian F JF
Nature communications 20171127 1
Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such ...[more]
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Project description:BackgroundFungal infections are a significant cause of mortality and morbidity in hospitalized preterm infants, yet little is known about eukaryotic colonization of infants and of the neonatal intensive care unit as a possible source of colonizing strains. This is partly because microbiome studies often utilize bacterial 16S rRNA marker gene sequencing, a technique that is blind to eukaryotic organisms. Knowledge gaps exist regarding the phylogeny and microdiversity of eukaryotes that colonize hospitalized infants, as well as potential reservoirs of eukaryotes in the hospital room built environment.ResultsGenome-resolved analysis of 1174 time-series fecal metagenomes from 161 premature infants revealed fungal colonization of 10 infants. Relative abundance levels reached as high as 97% and were significantly higher in the first weeks of life (p = 0.004). When fungal colonization occurred, multiple species were present more often than expected by random chance (p = 0.008). Twenty-four metagenomic samples were analyzed from hospital rooms of six different infants. Compared to floor and surface samples, hospital sinks hosted diverse and highly variable communities containing genomically novel species, including from Diptera (fly) and Rhabditida (worm) for which genomes were assembled. With the exception of Diptera and two other organisms, zygosity of the newly assembled diploid eukaryote genomes was low. Interestingly, Malassezia and Candida species were present in both room and infant gut samples.ConclusionsIncreased levels of fungal co-colonization may reflect synergistic interactions or differences in infant susceptibility to fungal colonization. Discovery of eukaryotic organisms that have not been sequenced previously highlights the benefit of genome-resolved analyses, and low zygosity of assembled genomes could reflect inbreeding or strong selection imposed by room conditions.
| S-EPMC6377789 | biostudies-literature
Project description:BACKGROUND:Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples. In this case study, we present a proof-of-concept using read cloud sequencing to describe bacterial strain diversity in the gut microbiome of one hematopoietic cell transplantation patient over a 2-month time course and highlight temporal strain variation of gut microbes during therapy. The treatment was accompanied by diet changes and administration of multiple immunosuppressants and antimicrobials. METHODS:We conducted short-read and read cloud metagenomic sequencing of DNA extracted from four longitudinal stool samples collected during the course of treatment of one hematopoietic cell transplantation (HCT) patient. After applying read cloud metagenomic assembly to discover strain-level sequence variants in these complex microbiome samples, we performed metatranscriptomic analysis to investigate differential expression of antibiotic resistance genes. Finally, we validated predictions from the genomic and metatranscriptomic findings through in vitro antibiotic susceptibility testing and whole genome sequencing of isolates derived from the patient stool samples. RESULTS:During the 56-day longitudinal time course that was studied, the patient's microbiome was profoundly disrupted and eventually dominated by Bacteroides caccae. Comparative analysis of B. caccae genomes obtained using read cloud sequencing together with metagenomic RNA sequencing allowed us to identify differences in substrain populations over time. Based on this, we predicted that particular mobile element integrations likely resulted in increased antibiotic resistance, which we further supported using in vitro antibiotic susceptibility testing. CONCLUSIONS:We find read cloud assembly to be useful in identifying key structural genomic strain variants within a metagenomic sample. These strains have fluctuating relative abundance over relatively short time periods in human microbiomes. We also find specific structural genomic variations that are associated with increased antibiotic resistance over the course of clinical treatment.
| S-EPMC7260799 | biostudies-literature
Project description:The gut microbiome of an individual can shape the local environmental surface microbiome. We sought to determine how the intensive care unit (ICU) patient gut microbiome shapes the ICU room surface microbiome, focusing on vancomycin-resistant Enterococcus (VRE), a common ICU pathogen. This was an ICU-based prospective cohort study. Rectal swabs were performed in adult ICU patients immediately at the time of ICU admission and environmental surface swabs were performed at five predetermined time points. All swabs underwent 16S rRNA gene sequencing and culture for VRE. 304 ICU patients and 24 ICU rooms were sampled (5 longitudinal samples per ICU room). Spatially adjacent ICU rooms were no more microbially similar than nonadjacent rooms. Microbial signatures within rooms diverged rapidly over time: in 14 days, ICU rooms were as similar to other ICU rooms as they were to their prior selves. This divergence over time was more pronounced in rooms with higher patient turnover. Examining VRE status by culture, patient VRE gut colonization had modest agreement with room surface VRE (kappa statistic 0.36). There were no ICU rooms that consistently cultured positive for VRE, including those that housed VRE positive patients. Individual ICU patients had a limited impact on ICU room surface microbiome, and rooms diverged similarly over time regardless of patients. Patient VRE gut colonization may have a modest influence on room surface VRE but there were no "bad rooms" that consistently cultured positive for VRE. These results may be useful in planning infection control measures. IMPORTANCE This study found that intensive care unit (ICU) room microbial signatures diverged from their baseline quickly: within 2 weeks, individual ICU rooms had lost distinguishing characteristics and were as similar to other ICU rooms as they were to their former selves. Patient turnover within rooms accelerated this drift. Patient gut colonization with vancomycin-resistant Enterococcus (VRE) was associated with ICU room surface contamination with VRE; again, within 2 weeks, this association was substantially diminished. These results provide dynamic information regarding how patients control the microbiota on local hospital room surfaces and may facilitate decision making for infection prevention and control measures targeting VRE or other organisms.
| S-EPMC8809377 | biostudies-literature
Project description:In cystic fibrosis, dynamic and complex communities of microbial pathogens and commensals can colonize the lung. Cultured isolates from lung sputum reveal high inter- and intraindividual variability in pathogen strains, sequence variants, and phenotypes; disease progression likely depends on the precise combination of infecting lineages. Routine clinical protocols, however, provide a limited overview of the colonizer populations. Therefore, a more comprehensive and precise identification and characterization of infecting lineages could assist in making corresponding decisions on treatment. Here, we describe longitudinal tracking for four cystic fibrosis patients who exhibited extreme clinical phenotypes and, thus, were selected from a pilot cohort of 11 patients with repeated sampling for more than a year. Following metagenomics sequencing of lung sputum, we find that the taxonomic identity of individual colonizer lineages can be easily established. Crucially, even superficially clonal pathogens can be subdivided into multiple sublineages at the sequence level. By tracking individual allelic differences over time, an assembly-free clustering approach allows us to reconstruct multiple lineage-specific genomes with clear structural differences. Our study showcases a culture-independent shotgun metagenomics approach for longitudinal tracking of sublineage pathogen dynamics, opening up the possibility of using such methods to assist in monitoring disease progression through providing high-resolution routine characterization of the cystic fibrosis lung microbiome.IMPORTANCE Cystic fibrosis patients frequently suffer from recurring respiratory infections caused by colonizing pathogenic and commensal bacteria. Although modern therapies can sometimes alleviate respiratory symptoms by ameliorating residual function of the protein responsible for the disorder, management of chronic respiratory infections remains an issue. Here, we propose a minimally invasive and culture-independent method to monitor microbial lung content in patients with cystic fibrosis at minimal additional effort on the patient's part. Through repeated sampling and metagenomics sequencing of our selected cystic fibrosis patients, we successfully classify infecting bacterial lineages and deconvolute multiple lineage variants of the same species within a given patient. This study explores the application of modern computational methods for deconvoluting lineages in the cystic fibrosis lung microbiome, an environment known to be inhabited by a heterogeneous pathogen population that complicates management of the disorder.
| S-EPMC8092271 | biostudies-literature
Project description:BackgroundVancomycin-resistant enterococci (VRE) are a major cause of morbidity and mortality in immunocompromised patients. Tracking the dissemination of VRE strains is crucial to understand the dynamics of emergence and spread of VRE in the hospital setting.MethodsWhole genome sequencing (WGS) and phylogenetic analyses were performed to identify dominant VRE strains and potential transmission networks between 35 patients with VRE-positive rectal swabs and their rooms (main rooms and bathrooms) on the leukemia (LKM) and the hematopoietic cell transplant (HCT) floors. Sequence types (STs), drug resistance genes, and patients' outcomes were also determined.ResultsA total of 89 VRE strains grouped into 10 different STs, of which newly described STs were isolated from both floors (ST736, ST494, ST772, and ST1516). We observed highly genetically related strains transmitted between rooms, floors, and time periods in an average period of 39 days (ranging from 3 to 90 days). Of 5 VRE bacteremia events, 3 strains were lacking the pili operon fms14-17-13 (ST203) and the remaining 2 were resistant to daptomycin (DAP; ST736, ST664). Of 10 patients harboring DAP-resistant strains, only 2 were exposed to DAP within 4 months before strain recovery.ConclusionsOur comparisons of VRE strains derived from the environment and immunocompromised patients confirmed horizontal transfer of highly related genetic lineages of multidrug-resistant (particularly to DAP) VRE strains between HCT and LKM patients and their room environment. Implementing WGS can be useful in distinguishing VRE reservoirs where interventions can be targeted to prevent and control the spread of highly resistant organisms.
| S-EPMC8677550 | biostudies-literature
Project description: Not available
| S-EPMC2078028 | biostudies-literature
Project description:Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome composition and the associated environmental characteristics have not been characterized in hotel environments. We presented here the first continental-scale microbiome study of hotel rooms (n?=?68) spanning Asia and Europe. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified in the same sequencing depth, but most fungal taxa showed a restricted distribution compared to bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for ?80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbiome and 16 indoor and outdoor environmental characteristics. Fungal composition and absolute quantity showed concordant associations with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea, and visible mold, while fungal richness was negatively associated with heavy traffic (95% confidence interval [CI] = -127.05 to -0.25) and wall-to-wall carpet (95% CI = -47.60 to -3.82). Bacterial compositional variation was associated with latitude, quality of the interior, and floor type, while bacterial richness was negatively associated with recent redecoration (95% CI -179.00 to -44.55) and mechanical ventilation (95% CI = -136.71 to -5.12).IMPORTANCE This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.
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Project description:BackgroundHospitalization in neonatal intensive care units with a single-family room design enables continuous maternal presence, but less is known regarding the association with milk production and breastfeeding.Research aimTo compare maternal milk production, breastfeeding self-efficacy, the extent to which infants received mother's milk, and rate of direct breastfeeding in a single-family room to an open bay neonatal intensive care unit.MethodsA longitudinal, prospective observational study comparing 77 infants born at 28- 32° weeks gestational age and their 66 mothers (n = 35 infants of n = 30 mothers in single family room and n = 42 infants of n = 36 mothers in open bay). Comparisons were made on milk volume produced, the extent to which infants were fed mother's milk, and rate of direct breastfeeding from birth to 4 months' corrected infant age. Breastfeeding self-efficacy was compared across mothers who directly breastfed at discharge (n = 45).ResultsFirst expression (6 hr vs. 30 hr, p < .001) and first attempt at breastfeeding (48 hr vs. 109 hr, p < .001) occurred significantly earlier, infants were fed a greater amount of mother's milk (p < .04), and significantly more infants having single-family room care were exclusively directly breastfed from discharge until 4 months' corrected age; OR 6.8 (95% CI [2.4, 19.1]). Volumes of milk produced and breastfeeding self-efficacy did not differ significantly between participants in either units.ConclusionTo increase the extent to which infants are fed mother's own milk and are exclusively directly breastfed, the design of neonatal intensive care units should facilitate continuous maternal presence and privacy for the mother-infant dyad.
| S-EPMC8414820 | biostudies-literature
Project description:The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling. We observed that several specific strains, including those of Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo gene expression of vertically transmitted microbes and found that transmitted strains of Bacteroides and Bifidobacterium species were transcriptionally active in the guts of both adult and infant. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we demonstrated that it is possible to track the vertical transmission of microbial strains from mother to infants and to characterize their transcriptional activity. Our work provides the foundation for larger-scale surveys to identify the routes of vertical microbial transmission and its influence on postinfancy microbiome development. IMPORTANCE Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.
| S-EPMC5264247 | biostudies-literature