Determining drug resistance trends will optimize treatment and public health responses.

Escherichia coli isolates were recovered from the National Antimicrobial Resistance Monitoring System retail meat program and examined for antimicrobial susceptibility. Retail meat samples (n ‫؍‬ 11,921) from four U.S. states collected during 2002 to 2008, consisting of 2,988 chicken breast, 2,942 ground turkey, 2,991 ground beef, and 3,000 pork chop samples, were analyzed. A total of 8,286 E. coli isolates were recovered. The greatest numbers of samples contaminated with the organism were chicken (83.5%) and turkey (82.0%), followed by beef (68.9%) and pork (44.0%). Resistance was most common to tetracycline (50.3%), followed by streptomycin (34.6%), sulfamethoxazole-sulfisoxazole (31.6%), ampicillin (22.5%), gentamicin (18.6%), kanamycin (8.4%), amoxicillin-clavulanic acid (6.4%), and cefoxitin (5.2%). Less than 5% of the isolates had resistance to trimethoprim, ceftriaxone, ceftiofur, nalidixic acid, chloramphenicol, and ciprofloxacin. All isolates were susceptible to amikacin. Compared to beef and pork isolates, the poultry meat isolates had a greater percentage of resistance to all tested drugs, with the exception of chloramphenicol, to which pork isolates had the most resistance. More than half of the turkey isolates (56%) were resistant to multidrugs (>3 classes) compared to 38.9% of chicken, 17.3% of pork, and 9.3% of beef isolates. The bla CMY gene was present in all ceftriaxone-and ceftiofur-resistant isolates. The cmlA, flo, and catI genes were present in 45%, 43%, and 40% of chloramphenicol-resistant isolates, respectively. Most nalidixic acid-resistant isolates (98.5%) had a gyrA mutation in S83 or D87 or both, whereas only 6.7% had a parC mutation in either S80 or E84. The results showed that E. coli was commonly present in the retail meats, and antimicrobial resistance profiles differed according to the animal origin of the isolates. E scherichia coli is a commensal bacterium in humans and animals and has a wide range of hosts. It is commonly present in the environment and is considered an indicator of fecal contamination in food and water. E. coli can acquire, maintain, and transmit resistance genes from other organisms in the environment. Due to its ubiquity in humans and animals and its role as a pathogenic and commensal organism, E. coli has become one of the microorganisms that are commonly resistant to antimicrobials.The level of antimicrobial resistance in E. coli represents a useful indicator of resistance dissemination in bacterial populations and of selective pressure imposed by the antimicrobials used in treatment of food animals and humans (2,25,28,30). Sáenz et al. (25) showed that the frequency of resistance to different antimicrobials in E. coli differed according to the source of the isolates. E. coli isolates from broilers were resistant to ciprofloxacin (CIP) (38%) and gentamicin (GEN) (40%) compared to 0% resistance to both drugs among E. coli isolates from healthy human volunteers versus 16% and 8% resistance among E. coli isolates from human clinical specimens. Kikuvi et al....

The emergence of antimicrobial resistance in Campylobacter spp. has been a growing public health concern globally. The objectives of this study were to determine the prevalence, antimicrobial susceptibility, and genetic relatedness of Campylobacter spp. recovered by the National Antimicrobial Resistance Monitoring System (NARMS) retail meat program. Retail meat samples (n ‫؍‬ 24,566) from 10 U.S. states collected between 2002 and 2007, consisting of 6,138 chicken breast, 6,109 ground turkey, 6,171 ground beef, and 6,148 pork chop samples, were analyzed. A total of 2,258 Campylobacter jejuni, 925 Campylobacter coli, and 7 Campylobacter lari isolates were identified. Chicken breast samples showed the highest contamination rate (49.9%), followed by ground turkey (1.6%), whereas both pork chops and ground beef had <0.5% contamination. The most common resistance was to doxycycline/tetracycline (46.6%), followed by nalidixic acid (18.5%), ciprofloxacin (17.4%), azithromycin and erythromycin (2.8%), telithromycin (2.4%), clindamycin (2.2%), and gentamicin (<0.1%). In a subset of isolates tested, no resistance to meropenem and florfenicol was seen. C. coli isolates showed higher resistance rates to antimicrobials, with the exception of doxycycline/tetracycline, than those seen for C. jejuni. Pulsed-field gel electrophoresis (PFGE) fingerprinting resulted in 1,226 PFGE profiles among the 2,318 isolates, with many clones being widely dispersed throughout the 6-year sampling period.

This study evaluated the effectiveness of formulary substitution from products or regimens containing name brand emtricitabine to alternative regimens containing generic lamivudine among virologically suppressed HIV-infected patients in a correctional managed health care system. Results of this retrospective cohort study showed that 94.9% of patients switched from emtricitabine to lamivudine ( n = 447) and 93.0% of emtricitabine control patients ( n = 449) had an undetectable viral load at last available test over a 2-year period. The two groups also showed similar values for CD4 counts, compliance, discontinuation, and M184V mutation; however, a slightly greater proportion of lamivudine patients experienced respiratory symptoms. Nonetheless, this study demonstrates that switching virologically suppressed HIV-infected patients from name brand emtricitabine-containing regimens to generic lamivudine-based regimens may reduce costs without compromising safety or effectiveness in correctional managed health care systems with directly observed therapy.

Adaptive metabolic switches are proposed to underlie conversions between cellular states during normal development as well as in cancer evolution, where they represent important therapeutic targets. However, the full spectrum, characteristics and regulation of existing metabolic switches are unknown. We propose that metabolic switches can be recognised by locating large alternating gene expression patterns and associate them with specific metabolic states. We developed a method to identify interspersed genesets by massive correlated biclustering (MCbiclust) and predict their metabolic wiring. Testing the method on major breast cancer transcriptome datasets we discovered a series of gene sets with switch-like behaviour, predicting mitochondrial content, activity and central carbon fluxes in tumours associated with different switch positions. The predictions were experimentally validated by bioenergetic profiling and metabolic flux analysis of 13C-labelled substrates, and were ultimately extended by geneset analysis to link metabolic alterations to cellular states, thus predicting tumour pathology, prognosis and chemosensitivity. The method is applicable to any large and heterogeneous transcriptome dataset to discover metabolic and associated pathophysiological states.