Abstract
Microbial source tracking (MST) describes a suite of methods and an investigative strategy for determination of fecal pollution sources in environmental waters that rely on the association ...of certain fecal microorganisms with a particular host. MST is used to assess recreational water quality and associated human health risk, and total maximum daily load allocations. Many methods rely on signature molecules (markers) such as DNA sequences of host-associated microorganisms. Human sewage pollution is among the greatest concerns for human health due to (1) the known risk of exposure to human waste and (2) the public and regulatory will to reduce sewage pollution; however, methods to identify animal sources are receiving increasing attention as our understanding of zoonotic disease potential improves. Here, we review the performance of MST methods in initial reports and field studies, with particular emphasis on quantitative PCR (qPCR). Relationships among human-associated MST markers, fecal indicator bacteria, pathogens, and human health outcomes are presented along with recommendations for future research. An integrated understanding of the advantages and drawbacks of the many MST methods targeting human sources advanced over the past several decades will benefit managers, regulators, researchers, and other users of this rapidly growing area of environmental microbiology.
This review of microbial source tracking (MST) methods for determining the dominant sources of fecal pollution in environmental waters focuses on qPCR-based assays, method performance, and the relationship of MST markers to fecal indicator bacteria, pathogens, and human health outcomes.
Fecal microbiota transplantation (FMT) from healthy donor to patient is a treatment for microbiome-associated diseases. Although the success of FMT requires donor bacteria to engraft in the patient's ...gut, the forces governing engraftment in humans are unknown. Here we use an ongoing clinical experiment, the treatment of recurrent Clostridium difficile infection, to uncover the rules of engraftment in humans. We built a statistical model that predicts which bacterial species will engraft in a given host, and developed Strain Finder, a method to infer strain genotypes and track them over time. We find that engraftment can be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient. Furthermore, donor strains within a species engraft in an all-or-nothing manner and previously undetected strains frequently colonize patients receiving FMT. We validated these findings for metabolic syndrome, suggesting that the same principles of engraftment extend to other indications.
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•Gut microbiota of 18 C. difficile patients profiled during fecal transplantation•Developed Strain Finder, a method to infer strain genotypes and track them over time•Bacterial abundance and phylogeny are the strongest determinants of engraftment•Unlike bacterial species, closely related strains engraft in an all-or-nothing pattern
Smillie et al. profile the gut microbiota of recurrent Clostridium difficile patients during fecal microbiota transplantation (FMT) and uncover the principles of microbiota engraftment in humans. They validate their findings across several FMT datasets and in another disease context, metabolic syndrome.
Intra-tumor microbiota have been implicated in pancreatic ductal adenocarcinoma (PDAC) development, treatment response and post-treatment survivorship. Moreover, therapeutic interventions targeting ...microbiota may improve the response to chemotherapy and immunotherapy, further emphasizing the critical need to understand the origins of and growth of bacteria within the pancreatic tumor microenvironment. Here, we studied the role of several clinical factors on the bacterial colonization of PDAC.
We obtained matched tumor and normal pancreatic tissue specimens from 27 patients who had undergone surgical resection for PDAC between 2011 and 2015 from the University of Minnesota Biological Materials Procurement Network (BioNet). We found that 26 (48%) out of 54 pancreatic tissue samples harbored detectable bacterial communities using real-time PCR targeting the 16S rRNA gene. Bacterial colonization was detected significantly more frequently in samples from patients who had pancreatic head tumors, underwent Whipple procedure, or had preoperative biliary stent placement. There was also a significantly greater relative abundance of microbiota from the family Enterobacteriaceae among samples from patients who underwent biliary stent placement or neoadjuvant treatment with a combination of Gemcitabine and Paclitaxel.
These findings suggest that biliary stent placement and neoadjuvant chemotherapy are associated with specific alterations that promote the infiltration and growth of intra-tumor bacteria in the setting of PDAC. Further studies exploring whether specific bacterial communities could contribute to increased chemoresistance will be essential for optimizing medical therapies in the future.
Fecal microbiota transplantation (FMT) is increasingly being used for treatment of recurrent Clostridium difficile infection (R-CDI) that cannot be cured with antibiotics alone. In addition, FMT is ...being investigated for a variety of indications where restoration or restructuring of the gut microbial community is hypothesized to be beneficial. We sought to develop a stable, freeze-dried encapsulated preparation of standardized fecal microbiota that can be used for FMT with ease and convenience in clinical practice and research.
We systematically developed a lyophilization protocol that preserved the viability of bacteria across the taxonomic spectrum found in fecal microbiota and yielded physicochemical properties that enabled consistent encapsulation. We also treated a cohort of R-CDI patients with a range of doses of encapsulated microbiota and analyzed the associated changes in the fecal microbiome of the recipients.
The optimized lyophilized preparation satisfied all our preset goals for physicochemical properties, encapsulation ease, stability at different temperatures, and microbiota viability in vitro and in vivo (germ-free mice). The capsule treatment was administered to 49 patients. Overall, 43/49 (88%) of patients achieved a clinical success, defined as no recurrence of CDI over 2 months. Analysis of the fecal microbiome demonstrated near normalization of the fecal microbial community by 1 month following FMT treatment. The simplest protocol using the lowest dose (2.1-2.5 × 10
bacteria in 2-3 capsules) without any colon purgative performed equally well in terms of clinical outcomes and microbiota engraftment.
A single administration of encapsulated, freeze-dried fecal microbiota from a healthy donor was highly successful in treating antibiotic-refractory R-CDI syndrome.
Compared with cast treatment, surgery may expose patients with distal radius fractures to undue risk. Surgical intervention in this cohort may offer less benefit than previously thought and ...appropriate patient selection is imperative. The modified Frailty Index (mFI) predicts complications after other orthopedic surgeries. We hypothesized that this index would predict, and might ultimately prevent, complications in patients older than 50 years with distal radius fractures.
We retrospectively reviewed the American College of Surgeons—National Surgery Quality Improvement Program (ACS-NSQIP) database, including patients older than 50 years who underwent open reduction and internal fixation of a distal radius fracture. A 5-item mFI score was then calculated for each patient. Postoperative complications, readmission and reoperation rates, as well as length of stay (LOS) were recorded. Bivariate and multivariable statistical analysis was then performed.
We identified 6,494 patients (mean age, 65 years). Compared with patients with mFI of 0, patients with mFI of 2 or greater were nearly 2.5 times as likely to incur a postoperative complication (1.7% vs 7.4%). Specifically, the rates of Clavien-Dindo IV, wound, cardiac, and renal complications were increased significantly in patients with mFI of 2 or greater. In addition, as mFI increased from 0 to 2 or greater, 30-day reoperation rate increased from 0.8% to 2.4%, 30-day readmission from 0.8% to 4.6%, and LOS from 0.5 days to 1.44 days. Frailty was associated with increased complications as well as rates of readmission and reoperation even when controlling for demographic data, LOS, and operative time. Age alone was not significantly associated with postoperative complications, readmission, reoperation, or LOS.
A state of frailty is highly predictive of postoperative complications, readmission, reoperation, and increased LOS following open reduction and internal fixation of distal radius fractures. Our data suggest that a simple frailty evaluation can help inform surgical decision making in patients older than 50 years with distal radius fractures.
Prognostic II.
Recent studies highlight the importance of intestinal fungal microbiota in the development of human disease. Infants, in particular, are an important population in which to study intestinal ...microbiomes because microbial community structure and dynamics during this formative window of life have the potential to influence host immunity and metabolism. When compared to bacteria, much less is known about the early development of human fungal communities, owing partly to their lower abundance and the relative lack of established molecular and taxonomic tools for their study. Herein, we describe the development, validation, and use of complementary amplicon-based genomic strategies to characterize infant fungal communities and provide quantitative information about Candida, an important fungal genus with respect to intestinal colonization and human disease. Fungal communities were characterized from 11 infant fecal samples using primers that target the internal transcribed spacer (ITS) 2 locus, a region that provides taxonomic discrimination of medically relevant fungi. Each sample yielded an average of 27,553 fungal sequences and Candida albicans was the most abundant species identified by sequencing and quantitative PCR (qPCR). Low numbers of Candida krusei and Candida parapsilosis sequences were observed in several samples, but their presence was detected by species-specific qPCR in only one sample, highlighting a challenge inherent in the study of low-abundance organisms. Overall, the sequencing results revealed that infant fecal samples had fungal diversity comparable to that of bacterial communities in similar-aged infants, which correlated with the relative abundance of C. albicans. We conclude that targeted sequencing of fungal ITS2 amplicons in conjunction with qPCR analyses of specific fungi provides an informative picture of fungal community structure in the human intestinal tract. Our data suggests that the infant intestine harbors diverse fungal species and is consistent with prior culture-based analyses showing that the predominant fungus in the infant intestine is C. albicans.
Bacterial community structure (BCS) in freshwater ecosystems varies seasonally and due to physicochemical gradients, but metacommunity structure of a major river remains understudied. Here we ...characterize the BCS along the Mississippi River and contributing rivers in Minnesota over three years using Illumina next-generation sequencing, to determine how changes in environmental conditions as well as inputs from surrounding land and confluences impacted community structure. Contributions of sediment to water microbial diversity were also evaluated. Long-term variation in community membership was observed, and significant shifts in relative abundances of major freshwater taxa, including α-Proteobacteria, Burkholderiales, and Actinomycetales, were observed due to temporal and spatial variations. Environmental parameters (e.g. temperature, rainfall, and nutrient concentrations) primarily contributed to differences in phyla abundances (88% of variance), with minimal influence from spatial distance alone (<1% of variance). Furthermore, an annually-recurrent BCS was observed in late summer, further suggesting that seasonal dynamics strongly influence community composition. Sediment communities differed from those in the water, but contributed up to 50% to community composition in the water column. Among water sampling sites, 34% showed significant variability in BCS of replicate samples indicating variability among riverine communities due to heterogeneity in the water column. Results of this study highlight the need for a better understanding of spatial and temporal variations in riverine bacterial diversity associated with physicochemical gradients and reveal how communities in sediments, and potentially other environmental reservoirs, impact waterborne BCS. Techniques used in this study may prove useful to determine sources of microbes from sediments and soils to waterways, which will facilitate best management practices and total maximum daily load determinations.
•Upper Mississippi River bacterial communities were characterized over three years.•Community structure was correlated with changes in physicochemical parameters.•A reproducible community structure was observed in the late summer.•Species sorting and seasonal dynamics primarily drove shifts in community structure.•Sediment communities may also contribute significantly to planktonic communities.
Vertebral compression fractures are the most common spine injury seen in elderly patients. Vertebral augmentation is considered a safe and effective treatment. The ability to predict outcomes based ...on comorbidities is lacking. The modified frailty index has been used to predict complications after orthopedic and surgical procedures. We hypothesized that despite a low rate of adverse outcomes, postoperative complications after kyphoplasty would be greater in patients who are frail.
The National Surgical Quality Improvement Program database was queried for patients who underwent kyphoplasty between 2006 and 2015. Complication data including 30-day complications, life-threatening complications, reoperation and readmission rate, and length of stay data was recorded, and 5-item modified frailty index (5i-mFI) scores were calculated. Univariate and multivariate logistic regression analyses were then conducted to analyze frailty as a predictor of postoperative complications after kyphoplasty.
In total, 2465 patients were identified (mean age = 73.98). As 5i-mFI increased from 0 to ≥2, the rate of overall complications increased nearly 3-fold from 3.7% to 10.4% (P < 0.001) and the rate of life-threatening complications increased from 0.8% to 2.4% (P = 0.042). In addition, 30-day readmission increased from 8.9% to 12.9% (P = 0.005), adverse hospital discharge increased from 7.6% to 25.6% (P < 0.001), and length of stay increased from 1.66 days to 3.75 days (P < 0.001). Frailty was associated with increased total complications, Clavien–Dindo IV complications, length of stay, and 30-day readmission rates.
The 5i-mFI is a straightforward assessment tool that correlates with outcomes after kyphoplasty. It can be used to help clinicians predict adverse events and facilitate informed discussions with their patients.
•The 5i-mFI is a straightforward assessment tool that correlates with outcomes after kyphoplasty.•The overall complication rate in our cohort of 2465 patients was 6.6%, is consistent with that reported in the literature.•The complication rate increased nearly 3-fold between patients with an mFI of 0 and those with a 5i-mFI of ≥2.•Frailty was associated with greater rates of overall and life-threatening complications, increased LOS, and readmission.
Frailty, as quantified by the modified frailty index (mFI), has emerged as a promising method to identify patients at high risk of complications after surgery. Several studies have shown that ...frailty, as opposed to age, is more predictive of adverse surgical outcomes. We hypothesized that a 5-item mFI could be used to identify patients at elevated risk of complications after total shoulder arthroplasty (TSA).
We identified patients aged 50 years or older who underwent TSA in the American College of Surgeons National Surgical Quality Improvement Program database. Pearson χ2 analysis and linear regression were used to determine the association of the mFI score with 30-day postoperative complications, reoperation, readmission, length of stay (LOS), adverse hospital discharge, and mortality rate.
The study included 9861 patients with a mean age of 70 years. As the mFI score increased from 0 to 2 or greater, the following rates increased: postoperative complications from 4.2% to 9.4%, readmission from 1.6% to 4.4%, adverse hospital discharge from 6.3% to 19.6%, and LOS from 1.88 days to 2.43 days (P < .001). Multivariate analysis showed that patients with an mFI score of 2 or greater were over twice as likely to sustain a postoperative complication (odds ratio OR, 2.4; 95% confidence interval CI, 1.86-3.10), readmission (OR, 2.80; 95% CI, 1.88-4.17), reoperation (OR, 1.82; 95% CI, 1.02-3.25), and adverse hospital discharge (OR, 3.14; 95% CI, 2.51-3.92). These effects were all significantly higher compared with age.
Frailty is associated with increased rates of 30-day postoperative complications, readmission, reoperation, adverse hospital discharge, and hospital LOS after TSA. Use of a simple frailty evaluation may help inform decision making and risk assessment when considering TSA.
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