Last data update: Jul 01, 2024. (Total: 47134 publications since 2009)
Records 1-27 (of 27 Records) |
Query Trace: Shirley H [original query] |
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Outbreak of Multidrug-Resistant Salmonella Heidelberg Infections Linked to Dairy Calf Exposure, United States, 2015-2018.
Nichols M , Gollarza L , Sockett D , Aulik N , Patton E , Francois Watkins LK , Gambino-Shirley KJ , Folster JP , Chen JC , Tagg KA , Stapleton GS , Trees E , Ellison Z , Lombard J , Morningstar-Shaw B , Schlater L , Elbadawi L , Klos R . Foodborne Pathog Dis 2022 19 (3) 199-208 In August 2016, the Wisconsin Department of Health Services notified the U.S. Centers for Disease Control and Prevention of multidrug-resistant (MDR) Salmonella enterica serovar Heidelberg infections in people who reported contact with dairy calves. Federal and state partners investigated this to identify the source and scope of the outbreak and to prevent further illnesses. Cases were defined as human Salmonella Heidelberg infection caused by a strain that had one of seven pulsed-field gel electrophoresis (PFGE) patterns or was related by whole genome sequencing (WGS), with illness onset from January 1, 2015, through July 2, 2018. Patient exposure and calf purchase information was collected and analyzed; calves were traced back from the point of purchase. Isolates obtained from animal and environmental samples collected on-farm were supplied by veterinary diagnostic laboratories and compared with patient isolates using PFGE and WGS. Antimicrobial susceptibility testing by standardized broth microdilution was performed. Sixty-eight patients from 17 states were identified. Forty (63%) of 64 patients noted cattle contact before illness. Thirteen (33%) of 40 patients with exposure to calves reported that calves were sick or had died. Seven individuals purchased calves from a single Wisconsin livestock market. One hundred forty cattle from 14 states were infected with the outbreak strain. WGS indicated that human, cattle, and environmental isolates from the livestock market were genetically closely related. Most isolates (88%) had resistance or reduced susceptibility to antibiotics of ≥5 antibiotic classes. This resistance profile included first-line antibiotic treatments for patients with severe salmonellosis, including ampicillin, ceftriaxone, and ciprofloxacin. In this outbreak, MDR Salmonella Heidelberg likely spread from sick calves to humans, emphasizing the importance of illness surveillance in animal populations to prevent future spillover of this zoonotic disease. |
Agritourism and Kidding Season: A Large Outbreak of Human Shiga Toxin-Producing Escherichia coli O157 (STEC O157) Infections Linked to a Goat Dairy Farm-Connecticut, 2016.
Nichols MC , Gacek P , Phan Q , Gambino-Shirley KJ , Gollarza LM , Schroeder MN , Mercante A , Mullins J , Blackstock A , Laughlin ME , Olson SM , Pizzo E , Nguyen TN , Mank L , Holmes-Talbot K , McNutt A , Noel D , Muyombwe A , Razeq JH , Lis MJ , Sherman B , Kasacek W , Whitlock L , Strockbine N , Martin H , Vidyaprakash E , McCormack P , Cartter M . Front Vet Sci 2021 8 744055 The objective of this study was to determine sources of Shiga toxin-producing Escherichia coli O157 (STEC O157) infection among visitors to Farm X and develop public health recommendations. A case-control study was conducted. Case-patients were defined as the first ill child (aged <18 years) in the household with laboratory-confirmed STEC O157, or physician-diagnosed hemolytic uremic syndrome with laboratory confirmation by serology, who visited Farm X in the 10 days prior to illness. Controls were selected from Farm X visitors aged <18 years, without symptoms during the same time period as case-patients. Environment and animal fecal samples collected from Farm X were cultured; isolates from Farm X were compared with patient isolates using whole genome sequencing (WGS). Case-patients were more likely than controls to have sat on hay bales at the doe barn (adjusted odds ratio: 4.55; 95% confidence interval: 1.41-16.13). No handwashing stations were available; limited hand sanitizer was provided. Overall, 37% (29 of 78) of animal and environmental samples collected were positive for STEC; of these, 62% (18 of 29) yielded STEC O157 highly related by WGS to patient isolates. STEC O157 environmental contamination and fecal shedding by goats at Farm X was extensive. Farms should provide handwashing stations with soap, running water, and disposable towels. Access to animal areas, including animal pens and enclosures, should be limited for young children who are at risk for severe outcomes from STEC O157 infection. National recommendations should be adopted to reduce disease transmission. |
Epidemiology of reported HIV and other sexually transmitted infections during the COVID-19 pandemic, New York City.
Braunstein SL , Slutsker JS , Lazar R , Shah D , Hennessy RR , Chen S , Pathela P , Daskalakis DC , Schillinger JA . J Infect Dis 2021 224 (5) 798-803 Early in the COVID-19 crisis, a statewide executive order ("PAUSE") severely restricted the movement of New Yorkers from March 23-June 7, 2020. We used NYC surveillance data for HIV, chlamydia, gonorrhea, and syphilis to describe trends in diagnosis and reporting surrounding PAUSE. During PAUSE, the volume of positive HIV/STI tests, and diagnoses of HIV, chlamydia, gonorrhea, and syphilis declined substantially, reaching a nadir in April before rebounding. Some shifts in characteristics of reported cases were identified. |
Notes from the Field: Impact of the COVID-19 Response on Scale-Up of HIV Viral Load Testing - PEPFAR-Supported Countries, January-June 2020.
Lecher SL , Naluguza M , Mwangi C , N'Tale J , Edgil D , Alemnji G , Alexander H . MMWR Morb Mortal Wkly Rep 2021 70 (21) 794-795 CDC and the U.S. President’s Emergency Plan for AIDS Relief (PEPFAR) are committed to maintaining an international response to the HIV epidemic even as countries face the challenge of controlling the COVID-19 pandemic (1). The Joint United Nations Programme on HIV/AIDS has set the following 95-95-95 targets for HIV infection control by 2030: 1) ensure that 95% of HIV-positive persons are aware of their HIV status, 2) ensure that 95% of these persons receive antiretroviral treatment (ART) and 3) facilitate viral load testing and suppression (viral load ≤1,000 HIV RNA copies per mL of blood) among 95% of persons with HIV infection (2). PEPFAR and international donors support 50 countries by investing in diagnostic testing, ART, and viral load testing to monitor treatment outcomes. Recent COVID-19–related stay-at-home orders and travel restrictions have affected essential HIV services worldwide. In the face of these challenges, CDC and PEPFAR are committed to sustaining the momentum necessary to achieve the target goal of facilitating testing and viral suppression among 95% of persons with HIV. |
Performance of Repeat BinaxNOW SARS-CoV-2 Antigen Testing in a Community Setting, Wisconsin, November-December 2020.
Shah MM , Salvatore PP , Ford L , Kamitani E , Whaley MJ , Kaitlin M , Currie DW , Morgan CN , Segaloff HE , Lecher S , Somers T , Van Dyke ME , Bigouette JP , Delaney A , DaSilva J , O'Hegarty M , Boyle-Estheimer L , Abdirizak F , Karpathy SE , Meece J , Ivanic L , Goffard K , Gieryn D , Sterkel A , Bateman A , Kahrs J , Langolf K , Zochert T , Knight NW , Hsu CH , Kirking HL , Tate JE . Clin Infect Dis 2021 73 S54-S57 Repeating the BinaxNOW antigen test for SARS-CoV-2 by two groups of readers within 30 minutes resulted in high concordance (98.9%) in 2,110 encounters. BinaxNOW test sensitivity was 77.2% (258/334) compared to real-time reverse transcription-polymerase chain reaction. Same day antigen testing did not significantly improve test sensitivity while specificity remained high. |
Systematic Review of Pooling Sputum as an Efficient Method for Xpert MTB/RIF Tuberculosis Testing during the COVID-19 Pandemic.
Cuevas LE , Santos VS , Lima Svma , Kontogianni K , Bimba JS , Iem V , Dominguez J , Adams E , Atienzar AC , Edwards T , Squire SB , Hall PJ , Creswell J . Emerg Infect Dis 2021 27 (3) 719-727 GeneXpert-based testing with Xpert MTB/RIF or Ultra assays is essential for tuberculosis diagnosis. However, testing may be affected by cartridge and staff shortages. More efficient testing strategies could help, especially during the coronavirus disease pandemic. We searched the literature to systematically review whether GeneXpert-based testing of pooled sputum samples achieves sensitivity and specificity similar to testing individual samples; this method could potentially save time and preserve the limited supply of cartridges. From 6 publications, we found 2-sample pools using Xpert MTB/RIF had 87.5% and 96.0% sensitivity (average sensitivity 94%; 95% CI 89.0%-98.0%) (2 studies). Four-sample pools averaged 91% sensitivity with Xpert MTB/RIF (2 studies) and 98% with Ultra (2 studies); combining >4 samples resulted in lower sensitivity. Two studies reported that pooling achieved 99%-100% specificity and 27%-31% in cartridge savings. Our results show that pooling may improve efficiency of GeneXpert-based testing. |
Characterization of COVID-19 in Assisted Living Facilities - 39 States, October 2020.
Yi SH , See I , Kent AG , Vlachos N , Whitworth JC , Xu K , Gouin KA , Zhang S , Slifka KJ , Sauer AG , Kutty PK , Perz JF , Stone ND , Stuckey MJ . MMWR Morb Mortal Wkly Rep 2020 69 (46) 1730-1735 The coronavirus disease 2019 (COVID-19) pandemic has highlighted the vulnerability of residents and staff members in long-term care facilities (LTCFs) (1). Although skilled nursing facilities (SNFs) certified by the Centers for Medicare & Medicaid Services (CMS) have federal COVID-19 reporting requirements, national surveillance data are less readily available for other types of LTCFs, such as assisted living facilities (ALFs) and those providing similar residential care. However, many state and territorial health departments publicly report COVID-19 surveillance data across various types of LTCFs. These data were systematically retrieved from health department websites to characterize COVID-19 cases and deaths in ALF residents and staff members. Limited ALF COVID-19 data were available for 39 states, although reporting varied. By October 15, 2020, among 28,623 ALFs, 6,440 (22%) had at least one COVID-19 case among residents or staff members. Among the states with available data, the proportion of COVID-19 cases that were fatal was 21.2% for ALF residents, 0.3% for ALF staff members, and 2.5% overall for the general population of these states. To prevent the introduction and spread of SARS-CoV-2, the virus that causes COVID-19, in their facilities, ALFs should 1) identify a point of contact at the local health department; 2) educate residents, families, and staff members about COVID-19; 3) have a plan for visitor and staff member restrictions; 4) encourage social (physical) distancing and the use of masks, as appropriate; 5) implement recommended infection prevention and control practices and provide access to supplies; 6) rapidly identify and properly respond to suspected or confirmed COVID-19 cases in residents and staff members; and 7) conduct surveillance of COVID-19 cases and deaths, facility staffing, and supply information (2). |
First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA.
Ghinai I , McPherson TD , Hunter JC , Kirking HL , Christiansen D , Joshi K , Rubin R , Morales-Estrada S , Black SR , Pacilli M , Fricchione MJ , Chugh RK , Walblay KA , Ahmed NS , Stoecker WC , Hasan NF , Burdsall DP , Reese HE , Wallace M , Wang C , Moeller D , Korpics J , Novosad SA , Benowitz I , Jacobs MW , Dasari VS , Patel MT , Kauerauf J , Charles EM , Ezike NO , Chu V , Midgley CM , Rolfes MA , Gerber SI , Lu X , Lindstrom S , Verani JR , Layden JE . Lancet 2020 395 (10230) 1137-1144 BACKGROUND: Coronavirus disease 2019 (COVID-19) is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first detected in China in December, 2019. In January, 2020, state, local, and federal public health agencies investigated the first case of COVID-19 in Illinois, USA. METHODS: Patients with confirmed COVID-19 were defined as those with a positive SARS-CoV-2 test. Contacts were people with exposure to a patient with COVID-19 on or after the patient's symptom onset date. Contacts underwent active symptom monitoring for 14 days following their last exposure. Contacts who developed fever, cough, or shortness of breath became persons under investigation and were tested for SARS-CoV-2. A convenience sample of 32 asymptomatic health-care personnel contacts were also tested. FINDINGS: Patient 1-a woman in her 60s-returned from China in mid-January, 2020. One week later, she was hospitalised with pneumonia and tested positive for SARS-CoV-2. Her husband (Patient 2) did not travel but had frequent close contact with his wife. He was admitted 8 days later and tested positive for SARS-CoV-2. Overall, 372 contacts of both cases were identified; 347 underwent active symptom monitoring, including 152 community contacts and 195 health-care personnel. Of monitored contacts, 43 became persons under investigation, in addition to Patient 2. These 43 persons under investigation and all 32 asymptomatic health-care personnel tested negative for SARS-CoV-2. INTERPRETATION: Person-to-person transmission of SARS-CoV-2 occurred between two people with prolonged, unprotected exposure while Patient 1 was symptomatic. Despite active symptom monitoring and testing of symptomatic and some asymptomatic contacts, no further transmission was detected. FUNDING: None. |
Molecular strain typing of the yaws pathogen, Treponema pallidum subspecies pertenue.
Katz SS , Chi KH , Nachamkin E , Danavall D , Taleo F , Kool JL , Addo KK , Ampofo W , Simpson SV , Ye T , Asiedu KB , Ballard RC , Chen CY , Pillay A . PLoS One 2018 13 (9) e0203632 Yaws is a neglected tropical disease caused by the bacterium Treponema pallidum subspecies pertenue. The disease primarily affects children under 15 years of age living in low socioeconomic conditions in tropical areas. As a result of a renewed focus on the disease owing to a recent eradication effort initiated by the World Health Organization, we have evaluated a typing method, adapted from and based on the enhanced Centers for Disease Control and Prevention typing method for T. pallidum subsp. pallidum, for possible use in epidemiological studies. Thirty DNA samples from yaws cases in Vanuatu and Ghana, 11 DNA samples extracted from laboratory strains, and 3 published genomic sequences were fully typed by PCR/RFLP analysis of the tpr E, G, and J genes and by determining the number of 60-bp repeats within the arp gene. Subtyping was performed by sequencing a homonucleotide "G" tandem repeat immediately upstream of the rpsA gene and an 84-bp region of tp0548. A total of 22 complete strain types were identified; two strain types in clinical samples from Vanuatu (5q11/ak and 5q12/ak), nine strain types in clinical samples from Ghana (3q12/ah, 4r12/ah, 4q10/j, 4q11/ah, 4q12/ah, 4q12/v, 4q13/ah, 6q10/aj, and 9q10/ai), and twelve strain types in laboratory strains and published genomes (2q11/ae, 3r12/ad, 4q11/ad, 4q12/ad, 4q12/ag, 4q12/v, 5r12/ad, 6r12/x, 6q11/af, 10q9/r, 10q12/r, and 12r12/w). The tpr RFLP patterns and arp repeat sizes were subsequently verified by sequencing analysis of the respective PCR amplicons. This study demonstrates that the typing method for subsp. pallidum can be applied to subsp. pertenue strains and should prove useful for molecular epidemiological studies on yaws. |
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. |
Multistate Outbreak of Salmonella Virchow Infections Linked to a Powdered Meal Replacement Product - United States, 2015-2016.
Gambino-Shirley KJ , Tesfai A , Schwensohn CA , Burnett C , Smith L , Wagner JM , Eikmeier D , Smith K , Stone JP , Updike D , Hines J , Shade LN , Tolar B , Fu TJ , Viazis S , Seelman SL , Blackshear K , Wise ME , Neil KP . Clin Infect Dis 2018 67 (6) 890-896 Background: Nontyphoidal Salmonella is the leading cause of bacterial gastroenteritis in the United States. Meal replacement products containing raw and 'superfood' ingredients have gained increasing popularity among consumers in recent years. In January 2016, we investigated a multistate outbreak of infections with a novel strain of Salmonella Virchow. Methods: Cases were defined using molecular subtyping procedures. Commonly reported exposures were compared with responses from healthy people interviewed in the 2006-2007 FoodNet Population Survey. Firm inspections and product traceback and testing were performed. Results: Thirty-five cases from 24 states were identified; 6 hospitalizations and no deaths were reported. Thirty-one (94%) of 33 ill people interviewed reported consuming a powdered supplement in the week before illness; of these, 30 (97%) reported consuming Product A, a raw organic powdered shake product consumed as a meal replacement. Laboratory testing isolated the outbreak strain of Salmonella Virchow from: leftover Product A collected from ill people's homes, organic moringa leaf powder (an ingredient in Product A), and finished product retained by the firm. Firm inspections at three facilities linked to Product A production did not reveal contamination at the facilities. Traceback identified that the contaminated moringa leaf powder was imported from South Africa. Conclusions: This investigation identified a novel outbreak vehicle and highlighted the potential risk with similar products not intended to be cooked by consumers before consuming. The company issued a voluntary recall of all implicated products. As this product has a long shelf-life, the recall likely prevented additional illnesses. |
Evaluation of TaqMan Array Card (TAC) for the Detection of Central Nervous System Infections in Kenya.
Onyango CO , Loparev V , Lidechi S , Bhullar V , Schmid DS , Radford K , Lo MK , Rota P , Johnson BW , Munoz J , Oneko M , Burton D , Black CM , Neatherlin J , Montgomery JM , Fields B . J Clin Microbiol 2017 55 (7) 2035-2044 Infections of the central nervous system (CNS) are often acute with significant morbidity and mortality. Routine diagnosis of such infections is limited in developing countries and requires modern equipment in advanced laboratories that may be unavailable to a number of patients in sub-Saharan Africa. We developed a TaqMan Array Card (TAC) that detects multiple pathogens simultaneously from cerebrospinal fluid (CSF). The 21-pathogen TAC assays include two parasites (Balamuthia mandrillaris and Acanthamoeba), six bacterial pathogens (Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Mycoplasma pneumoniae, Mycobacterium tuberculosis, and Bartonella) and 13 viruses (parechovirus, dengue, nipah, varicella zoster, mumps, measles, lyssa, herpes simplex virus 1 and 2, Epstein Barr virus, enterovirus, cytomegalovirus and chikungunya). The card also includes human RNAse P as a nucleic acid extraction control and an internal manufacturer control (glyceraldehyde 3-phosphate dehydrogenase (GAPDH)). This CNS-TAC can test up to eight samples for all 21 agents within 2.5 hours following nucleic acid extraction. The assay was validated for linearity, limit of detection, sensitivity and specificity by either using live viruses (dengue, mumps and measles) or nucleic acid material (nipah and chikungunya). Of the 120 samples tested by individual real-time PCR (IRTP), 35 were positive for eight different targets while CNS-TAC detected 37 positive samples across nine different targets. The TAC assays showed 85.6% sensitivity and 96.7% specificity across the assays. This assay may be useful for outbreak investigation and surveillance of suspected neurological disease. |
State laws requiring hand sanitation stations at animal contact exhibits - United States, March-April 2016
Hoss A , Basler C , Stevenson L , Gambino-Shirley K , Robyn MP , Nichols M . MMWR Morb Mortal Wkly Rep 2017 66 (1) 16-18 In the United States, animal contact exhibits, such as petting zoos and agricultural fairs, have been sources of zoonotic infections, including infections with Escherichia coli, Salmonella, and Cryptosporidium. The National Association of State Public Health Veterinarians recommends handwashing after contact with animals as an effective prevention measure to disease transmission at these exhibits. This report provides a list of states that have used law, specifically statutes and regulations, as public health interventions to increase hand sanitation at animal contact exhibits. The report is based on an assessment conducted by CDC's Public Health Law Program, in collaboration with the Division of Foodborne, Waterborne, and Environmental Diseases in CDC's National Center for Emerging and Zoonotic Infectious Diseases. The assessment found that seven states have used statutes or regulations to require hand sanitation stations at these exhibits (5). Jurisdictions seeking to improve rates of hand sanitation at animal contact exhibits can use this report as a resource in developing their own legal interventions. |
Notes from the field: Outbreak of Escherichia coli O157 infections associated with goat dairy farm visits - Connecticut, 2016
Laughlin M , Gambino-Shirley K , Gacek P , Phan Q , Stevenson L , Mercante A , Mullins J , Burnworth L , Blackstock A , Razeq JH , Cartter M , Nichols M . MMWR Morb Mortal Wkly Rep 2016 65 (5051) 1453-1454 On March 24, 2016, the Connecticut Department of Public Health (DPH) identified a cluster of seven culture-confirmed Shiga toxin–producing Escherichia coli (STEC) infections in patients ranging in age from 2 to 25 years. All seven patients reported bloody diarrhea; four were evaluated in an emergency department, three were hospitalized, and two developed hemolytic uremic syndrome (HUS). Six of the seven patients reported visiting the same goat dairy farm in southeastern Connecticut during the week preceding illness onset. An investigation was initiated by DPH, the Connecticut Department of Agriculture, CDC, and the local health district to determine the magnitude of the outbreak, identify risk factors and potential sources of infection, and develop recommendations to prevent further illnesses. A total of 50 confirmed cases of E. coli infection were associated with the outbreak, including 47 with an epidemiologic link to the goat farm. | PulseNet, the national molecular subtyping laboratory network for foodborne disease surveillance, and pulsed-field gel electrophoresis (PFGE) were used to identify the outbreak strains as STEC O157. A confirmed case was defined as 1) laboratory-confirmed E. coli O157 infection with the PFGE-identified outbreak strain or 2) physician-diagnosed HUS during March–April 2016 in a person with an epidemiologic link to the goat farm. Ill farm visitors were encouraged to contact DPH through a public statement released on March 28, 2016, and were interviewed about their visit. Environmental samples were collected at the farm and cultured, and the resulting bacterial isolates were compared with patient isolates using PFGE and whole genome sequencing. Genetic relatedness of isolates was determined by high-quality single nucleotide polymorphism analysis. The 2013 Compendium of Measures to Prevent Disease Associated with Animals in Public Settings was used to evaluate practices at the farm (1). |
Raccoon roundworm infection associated with central nervous system disease and ocular disease - six states, 2013-2015
Sircar AD , Abanyie F , Blumberg D , Chin-Hong P , Coulter KS , Cunningham D , Huskins WC , Langelier C , Reid M , Scott BJ , Shirley DA , Babik JM , Belova A , Sapp SG , McAuliffe I , Rivera HN , Yabsley MJ , Montgomery SP . MMWR Morb Mortal Wkly Rep 2016 65 (35) 930-933 Baylisascaris procyonis, predominantly found in raccoons, is a ubiquitous roundworm found throughout North America. Although raccoons are typically asymptomatic when infected with the parasite, the larval form of Baylisascaris procyonis can result in fatal human disease or severe neurologic outcomes if not treated rapidly. In the United States, Baylisascaris procyonis is more commonly enzootic in raccoons in the midwestern and northeastern regions and along the West Coast. However, since 2002, infections have been documented in other states (Florida and Georgia) and regions. Baylisascariasis is not a nationally notifiable disease in the United States, and little is known about how commonly it occurs or the range of clinical disease in humans. Case reports of seven human baylisascariasis cases in the United States diagnosed by Baylisascaris procyonis immunoblot testing at CDC are described, including review of clinical history and laboratory data. Although all seven patients survived, approximately half were left with severe neurologic deficits. Prevention through close monitoring of children at play, frequent handwashing, and clearing of raccoon latrines (communal sites where raccoons defecate) are critical interventions in curbing Baylisascaris infections. Early treatment of suspected cases is critical to prevent permanent sequelae. |
Complete Genome Sequences of 11 Haemophilus ducreyi Isolates from Children with Cutaneous Lesions in Vanuatu and Ghana.
Pillay A , Katz SS , Abrams AJ , Ballard RC , Simpson SV , Taleo F , Lahra MM , Batra D , Rowe L , Trees DL , Asiedu K , Chen CY . Genome Announc 2016 4 (4) Haemophilus ducreyi causes chancroid and has recently been shown to be a significant cause of cutaneous lesions in tropical or subtropical regions where yaws is endemic. Here, we report the draft genome assemblies for 11 cutaneous strains of Haemophilus ducreyi, isolated from children in Vanuatu and Ghana. |
Notes from the field: Four multistate outbreaks of human Salmonella infections linked to small turtle exposure - United States, 2015
Gambino-Shirley K , Stevenson L , Wargo K , Burnworth L , Roberts J , Garrett N , Van Duyne S , McAllister G , Nichols M . MMWR Morb Mortal Wkly Rep 2016 65 (25) 655-6 In August 2015, the Food and Drug Administration (FDA) notified CDC of a consumer complaint involving Salmonella Sandiego infection in a child (the index patient), who had acquired a small turtle (shell length <4 inches [<10 cm]) at an Alabama flea market. The subsequent investigation, which included examining data from PulseNet, the national molecular subtyping network for foodborne disease surveillance, identified four multistate Salmonella outbreaks: two involving Salmonella Sandiego and two involving Salmonella Poona. These serotypes have been linked to small turtles in previous outbreaks. Although selling small turtles as pets in the United States has been banned since 1975, illegal sales still occur at discount stores and flea markets and by street vendors. CDC investigated to determine the extent of the outbreaks and prevent additional infections. |
Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana.
Forbi JC , Layden JE , Phillips RO , Mora N , Xia GL , Campo DS , Purdy MA , Dimitrova ZE , Owusu DO , Punkova LT , Skums P , Owusu-Ofori S , Sarfo FS , Vaughan G , Roh H , Opare-Sem OK , Cooper RS , Khudyakov YE . PLoS One 2015 10 (12) e0145530 Globally, hepatitis C Virus (HCV) infection is responsible for a large proportion of persons with liver disease, including cancer. The infection is highly prevalent in sub-Saharan Africa. West Africa was identified as a geographic origin of two HCV genotypes. However, little is known about the genetic composition of HCV populations in many countries of the region. Using conventional and next-generation sequencing (NGS), we identified and genetically characterized 65 HCV strains circulating among HCV-positive blood donors in Kumasi, Ghana. Phylogenetic analysis using consensus sequences derived from 3 genomic regions of the HCV genome, 5'-untranslated region, hypervariable region 1 (HVR1) and NS5B gene, consistently classified the HCV variants (n = 65) into genotypes 1 (HCV-1, 15%) and genotype 2 (HCV-2, 85%). The Ghanaian and West African HCV-2 NS5B sequences were found completely intermixed in the phylogenetic tree, indicating a substantial genetic heterogeneity of HCV-2 in Ghana. Analysis of HVR1 sequences from intra-host HCV variants obtained by NGS showed that three donors were infected with >1 HCV strain, including infections with 2 genotypes. Two other donors share an HCV strain, indicating HCV transmission between them. The HCV-2 strain sampled from one donor was replaced with another HCV-2 strain after only 2 months of observation, indicating rapid strain switching. Bayesian analysis estimated that the HCV-2 strains in Ghana were expanding since the 16th century. The blood donors in Kumasi, Ghana, are infected with a very heterogeneous HCV population of HCV-1 and HCV-2, with HCV-2 being prevalent. The detection of three cases of co- or super-infections and transmission linkage between 2 cases suggests frequent opportunities for HCV exposure among the blood donors and is consistent with the reported high HCV prevalence. The conditions for effective HCV-2 transmission existed for ~ 3-4 centuries, indicating a long epidemic history of HCV-2 in Ghana. |
Incidence of medically-attended norovirus-associated acute gastroenteritis in four Veteran's Affairs Medical Center populations in the United States, 2011-2012
Grytdal SP , Rimland D , Shirley SH , Rodriguez-Barradas MC , Goetz MB , Brown ST , Lucero-Obusan C , Holodniy M , Graber C , Parashar U , Vinje J , Lopman B . PLoS One 2015 10 (5) e0126733 An estimated 179 million acute gastroenteritis (AGE) illnesses occur annually in the United States. The role of noroviruses in hospital-related AGE has not been well-documented in the U. S. We estimated the population incidence of community- acquired outpatient and inpatient norovirus AGE encounters, as well as hospital-acquired inpatient norovirus AGE among inpatients at four Veterans Affairs (VA) Medical Centers (VAMCs). Fifty (4%) of 1,160 stool specimens collected ≤7 days from symptom onset tested positive for norovirus. During a one year period, the estimated incidence of outpatient, community- and hospital-acquired inpatient norovirus AGE was 188 cases, 11 cases, and 54 cases/ 100,000 patients, respectively. This study demonstrates the incidence of outpatient and community- and hospital-acquired inpatient norovirus AGE among the VA population seeking care at these four VAMCs. |
Innate susceptibility to norovirus infections influenced by FUT2 genotype in a United States pediatric population.
Currier RL , Payne DC , Staat MA , Selvarangan R , Shirley SH , Halasa N , Boom JA , Englund JA , Szilagyi PG , Harrison CJ , Klein EJ , Weinberg GA , Wikswo ME , Parashar U , Vinje J , Morrow AL . Clin Infect Dis 2015 60 (11) 1631-8 BACKGROUND: Norovirus is a leading cause of acute gastroenteritis (AGE). Noroviruses bind to gut histo-blood group antigens (HBGAs), but only 70-80% of individuals have a functional copy of the FUT2 ("secretor") gene required for gut HBGA expression; these individuals are known as "secretors." Susceptibility to some noroviruses depends on FUT2 secretor status, but the population impact of this association is not established. METHODS: From 12/2011 to 11/2012, active AGE surveillance was performed at six geographically diverse US pediatric sites. Cases under five years were recruited from emergency departments and inpatient units; age-matched healthy controls were recruited at well-child visits. Salivary DNA was collected to determine secretor status and genetic ancestry. Stool was tested for norovirus by realtime RT-PCR. Norovirus genotype was then determined by sequencing. RESULTS: Norovirus was detected in 302 (21%) of 1465 AGE cases and 52 (6%) of 826 healthy controls. Norovirus AGE cases were 2.8-fold more likely than norovirus-negative controls to be secretors (p<0.001) in a logistic regression model adjusted for ancestry, age, site, and health insurance. Secretors comprised all 155 cases and 21 asymptomatic infections with the most prevalent norovirus, GII.4. Control children of Meso-American ancestry were more likely than children of European or African ancestry to be secretors (96% versus 74%, p<0.001). CONCLUSIONS: FUT2 status is associated with norovirus infection and varies by ancestry. GII.4 norovirus exclusively infected secretors. These findings are important to norovirus vaccine trials and design of agents that may block norovirus-HBGA binding. |
Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
Neafsey DE , Waterhouse RM , Abai MR , Aganezov SS , Alekseyev MA , Allen JE , Amon J , Arca B , Arensburger P , Artemov G , Assour LA , Basseri H , Berlin A , Birren BW , Blandin SA , Brockman AI , Burkot TR , Burt A , Chan CS , Chauve C , Chiu JC , Christensen M , Costantini C , Davidson VL , Deligianni E , Dottorini T , Dritsou V , Gabriel SB , Guelbeogo WM , Hall AB , Han MV , Hlaing T , Hughes DS , Jenkins AM , Jiang X , Jungreis I , Kakani EG , Kamali M , Kemppainen P , Kennedy RC , Kirmitzoglou IK , Koekemoer LL , Laban N , Langridge N , Lawniczak MK , Lirakis M , Lobo NF , Lowy E , MacCallum RM , Mao C , Maslen G , Mbogo C , McCarthy J , Michel K , Mitchell SN , Moore W , Murphy KA , Naumenko AN , Nolan T , Novoa EM , O'Loughlin S , Oringanje C , Oshaghi MA , Pakpour N , Papathanos PA , Peery AN , Povelones M , Prakash A , Price DP , Rajaraman A , Reimer LJ , Rinker DC , Rokas A , Russell TL , Sagnon N , Sharakhova MV , Shea T , Simao FA , Simard F , Slotman MA , Somboon P , Stegniy V , Struchiner CJ , Thomas GW , Tojo M , Topalis P , Tubio JM , Unger MF , Vontas J , Walton C , Wilding CS , Willis JH , Wu YC , Yan G , Zdobnov EM , Zhou X , Catteruccia F , Christophides GK , Collins FH , Cornman RS , Crisanti A , Donnelly MJ , Emrich SJ , Fontaine MC , Gelbart W , Hahn MW , Hansen IA , Howell PI , Kafatos FC , Kellis M , Lawson D , Louis C , Luckhart S , Muskavitch MA , Ribeiro JM , Riehle MA , Sharakhov IV , Tu Z , Zwiebel LJ , Besansky NJ . Science 2015 347 (6217) 1258522 Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts. |
High frequency of active HCV infection among seropositive cases in west Africa and evidence for multiple transmission pathways.
Layden JE , Phillips RO , Owusu-Ofori S , Sarfo FS , Kliethermes S , Mora N , Owusu D , Nelson K , Opare-Sem O , Dugas L , Luke A , Shoham D , Forbi JC , Khudyakov YE , Cooper RS . Clin Infect Dis 2014 60 (7) 1033-41 BACKGROUND: Sub-Saharan Africa (SSA) has among the highest global Hepatitis C Virus (HCV) prevalence estimates. However, reports suggesting high rates of serologic false positives and low levels of viremia have led to uncertainty regarding the burden of active infection in this region. Additionally, little is known about the predominant transmission risk factors in SSA. METHODS: We prospectively recalled 363 past blood donors (180 who were rapid screen assay (RSA) positive and 183 that were RSA negative at time of donation) to identify the level of active infection and risk factors for infection at a teaching hospital in Kumasi, Ghana. Participants had repeat blood testing and were administered a questionnaire on risk factors. RESULTS: The frequency of HCV active infection ranged from 74.4% to 88% depending on the criteria used to define serologically positive cases. Individuals with active disease had biochemical evidence of liver inflammation and median viral loads of 5.7 log copies/ml. Individuals from the northern and upper regions of Ghana had greater risks of infection compared to participants from other areas. Additional risk factors included traditional circumcision, home birth, tribal scarring and HBV co-infection. CONCLUSIONS: Viremic infection was common among serologically confirmed cases. Attention to testing algorithms is needed to define the true HCV burden in SSA. These data also suggest that several transmission modes are likely contributing to the current HCV epidemic in Ghana, and the distribution of these practices may result in substantial regional variation in prevalence. |
Genomic analysis of the causative agents of coccidiosis in domestic chickens.
Reid AJ , Blake DP , Ansari HR , Billington K , Browne HP , Bryant JM , Dunn M , Hung SS , Kawahara F , Miranda-Saavedra D , Malas T , Mourier T , Naghra H , Nair M , Otto TD , Rawlings ND , Rivailler P , Sanchez-Flores A , Sanders M , Subramaniam C , Tay YL , Woo Y , Wu X , Barrell B , Dear PH , Doerig C , Gruber A , Ivens AC , Parkinson J , Rajandream MA , Shirley MW , Wan KL , Berriman M , Tomley FM , Pain A . Genome Res 2014 24 (10) 1676-85 Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding. |
Genotypic and epidemiologic trends of norovirus outbreaks in the United States, 2009 to 2013.
Vega E , Barclay L , Gregoricus N , Shirley SH , Lee D , Vinje J . J Clin Microbiol 2013 52 (1) 147-55 Noroviruses are the leading cause of epidemic acute gastroenteritis in the United States. From September 2009 through August 2013, 3,960 norovirus outbreaks were reported to CaliciNet. Of the 2,895 outbreaks with a known transmission route, person-to-person and foodborne transmission were reported for 2,425 (83.7%) and 465 (16.1%) of the outbreaks, respectively. A total of 2,475 (62.5%) of outbreaks occurred in long term care facilities (LTCF) followed by 389 (9.8%) in restaurants and 227 (5.7%) in schools. A total of 435 (11%) outbreaks were typed as GI and 3,525 (89%) as GII norovirus. GII.4 viruses caused 2,853 (72%) of all outbreaks, of which 94% typed as either GII.4 New Orleans or GII.4 Sydney. In addition, three non-GII.4 viruses, GII.12, GII.1, and GI.6, caused 528 (13%) of all outbreaks. Several non-GII.4 genotypes (GI.3, GI.6, GI.7, GII.3, GII.6, and GII.12) were significantly more associated with foodborne transmission (P < 0.05; OR: 1.9 - 7.1). Patients in LTCF and people ≥ 65 years of age were at a higher risk for GII.4 infections compared to other settings and genotypes (P < 0.05). Phylogeographic analysis identified three major dispersions from two geographic locations responsible for the GI.6 outbreaks from 2011 -- 2013. In conclusion, our data demonstrate the cyclic emergence of new (non-GII.4) norovirus strains, and several genotypes are more often associated with foodborne outbreaks. These surveillance data can be used to improve viral foodborne surveillance and help guide studies to develop and evaluate targeted prevention methods such as norovirus vaccines, antivirals and environmental decontamination methods. |
Etiology of viral gastroenteritis infections in children <5 years of age in the United States, 2008-2009
Chhabra P , Payne DC , Szilagyi PG , Edwards KM , Staat MA , Shirley SH , Wikswo M , Nix WA , Lu X , Parashar UD , Vinje J . J Infect Dis 2013 208 (5) 790-800 BACKGROUND: Although rotavirus and norovirus cause nearly 40% of severe endemic acute gastroenteritis (AGE) in children <5 years of age in the United States (US), there are limited data on the etiologic role of other enteric viruses in this age group. METHODS: We conducted active population-based surveillance in children presenting with AGE to hospitals, emergency departments, and primary care clinics in three US counties. Stool specimens from these children and from age-matched healthy controls collected between October 2008 and September 2009 were tested for enteric adenovirus, astrovirus, sapovirus, parechovirus, bocavirus and aichivirus. Typing was carried out by sequencing and phylogenetic analysis. RESULTS: Adenovirus, astrovirus, sapovirus, parechovirus, bocavirus and aichivirus were detected in the stool specimens of 11.8%, 4.9%, 5.4%, 4.8%, 1.4% and 0.2% of AGE patients and 1.8%, 3.0%, 4.2%, 4.4%, 2.4% and 0% of healthy controls, respectively. Adenovirus [type-41], astrovirus [types-1, 2, 3, 4, 8], sapovirus [GI and GII], parechovirus [types-1, 3, 4, 5] and bocavirus [types-1, 2, 3] were found co-circulating. CONCLUSIONS: Adenovirus, astrovirus, and sapovirus infections were detected in 22.1% of the specimens from children <5 years of age who had medical visits for AGE and tested negative for rota- and norovirus. No causal role for parechovirus and bocavirus was found. |
Norovirus and medically attended gastroenteritis in U.S. children
Payne DC , Vinje J , Szilagyi PG , Edwards KM , Staat MA , Weinberg GA , Hall CB , Chappell J , Bernstein DI , Curns AT , Wikswo M , Shirley SH , Hall AJ , Lopman B , Parashar UD . N Engl J Med 2013 368 (12) 1121-30 BACKGROUND: Cases of rotavirus-associated acute gastroenteritis have declined since the introduction of rotavirus vaccines, but the burden of norovirus-associated acute gastroenteritis in children remains to be assessed. METHODS: We conducted active surveillance for laboratory-confirmed cases of norovirus among children younger than 5 years of age with acute gastroenteritis in hospitals, emergency departments, and outpatient clinical settings. The children resided in one of three U.S. counties during the years 2009 and 2010. Fecal specimens were tested for norovirus and rotavirus. We calculated population-based rates of norovirus-associated acute gastroenteritis and reviewed billing records to determine medical costs; these data were extrapolated to the U.S. population of children younger than 5 years of age. RESULTS: Norovirus was detected in 21% of young children (278 of 1295) seeking medical attention for acute gastroenteritis in 2009 and 2010, with norovirus detected in 22% (165 of 742) in 2009 and 20% (113 of 553) in 2010 (P=0.43). The virus was also detected in 4% of healthy controls (19 of 493) in 2009. Rotavirus was identified in 12% of children with acute gastroenteritis (152 of 1295) in 2009 and 2010. The respective rates of hospitalization, emergency department visits, and outpatient visits for the norovirus were 8.6, 146.7, and 367.7 per 10,000 children younger than 5 years of age in 2009 and 5.8, 134.3, and 260.1 per 10,000 in 2010, with an estimated cost per episode of $3,918, $435, and $151, respectively, in 2009. Nationally, we estimate that the average numbers of annual hospitalizations, emergency department visits, and outpatient visits due to norovirus infection in 2009 and 2010 among U.S. children in this age group exceeded 14,000, 281,000, and 627,000, respectively, with more than $273 million in treatment costs each year. CONCLUSIONS: Since the introduction of rotavirus vaccines, norovirus has become the leading cause of medically attended acute gastroenteritis in U.S. children and is associated with nearly 1 million health care visits annually. (Funded by the Centers for Disease Control and Prevention.). |
Detection and molecular characterization of noroviruses and sapoviruses in children admitted to hospital with acute gastroenteritis in Vietnam
Trang NV , Luan le T , Kim-Anh le T , Hau VT , Nhung le TH , Phasuk P , Setrabutr O , Shirley H , Vinje J , Anh DD , Mason CJ . J Med Virol 2012 84 (2) 290-7 Noroviruses (NoV) and sapoviruses (SaV) are recognized as important causes of acute gastroenteritis in children worldwide. In this study, the prevalence and genetic variability of NoV and SaV were determined in hospitalized children <5 years of age with acute gastroenteritis in Hanoi, Vietnam. A total of 501 fecal specimens collected between November-2007 and October-2008, that previously had been tested for rotavirus (RV), were tested for NoV and SaV by realtime RT-PCR. Positive samples were genotyped by conventional RT-PCR followed by sequencing. GII NoV was detected in 180 (36%) and SaV in 7 (1.4%) of the samples. NoV was detected year-round ranging from 9.5% in April to 81.5% in September among RV negative samples. NoV GII.4 Minerva (2006b) was the dominant genotype (93%) with a few other genotypes detected including GII.3 (4.4%), GII.13 (1.7%), and GII.2 (0.6%) but no GI strains. Only GI and GII SaV strains were detected in this study. No difference in NoV prevalence between age groups was noted. Frequency of vomiting or fever was similar between children with NoV and RV infection, yet, NoV caused diarrhea with longer duration. In conclusion, NoV is the second most frequent cause of diarrhea in hospitalized children in North Vietnam. (J. Med. Virol. 84:290-297, 2012. (c) 2011 Wiley Periodicals, Inc.) |
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