Design of a Bacteriophage Cocktail Active against Species and Testing of Its Therapeutic Potential in .

Shigellosis is a leading global cause of diarrheal disease and travelers' diarrhea now being complicated by the dissemination of antibiotic resistance, necessitating the development of alternative antibacterials such as therapeutic bacteriophages (phages). Phages with lytic activity against strains were isolated from sewage. The genomes of 32 phages were sequenced, and based on genomic comparisons belong to seven taxonomic genera: , , , , , and .

IS-mediated plasmid reshuffling results in convergence of toxin-antitoxin systems but loss of resistance genes in XDR from a chronic infection.

Carbapenem-resistant pose an urgent threat to human health worldwide. sequence type (ST) 14, initially identified in the Middle East and South-Asia and co-harbouring the carbapenemase genes and is now emerging globally. One such strain was detected in the USA in 2013 from a patient initially treated in India that also carried , a 16S rRNA methyltransferase that confers resistance to all clinically relevant aminoglycosides.

A panel of diverse clinical isolates for research and development.

Objectives: is a leading cause of community- and hospital-acquired infections. Successful treatment is hampered by its remarkable ability to rapidly develop resistance to antimicrobial agents, primarily through mutation. In response, WHO listed carbapenem-resistant as a Priority 1 (Critical) pathogen for research and development of new treatments.

TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis.

We describe here the structure and organization of TnCentral (https://tncentral.proteininformationresource.org/ [or the mirror link at https://tncentral.

A Longitudinal Evaluation of the Bacterial Pathogens Colonizing Chronic Non-Healing Wound Sites at a United States Military Treatment Facility in the Pacific Region.

Purpose: The biology of chronic wounds is complex and many factors act concurrently to impede healing progress. In this study, the dynamics of microflora changes and their antibiotic susceptibility patterns were evaluated longitudinally over 30 days using data from 28 patients with a total of 47 chronic lower extremity wounds.

Materials And Methods: In this study, colonized wound isolates were characterized using cultural, biochemical, and VITEK 2 methods.

A Diverse Panel of Clinical Acinetobacter baumannii for Research and Development.

Over the past two decades, has emerged as a leading cause of nosocomial infections worldwide. Of particular concern are panresistant strains, leading the World Health Organization (WHO) to designate carbapenem-resistant as a priority 1 (critical) pathogen for research and development of new antibiotics. A key component in supporting this effort is accessibility to diverse and clinically relevant strains for testing.

Vertebral Osteomyelitis and Discitis: "Back" to Susceptibility Testing.

Genetic testing of anaerobic isolates can be important for proper antimicrobial stewardship to identify the appropriate narrow-spectrum treatment for a polymicrobial infection.

Comparison of Pseudomonas aeruginosa strains reveals that Exolysin A toxin plays an additive role in virulence.

Background: Pseudomonas aeruginosa possesses an array of virulence genes ensuring successful infection development. A two-partner secretion system Exolysin BA (ExlBA) is expressed in the PA7-like genetic outliers consisting of ExlA, a pore-forming toxin and ExlB transporter protein. Presence of exlBA in multidrug-resistant (MDR) strains has not been investigated, particularly in the strains isolated from wounded soldiers.

Genomic and epidemiological evidence of bacterial transmission from probiotic capsule to blood in ICU patients.

Probiotics are routinely administered to hospitalized patients for many potential indications but have been associated with adverse effects that may outweigh their potential benefits. It is particularly alarming that probiotic strains can cause bacteremia, yet direct evidence for an ancestral link between blood isolates and administered probiotics is lacking. Here we report a markedly higher risk of Lactobacillus bacteremia for intensive care unit (ICU) patients treated with probiotics compared to those not treated, and provide genomics data that support the idea of direct clonal transmission of probiotics to the bloodstream.

A novel plasmid-encoded mcr-4.3 gene in a colistin-resistant Acinetobacter baumannii clinical strain.

Objectives: To identify the molecular mechanism of colistin resistance in an MDR Acinetobacter baumannii clinical strain isolated in 2008 from a meningitis case in Brazil.

Methods: Long- and short-read WGS was used to identify colistin resistance genes in A. baumannii strain 597A with a colistin MIC of 64 mg/L.

An intervention to control an ICU outbreak of carbapenem-resistant Acinetobacter baumannii: long-term impact for the ICU and hospital.

Background: Following a fatal intensive care unit (ICU) outbreak of carbapenem-resistant Acinetobacter baumanii (CRAB) in 2015, an aggressive infection control intervention was instituted. We outline the intervention and long-term changes in the incidence and prevalence of CRAB.

Methods: The infection control intervention included unit closure (3 days), environmental cleaning, hand hygiene interventions, and environmental culturing.

Clinical and Genomic Features of the First Cases of Elizabethkingia anophelis Infection in New York, Including the First Case in a Healthy Infant Without Previous Nosocomial Exposure.

Elizabethkingia spp are Gram-negative bacteria associated with neonatal meningitis. In 2015-2016, an outbreak of Elizabethkingia anophelis infection that involved 63 patients and 18 deaths occurred in Wisconsin. Despite a multistate investigation, as of September 2016 the source remained undetermined, and experts warned of reemergence.

Chromosomally Encoded in Colistin-Nonsusceptible Pseudomonas aeruginosa.

Whole-genome sequencing (WGS) of historical clinical isolates identified a chromosomal copy of within a Tn-like transposon in MRSN 12280. The isolate was nonsusceptible to colistin by broth microdilution, and genome analysis revealed no mutations known to confer colistin resistance. To the best of our knowledge, this is the first report of in colistin-nonsusceptible .

Genomic Characterization of Nonclonal mcr-1-Positive Multidrug-Resistant Klebsiella pneumoniae from Clinical Samples in Thailand.

Multidrug-resistant Klebsiella pneumoniae strains are one of the most prevalent causes of nosocomial infections and pose an increasingly dangerous public health threat. The lack of remaining treatment options has resulted in the utilization of older drug classes, including colistin. As a drug of last resort, the discovery of plasmid-mediated colistin resistance by mcr-1 denotes the potential development of pandrug-resistant bacterial pathogens.

The Birth and Demise of the IS--IS Composite Transposon: the Vehicle for Transferable Colistin Resistance.

The origin and mobilization of the ~2,609-bp DNA segment containing the mobile colistin resistance gene continue to be sources of uncertainty, but recent evidence suggests that the gene originated in species. Moreover can be mobilized as an IS-flanked composite transposon (Tn), but many sequences have been identified without IS or with just a single copy (single ended). To further clarify the origins and mobilization of , we employed the Geneious R8 software suite to comprehensively analyze the genetic environment of every complete structure deposited in GenBank as of this writing (September 2017) both with and without associated IS ( = 273).

s Endocarditis with an unstable phenotype: the challenges of isolate characterization and Carbapenem stewardship with a partial review of the literature.

Background: endocarditis is exceedingly rare, especially in patients without predisposing risks. We present such a case that included unexpected switches in antibacterial resistance profiles in two (PA) strains with the same whole-genome sequence. The case also involved diagnostic and treatment challenges, such as issues with automated testing platforms, choosing the optimal aminoglycoside, minimizing unnecessary carbapenem exposure, and the need for faster, more informative laboratory tests.

Analysis of Serial Isolates of -Positive Escherichia coli Reveals a Highly Active IS Transposon.

The emergence of a transferable colistin resistance gene () is of global concern. The insertion sequence IS is a key component in the mobilization of this gene, but its role remains poorly understood. Six isolates were cultured from the same patient over the course of 1 month in Germany and the United States after a brief hospitalization in Bahrain for an unconnected illness.

Clostridium sphenoides Chronic Osteomyelitis Diagnosed Via Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry, Conflicting With 16S rRNA Sequencing but Confirmed by Whole Genome Sequencing.

We report a case of successful treatment of chronic osteomyelitis (emanating from contaminated soil exposure) caused by Clostridium sphenoides, an organism infrequently identified as a cause of human infection and more saliently osteomyelitis (only 1 reported case in the literature). Additional impetus for reporting this case resides in the insights gained regarding pathogen identification exploiting sophisticated molecular platforms coupled to traditional microbial culture-based methods. The fastidious nature of cultivating anaerobic organisms required initial attempts at 16S rRNA sequencing to identify a Clostridium species (Clostridium celerecrescens).

A Model for Transposition of the Colistin Resistance Gene mcr-1 by ISApl1.

Analysis of mcr-1-containing sequences identified a common ∼2,607-bp DNA segment that in many cases is flanked on one or both ends by ISApl1 We present evidence that mcr-1 is mobilized by an ISApl1 composite transposon which has, in some cases, subsequently lost one or both copies of ISApl1 We also show that mcr-1 can be mobilized in some circumstances by a single upstream copy of ISApl1 in conjunction with the remnants of a downstream ISApl1.

From the Battlefield to the Bedside: Supporting Warfighter and Civilian Health With the "ART" of Whole Genome Sequencing for Antibiotic Resistance and Outbreak Investigations.

Awareness, responsiveness, and throughput characterize an approach for enhancing the clinical impact of whole genome sequencing for austere environments and for large geographically dispersed health systems. This Department of Defense approach is informing interagency efforts linking antibiograms of multidrug-resistant organisms to their genome sequences in a public database.

Isolation of Rapidly Growing Nontuberculous Mycobacteria in Wounds Following Combat-Related Injury.

Objectives: Rapidly growing nontuberculous mycobacteria (RGNTM) have yet to be described in combat-related injuries. This study investigates the epidemiology, clinical findings, treatment, and outcomes of RGNTM infections among combat casualties wounded in Afghanistan from 2010 to 2012.

Methods: Patients with RGNTM were identified from the Department of Defense Trauma Registry through the Trauma Infectious Disease Outcomes Study.