Bacteroides and related species: The keystone taxa of the human gut microbiota.

Microbial communities play a significant role in maintaining ecosystems in a healthy homeostasis. Presently, in the human gastrointestinal tract, there are certain taxonomic groups of importance, though there is no single species that plays a keystone role. Bacteroides spp.

The Application of Transposon Insertion Sequencing in Identifying Essential Genes in B. fragilis.

Essential genes are those that are indispensable for the survival of organism under specific growth conditions. Investigating essential genes in pathogenic bacteria not only helps to understand vital biological networks but also provides novel targets for drug development. Availability of genetic engineering tools and high-throughput sequencing methods has enabled essential genes identification in many pathogenic gram-positive and gram-negative bacteria.

Complete hybrid genome assembly of clinical multidrug-resistant isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids.

constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen. Antimicrobial resistance (AMR) and the prevalence of AMR genes are increasing, and prediction of antimicrobial susceptibility based on sequence information could support targeted antimicrobial therapy in a clinical setting. Complete identification of insertion sequence (IS) elements carrying promoter sequences upstream of resistance genes is necessary for prediction of AMR.

Transposon Mutagenesis of Bacteroides fragilis.

Bacteroides fragilis is Gram-negative obligatory anaerobe which usually resides in the gut of humans and animals. As an important member of the human gut microbiota it plays a vital role in digestion and absorption of nutrients as well as shaping of host immune system. B.

CRISPR-Cas Systems in , an Important Pathobiont in the Human Gut Microbiome.

While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus make up ~25% of the total gut microbiome. comprises only 2% of the total in the gut, yet causes of >70% of infections.

Novel large-scale chromosomal transfer in Bacteroides fragilis contributes to its pan-genome and rapid environmental adaptation.

Bacteroides fragilis, an important component of the human gastrointestinal microbiota, can cause lethal extra-intestinal infection upon escape from the gastrointestinal tract. We demonstrated transfer and recombination of large chromosomal segments from B. fragilis HMW615, a multidrug resistant clinical isolate, to B.

Changes in the antibiotic susceptibility of anaerobic bacteria from 2007-2009 to 2010-2012 based on the CLSI methodology.

Antimicrobial susceptibility testing of anaerobic isolates was conducted at four independent sites from 2010 to 2012 and compared to results from three sites during the period of 2007-2009. This data comparison shows significant changes in antimicrobial resistance in some anaerobic groups. Therefore, we continue to recommend institutions regularly perform susceptibility testing when anaerobes are cultured from pertinent sites.

Co-occurring substance use and mental disorders in the criminal justice system: a new frontier of clinical practice and research.

This editorial introduces this special section of the Psychiatric Rehabilitation Journal, which focuses on justice-involved persons with co-occurring mental and substance use disorders (CODs). It contains seven original articles examining CODs among justice-involved populations that vary by gender, age, setting (e.g.

The Ellis Island Effect: A novel mobile element in a multi-drug resistant clinical isolate includes a mosaic of resistance genes from Gram-positive bacteria.

 , a Gram-negative anaerobic bacterium, is alternately a gut commensal or virulent pathogen and is an important reservoir for horizontal gene transfer (HGT) of bacterial resistance and virulence genes in the human gastrointestinal tract. We identified a unique conjugative transposon (CTn) in a multidrug resistant clinical isolate of (BF-HMW615); we named this element CTnHyb because it included a hybrid mosaic of foreign elements. This study reports the characterization of CTnHyb and discusses the potential impact on horizontal spread of resistance genes.

Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library.

Background: Bacteroides fragilis is a Gram-negative anaerobe that is normally a human gut commensal; it comprises a small percentage of the gut Bacteroides but is the most frequently isolated Bacteroides from human infections. Identification of the essential genes necessary for the survival of B. fragilis provides novel information which can be exploited for the treatment of bacterial infections.

Antianaerobic antimicrobials: spectrum and susceptibility testing.

Susceptibility testing of anaerobic bacteria recovered from selected cases can influence the choice of antimicrobial therapy. The Clinical and Laboratory Standards Institute (CLSI) has standardized many laboratory procedures, including anaerobic susceptibility testing (AST), and has published documents for AST. The standardization of testing methods by the CLSI allows comparisons of resistance trends among various laboratories.

Two multidrug-resistant clinical isolates of Bacteroides fragilis carry a novel metronidazole resistance nim gene (nimJ).

Two multidrug-resistant Bacteroides fragilis clinical isolates contain and express a novel nim gene, nimJ, that is not recognized by the "universal" nim primers and can confer increased resistance to metronidazole when introduced into a susceptible strain on a multicopy plasmid. HMW615, an appendiceal isolate, contains at least two copies of nimJ on its genome, while HMW616, an isolate from a patient with sepsis, contains one genomic copy of nimJ. B.

Transposon mutagenesis of Bacteroides fragilis using a mariner transposon vector.

The mariner transposon vector pYV07 was tested for use in the mutagenesis of Bacteroides fragilis 638R. The transposon vector efficiently generated mutants in B. fragilis 638R.

Transposon mutagenesis of the anaerobic commensal, Bacteroides fragilis, using the EZ::TN5 transposome.

Genetic analysis of Bacteroides fragilis (BF) is hindered because of the lack of efficient transposon mutagenesis methods. Here, we describe a simple method for transposon mutagenesis using EZ::TN5, a commercially available system that we optimized for use in BF638R. The modified EZ::TN5 transposon contains an Escherichia coli conditional origin of replication, a kanamycin resistance gene for E.

Pump it up: occurrence and regulation of multi-drug efflux pumps in Bacteroides fragilis.

Bacteroides fragilis is a gram-negative anaerobic commensal that can be a virulent pathogen when it escapes its normal niche in the human gut. Recent increases in reports of multi-drug resistance strains of this organism have lent urgency to understanding its mechanisms of antimicrobial resistance. We have identified and characterized RND-type multi-drug efflux pumps in B.

Racial disparities in substance abuse treatment and the ecological fallacy.

This study examined engagement in treatment in substance abuse treatment programs that treated primarily either African American or White clients. Findings showed higher levels of engagement in White programs; however, engagement of African Americans in White programs was similar to that of Whites and was greater than Whites in African American programs. No significant differences emerged when a mixed model analysis considered additional variables of staff consensus (regarding treatment elements), treatment climate, acceptance of Medicaid clients, the proportion mandated to treatment, and the quality of the physical space.

What does not work? Expert consensus on discredited treatments in the addictions.

Evidence-based practice promotes those research-supported treatments that have proven effective, but it rarely identifies discredited treatments that are to be avoided. We sought to establish a professional consensus on discredited addiction treatments using Delphi methodology. A panel of 75 experts participated in a 2-stage study, reporting familiarity with 65 treatments and rating these on a continuum from "not at all discredited" to "certainly discredited.

Antimicrobial resistance and prevalence of resistance genes in intestinal Bacteroidales strains.

Objective: This study examined the antimicrobial resistance profile and the prevalence of resistance genes in Bacteroides spp. and Parabacteroides distasonis strains isolated from children's intestinal microbiota.

Methods: The susceptibility of these bacteria to 10 antimicrobials was determined using an agar dilution method.

Multi-drug resistant Bacteroides fragilis recovered from blood and severe leg wounds caused by an improvised explosive device (IED) in Afghanistan.

This report summarizes the case of a 23 year-old otherwise healthy male that was injured in an improvised explosive device (IED) blast in support of Operation Enduring Freedom (OEF). He sustained bilateral open tibia and fibula fractures in the setting of being exposed to water contaminated with raw sewage. Despite long-term carbapenem therapy, the patient's wounds were repeatedly noted to have purulent drainage during surgical debridement and cultures from these wounds were persistently positive for Bacteroides fragilis.

Measuring collaboration and integration activities in criminal justice and substance abuse treatment agencies.

Individuals with substance abuse problems who are involved in the criminal justice system frequently need community-based drug and alcohol abuse treatment and other services. To reduce the risk of relapse to illicit drugs and criminal recidivism, criminal justice agencies may need to establish collaborations with substance abuse treatment and other community-based service providers. Although there are many variations of interorganizational relationships, the nature of these interagency collaborations among justice agencies and treatment providers has received little systematic study.

Characteristics of Bacteroides fragilis lacking the major outer membrane protein, OmpA.

OmpA1 is the major outer membrane protein of the Gram-negative anaerobic pathogen Bacteroides fragilis. We identified three additional conserved ompA homologues (ompA2-ompA4) and three less homologous ompA-like genes (ompAs 5, 6 and 7) in B. fragilis.

Organizational factors and collaboration and integration activities in criminal justice and drug abuse treatment agencies.

Despite strong interest in improving collaborations between correctional and substance abuse treatment organizations, there is a lack of empirical data describing the existing practices. The current study used a national survey of correctional administrators to examine organizational factors related to cross-agency collaboration and integration activities between corrections and substance abuse treatment organizations. Using a measure of collaboration that scaled cross-agency activities from less structured, informal networking and coordination to more structured and formalized levels of cooperation and collaboration, we found that different correctional settings (e.

When goals diverge: Staff consensus and the organizational climate.

A sample of correctional officers and prison substance abuse treatment staff collected by the National Criminal Justice Treatment Practices Survey is used to provide an exploratory study of an aspect of organizational culture consisting of consensus (agreement) among prison personnel regarding their beliefs about rehabilitation in the presence of conflicting organizational goals and aspects of the organizational climate important to change. Findings show that among those staff members responding to the survey, the belief in rehabilitation scale mean score was associated with higher levels of organizational commitment, and interdepartmental coordination. However, an hierarchical linear modeling (HLM) analysis that used an index score derived from the standard deviation for staff consensus regarding these same beliefs about rehabilitation produced a different pattern of results, showing that high levels of consensus were associated with job frustration, cynicism towards the ability of the institution to change, and lower levels of organizational commitment.