The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

FRED C. TENOVER,* ROBERT D. ARBEIT, RICHARD V. GOERING, PATRICIA A. MICKELSEN, BARBARA E. MURRAY, DAVID H. PERSING, AND BALA SWAMINATHAN National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333; Veterans Affairs Medical Center, Boston, Massachusetts 02130; Creighton University, Omaha, Nebraska 68178; Stanford University Medical Center, Stanford, California 94305; University of Texas Medical School, Houston, Texas 77030; and Mayo Clinic, Rochester, Minnesota 55905

https://courses.washington.edu/pabio568/files/tenover.pdf

Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing.

Escherichia coli is the predominant nonpathogenic facultative flora of the human intestine. Some E. coli strains, however, have developed the ability to cause disease of the gastrointestinal, urinary, or central nervous system in even the most robust human hosts. Diarrheagenic strains of E. coli can be divided into at least six different categories with corresponding distinct pathogenic schemes. Taken together, these organisms probably represent the most common cause of pediatric diarrhea worldwide. Several distinct clinical syndromes accompany infection with diarrheagenic E. coli categories, including traveler’s diarrhea (enterotoxigenic E. coli), hemorrhagic colitis and hemolytic-uremic syndrome (enterohemorrhagic E. coli), persistent diarrhea (enteroaggregative E. coli), and watery diarrhea of infants (enteropathogenic E. coli). This review discusses the current level of understanding of the pathogenesis of the diarrheagenic E. coli strains and describes how their pathogenic schemes underlie the clinical manifestations, diagnostic approach, and epidemiologic investigation of these important pathogens.

Diarrheagenic Escherichia coli

Few microorganisms are as versatile as Escherichia coli. An important member of the normal intestinal microflora of humans and other mammals, E. coli has also been widely exploited as a cloning host in recombinant DNA technology. But E. coli is more than just a laboratory workhorse or harmless intestinal inhabitant; it can also be a highly versatile, and frequently deadly, pathogen. Several different E. coli strains cause diverse intestinal and extraintestinal diseases by means of virulence factors that affect a wide range of cellular processes.

Pathogenic Escherichia coli

To provide an update to “Surviving Sepsis Campaign Guidelines for Management of Sepsis and Septic Shock: 2012”. A consensus committee of 55 international experts representing 25 international organizations was convened. Nominal groups were assembled at key international meetings (for those committee members attending the conference). A formal conflict-of-interest (COI) policy was developed at the onset of the process and enforced throughout. A stand-alone meeting was held for all panel members in December 2015. Teleconferences and electronic-based discussion among subgroups and among the entire committee served as an integral part of the development. The panel consisted of five sections: hemodynamics, infection, adjunctive therapies, metabolic, and ventilation. Population, intervention, comparison, and outcomes (PICO) questions were reviewed and updated as needed, and evidence profiles were generated. Each subgroup generated a list of questions, searched for best available evidence, and then followed the principles of the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system to assess the quality of evidence from high to very low, and to formulate recommendations as strong or weak, or best practice statement when applicable. The Surviving Sepsis Guideline panel provided 93 statements on early management and resuscitation of patients with sepsis or septic shock. Overall, 32 were strong recommendations, 39 were weak recommendations, and 18 were best-practice statements. No recommendation was provided for four questions. Substantial agreement exists among a large cohort of international experts regarding many strong recommendations for the best care of patients with sepsis. Although a significant number of aspects of care have relatively weak support, evidence-based recommendations regarding the acute management of sepsis and septic shock are the foundation of improved outcomes for these critically ill patients with high mortality.

https://link.springer.com/content/pdf/10.1007%2Fs00134-017-4683-6.pdf

Surviving Sepsis Campaign: International Guidelines for Management of Sepsis and Septic Shock: 2016

Treatment of enterococcal infections has long been recognized as an important clinical challenge, particularly in the setting of infective endocarditis (IE). Furthermore, the increase prevalence of isolates exhibiting multidrug resistance (MDR) to traditional anti-enterococcal antibiotics such as ampicillin, vancomycin and aminoglycosides (high-level resistance) poses immense therapeutic dilemmas in hospitals around the world. Unlike IE caused by most isolates of Enterococcus faecalis, which still retain susceptibility to ampicillin and vancomycin, the emergence and dissemination of a hospital-associated genetic clade of multidrug resistant Enterococcus faecium, markedly limits the therapeutic options. The best treatment of IE MDR enterococcal endocarditis is unknown and the paucity of antibiotics with bactericidal activity against these organisms is a cause of serious concern. Although it appears that we are winning the war against E. faecalis, the battle rages on against isolates of multidrug-resistant E. faecium.

/pdf/enterococcal-endocarditis-can-we-win-the-war-2gvzs0djqb.pdf

Enterococcal Endocarditis: Can We Win the War?

Enterococci have become a significant cause of nosocomial infections in the past two decades. Moreover, acquisition of new resistance traits such as aminoglycoside resistance, β-lactamase production, high-level resistance to penicillins due to penicillin-binding protein changes and glycopeptide resistance has dramatically limited therapeutic options for disease caused by these organisms. Although hospital-associated enterococcal infections were previously thought to be derived from endogenous flora, recent epidemiologic studies, assisted in some instances by the application of new molecular techniques, have identified both intra- and inter-hospital spread of strains of enterococci. These studies have indicated that person-to-person transmission via the hands of health care personnel may occur and have implicated inanimate objects as a possible source of enterococcal infection. It has also been shown that a major risk factor for nosocomial acquisition of enterococci is the use of antibiotics, presumably because enterococci are resistant to many of the commonly used antimicrobial regimens. With the information currently available, there can be little doubt that nosocomial infections due to enterococci will continue to be important in the future. Rapid identification of patients infected or colonized by multi-resistant enterococci, strict adherence to infection control practices, and prudent use of antibiotics all seem necessary to control and prevent nosocomial infections due to enterococci.

The nosocomial transmission of enterococci

In enterococci, the structural gene for beta-lactamase (blaZ) is identical to blaZ from Staphylococcus aureus. However, in the enterococci studied to date, beta-lactamase is produced constitutively, whereas in staphylococci it is often inducible. Recent reports have revealed the presence of two adjacent genes upstream of the staphylococcal blaZ thought to be the antirepressor (blaR1) and repressor (blaI) genes. In the present study, beta-lactamase expression mutants of the staphylococcal beta-lactamase plasmid pI524 were generated by transposon mutagenesis with the transposon Tn917. Tn917 insertions upstream of blaZ in either blaR1 or blaI resulted in constitutive beta-lactamase production, indicating that the repressor function is lost with insertion of Tn917 into either gene. This finding supports the concept that the staphylococcal beta-lactamase regulatory genes are encoded on a polycistronic mRNA. The corresponding region upstream of the enterococcal blaZ from Enterococcus faecalis HH22 was sequenced and compared with the staphylococcal blaR1 sequence. The two sequences were identical for 893 nucleotides, and then the sequences diverged completely. Therefore, in strain HH22, only 51% of the putative antirepressor gene is present and the repressor gene is also absent. In conclusion, constitutive beta-lactamase production in HH22 appears to be due to a lack of the regulatory genes blaR1 and blaI which regulate expression of blaZ in staphylococci.

Genes involved in the regulation of beta-lactamase production in enterococci and staphylococci.

Vancomycin-resistant enterococci: recent advances in genetics, epidemiology and therapeutic options.

Previously, TX5179, a disruption mutant of the enterococcal polysaccharide antigen (epa) gene cluster of Enterococcus faecalis strain OG1RF was shown to be attenuated in translocation, biofilm, mouse peritonitis and was more susceptible to polymorphonuclear leukocyte phagocytic killing. Here, wild-type E. faecalis OG1RF and TX5179 strains were tested in a mixed-infection (inoculum, approximately 1:1) mouse urinary tract infection model. Wild-type OG1RF outnumbered TX5179 in the kidneys (P < .001) and bladder (P < .001). In conclusion, the epa locus of E. faecalis OG1RF contributes to murine urinary tract infection and is the first such enterococcal polysaccharide locus shown to be important in this site.

/pdf/importance-of-the-epa-locus-of-enterococcus-faecalis-og1rf-2p37ypau3w.pdf

Barbara E. Murray

Papers

Enterococcal Endocarditis: Can We Win the War?

The nosocomial transmission of enterococci

Genes involved in the regulation of beta-lactamase production in enterococci and staphylococci.

Vancomycin-resistant enterococci: recent advances in genetics, epidemiology and therapeutic options.

Importance of the epa Locus of Enterococcus faecalis OG1RF in a Mouse Model of Ascending Urinary Tract Infection