Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population.

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.

The Gut Microbiome of Healthy Vietnamese Adults and Children Is a Major Reservoir for Resistance Genes Against Critical Antimicrobials.

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 <2 years) exhibiting a unique structure in comparison to adults and older children. We identified a total of 132 unique AMR genes, with macrolide, lincosamide, and streptogramin class resistance genes (ermB and lnuC) and tetracycline resistance genes being almost ubiquitous across the study population. Notably, samples from younger children were significantly associated with a greater number of AMR genes than other age groups, including key signature genes associated with AMR pathogens (eg, blaCTX-M, mphA). Our data suggest that the gut microbiome of those living in Vietnam, particularly young children, is a substantial reservoir of AMR genes, which can be transferred to circulating enteric pathogens. Our data support the generation of longitudinal cohort studies of those living in urban and rural areas of developing countries to understand the behavior of these AMR reservoirs and their role in generating multidrug-resistant and extensively drug-resistant pathogens.

Shiga Toxin-Producing Escherichia coli Transmission via Fecal Microbiota Transplant.

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.

Framework for rational donor selection in fecal microbiota transplant clinical trials.

Early clinical successes are driving enthusiasm for fecal microbiota transplantation (FMT), the transfer of healthy gut bacteria through whole stool, as emerging research is linking the microbiome to many different diseases. However, preliminary trials have yielded mixed results and suggest that heterogeneity in donor stool may play a role in patient response. Thus, clinical trials may fail because an ineffective donor was chosen rather than because FMT is not appropriate for the indication. Here, we describe a conceptual framework to guide rational donor selection to increase the likelihood that FMT clinical trials will succeed. We argue that the mechanism by which the microbiome is hypothesized to be associated with a given indication should inform how healthy donors are selected for FMT trials, categorizing these mechanisms into four disease models and presenting associated donor selection strategies. We next walk through examples based on previously published FMT trials and ongoing investigations to illustrate how donor selection might occur in practice. Finally, we show that typical FMT trials are not powered to discover individual taxa mediating patient responses, suggesting that clinicians should develop targeted hypotheses for retrospective analyses and design their clinical trials accordingly. Moving forward, developing and applying novel clinical trial design methodologies like rational donor selection will be necessary to ensure that FMT successfully translates into clinical impact.

Investigation of a Cluster of Sphingomonas koreensis Infections.

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.).

On the hands of patients with Clostridium difficile: A study of spore prevalence and the effect of hand hygiene on C difficile removal.

The prevalence of Clostridium difficile spores was assessed in 48 observations of infected inpatients. Participants were randomized to hand hygiene with either alcohol-based handrub or soap and water. C difficile was recovered in 14.6% of pre-hand hygiene observations. It was still present on 5 of these 7 participants after hand hygiene (3/3 using alcohol-based handrub; 2/4 using soap and water).

Patient Perspectives on Fecal Microbiota Transplantation for Clostridium Difficile Infection.

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.

Variation in health care worker removal of personal protective equipment.

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.

Understanding the current state of infection prevention to prevent Clostridium difficile infection: a human factors and systems engineering approach.

BACKGROUND: 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. METHODS: 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. RESULTS: 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). CONCLUSIONS: 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.

Impact of sink location on hand hygiene compliance for Clostridium difficile infection.

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.

Evaluating the usefulness of patient education materials on surgical site infection: a systematic assessment.

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.