Identification of novel antimicrobial resistance genes from microbiota on retail spinach

BackgroundDrug resistance genes and their mobile genetic elements are frequently identified from environmental saprophytic organisms. It is widely accepted that the use of antibiotics in animal husbandry selects for drug resistant microorganisms, which are then spread from the farm environment to humans through the consumption of contaminated food products. We wished to identify novel drug resistance genes from microbial communities on retail food products. Here, we chose to study the microbial communities on retail spinach because it is commonly eaten raw and has previously been associated with outbreaks of bacterial infections.ResultsWe created metagenomic plasmid libraries from microbiota isolated from retail spinach samples. We identified five unique plasmids that increased resistance to antimicrobial drugs in the E. coli host. These plasmids were identified in E. coli that grew on plates that contained ampicillin (pAMP), aztreonam (pAZT), ciprofloxacin (pCIP), trimethoprim (pTRM), and trimethoprim-sulfamethoxazole (pSXT). We identified open reading frames with similarity to known classes of drug resistance genes in the DNA inserts of all 5 plasmids. These drug resistance genes conferred resistance to fluoroquinolones, cephalosporins, and trimethoprim, which are classes of antimicrobial drugs frequently used to treat human Gram negative bacterial infections. These results show that novel drug resistance genes are found in microbiota on retail produce items.ConclusionsHere we show that microbiota of retail spinach contains DNA sequences previously unidentified as conferring antibiotic resistance. Many of these novel sequences show similarity to genes found in species of bacteria, which have previously been identified as commensal or saprophytic bacteria found on plants. We showed that these resistance genes are capable of conferring clinically relevant levels of resistance to antimicrobial agents. Food saprophytes may serve as an important reservoir for new drug-resistance determinants in human pathogens

Characterization of an Outbreak of Hand, Foot, and Mouth Disease in Nanchang, China in 2010

Recent outbreaks of human enterovirus 71 (EV71) infection and EV71-associated hand, foot, and mouth disease (HFMD) in China have affected millions and potentially lead to life-threatening complications in newborns. Furthermore, these outbreaks represent a significant global public health issue in the world. Understanding the epidemiology of HFMD and EV71 infection and their transmission patterns in China is essential for controlling outbreaks. However, no studies on the outbreaks of HFMD and EV71 infection in China during 2010 have been reported. In this report, we carried out an epidemiological analysis to study an outbreak of HFMD and EV71 infection in 2010 in the city of Nanchang in the Jiangxi province of People's Republic of China. From April 7 to May 11, 2010, a total of 109 HFMD cases were reported, and in this report the HFMD cases were studied by both epidemiological and laboratory analyses. The epidemiological study indicates that children aged younger than 8 years old represented more than 90% of the reported cases, with the age group of 1–3 years containing the highest number of cases. Laboratory studies detected a high prevalence of EV71 amongst the cases in our study, suggesting EV71 as a common enterovirus found in HFMD cases in Nanchang. Phylogenetic analysis of the sequence of the VP1 region of four EV71 isolates indicated that the Nanchang strains belong to the C4 subgenotype commonly found in China during outbreaks in 2008 but contain distinct variations from these strains. Our study for the first time characterizes the epidemiology of HFMD and EV71 infection in China in 2010 and furthermore, provides the first direct evidence of the genotype of EV71 circulating in Nanchang, China. Our study should facilitate the development of public health measures for the control and prevention of HFMD and EV71 infection in at-risk individuals in China

The Spread of Drug Resistance in Gram Negative Bacteria

Drug resistant infections with Gram negative bacteria have become increasingly common. Some of these Gram negative bacteria are pan resistant. To better understand the spread of drug resistant infections we used E. coli as a model system. By using this system we investigated both the spread of drug resistance genes and bacteria that are drug resistant.Drug resistance genes and their mobile genetic elements are frequently identified from environmental saprophytic organisms. It is widely accepted that the use of antibiotics in agriculture selects for drug resistant microorganisms, which are then spread from the farm environment to humans through the consumption of contaminated food products. We wished to identify novel drug resistance genes from microbial communities on retail food products. To do this, we created metagenomic plasmid libraries from microbiota isolated from retail spinach samples. From these libraries we identified five unique plasmids that increased resistance to antimicrobial drugs. These plasmids were identified in E. coli that grew on plates that contained ampicillin (pAMP), aztreonam (pAZT), ciprofloxacin (pCIP), trimethoprim (pTRM), and trimethoprim-sulfamethoxazole (pSXT). We identified open reading frames with similarity to known classes of drug resistance genes in the DNA inserts of all five plasmids. These drug resistance genes conferred resistance to fluoroquinolones, cephalosporins, and trimethoprim, which are classes of antimicrobial drugs frequently used to treat human Gram negative bacterial infections. These results show that novel drug resistance genes are found in microbiota on retail produce items. Food saprophytes may serve as an important reservoir for new drug-resistance determinants in human pathogens.The clinical management of infections caused by E. coli, including meningitis, is greatly complicated when the organism becomes resistant to broad-spectrum antibiotics. We sought to characterize the antimicrobial susceptibility, multilocus sequence type (MLST), and presence of known drug resistance genes of E. coli that caused meningitis between 1996 and 2011 in Salvador, Brazil. We then compared these findings to E. coli isolates from community acquired urinary tract infections (UTI) that occurred during the same time period and in the same city. We found 19% of E. coli from cases of meningitis and less than 1% of isolates from UTI to be resistant to third-generation cephalosporins. The sequence types of E. coli from cases of meningitis included ST 131, ST 69, ST 405, and ST 62, which were also found among isolates from UTI. These sequence types of E. coli have previously been isolated from produce items and food animals. Additionally, among the E. coli isolates that were resistant to third-generation cephalosporins, we found genes that encode the extended-spectrum beta-lactamases CTX-M-2, CTX-M-14, and CTX-M-15. These observations demonstrate that, compared to E. coli isolated from cases of community acquired UTI, those isolated from cases of meningitis are more resistant to third-generation cephalosporins, even though the same sequence types are shared between the two forms of extraintestinal infections.The results of our investigation of retail food products indicate that drug resistant genes are frequently found in these products and that these food items may be a reservoir for drug resistance genes found in human pathogens. We also found that many of the sequence types of E. coli that cause both UTI and meningitis have previously been isolated from retail food products. These findings suggest that bacteria that are considered to be normal flora of food products may play an important role of the spread of drug resistant genes and drug resistant bacteria

HIV Nef and Antiretroviral Therapy Have an Inhibitory Effect on Autophagy in Human Astrocytes that May Contribute to HIV-Associated Neurocognitive Disorders

A significant number of people living with HIV (PLWH) develop HIV-associated neurocognitive disorders (HAND) despite highly effective antiretroviral therapy (ART). Dysregulated macroautophagy (autophagy) is implicated in HAND pathogenesis. The viral protein Nef, expressed even with suppressive ART, and certain antiretrovirals affect autophagy in non-CNS cells. Astrocytes, vital for CNS microenvironment homeostasis and neuronal health, require autophagy for their own homeostasis. We hypothesized that extracellular Nef and/or ART impact astrocyte autophagy, thus contributing to HAND. We studied in-bulk and selective autophagic flux in primary human astrocytes treated with extracellular Nef and/or a combination of tenofovir+emtricitabine+raltegravir (ART) using Western blotting, a tandem fluorescent LC3 reporter, and transmission electron microscopy/morphometry. We show that after 24 h treatment, Nef and ART decrease autophagosomes through different mechanisms. While Nef accelerates autophagosome degradation without inducing autophagosome formation, ART inhibits autophagosome formation. Combination Nef+ART further depletes autophagosomes by inducing both abnormalities. Additionally, extracellular Nef and/or ART inhibit lysosomal degradation of p62, indicating Nef and/or ART affect in-bulk and selective autophagy differently. Dysregulation of both autophagic processes is maintained after 7 days of Nef and/or ART treatment. Persistent autophagy dysregulation due to chronic Nef and/or ART exposure may ultimately result in astrocyte and neuronal dysfunction, contributing to HAND

Distribution of superantigens in group A streptococcal isolates from Salvador, Brazil.

BackgroundGroup A streptococcus (GAS) causes invasive disease, superficial disease, and can asymptomatically colonize humans. Superantigens are one virulence factor found in GAS. Previous studies found associations between the genes that encode superantigens and emm type of GAS. It is unknown if these associations are due to underlying biological factors that limit the distribution of superantigens or, alternatively, if these associations are due to the expansion of local GAS linages where these studies took place. To further address this question we screened GAS isolates collected from Salvador, Brazil for 11 known superantigen genes.MethodsSeventy-seven GAS isolates were screened by PCR for superantigen genes. These superantigen genes were speA, speC, speG, speH, speI, speJ, speK, speL, speM, ssa, and smeZ. We used Fisher's two-sided exact test to identify associations between superantigens and GAS emm type. We then compared our results to previous reports of superantigen prevalence and superantigen association with emm type.ResultsIn our collection we found several emm type and superantigen genotype combinations that have previously been reported in isolates from Europe and Australia. We also found that speA was significantly associated with emm type 1, and that speC was significantly associated with emm type 12.ConclusionsOur study reports superantigen genotypes of GAS from a region of the world that is lacking this information. We found evidence of common GAS superantigen genotypes that are spread worldwide as well as novel superantigen genotypes that, so far, are unique to Brazil

Distribution of superantigens in group A streptococcal isolates from Salvador, Brazil

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2018-02-27T16:26:25Z No. of bitstreams: 1 Berman HF Distribution of superantigens....pdf: 197957 bytes, checksum: fe310ef26181ee406383d2386dcb5b96 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2018-02-27T16:37:13Z (GMT) No. of bitstreams: 1 Berman HF Distribution of superantigens....pdf: 197957 bytes, checksum: fe310ef26181ee406383d2386dcb5b96 (MD5)Made available in DSpace on 2018-02-27T16:37:14Z (GMT). No. of bitstreams: 1 Berman HF Distribution of superantigens....pdf: 197957 bytes, checksum: fe310ef26181ee406383d2386dcb5b96 (MD5) Previous issue date: 2014Fogarty International Center, NIH, Grant number TW006563.University of California. School of Public Health. Division of Infectious Disease and Vaccinology. Berkeley, CA, USAUniversity of California. School of Public Health. Division of Infectious Disease and Vaccinology. Berkeley, CA, USA / Kaiser Permanente Southern California Research and Evaluation. Pasadena, CA, USAFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrasilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrasilUniversity of California. School of Public Health. Division of Infectious Disease and Vaccinology. Berkeley, CA, USAGroup A streptococcus (GAS) causes invasive disease, superficial disease, and can asymptomatically colonize humans. Superantigens are one virulence factor found in GAS. Previous studies found associations between the genes that encode superantigens and emm type of GAS. It is unknown if these associations are due to underlying biological factors that limit the distribution of superantigens or, alternatively, if these associations are due to the expansion of local GAS linages where these studies took place. To further address this question we screened GAS isolates collected from Salvador, Brazil for 11 known superantigen genes. Methods: Seventy-seven GAS isolates were screened by PCR for superantigen genes. These superantigen genes were speA, speC, speG, speH, speI, speJ, speK, speL, speM, ssa, and smeZ. We used Fisher’s two-sided exact test to identify associations between superantigens and GAS emm type. We then compared our results to previous reports of superantigen prevalence and superantigen association with emm type. Results: In our collection we found several emm type and superantigen genotype combinations that have previously been reported in isolates from Europe and Australia. We also found that speA was significantly associated with emm type 1, and that speC was significantly associated with emm type 12. Conclusions: Our study reports superantigen genotypes of GAS from a region of the world that is lacking this information. We found evidence of common GAS superantigen genotypes that are spread worldwide as well as novel superantigen genotypes that, so far, are unique to Brazil

Distribution of strain type and antimicrobial susceptibility of Escherichia coli isolates causing meningitis in a large urban setting in Brazil

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2014-09-29T17:43:30Z No. of bitstreams: 1 Berman H Distribution....pdf: 631104 bytes, checksum: a03fc22fb8394fe9d8a832d47033a4f4 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2014-09-29T17:43:46Z (GMT) No. of bitstreams: 1 Berman H Distribution....pdf: 631104 bytes, checksum: a03fc22fb8394fe9d8a832d47033a4f4 (MD5)Made available in DSpace on 2014-09-29T18:21:17Z (GMT). No. of bitstreams: 1 Berman H Distribution....pdf: 631104 bytes, checksum: a03fc22fb8394fe9d8a832d47033a4f4 (MD5) Previous issue date: 2014University of California. School of Public Health. Division of Infectious Disease and Vaccinology. Berkeley, California, USA.Fundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, Brasil.University of California. School of Public Health. Division of Infectious Disease and Vaccinology. Berkeley, California, USA.Fundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Salvador, BA, Brasil.The clinical management of meningitis caused by Escherichia coli is greatly complicated when the organism becomes resistant to broad-spectrum antibiotics. We sought to characterize the antimicrobial susceptibilities, sequence types (ST), and presence of known drug resistance genes of E. coli isolates that caused meningitis between 1996 and 2011 in Salvador, Brazil. We then compared these findings to those for E. coli isolates from community-acquired urinary tract infections (UTI) that occurred during the same time period and in the same city. We found that 19% of E. coli isolates from cases of meningitis and less than 1% of isolates from UTI were resistant to third-generation cephalosporins. The sequence types of E. coli isolates from cases of meningitis included ST131, ST69, ST405, and ST62, which were also found among isolates from UTI. Additionally, among the E. coli isolates that were resistant to third-generation cephalosporins, we found genes that encode the extended-spectrum beta-lactamases CTX-M-2, CTX-M-14, and CTX-M-15. These observations demonstrate that compared to E. coli strains isolated from cases of community-acquired UTI, those isolated from cases of meningitis are more resistant to third-generation cephalosporins, even though the same sequence types are shared between the two forms of extraintestinal infections

New Primitive Caseid (Synapsida, Caseasauria) from the Early Permian of Germany

A new genus and species of a basal synapsid Caseidae, Martensius bromackerensis, is described based on four partial to nearly complete mostly articulated skeletons that provide a comprehensive knowledge of the skeletal morphology. All four specimens were collected from a single site, the Bromacker quarry, in the Lower Permian Artinskian Tambach Formation, Germany. The Bromacker caseid is the first to be reported from Germany and can be easily distinguished from all other caseids based on substantial lists of autapomorphic and plesiomorphic characters. Of the four caseid specimens only the smallest, a juvenile, and the largest, an adult designated as the holotype, are nearly complete, articulated, and possess skull material: in the juvenile a small partially articulated portion of the skull, and in the adult a nearly complete but dorsoventrally crushed skull. The two specimens are distinguished from one another by features attributed to different ontogenetic stages of development, which include skeletal ossification, proportional dimensions of elements, and most interestingly marginal dentitions. The last category includes a feature unique among caseids of an ontogenetic change in the dentition from insectivorous in the juvenile specimen to what is believed to be an omnivorous dentition in the adult. A phylogenetic analysis posits the Late Pennsylvanian Eocasea martiniReisz and Fröbisch, 2014, as the basalmost member of the monophyletic Caseidae and the later occurring middle Early Permian Bromacker caseid as the sister taxon of the remaining late Early and Middle Permian members of the clade. This series of relationships parallels a proposed chronology of evolutionary changes in the dentitions and associated diets of caseids

Do state minimum markup/price laws work? Evidence from retail scanner data and TUS-CPS

BACKGROUND: Minimum markup/price laws (MPLs) have been proposed as an alternative non-tax pricing strategy to reduce tobacco use and access. However, the empirical evidence on the effectiveness of MPLs in increasing cigarette prices is very limited. This study aims to fill this critical gap by examining the association between MPLs and cigarette prices. METHODS: State MPLs were compiled from primary legal research databases and were linked to cigarette prices constructed from the Nielsen retail scanner data and the self-reported cigarette prices from the Tobacco Use Supplement to the Current Population Survey. Multivariate regression analyses were conducted to examine the association between MPLs and the major components of MPLs and cigarette prices. RESULTS: The presence of MPLs was associated with higher cigarette prices. In addition, cigarette prices were higher, above and beyond the higher prices resulting from MPLs, in states that prohibit below-cost combination sales; do not allow any distributing party to use trade discounts to reduce the base cost of cigarettes; prohibit distributing parties from meeting the price of a competitor, and prohibit distributing below-cost coupons to the consumer. Moreover, states that had total markup rates >24% were associated with significantly higher cigarette prices. CONCLUSIONS: MPLs are an effective way to increase cigarette prices. The impact of MPLs can be further strengthened by imposing greater markup rates and by prohibiting coupon distribution, competitor price matching, and use of below-cost combination sales and trade discounts