The Mesh Archetype

A parallel program archetype [2] aids in the development of reliable, efficient parallel applications with common computation/communication structures by providing development methods and code libraries specific to the structure. This document presents an archetype for mesh-spectral computations. It describes the common structure captured by the archetype abstraction, discusses a parallelization strategy for such computations, documents our code library to support this parallelization strategy, and presents a collection of tutorial example application programs

Prospectus, October 25, 2000

https://spark.parkland.edu/prospectus_2000/1028/thumbnail.jp

Antibiotic-resistant Escherichia Coli from Retail Poultry Meat with Different Antibiotic Use Claims

Background We sought to determine if the prevalence of antibiotic-resistant Escherichia coli differed across retail poultry products and among major production categories, including organic, “raised without antibiotics”, and conventional. Results We collected all available brands of retail chicken and turkey—including conventional, “raised without antibiotic”, and organic products—every two weeks from January to December 2012. In total, E. coli was recovered from 91% of 546 turkey products tested and 88% of 1367 chicken products tested. The proportion of samples contaminated with E. coli was similar across all three production categories. Resistance prevalence varied by meat type and was highest among E. coli isolates from turkey for the majority of antibiotics tested. In general, production category had little effect on resistance prevalence among E. coli isolates from chicken, although resistance to gentamicin and multidrug resistance did vary. In contrast, resistance prevalence was significantly higher for 6 of the antibiotics tested—and multidrug resistance—among isolates from conventional turkey products when compared to those labelled organic or “raised without antibiotics”. E. coli isolates from chicken varied strongly in resistance prevalence among different brands within each production category. Conclusion The high prevalence of resistance among E. coli isolates from conventionally-raised turkey meat suggests greater antimicrobial use in conventional turkey production as compared to “raised without antibiotics” and organic systems. However, among E. coli from chicken meat, resistance prevalence was more strongly linked to brand than to production category, which could be caused by brand-level differences during production and/or processing, including variations in antimicrobial use

Colonizing opportunistic pathogens (COPs): The beasts in all of us.

Colonizing opportunistic pathogens (COPs) are microbes that asymptomatically colonize the human body and, when the conditions are right, can cause infections. Their ability to persist indefinitely and to be transmitted without detection [1] gives COPs a unique epidemiology that warrants special consideration. There are examples of COPs among bacteria, fungi (e.g., Candida albicans [2]), protozoa (e.g., Blastocystis [3, 4]), and viruses (e.g., Rhinovirus [5]), but bacterial COPs are of particular relevance because of their major contribution to today’s antibiotic resistance crisis. The COPs include a long list of notorious bacteria that live double lives as passive stowaways and virulent foes. Some of the best-known COPs include Staphylococcus aureus, extraintestinal pathogenic Escherichia coli (ExPEC), Klebsiella pneumoniae, and Streptococcus pneumoniae (Table 1). Their capacity for benign coexistence with humans belies their alter egos that exact a heavy burden of human disease. For example, in the United States, ExPEC bloodstream infections kill as many as 40,000 people annually [6], but, ExPEC are also benign colonizers in the gastrointestinal tract [7]. Host factors, including age, sex, health status, anatomy, and behavior, all play profound roles in infection susceptibility and severity [8–10]. In particular, immunocompromised individuals are at excess risk for infections caused by diverse bacteria, including COPs [11, 12] and even commensals. Yet, health status is not the sole determinant of infection by COPs. For example, healthy women more frequently suffer from urinary tract infections than men because of anatomical differences, including shorter urethrae. Likewise, healthy children more commonly suffer from acute otitis media than adults due to their shorter, flatter eustachian tubes [13]

Intermingled Klebsiella pneumoniae Populations Between Retail Meats and Human Urinary Tract Infections

Background. Klebsiella pneumoniae is a common colonizer of the gastrointestinal tract of humans, companion animals, and livestock. To better understand potential contributions of foodborne K. pneumoniae to human clinical infections, we compared K. pneumoniae isolates from retail meat products and human clinical specimens to assess their similarity based on antibiotic resistance, genetic relatedness, and virulence. Methods. Klebsiella pneumoniae was isolated from retail meats from Flagstaff grocery stores in 2012 and from urine and blood specimens from Flagstaff Medical Center in 2011–2012. Isolates underwent antibiotic susceptibility testing and whole-genome sequencing. Genetic relatedness of the isolates was assessed using multilocus sequence typing and phylogenetic analyses. Extraintestinal virulence of several closely related meat-source and urine isolates was assessed using a murine sepsis model. Results. Meat-source isolates were significantly more likely to be multidrug resistant and resistant to tetracycline and gentamicin than clinical isolates. Four sequence types occurred among both meat-source and clinical isolates. Phylogenetic analyses confirmed close relationships among meat-source and clinical isolates. Isolates from both sources showed similar virulence in the mouse sepsis model. Conclusions. Meat-source K. pneumoniae isolates were more likely than clinical isolates to be antibiotic resistant, which could reflect selective pressures from antibiotic use in food-animal production. The close genetic relatedness of meat-source and clinical isolates, coupled with similarities in virulence, suggest that the barriers to transmission between these 2 sources are low. Taken together, our results suggest that retail meat is a potential vehicle for transmitting virulent, antibiotic-resistant K. pneumoniae from food animals to humans

Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis

Background. Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but has been assessed minimally using whole genome sequence (WGS) analysis. Methods. Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in six households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates. Results. In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only one household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these two groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In one instance the household\u27s index strain persisted for 6 years before causing a new infection in a different household member. Conclusions. Within-household sharing of E. coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members

Evolution of Lyman Alpha Galaxies: Stellar Populations at z ~ 0.3

We present the results of a stellar population analysis of 30 Lyman alpha emitting galaxies (LAEs) at z ~ 0.3, previously discovered with the Galaxy Evolution Explorer (GALEX). With a few exceptions, we can accurately fit model spectral energy distributions to these objects, representing the first time this has been done for a large sample of LAEs at z < 3, a gap of ~ 8 Gyr in the history of the Universe. From the 26/30 LAEs which we can fit, we find an age and stellar mass range of 200 Myr - 10 Gyr and 10^9 - 10^11 Msol, respectively. These objects thus appear to be significantly older and more massive than LAEs at high-redshift. We also find that these LAEs show a mild trend towards higher metallicity than those at high redshift, as well as a tighter range of dust attenuation and interstellar medium geometry. These results suggest that low-redshift LAEs have evolved significantly from those at high redshift.Comment: Accepted for publication in the Astrophysical Journal. Replaced with accepted version. Eight pages, four figures, in emulateapj forma