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]

Testing interactive effects of global environmental changes on soil nitrogen cycling

Responses of soil nitrogen (N) cycling to simultaneous and potentially interacting global environmental changes are uncertain. Here, we investigated the combined effects of elevated CO2, warming, increased precipitation and enhanced N supply on soil N cycling in an annual grassland ecosystem as part of the Jasper Ridge Global Change Experiment (CA, USA). This field experiment included four treatments-CO2, temperature, precipitation, nitrogen-with two levels per treatment (ambient and elevated), and all their factorial combinations replicated six times. We collected soil samples after 7 and 8 years of treatments, and measured gross rates of N mineralization, N immobilization and nitrification, along with potential rates of ammonia oxidation, nitrite oxidation and denitrification. We also determined the main drivers of these microbial activities (soil ammonium and nitrate concentrations, soil moisture, soil temperature, soil pH, and soil CO2 efflux, as an indicator of soil heterotrophic activity). We found that gross N mineralization responded to the interactive effects of the CO2, precipitation and N treatments: N addition increased gross N mineralization when CO2 and precipitation were either both at ambient or both at elevated levels. However, we found limited evidence for interactions among elevated CO2, warming, increased precipitation, and enhanced N supply on the other N cycling processes examined: statistically significant interactions, when found, tended not to persist across multiple dates. Soil N cycling responded mainly to single-factor effects: long-term N addition increased gross N immobilization, potential ammonia oxidation and potential denitrification, while increased precipitation depressed potential nitrite oxidation and increased potential ammonia oxidation and potential denitrification. In contrast, elevated CO2 and modest warming did not significantly affect any of these microbial N transformations. These findings suggest that global change effects on soil N cycling are primarily additive, and therefore generally predictable from single factor studies

Penile Microbiota and Female Partner Bacterial Vaginosis in Rakai, Uganda

Bacterial vaginosis (BV) is a common vaginal bacterial imbalance associated with risk for HIV and poor gynecologic and obstetric outcomes. Male circumcision reduces BV-associated bacteria on the penis and decreases BV in female partners, but the link between penile microbiota and female partner BV is not well understood. We tested the hypothesis that having a female partner with BV increases BV-associated bacteria in uncircumcised men. We characterized penile microbiota composition and density (i.e., the quantity of bacteria per swab) by broad-coverage 16S rRNA gene-based sequencing and quantitative PCR (qPCR) in 165 uncircumcised men from Rakai, Uganda. Associations between penile community state types (CSTs) and female partner’s Nugent score were assessed. We found seven distinct penile CSTs of increasing density (CST1 to 7). CST1 to 3 and CST4 to 7 were the two major CST groups. CST4 to 7 had higher prevalence and abundance of BV-associated bacteria, such as Mobiluncus and Dialister, than CST1 to 3. Men with CST4 to 7 were significantly more likely to have a female partner with a high Nugent score (P = 0.03). Men with two or more extramarital partners were significantly more likely to have CST4 to 7 than men with only marital partners (CST4 to 7 prevalence ratio, 1.84; 95% confidence interval [CI], 1.16 to 2.92). Female partner Nugent BV is significantly associated with penile microbiota. Our data support the exchange of BV-associated bacteria through intercourse, which may explain BV recurrence and persistence. IMPORTANCE Bacterial vaginosis (BV) is sexually associated but not considered a sexually transmitted disease. Our findings suggest that the uncircumcised penis is an important niche for BV-associated genital anaerobes. In addition, we found a link between extramarital sexual relationships and BV-associated bacteria in men, which parallels earlier findings of the association between sexual activity and BV in women. This suggests the sexual transmissibility of BV-associated bacteria. Reducing bacterial exchange by barrier methods and managing carriage of BV-associated bacteria in men may decrease BV persistence and recurrence in women

Prevalence of antibiotic-resistant E. coli in retail chicken: Comparing conventional, organic, kosher, and raised without antibiotics

Retail poultry products are known sources of antibiotic-resistant Escherichia coli, a major human health concern. Consumers have a range of choices for poultry, including conventional, organic, kosher, and raised without antibiotics (RWA) – designations that are perceived to indicate differences in quality and safety. However, whether these categories vary in the frequency of contamination with antibiotic-resistant E. coli is unknown. We examined the occurrence of antibiotic-resistant E. coli on raw chicken marketed as conventional, organic, kosher and RWA. From April – June 2012, we purchased 213 samples of raw chicken from 15 locations in the New York City metropolitan area. We screened E. coli isolates from each sample for resistance to 12 common antibiotics. Although the organic and RWA labels restrict the use of antibiotics, the frequency of antibiotic-resistant E. coli tended to be only slightly lower for RWA, and organic chicken was statistically indistinguishable from conventional products that have no restrictions. Kosher chicken had the highest frequency of antibiotic-resistant E. coli, nearly twice that of conventional products, a result that belies the historical roots of kosher as a means to ensure food safety. These results indicate that production methods influence the frequency of antibiotic-resistant E. coli on poultry products available to consumers. Future research to identify the specific practices that cause the high frequency of antibiotic-resistant E. coli in kosher chicken could promote efforts to reduce consumer exposure to this potential pathogen

Prevalence of antibiotic-resistant E. coli in retail chicken: Comparing conventional, organic, kosher, and raised without antibiotics

Retail poultry products are known sources of antibiotic-resistant Escherichia coli, a major human health concern. Consumers have a range of choices for poultry, including conventional, organic, kosher, and raised without antibiotics (RWA) – designations that are perceived to indicate differences in quality and safety. However, whether these categories vary in the frequency of contamination with antibiotic-resistant E. coli is unknown. We examined the occurrence of antibiotic-resistant E. coli on raw chicken marketed as conventional, organic, kosher and RWA. From April – June 2012, we purchased 213 samples of raw chicken from 15 locations in the New York City metropolitan area. We screened E. coli isolates from each sample for resistance to 12 common antibiotics. Although the organic and RWA labels restrict the use of antibiotics, the frequency of antibiotic-resistant E. coli tended to be only slightly lower for RWA, and organic chicken was statistically indistinguishable from conventional products that have no restrictions. Kosher chicken had the highest frequency of antibiotic-resistant E. coli, nearly twice that of conventional products, a result that belies the historical roots of kosher as a means to ensure food safety. These results indicate that production methods influence the frequency of antibiotic-resistant E. coli on poultry products available to consumers. Future research to identify the specific practices that cause the high frequency of antibiotic-resistant E. coli in kosher chicken could promote efforts to reduce consumer exposure to this potential pathogen

Carbon and water fluxes from ponderosa pine forests disturbed by wildfire and thinning

Disturbances alter ecosystem carbon dynamics, often by reducing carbon uptake and stocks. We compared the impact of two types of disturbances that represent the most likely future conditions of currently dense ponderosa pine forests of the southwestern United States: (1) high-intensity fire and (2) thinning, designed to reduce fire intensity. High- severity fire had a larger impact on ecosystem carbon uptake and storage than thinning. Total ecosystem carbon was 42% lower at the intensely burned site, 10 years after burning, than at the undisturbed site. Eddy covariance measurements over two years showed that the burned site was a net annual source of carbon to the atmosphere whereas the undisturbed site was a sink. Net primary production (NPP), evapotranspiration (ET), and water use efficiency were lower at the burned site than at the undisturbed site. In contrast, thinning decreased total ecosystem carbon by 18%, and changed the site from a carbon sink to a source in the first post- treatment year. Thinning also decreased ET, reduced the limitation of drought on carbon uptake during summer, and did not change water use efficiency. Both disturbances reduced ecosystem carbon uptake by decreasing gross primary production (55% by burning, 30% by thinning) more than total ecosystem respiration (TER; 33–47% by burning, 18% by thinning), and increased the contribution of soil carbon dioxide efflux to TER. The relationship between TER and temperature was not affected by either disturbance. Efforts to accurately estimate regional carbon budgets should consider impacts on carbon dynamics of both large disturbances, such as high-intensity fire, and the partial disturbance of thinning that is often used to prevent intense burning. Our results show that thinned forests of ponderosa pine in the southwestern United States are a desirable alternative to intensively burned forests to maintain carbon stocks and primary production

<i>Staphylococcus aureus</i> and the ecology of the nasal microbiome

The human microbiome can play a key role in host susceptibility to pathogens, including in the nasal cavity, a site favored by Staphylococcus aureus. However, what determines our resident nasal microbiota—the host or the environment—and can interactions among nasal bacteria determine S. aureus colonization? Our study of 46 monozygotic and 43 dizygotic twin pairs revealed that nasal microbiota is an environmentally derived trait, but the host’s sex and genetics significantly influence nasal bacterial density. Although specific taxa, including lactic acid bacteria, can determine S. aureus colonization, their negative interactions depend on thresholds of absolute abundance. These findings demonstrate that nasal microbiota is not fixed by host genetics and opens the possibility that nasal microbiota may be manipulated to prevent or eliminate S. aureus colonization

Staphylococcus aureus and the ecology of the nasal microbiome

The human microbiome can play a key role in host susceptibility to pathogens, including in the nasal cavity, a site favored by Staphylococcus aureus. However, what determines our resident nasal microbiota—the host or the environment—and can interactions among nasal bacteria determine S. aureus colonization? Our study of 46 monozygotic and 43 dizygotic twin pairs revealed that nasal microbiota is an environmentally derived trait, but the host’s sex and genetics significantly influence nasal bacterial density. Although specific taxa, including lactic acid bacteria, can determine S. aureus colonization, their negative interactions depend on thresholds of absolute abundance. These findings demonstrate that nasal microbiota is not fixed by host genetics and opens the possibility that nasal microbiota may be manipulated to prevent or eliminate S. aureus colonization

The Effect of Basal Diet on Lactate-Producing Bacteria and the Susceptibility of Sheep to Lactic Acidosis

The influence of a diet of either pasture or hay on the development of lactic acidosis in sheep was investigated using a grain challenge approach. Twenty-four Merino wethers with a mean live weight of 36.7 (s.e. 3.6) kg were used; 12 were adapted to grass pasture and 12 to hay (lucerne and oaten hay, 60 : 40) for 4 weeks before being given 1 kg of crushed barley via stomach tube. Six sheep in each group were also given virginiamycin (VM; 50 mg/kg barley) with the grain to test the efficacy of this antibiotic in controlling the bacteria responsible for the development of acidosis. Changes in volatile fatty acid (VFA), pH, lactate and bacterial count in the rumen and faecal pH and dry matter (DM) were measured for a 24-h period following administration of the barley. Daily intakes of hay were measured for a 10-day period following grain engorgement. Total ruminal VFA increased (P < 0.01) over time and tended (P = 0.08) to be higher in sheep adapted to hay than in those adapted to pasture (67.5 v. 59.8 mmol/l). The molar proportions of VFA changed (P< 0.01) over time in favour of propionate in both groups. Ruminal pH was higher (P< 0.001) in pasture-adapted sheep, but declined (P< 0.001) in both groups over time following the introduction of barley. This decline in pH was associated with increases in ruminal concentration of VFA in pasture-adapted sheep and VFA and lactate in hay-adapted sheep. The addition of VM resulted in a higher (P < 0.001) proportion of propionate and a trend towards higher (P = 0.24) faecal pH and DM content. Faecal pH and DM content declined (P < 0.001) over time and was lower for the pasture-adapted sheep. The introduction of either barley alone or barley with VM from both hay and pasture diets increased (P < 0.05) the viable counts of total bacteria, Streptococcus bovis and lactic acid bacteria. Bacterial isolates were purified and identified by complete sequencing of the 16S rRNA gene to determine the predominant bacteria during the overfeeding of grain. Isolates from medium selective for S. bovis were all identified as this species when VM was not given. VM had no effect on counts of viable bacteria, but inhibited the growth of S. bovis