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Fecal microbiota transplantation (FMT) is recommended therapy for multiply recurrent Clostridioides difficile infection. We report adverse events in 7 patients who received FMT from a stool donor who was colonized with Shiga toxin–producing Escherichia coli (STEC). No patients died of FMT-transmitted STEC. Improved screening can likely avoid future transmission.

Antimicrobials are a key group of therapeutic agents. Given the animal/human population density and high antimicrobial consumption rate in Southeast Asia, the region is a focal area for monitoring antimicrobial resistance (AMR). Hypothesizing that the gastrointestinal tract of healthy individuals in Vietnam is a major source of AMR genes that may be transferred to pathogens, we performed shotgun metagenomic sequencing on fecal samples from 42 healthy Vietnamese people (21 children and 21 adults). We compared their microbiome profiles by age group and determined the composition of AMR genes. An analysis of the taxonomic profiles in the gut microbiome showed a clear differentiation by age, with young children (age

Bifidobacterium pseudocatenulatum is a member of the human gut microbiota, and specific variants of B. pseudocatenulatum have been associated with health benefits such as improving gut integrity and reducing inflammatory responses. Here, we aimed to assess the genomic diversity and predicted metabolic profiles of B. pseudocatenulatum cells found colonizing the gut of healthy Vietnamese adults and children. We found that the population of B. pseudocatenulatum from each individual was distinct and highly diverse, with intraclonal variation attributed largely to a gain or loss of carbohydrate-utilizing enzymes. The B. pseudocatenulatum genomes were enriched with glycosyl hydrolases predicted to target plant-based nondigestible carbohydrates (GH13, GH43) but not host-derived glycans. Notably, the exopolysaccharide biosynthesis region from organisms isolated from healthy children showed extensive genetic diversity and was subject to a high degree of genetic modification. Antimicrobial susceptibility profiling revealed that the Vietnamese B. pseudocatenulatum cells were uniformly susceptible to beta-lactams but exhibited variable resistance to azithromycin, tetracycline, ciprofloxacin, and metronidazole. The genomic presence of ermX and tet variants conferred resistance against azithromycin and tetracycline, respectively; ciprofloxacin resistance was associated with a mutation(s) in the quinolone resistance-determining region (GyrA, S115, and/or D119). Our work provides the first detailed genomic and antimicrobial resistance characterization of B. pseudocatenulatum found in the Vietnamese population, which can be exploited for the rational design of probiotics. IMPORTANCE Bifidobacterium pseudocatenulatum is a beneficial member of the human gut microbiota. The organism can modulate inflammation and has probiotic potential, but its characteristics are largely strain dependent and associated with distinct genomic and biochemical features. Population-specific beneficial microbes represent a promising avenue for the development of potential probiotics, as they may exhibit a more suitable profile in the target population. This study investigates the underexplored diversity of B. pseudocatenulatum in Vietnam and provides more understanding of its genomic diversity, metabolic potential, and antimicrobial susceptibility. Such data from indigenous populations are essential for selecting probiotic candidates that can be accelerated into further preclinical and clinical investigations.

BACKGROUND: Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted an investigation. METHODS: We performed whole-genome DNA sequencing on clinical isolates of multidrug-resistant Sphingomonas koreensis identified from 2006 through 2016 at the National Institutes of Health (NIH) Clinical Center. We cultured S. koreensis from the sinks in patient rooms and performed both whole-genome and shotgun metagenomic sequencing to identify a reservoir within the infrastructure of the hospital. These isolates were compared with clinical and environmental S. koreensis isolates obtained from other institutions. RESULTS: The investigation showed that two isolates of S. koreensis obtained from the six patients identified in the 2016 cluster were unrelated, but four isolates shared more than 99.92% genetic similarity and were resistant to multiple antibiotic agents. Retrospective analysis of banked clinical isolates of sphingomonas from the NIH Clinical Center revealed the intermittent recovery of a clonal strain over the past decade. Unique single-nucleotide variants identified in strains of S. koreensis elucidated the existence of a reservoir in the hospital plumbing. Clinical S. koreensis isolates from other facilities were genetically distinct from the NIH isolates. Hospital remediation strategies were guided by results of microbiologic culturing and fine-scale genomic analyses. CONCLUSIONS: This genomic and epidemiologic investigation suggests that S. koreensis is an opportunistic human pathogen that both persisted in the NIH Clinical Center infrastructure across time and space and caused health care-associated infections. (Funded by the NIH Intramural Research Programs.)

Bifidobacterium pseudocatenulatum is a member of the human gut microbiota, and has previously been used as a probiotic to improve gut integrity and reduce inflammatory responses. We showed previously that B. pseudocatenulatum was significantly depleted during dysenteric diarrhea, suggesting the organism may aid in recovery from diarrhea. Here, in order to investigate its probiotic potential, we aimed to assess the genomic diversity and predicted metabolic profiles of B. pseudocatenulatum found colonizing the gut of healthy Vietnamese adults and children. We found that the population of B. pseudocatenulatum from each individual was distinct and highly diverse, with intra-clonal variation attributed to gain or loss of carbohydrate utilizing enzymes. The B. pseudocatenulatum genomes were enriched with glycosyl hydrolases that target plant-based non-digestible carbohydrates (GH13, GH43), but not host-derived glycans. Notably, the exopolysaccharide biosynthesis region from organisms isolated from healthy children showed greater genetic diversity, and was subject to a high degree of genetic modification. Antimicrobial susceptibility testing revealed that the Vietnamese B. pseudocatenulatum were uniformly susceptible to beta-lactams, but exhibited variable resistance to azithromycin, tetracycline, ciprofloxacin and metronidazole. The genomic presence of ermX and tet variants conferred resistance against azithromycin and tetracycline, respectively; ciprofloxacin resistance was associated with mutation(s) in the quinolone resistance determining region (GyrA, S115 and/or D119). Our work provides the first detailed genomic and antimicrobial resistance characterization of B. pseudocatenulatum found in the Vietnamese population, which could inform the next phase of rational probiotic design.ImportanceBifidobacterium pseudocatenulatum is a probiotic candidate with potential applications in several health conditions, but its efficacy is largely strain-dependent and associated with distinct genomic and biochemical features. However, most commercial probiotics have been developed by Western institutions, which may not have ideal efficacy when administered in developing countries. This study taps into the underexplored diversity of the organism in Vietnam, and provides more understanding to its lifestyles and antimicrobial susceptibility. These data are key for selecting an optimal probiotic candidate, from our established collection, for downstream investigations and validation. Thus, our work represents a model in identifying and characterizing bespoke probiotics from an indigenous population in a developing setting.

This month’s Genome Watch highlights the need for improved phenotypic approaches to complement the power of genomics.

Introduction Clostridium difficile infection (CDI) is a severe and increasingly frequent healthcare-associated infection that develops after disruption of the gut microbiota. Immunocompromised, hospitalized patients have an increased likelihood of acquiring CDI, leading to lengthened hospital stays, increased medical fees, and higher rates of morbidity and mortality. Treatment of CDI is challenging because of limited treatment options and a 19–20% recurrence rate. Thus, there is a need for effective, affordable and safe treatments for CDI. Fecal microbiota transplantation (FMT) is the transplantation of donor stool into the intestine of a CDI patient to restore the structure and function of the gut microbiota and eradicate CDI. Recently, FMT has become an attractive alternative treatment for CDI due to its overwhelming success rate. However, the patient perspective on the effect of CDI and the role of FMT in that context is lacking. Methods We undertook a patient survey to gather qualitative and quantitative data on the short-term social, physical, emotional outcomes for patients with CDI who have undergone FMT. Results We found in all patients interviewed that the social implications of CDI were generally more severe than the emotional and physical aspects. Conclusion Future studies should consider evaluating these important patient-centered factors as outcomes. Moreover, patients are willing to undergo FMT as treatment for CDI.

Achieving and sustaining high levels of health care worker (HCW) compliance with contact isolation precautions is challenging. The aim of this study was to determine HCW work system barriers to and facilitators of adherence to contact isolation for patients with suspected or confirmed Clostridium difficile infection (CDI) using a human factors and systems engineering approach.This prospective cohort study took place between September 2013 and November 2013 at a large academic medical center (hospital A) and an affiliated Veterans Administration hospital (hospital B). A human factors engineering (HFE) model for patient safety, the Systems Engineering Initiative for Patient Safety model, was used to guide work system analysis and direct observation data collection. There were 288 observations conducted. HCWs and visitors were assessed for compliance with all components of contact isolation precautions (hand hygiene, gowning, and gloving) before and after patient contact. Time required to complete contact isolation precautions was measured, and adequacy of contact isolation supplies was assessed.Full compliance with contact isolation precautions was low at both hospitals A (7%) and B (22%). Lack of appropriate hand hygiene prior to room entry (compliance for hospital A: 18%; compliance for hospital B: 29%) was the most common reason for lack of full compliance. More time was required for full compliance compared with compliance with no components of contact isolation precautions before patient room entry, inside patient room, and after patient room exit (59.9 vs 3.2 seconds, P.001; 507.3 vs 149.7 seconds, P = .006; 15.2 vs 1.3 seconds, P.001, respectively). Compliance was lower when contact isolation supplies were inadequate (4% vs 16%, P = .005).Adherence to contact isolation precautions for CDI is a complex, time-consuming process. HFE analysis indicates that multiple work system components serve as barriers and facilitators to full compliance with contact isolation precautions and should be addressed further to prevent CDI.

The prevalence of Clostridium difficile (C. difficile) spores was assessed in 48 observations of infected inpatients. Participants were randomized to hand hygiene with either alcohol based hand rub or soap and water. C. difficile was recovered in 14.6% of pre-hand hygiene observations. It was still present on five of these seven participants after hand hygiene (3/3 alcohol based hand rub; 2/4 soap and water).

Hand hygiene with soap and water after the care of a patient with Clostridium difficile infection is essential to reduce nosocomial transmission in an outbreak situation. Factors that may pose barriers to user completion of infection prevention measures, such as hand hygiene, are of interest. We undertook a quantitative study to evaluate the relationship between sink location and compliance with handwashing among health care workers and visitors in a surgical transplant unit. We found that placement of 2 more easily visible sinks in a surgical transplant unit was associated with improved adherence to handwashing.

Background The NIH Clinical Center conducts patient and environmental surveillance for carbapenemase-producing organisms (CPO). Previous investigation revealed that sink drains can become colonized with CPO. Subsequent surveillance targets included potential aqueous reservoirs, such as floor drains of environmental services (EVS) closets. Methods Premoistened swabs were used to culture sink drains, floor drains, and equipment for CPO. Perirectal swabs were ordered monthly for all patients in non-behavioral health wards. Specimens were plated to CRE- and ESBL-selective media, and colonies identified by MALDI-TOF. The presence of the blaKPC gene was confirmed by PCR. When environmental CPO isolates were detected, EVS procedures and practices were reviewed. Results In June 2016, blaKPC+ Leclercia adecarboxylata was isolated from an EVS closet floor drain, and in August 2016, from drains in four additional closets. In the previous 10 years, Leclercia sp. was isolated just once from a clinical culture. In September 2016, routine surveillance revealed new-onset blaKPC+ L. adecarboxylata colonization in a stem cell transplant recipient. Investigation included 33 cultures collected from sink and floor drains, EVS equipment, and other items. EVS equipment, especially mop buckets, were identified as a likely point source due to their use in patient care areas and closets with contaminated floor drains. Among seven mop buckets sampled, one grew blaKPC+ L. adecarboxylata. Whole genome sequencing demonstrated genetic relatedness of the Leclercia isolates. Floor cleaner was changed to a disinfectant solution. Extensive decontamination of 67 EVS closets and equipment was performed urgently. No further patient or environmental cultures have grown blaKPC+ L. adecarboxylata. Conclusion The recovery of a highly unusual organism, rarely found in clinical specimens, that was also carrying a blaKPC+ plasmid, allowed us to detect environmental spread of this organism in the hospital. The ability to track this organism using genome sequencing provided strong evidence of the mode of spread, leading to effective remediation. No evidence-based methods exist for remediating drain contamination, which can serve as a potential reservoir for transmission. Disclosures All authors: No reported disclosures.

Background The rising prevalence of recurrent Clostridium difficile infection (CDI) in pediatrics is a public health concern. Fecal microbiota transplantation (FMT) is an effective treatment and is recommended in US guidelines. Universal stool banks (USB) have enabled widespread FMT access among adult patients; however, the progression of FMT uptake in pediatrics is unknown. We present a geospatial timeseries analysis of growth in pediatric FMT providers within the United States between 2013 and 2018. Methods A list of healthcare facilities associated with a USB and an FMT special interest group was geocoded using Google Maps. Spatial network analysis methods were used to create drive-time polygons for each healthcare facility with simulated traffic for 12 pm on a Wednesday. US Census data were used to estimate the percentage population living within 1, 2, and 4-hour drive time to a pediatric FMT provider cumulatively from 2013 to March 2018. Results Between 2013 and 2018, there was a rapid expansion in access to FMT to include 45 pediatric healthcare facilities (Figure 1). As of March 2018, 40.51% of the US population lives within a 1-hour drive, 62.73% within a 2-hour drive, and 89.38% within a 4-hour drive of an FMT provider (Table 1). The largest percentage increases in access occurred between 2013 and 2014 (28.43% increase within a 1-hour drive time). These 45 FMT providers include 6 community hospitals, seven private practices, and 32 academic centers. Conclusion Although these results demonstrate a rise in pediatric FMT providers across the United States, there remains a significant discrepancy in access between adult and pediatric populations, despite growing evidence of safety and efficacy of FMT. Additional efforts are needed to address barriers to FMT and improve access for pediatric patients with recurrent CDI. Table 1: Pediatric FMT Facilities Within a 1, 2, and 4-Hour Drive Time Year No. of Partners Time (hours) % of US Population 2013 10 1 17.74 2 28.28 4 44.09 2014 15 1 22.79 2 36.88 4 60.74 2015 23 1 28.54 2 45.54 4 70.17 2016 33 1 34.14 2 55.23 4 79.57 2017 41 1 39.20 2 61.26 4 88.76 2018 45 1 40.51 2 62.73 4 89.38 Figure 1. Pediatric Access to FMT From 2013 to 2018. Disclosures P. Panchal, OpenBiome: Employee, Salary.

Background Following a rise in nosocomial infections due to Sphingomonas, a waterborne Gram-negative organism, we undertook an epidemiological investigation to identify possible sources and develop a remediation strategy. Methods We analyzed Sphingomonas isolates from 30 inpatients in the past 11 years, and we reviewed each patient’s chart. We collected swabs of faucets, water samples, and free and total chlorine levels from rooms of Sphingomonas patients from 2016, using unrelated rooms as controls. Water samples and chlorine levels were collected from hospital pipes. Swabs were placed into 1 mL TSB and cultured to sheep blood agar. Isolates were identified by MALDI-TOF MS. Water samples were tested via membrane filtration (500 mL) and spread plate method (1 mL). Patient and environmental Sphingomonas isolates underwent whole genome sequencing, and were analyzed with Mash and Snippy for overall genomic sequence and single-nucleotide polymorphisms comparisons, respectively, to assess relatedness. Results Of 27 faucets examined, 59% grew Sphingomonas spp., and 33% grew highly-resistant S. koreensis. Of 21 water samples, 76% grew Sphingomonas spp., and 48% grew S. koreensis. Sequence analysis demonstrated strong genetic similarity among S. koreensis clinical isolates from the past 11 years and recent faucet and water isolates. One patient’s S. koreensis isolate was genetically related to isolates from faucets in his room. Sphingomonas did not grow from samples collected from municipal water or some of the far upstream water pipes within the hospital. Free chlorine levels were extremely low in hot water, leading to a program of flushing in order to restore and maintain adequate levels. Among 7 contaminated faucets that were replaced, 3 became recolonized within 4 weeks, and continued to grow Sphingomonas from water. Conclusion Investigation and genome sequencing suggest long-standing S. koreensis colonization within the hospital plumbing system that has served as a reservoir for sporadic infections among immunosuppressed patients. Remediation of Sphingomonas plumbing contamination is an ongoing challenge guided by few published data. Hospital water must be rendered safe for even the most immunosuppressed patients. Disclosures All authors: No reported disclosures.

Patient education is important for the prevention of surgical site infections (SSIs). The usefulness of available patient education materials is unclear. Using a validated evaluation tool, the Patient Education Materials Assessment Tool, we systematically assessed patient education materials for SSI. We found that available materials performed poorly, and further research is needed in this area.

In the current era of emerging pathogens such as Ebola virus, removal of personal protective equipment (PPE) is crucial to reduce contamination of health care workers. However, current removal practices are not well described. We undertook a systematic evaluation of health care worker removal of PPE for contact isolation to examine variation in removal procedures. Findings indicate that under usual conditions, only about half of health care workers correctly remove their PPE, and very few remove their PPE in the correct order and dispose of it in the proper location.