Last data update: Oct 28, 2024. (Total: 48004 publications since 2009)
Records 1-21 (of 21 Records) |
Query Trace: Peralta G [original query] |
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A compendium of multi-omics data illuminating host responses to lethal human virus infections
Eisfeld AJ , Anderson LN , Fan S , Walters KB , Halfmann PJ , Westhoff Smith D , Thackray LB , Tan Q , Sims AC , Menachery VD , Schäfer A , Sheahan TP , Cockrell AS , Stratton KG , Webb-Robertson BM , Kyle JE , Burnum-Johnson KE , Kim YM , Nicora CD , Peralta Z , N'Jai A U , Sahr F , van Bakel H , Diamond MS , Baric RS , Metz TO , Smith RD , Kawaoka Y , Waters KM . Sci Data 2024 11 (1) 328 Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology. |
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.
Walker K , Kalra D , Lowdon R , Chen G , Molik D , Soto DC , Dabbaghie F , Khleifat AA , Mahmoud M , Paulin LF , Raza MS , Pfeifer SP , Agustinho DP , Aliyev E , Avdeyev P , Barrozo ER , Behera S , Billingsley K , Chong LC , Choubey D , De Coster W , Fu Y , Gener AR , Hefferon T , Henke DM , Höps W , Illarionova A , Jochum MD , Jose M , Kesharwani RK , Kolora SRR , Kubica J , Lakra P , Lattimer D , Liew CS , Lo BW , Lo C , Lötter A , Majidian S , Mendem SK , Mondal R , Ohmiya H , Parvin N , Peralta C , Poon CL , Prabhakaran R , Saitou M , Sammi A , Sanio P , Sapoval N , Syed N , Treangen T , Wang G , Xu T , Yang J , Zhang S , Zhou W , Sedlazeck FJ , Busby B . F1000Res 2022 11 530 In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics. |
Multistate outbreak of turtle-associated salmonellosis highlights ongoing challenges with the illegal sale and distribution of small turtles
Nemechek K , Stapleton GS , Waltenburg MA , Low MSF , Gollarza L , Adams J , Peralta V , Lopez K , Morrison A , Schnitzler H , Kline KE , McGinnis S , Nichols M . Zoonoses Public Health 2023 70 (8) 684-691 The sale and distribution of small turtles (shell length <4 inches) as pets has been banned in the United States since 1975 because of the risk of Salmonella transmission, especially to children. Despite this 48-year-old ban, salmonellosis outbreaks continue to be linked to contact with small turtles. During investigations of turtle-associated outbreaks, information regarding the turtle farm of origin is difficult to obtain because turtles are commonly sold by transient vendors. During 2020-2021, public health officials investigated a multistate illness outbreak caused by Salmonella enterica serotype Typhimurium linked to pet small turtles. Cases were defined as a laboratory-confirmed Salmonella Typhimurium infection highly related (within 0-6 allele differences) to the outbreak strain based on whole-genome sequencing analysis by core-genome multilocus sequence typing with illness onset occurring during 27 August 2020-14 May 2021. Forty-three patients were identified from 12 states; of these, 35% (15/43) were children <5 years old. Among patients with available information, 37% (14/38) were hospitalized, and one death was reported. Seventy-four percent (25/34) of patients reported turtle exposure in the week before illness onset, and 84% (16/19) specified exposure to small turtles. The outbreak strain was isolated from samples collected from a Pennsylvania patient's small turtle tank. Two patients reported purchasing their small turtles from pet stores. Salmonella Braenderup was isolated from samples collected from small turtles and their habitat at one of these stores; however, at that time, this strain was not associated with any human illnesses. This investigation was notable because of the documented sale of small turtles from several pet stores combined with the identification of a single small turtle supplier to these pet stores. The high proportion of children involved in this outbreak highlights the continued need to educate the pet industry as well as parents and caregivers about the risk of turtle-associated salmonellosis especially in children. Understanding and addressing the persisting challenges related to the illegal sale and distribution of small turtles could reduce the burden of turtle-associated salmonellosis. |
Two multistate outbreaks of a reoccurring Shiga toxin-producing Escherichia coli strain associated with romaine lettuce - United States, 2018-2019
Waltenburg MA , Schwensohn C , Madad A , Seelman SL , Peralta V , Koske SE , Boyle MM , Arends K , Patel K , Mattioli M , Gieraltowski L , Neil KP . Epidemiol Infect 2021 150 e16 Leafy green vegetables are a common source of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) foodborne illness outbreaks. Ruminant animals, primarily cattle, are the major reservoir of STEC O157. Epidemiological, traceback, and field investigations were conducted to identify potential outbreak sources. Product and environmental samples were tested for STEC. A reoccurring strain of STEC O157 caused two multistate outbreaks linked to romaine lettuce in 2018 and 2019, resulting in 234 illnesses in 33 states. Over 80% of patients interviewed consumed romaine lettuce before illness. The romaine lettuce was sourced from two California growing regions: Santa Maria and Salinas Valley in 2018 and Salinas Valley in 2019. The outbreak strain was isolated from environmental samples collected at sites >90 miles apart across growing regions, as well as from romaine-containing products in 2019. Although the definitive route of romaine contamination was undetermined, use of a contaminated agricultural water reservoir in 2018 and contamination from cattle grazing on adjacent land in 2019 were suspected as possible factors. Preventing lettuce contamination from growth to consumption is imperative to preventing illness. These outbreaks highlight the need to further understand mechanisms of romaine contamination, including the role of environmental or animal reservoirs for STEC O157. © 2021 Cambridge University Press. All rights reserved. |
Implementation of Rapid Diagnostics Assays for Detection of Histoplasmosis and Cryptococcosis in Central American People Living with HIV
Caceres DH , Arauz AB , Flores C , Santiago E , Montoya S , Saenz C , Torres-Meneses FA , Peralta H , Zuniga-Moya JC , Lainez Arteaga IZ , Garcia A , Abdo J , Verweij PE , Chiller TM , Forno D . Mycoses 2021 64 (11) 1396-1401 OBJECTIVES: Histoplasmosis and cryptococcosis are important public health problems in people living with HIV (PLHIV) in Central America. Conventional laboratory assays, based on microscopy and culture, are not optimal for the diagnosis of either disease. However, antigen (Ag) assays are rapid and highly accurate for the diagnosis of these infections. METHODS: Laboratory surveillance of PLHIV was carried out in four hospitals in Panama, Honduras, and Nicaragua, between 2015 and 2019. Detection of Histoplasma antigens in urine was performed by enzyme immunoassay (EIA), and Cryptococcus antigen detection in sera and cerebrospinal fluid specimens was performed by lateral flow assay (LFA). RESULTS: A total of 4,453 PLHIV with clinical suspicion of histoplasmosis (n=1,343) or cryptococcosis (n=3,110; 2,721 sera and 389 CSF) were tested. Of 1,343 patients suspected of having histoplasmosis, 269 (20%) were Histoplasma Ag positive. Of 3,110 patients tested using the Cryptococcus Ag assay, 329 (11%) were positive. Honduras reported the highest positivity rates (32% for Histoplasma Ag, and 16% for Cryptococcus Ag); Panama reported the largest number of patients testing positive using the Histoplasma Ag assay (n=201); and Nicaragua reported the largest number of patients testing positive using the Cryptococcus Ag assay (n=170). CONCLUSION: Here we show how the implementation of rapid diagnostics assays impacted case detection and were useful for the care of people with advanced HIV. Rapid and accurate diagnosis could reduce mortality associated with histoplasmosis and cryptococcosis in PLHIV. |
Lessons learned from a decade of investigations of shiga toxin-producing Escherichia coli outbreaks linked to leafy greens, United States and Canada
Marshall KE , Hexemer A , Seelman SL , Fatica MK , Blessington T , Hajmeer M , Kisselburgh H , Atkinson R , Hill K , Sharma D , Needham M , Peralta V , Higa J , Blickenstaff K , Williams IT , Jhung MA , Wise M , Gieraltowski L . Emerg Infect Dis 2020 26 (10) 2319-2328 Shiga toxin-producing Escherichia coli (STEC) cause substantial and costly illnesses. Leafy greens are the second most common source of foodborne STEC O157 outbreaks. We examined STEC outbreaks linked to leafy greens during 2009-2018 in the United States and Canada. We identified 40 outbreaks, 1,212 illnesses, 77 cases of hemolytic uremic syndrome, and 8 deaths. More outbreaks were linked to romaine lettuce (54%) than to any other type of leafy green. More outbreaks occurred in the fall (45%) and spring (28%) than in other seasons. Barriers in epidemiologic and traceback investigations complicated identification of the ultimate outbreak source. Research on the seasonality of leafy green outbreaks and vulnerability to STEC contamination and bacterial survival dynamics by leafy green type are warranted. Improvements in traceability of leafy greens are also needed. Federal and state health partners, researchers, the leafy green industry, and retailers can work together on interventions to reduce STEC contamination. |
Extragenital gonorrhea and chlamydia positivity and the potential for missed extragenital gonorrhea with concurrent urethral chlamydia among men who have sex with men attending STD clinics - STD Surveillance Network, 2015-2019
Abara WE , Llata EL , Schumacher C , Carlos-Henderson J , Peralta AM , Huspeni D , Kerani RP , Elder H , Toevs K , Pathela P , Asbel L , Nguyen TQ , Bernstein KT , Torrone EA , Kirkcaldy RD . Sex Transm Dis 2020 47 (6) 361-368 BACKGROUND: Extragenital gonorrhea (GC) and chlamydia (CT) are usually asymptomatic and only detected through screening. Ceftriaxone plus azithromycin is the recommended GC treatment; monotherapy (azithromycin or doxycycline) is recommended for CT. In urethral CT-positive/urethral GC-negative persons who are not screened extragenitally, CT monotherapy can lead to GC undertreatment and may foster the development of gonococcal antimicrobial resistance. We assessed urethral and extragenital GC and CT positivity among men who have sex with men (MSM) attending sexually transmitted disease (STD) clinics. METHODS: We included visit data for MSM tested for GC and CT at 30 STD clinics in 10 jurisdictions during 1/1/2015-6/30/2019. Using an inverse-variance random effects model to account for heterogeneity between jurisdictions, we calculated weighted test visit positivity estimates and 95% confidence intervals (CI) for GC and CT at urethral and extragenital sites, and extragenital GC among urethral CT-positive/GC-negative test visits. RESULTS: Of 139,718 GC and CT test visits, we calculated overall positivity (GC=16.7% [95% CI=14.4-19.1]; CT=13.3% [95% CI=12.7-13.9]); urethral positivity (GC=7.5% [95% CI=5.7-9.3]; CT=5.2% [95% CI=4.6-5.8]); rectal positivity (GC=11.8% [95% CI=10.4-13.2]; CT=12.6% [95% CI=11.8-13.4]); and pharyngeal positivity (GC=9.1% [95% CI=7.9-10.3]; CT=1.8% [95% CI=1.6-2.0]). Of 4,566 urethral CT-positive/GC-negative test visits with extragenital testing, extragenital GC positivity was 12.5% (95% CI=10.9-14.1). CONCLUSION: Extragenital GC and CT were common among MSM. Without extragenital screening of MSM with urethral CT, extragenital GC would have been undetected and undertreated in ~13% of these men. Undertreatment could potentially select for antimicrobial resistance. These findings underscore the importance of extragenital screening in MSM. |
Extragenital gonorrhea and chlamydia positivity and the potential for missed extragenital gonorrhea with concurrent urethral chlamydia among men who have sex with men attending STD clinics - STD Surveillance Network, 2015-2019
Abara WE , Llata EL , Schumacher C , Carlos-Henderson J , Peralta AM , Huspeni D , Kerani RP , Elder H , Toevs K , Pathela P , Asbel L , Nguyen TQ , Bernstein KT , Torrone EA , Kirkcaldy RD . Sex Transm Dis 2020 47 (6) 361-368 BACKGROUND: Extragenital gonorrhea (GC) and chlamydia (CT) are usually asymptomatic and only detected through screening. Ceftriaxone plus azithromycin is the recommended GC treatment; monotherapy (azithromycin or doxycycline) is recommended for CT. In urethral CT-positive/urethral GC-negative persons who are not screened extragenitally, CT monotherapy can lead to GC undertreatment and may foster the development of gonococcal antimicrobial resistance. We assessed urethral and extragenital GC and CT positivity among men who have sex with men (MSM) attending sexually transmitted disease (STD) clinics. METHODS: We included visit data for MSM tested for GC and CT at 30 STD clinics in 10 jurisdictions during 1/1/2015-6/30/2019. Using an inverse-variance random effects model to account for heterogeneity between jurisdictions, we calculated weighted test visit positivity estimates and 95% confidence intervals (CI) for GC and CT at urethral and extragenital sites, and extragenital GC among urethral CT-positive/GC-negative test visits. RESULTS: Of 139,718 GC and CT test visits, we calculated overall positivity (GC=16.7% [95% CI=14.4-19.1]; CT=13.3% [95% CI=12.7-13.9]); urethral positivity (GC=7.5% [95% CI=5.7-9.3]; CT=5.2% [95% CI=4.6-5.8]); rectal positivity (GC=11.8% [95% CI=10.4-13.2]; CT=12.6% [95% CI=11.8-13.4]); and pharyngeal positivity (GC=9.1% [95% CI=7.9-10.3]; CT=1.8% [95% CI=1.6-2.0]). Of 4,566 urethral CT-positive/GC-negative test visits with extragenital testing, extragenital GC positivity was 12.5% (95% CI=10.9-14.1). CONCLUSION: Extragenital GC and CT were common among MSM. Without extragenital screening of MSM with urethral CT, extragenital GC would have been undetected and undertreated in ~13% of these men. Undertreatment could potentially select for antimicrobial resistance. These findings underscore the importance of extragenital screening in MSM. |
A multistate outbreak of E Coli O157:H7 infections linked to soy nut butter
Hassan R , Seelman S , Peralta V , Booth H , Tewell M , Melius B , Whitney B , Sexton R , Dwarka A , Vugia D , Vidanes J , Kiang D , Gonzales E , Dowell N , Olson SM , Gladney LM , Jhung MA , Neil KP . Pediatrics 2019 144 (4) BACKGROUND: In 2017, we conducted a multistate investigation to determine the source of an outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infections, which occurred primarily in children. METHODS: We defined a case as infection with an outbreak strain of STEC O157:H7 with illness onset between January 1, 2017, and April 30, 2017. Case patients were interviewed to identify common exposures. Traceback and facility investigations were conducted; food samples were tested for STEC. RESULTS: We identified 32 cases from 12 states. Twenty-six (81%) cases occurred in children <18 years old; 8 children developed hemolytic uremic syndrome. Twenty-five (78%) case patients ate the same brand of soy nut butter or attended facilities that served it. We identified 3 illness subclusters, including a child care center where person-to-person transmission may have occurred. Testing isolated an outbreak strain from 11 soy nut butter samples. Investigations identified violations of good manufacturing practices at the soy nut butter manufacturing facility with opportunities for product contamination, although the specific route of contamination was undetermined. CONCLUSIONS: This investigation identified soy nut butter as the source of a multistate outbreak of STEC infections affecting mainly children. The ensuing recall of all soy nut butter products the facility manufactured, totaling >1.2 million lb, likely prevented additional illnesses. Prompt diagnosis of STEC infections and appropriate specimen collection aids in outbreak detection. Child care providers should follow appropriate hygiene practices to prevent secondary spread of enteric illness in child care settings. Firms should manufacture ready-to-eat foods in a manner that minimizes the risk of contamination. |
Building a network for multicenter, prospective research of central nervous system infections in South America: Process and lessons learned
Nelson C , Mori N , Ton T , Zunt J , Kochel T , Romero A , Gadea N , Tilley D , Ticona E , Soria J , Celis V , Huanca D , Delgado A , Rivas M , Stiglich M , Sihuincha M , Donayre G , Celis J , Romero R , Tam N , Tipismana M , Espinoza I , Rozas M , Peralta A , Sanchez E , Vasquez L , Muñoz P , Ramirez G , Reyes Ifgt . eNeurologicalSci 2018 13 63-69 Multicenter collaborative networks are essential for advancing research and improving clinical care for a variety of conditions. Research networks are particularly important for central nervous system infections, which remain difficult to study due to their sporadic occurrence and requirement for collection and testing of cerebrospinal fluid. Establishment of long-term research networks in resource-limited areas also facilitates diagnostic capacity building, surveillance for emerging pathogens, and provision of appropriate treatment where needed. We review our experience developing a research network for encephalitis among twelve hospitals in five Peruvian cities since 2009. We provide practical suggestions to aid other groups interested in advancing research on central nervous system infections in resource-limited areas. |
Fentanyl-associated illness among substance users - Fulton County, Georgia, 2015
Angela Parham M , Pomerleau AC , Peralta G , Drenzek CL , Edison LS . Am J Emerg Med 2018 36 (11) 2115-2117 In early 2015, Hospital A emergency physicians subjectively noticed an increase in opioid overdoses presenting to the emergency department (ED) that corresponded with an increase in fentanyl-positive substance-related deaths documented by the Fulton County medical examiner (ME). This prompted Hospital A emergency physicians to begin selective fentanyl urine drug screening (UDS) for patients with clinical signs of opioid intoxication. After testing revealed that some patients had UDS positive for fentanyl, Hospital A began testing for fentanyl as part of all routine UDS in May 2015 and notified the Georgia Department of Public Health (DPH) of their findings. Fentanyl had not been commonly reported as associated with substance abuse and overdose in Georgia before this cluster. DPH initiated an epidemiologic investigation to characterize events and guide prevention efforts. |
Flea market finds and global exports: Four multistate outbreaks of human Salmonella infections linked to small turtles, United States-2015
Gambino-Shirley K , Stevenson L , Concepcion-Acevedo J , Trees E , Wagner D , Whitlock L , Roberts J , Garrett N , Van Duyne S , McAllister G , Schick B , Schlater L , Peralta V , Reporter R , Li L , Waechter H , Gomez T , Fernandez Ordenes J , Ulloa S , Ragimbeau C , Mossong J , Nichols M . Zoonoses Public Health 2018 65 (5) 560-568 Zoonotic transmission of Salmonella infections causes an estimated 11% of salmonellosis annually in the United States. This report describes the epidemiologic, traceback and laboratory investigations conducted in the United States as part of four multistate outbreaks of Salmonella infections linked to small turtles. Salmonella isolates indistinguishable from the outbreak strains were isolated from a total of 143 ill people in the United States, pet turtles, and pond water samples collected from turtle farm A, as well as ill people from Chile and Luxembourg. Almost half (45%) of infections occurred in children aged <5 years, underscoring the importance of the Centers for Disease Control and Prevention recommendation to keep pet turtles and other reptiles out of homes and childcare settings with young children. Although only 43% of the ill people who reported turtle exposure provided purchase information, most small turtles were purchased from flea markets or street vendors, which made it difficult to locate the vendor, trace the turtles to a farm of origin, provide education and enforce the United States federal ban on the sale and distribution of small turtles. These outbreaks highlight the importance of improving public awareness and education about the risk of Salmonella from small turtles not only in the United States but also worldwide. |
Utility of Combining Whole Genome Sequencing with Traditional Investigational Methods To Solve Foodborne Outbreaks of Salmonella Infections Associated with Chicken: A New Tool for Tackling This Challenging Food Vehicle.
Crowe SJ , Green A , Hernandez K , Peralta V , Bottichio L , Defibaugh-Chavez S , Douris A , Gieraltowski L , Hise K , La-Pham K , Neil KP , Simmons M , Tillman G , Tolar B , Wagner D , Wasilenko J , Holt K , Trees E , Wise ME . J Food Prot 2017 80 (4) 654-660 High consumption rates and a multitude of brands make multistate foodborne outbreaks of Salmonella infections associated with chicken challenging to investigate, but whole genome sequencing is a powerful tool that can be used to assist investigators. Whole genome sequencing of pathogens isolated from clinical, environmental, and food samples is increasingly being used in multistate foodborne outbreak investigations to determine with unprecedented resolution how closely related these isolates are to one another genetically. In 2014, federal and state health officials investigated an outbreak of 146 Salmonella Heidelberg infections in 24 states. A follow-up analysis was conducted after the conclusion of the investigation in which 27 clinical and 24 food isolates from the outbreak underwent whole genome sequencing. These isolates formed seven clades, the largest of which contained clinical isolates from a subcluster of case patients who attended a catered party. One isolate from a chicken processed by a large producer was closely related genetically (zero to three single-nucleotide polymorphism differences) to the clinical isolates from these subcluster case patients. Chicken from this large producer was also present in the kitchen of the caterer on the day before the event, thus providing additional evidence that the chicken from this producer was the outbreak source. This investigation highlights how whole genome sequencing can be used with epidemiologic and traceback evidence to identify chicken sources of foodborne outbreaks. |
National outbreak of multidrug resistant Salmonella Heidelberg infections linked to a single poultry company
Gieraltowski L , Higa J , Peralta V , Green A , Schwensohn C , Rosen H , Libby T , Kissler B , Marsden-Haug N , Booth H , Kimura A , Grass J , Bicknese A , Tolar B , Defibaugh-Chavez S , Williams I , Wise M . PLoS One 2016 11 (9) e0162369 IMPORTANCE: This large outbreak of foodborne salmonellosis demonstrated the complexity of investigating outbreaks linked to poultry products. The outbreak also highlighted the importance of efforts to strengthen food safety policies related to Salmonella in chicken parts and has implications for future changes within the poultry industry. OBJECTIVE: To investigate a large multistate outbreak of multidrug resistant Salmonella Heidelberg infections. DESIGN: Epidemiologic and laboratory investigations of patients infected with the outbreak strains of Salmonella Heidelberg and traceback of possible food exposures. SETTING: United States. Outbreak period was March 1, 2013 through July 11, 2014. PATIENTS: A case was defined as illness in a person infected with a laboratory-confirmed Salmonella Heidelberg with 1 of 7 outbreak pulsed-field gel electrophoresis (PFGE) XbaI patterns with illness onset from March 1, 2013 through July 11, 2014. A total of 634 case-patients were identified through passive surveillance; 200/528 (38%) were hospitalized, none died. RESULTS: Interviews were conducted with 435 case-patients: 371 (85%) reported eating any chicken in the 7 days before becoming ill. Of 273 case-patients interviewed with a focused questionnaire, 201 (74%) reported eating chicken prepared at home. Among case-patients with available brand information, 152 (87%) of 175 patients reported consuming Company A brand chicken. Antimicrobial susceptibility testing was completed on 69 clinical isolates collected from case-patients; 67% were drug resistant, including 24 isolates (35%) that were multidrug resistant. The source of Company A brand chicken consumed by case-patients was traced back to 3 California production establishments from which 6 of 7 outbreak strains were isolated. CONCLUSIONS: Epidemiologic, laboratory, traceback, and environmental investigations conducted by local, state, and federal public health and regulatory officials indicated that consumption of Company A chicken was the cause of this outbreak. The outbreak involved multiple PFGE patterns, a variety of chicken products, and 3 production establishments, suggesting a reservoir for contamination upstream from the production establishments. Sources of bacteria and genes responsible for resistance, such as farms providing birds for slaughter or environmental reservoir on farms that raise chickens, might explain how multiple PFGE patterns were linked to chicken from 3 separate production establishments and many different poultry products. |
Streptococcus pneumoniae of Serotypes 9 and 14 Circulating in Brazil Over a 23-Year Period Prior to the Introduction of PCV10: Role of International Clones in the Evolution of Antimicrobial Resistance and Description of a Novel Genotype.
Pinto TC , Kegele FC , Dias CA , Barros RR , Peralta JM , Merquior VL , Carvalho MD , Chochua S , Hawkins P , McGee L , Teixeira LM . Antimicrob Agents Chemother 2016 60 (11) 6664-6672 Antimicrobial resistant pneumococcal strains have been detected worldwide since the 1960's. In Brazil, the first penicillin non-susceptible pneumococci (PNSP) were reported in the 1980's, and their emergence and dissemination have been mainly attributed to serogroup 9 and serotype 14 strains, especially those highly related to recognized international clones. In the present study, antimicrobial susceptibility testing and Multilocus Sequence Typing (MLST) were performed on 315 pneumococcal isolates belonging to serogroup 9 (n=99) or serotype 14 (n=216), recovered from patients or asymptomatic carriers between 1988 and 2011 in Brazil, in order to trace changes in antimicrobial resistance and genotypes prior to the full introduction of the pneumococcal conjugate vaccine in the country. Over the 23-year study period, PNSP levels increased and four clonal complexes (CC156, CC66, CC15 and CC5401) have played important roles in the evolution and dissemination of pneumococcal isolates belonging to serogroup 9 and serotype 14, as well as in the emergence of antimicrobial resistance, in the pre-pneumococcal vaccination era. The earliest PNSP strains detected in this study belonged to serotype 9N/ST66 and were single locus variants of the international clone Tennesse14-18 ST67 (CC66). The first serotype 14 PNSP isolates were identified in 1990, and were related to the England14-9 ST9 (CC15) clone. Serotype 14 PNSP variants of the Spain9V-3 ST156 clone with elevated penicillin MICs and non-susceptibility to other beta-lactams were detected in 1995, and showed an increasing trend over the years. The results also indicated that introduction of ST156 in our region was preceded by the emergence of trimethoprim/sulfamethoxazole resistance and by the dissemination of ST162. In addition to the presence of successful international clones, a novel regional serotype 14 genotype (CC5401) has emerged in 1996. |
Notes from the field: Mycobacterium abscessus infections among patients of a pediatric dentistry practice - Georgia, 2015
Peralta G , Tobin-D'Angelo M , Parham A , Edison L , Lorentzson L , Smith C , Drenzek C . MMWR Morb Mortal Wkly Rep 2016 65 (13) 355-356 On September 13, 2015, the Georgia Department of Public Health (DPH) was notified by hospital A of a cluster of pediatric Mycobacterium abscessus odontogenic infections. Hospital A had provided care for nine children who developed presumptive or confirmed M. abscessus infection after having a pulpotomy at pediatric dentistry practice A (dates of onset: July 23, 2014-September 4, 2015). During a pulpotomy procedure, decay and the diseased pulp are removed to preserve a deciduous tooth. DPH initiated an investigation to identify the outbreak source and recommend prevention and control measures. |
Varicella hospitalizations in Los Angeles during the varicella vaccination era, 2003-2011: are they preventable?
Agopian A , Lopez A , Wilson D , Peralta V , Amin AN , Bialek S . Vaccine 2014 32 (41) 5353-6 Characteristics of varicella-related hospitalizations in the mature varicella vaccination era, including the proportion vaccinated and the severity of disease, are not well described. We present the vaccination status, severity and reasons for hospitalization of the hospitalized varicella cases reported to the Los Angeles County Health Department from 2003 to 2011, the period which includes the last 4 years of the mature one-dose program and the first 5 years after introduction of the routine two-dose program. A total of 158 hospitalized varicella cases were reported overall, of which 52.5% were potentially preventable and eligible for vaccination, 41.8% were not eligible for vaccination, and 5.7% were vaccinated. Most hospitalizations (72.2%) occurred among healthy persons, 54.4% occurred among persons ≥20 years of age, and 3.8% of hospitalizations resulted in death. Our data suggest that as many as half of the hospitalized varicella cases, including half of the deaths, may have been preventable given that they occurred in persons who were eligible for vaccination. More complete implementation of the routine varicella vaccination program could further reduce the disease burden of severe varicella. |
LUMINEX(R): a new technology for the simultaneous identification of five Entamoeba spp. commonly found in human stools
Santos HL , Bandyopadhyay K , Bandea R , Peralta RH , Peralta JM , Da Silva AJ . Parasit Vectors 2013 6 69 BACKGROUND: Six species of the genus Entamoeba, i.e., E. histolytica, E. dispar, E. moshkovskii, E. polecki, E. coli, and E. hartmanii can be found in human stools. Among these, only E. histolytica is considered to be pathogenic, causing intestinal and extra-intestinal disease, but it is morphologically identical to E. dispar and E. moshkovskii. In general, E. polecki, E. coli, and E. hartmanii can be differentiated morphologically from E. histolytica, but some of their diagnostic morphologic features may overlap creating issues for the differential diagnosis. Moreover, the previous inability to differentiate among Entamoeba species has limited epidemiologic information on E histolytica. The objective of this study was to develop a rapid, high-throughput screening method using Luminex technique for the simultaneous detection and differentiation of Entamoeba species. METHODS: PCR amplification was performed with biotinylated Entamoeba sp 18S rRNA gene primers, designed to amplify a fragment ranging from 382 to 429 bp of the Entamoeba spp studied. Regions of this fragment that could differentiate among E. histolytica, E. moshkovskii, E. dispar, E. hartmanii and E. coli were selected to design hybridization probes to link to Luminex beads. The assay was standardized with cloned DNA samples of each species and evaluated with 24 DNA extracts from samples obtained from individuals diagnosed with these amebas in their stools. RESULTS: Using this approach we were able to correctly identify E. histoltyica, E. dispar, E hartmanni, E. coli and E. moshkovskii in all specimens studied. From twenty four samples tested by microscopy, PCR/DNA Sequencing and real-time PCR, 100% agreed with PCR-Luminex assay for identification of E. dispar, E. moshkovskii, E. hartmanni, E. histolytica, and E. coli. CONCLUSION: These results show that this method could be used in the diagnostic detection of Entamoeba spp in fecal samples. This diagnostic test was useful to clearly distinguish E histolytica from other species and also to strengthen epidemiologic data on Entamoeba spp. |
Prevalence and predictors of drug use among adolescents with HIV infection acquired perinatally or later in life
Conner LC , Wiener J , Lewis JV , Phill R , Peralta L , Chandwani S , Koenig LJ . AIDS Behav 2013 17 (3) 976-86 We examined the prevalence and predictors of drug use among a diverse group of adolescents living with HIV infection acquired perinatally or through sexual risk behaviors ("behaviorally acquired"). Adolescents ages 13-21 (n = 166) who were receiving care at one of five pediatric/adolescent HIV clinics in three US cities (Baltimore MD, Washington DC, and New York NY) and were enrolled in a behavioral intervention were interviewed at baseline regarding lifetime drug use experiences and depression symptoms. A majority of study participants reported using alcohol (57.2%) and marijuana (51.2%); 48.8% reported tobacco/cigarette use. The mean age of onset of use for each type of drug was 14 years or younger. A larger proportion of participants with behaviorally acquired HIV than adolescents with perinatally acquired HIV reported lifetime use of alcohol (76.1 vs. 44.4%), marijuana (73.1 vs. 36.4%), tobacco (70.2 vs. 34.3%), and club drugs (22.4 vs. 3%) (all p < 0.001). |
The identification and characterization of epitopes in the 30-34kDa Trypanosoma cruzi proteins recognized by antibodies in the serum samples of chagasic patients
Verissimo da Costa GC , Lery LM , da Silva ML , Moura H , Peralta RH , von Kruger WM , Bisch PM , Barr JR , Peralta JM . J Proteomics 2012 80C 34-42 Trypanosoma cruzi proteins with molecular weight between 30 and 34kDa have shown high reactivity in western blot assays with serum samples from chagasic individuals. However, in-depth analysis of the constituents of these protein fractions has not been performed. This is the first report of an immunoaffinity proteomic approach to identify the immunodominant 30-34kDa proteins of T. cruzi that could eventually be used for the diagnosis of Chagas disease. We used two different sample preparation protocols for protein digestion coupled to mass spectrometry to identify proteins in the protein fraction. The immunodominant proteins and their respective epitopes were then identified by co-immunoprecipitation and excision-epitope mapping/mass spectrometry, using human sera followed by the prediction and three-dimensional structural modeling of reactive epitopes. The use of different sample preparation methods allowed the identification of a relatively high number of proteins, some of which were only identified after one or multiple sample preparation and digestion protocols. Seven immunodominant proteins were identified by co-immunoprecipitation with purified IgGs from chagasic serum samples. Moreover, six reactive peptide epitopes were detected in four of these proteins by excision-epitope mapping/mass spectrometry. Three-dimensional structural models were obtained for the immunoreactive peptides, which correlated well with the linear B-cell epitope prediction tools. |
Taenia crassiceps cysticerci: characterization of the 14-kDa glycoprotein with homologies to antigens from Taenia solium cysticerci
Peralta RH , Espindola NM , Pardini AX , Iha AH , Moura H , Barr JR , Vaz AJ , Peralta JM . Exp Parasitol 2010 124 (3) 295-300 Glycoproteins from the total vesicular fluid of Taenia crassiceps (VF-Tc) were prepared using three different purification methods, consisting of ConA-lectin affinity chromatography (ConA-Tc), preparative electrophoresis (SDS-PAGE) (14 gp-Tc), and monoclonal antibody immunoaffinity chromatography (18/14-Tc). The complex composition represented by the VF-Tc and ConA-Tc antigens revealed peptides ranging from 101- to 14-kDa and from 92- to 12-kDa, respectively. Immunoblotting using lectins confirmed glucose/mannose (glc/man) residues in the 18- and 14-kDa peptides, which are considered specific and immunodominant for the diagnosis of cysticercosis, and indicated that these fractions are glycoproteins. Serum antibodies from a patient with neurocysticercosis that reacted to the 14 gp band from T. crassiceps (Tc) were eluted from immunoblotting membranes and showed reactivity to 14 gp from Taenia solium. In order to determine the similar peptide sequence, the N-terminal amino acid was determined and analyzed with sequences available in public databases. This sequence revealed partial homology between T. crassiceps and T. solium peptides. In addition, mass spectrometry along with theoretical M(r) and pI of the 14 gp-Tc point suggested a close relationship to some peptides of a 150-kDa protein complex of the T. solium previously described. The identification of these common immunogenic sites will contribute to future efforts to develop recombinant antigens and synthetic peptides for immunological assays. |
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