Last data update: Sep 16, 2024. (Total: 47680 publications since 2009)
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Query Trace: Boxrud D [original query] |
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Reported incidence of infections caused by pathogens transmitted commonly through food: Impact of increased use of culture-independent diagnostic tests - Foodborne Diseases Active Surveillance Network, 1996-2023
Shah HJ , Jervis RH , Wymore K , Rissman T , LaClair B , Boyle MM , Smith K , Lathrop S , McGuire S , Trevejo R , McMillian M , Harris S , Zablotsky Kufel J , Houck K , Lau CE , Devine CJ , Boxrud D , Weller DL . MMWR Morb Mortal Wkly Rep 2024 73 (26) 584-593 Reducing foodborne disease incidence is a public health priority. This report summarizes preliminary 2023 Foodborne Diseases Active Surveillance Network (FoodNet) data and highlights efforts to increase the representativeness of FoodNet. During 2023, incidences of domestically acquired campylobacteriosis, Shiga toxin-producing Escherichia coli infection, yersiniosis, vibriosis, and cyclosporiasis increased, whereas those of listeriosis, salmonellosis, and shigellosis remained stable compared with incidences during 2016-2018, the baseline used for tracking progress towards federal disease reduction goals. During 2023, the incidence and percentage of infections diagnosed by culture-independent diagnostic tests (CIDTs) reported to FoodNet continued to increase, and the percentage of cases that yielded an isolate decreased, affecting observed trends in incidence. Because CIDTs allow for diagnosis of infections that previously would have gone undetected, lack of progress toward disease reduction goals might reflect changing diagnostic practices rather than an actual increase in incidence. Continued surveillance is needed to monitor the impact of changing diagnostic practices on disease trends, and targeted prevention efforts are needed to meet disease reduction goals. During 2023, FoodNet expanded its catchment area for the first time since 2004. This expansion improved the representativeness of the FoodNet catchment area, the ability of FoodNet to monitor trends in disease incidence, and the generalizability of FoodNet data. |
Laboratory criteria for exclusion and readmission of potentially infectious persons in sensitive settings in the age of culture-independent diagnostic tests: Report of a multidisciplinary workgroup
Besser J , Singer R , Jervis R , Boxrud D , Smith K , Daly ER . J Food Prot 2023 86 (12) 100173 Culture-independent diagnostic tests (CIDTs) are increasingly used for clinical diagnosis of gastrointestinal diseases such as salmonellosis, Shiga toxin-producing E. coli disease, and shigellosis because of their speed, convenience, and generally high-performance characteristics. These tests are also used to screen potentially infectious asymptomatic persons during outbreak investigations in sensitive settings such as childcare, food service, and healthcare. However, only limited performance data are available for CIDTs used on specimens from asymptomatic persons. The Association of Public Health Laboratories (APHL) and Council of State and Territorial Epidemiologists (CSTE) convened a workgroup to examine the available scientific data to inform interim decision-making related to exclusion and readmission criteria for potentially infectious persons in sensitive settings, the risks and benefits of different testing strategies, and to identify knowledge gaps for further research. This is the report on the Workgroup findings. |
Emergence of a novel Salmonella enterica serotype Reading clone is linked to its expansion in commercial turkey production, resulting in unanticipated human illness in North America (preprint)
Miller EA , Elnekave E , Flores-Figueroa C , Johnson A , Kearney A , Munoz-Aguayo J , Tagg KA , Tschetter L , Weber BP , Nadon CA , Boxrud D , Singer RS , Folster JP , Johnson TJ . bioRxiv 2019 855734 Concurrent separate human outbreaks of Salmonella enterica serotype Reading occurred in 2017-2019 in the United States and Canada, which were both linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys, and to determine the genomic context of outbreaks involving this rarely isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade isolates clustered into three subclades, including an “emergent” clade that only contained isolates dated 2016 or later, including many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades suggesting that the apparent success of currently circulating subclades clade is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S. Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source.Importance Increasingly, outbreak investigations involving foodborne pathogens are confounded by the inter-connectedness of food animal production and distribution, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincides with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in the barn environment, and ability to cause illness in humans. |
Evidence of False Positivity for Vibrio Species Tested by Gastrointestinal Multiplex PCR Panels, Minnesota, 2016-2018.
Decuir M , Fowler RC , Cebelinski E , Smith K , Boxrud D , Medus C . Open Forum Infect Dis 2021 8 (6) ofab247 BACKGROUND: Syndromic gastrointestinal multiplex polymerase chain reaction (PCR) panels (GMPPs) are used by an increasing number of clinical laboratories to identify enteric pathogens. Vibrio species are included on GMPPs, but because of the low prevalence of vibriosis, performance characteristics for these panels have been difficult to measure. METHODS: All Vibrio spp. cases identified by GMPPs in Minnesota during 2016-2018 (n = 100) were assessed to identify differences between culture-confirmed cases and those that were PCR-positive only. RESULTS: Overall, 47% of cases had Vibrio species recovered by culture. Two GMPPs were used in Minnesota, Verigene EPT and FilmArray GIP, and the recovery rate of Vibrio spp. was significantly different between these platforms (Verigene EPT 63%, compared with FilmArray GIP 28%). No distinct seasonality was identified among GMPP-positive, culture-negative cases, whereas culture-confirmed case incidence peaked during July and August. Among cases with no other pathogen detected by the GMPP, confirmed cases reported a lower rate of bloody diarrhea (odds ratio [OR], 0.7; P = .004) and were less likely to have a symptom duration >14 days (OR, 0.3; P = .04). Confirmed cases were also more likely to include reports of consuming food items typically associated with Vibrio spp. infection or to have another likely source of infection (eg, international travel or contact with an untreated body of fresh or salt water or marine life; OR, 9.6; P = .001). CONCLUSIONS: The combined findings indicate that cases identified by GMPP that did not have culture confirmation were less likely to include symptoms or exposures consistent with vibriosis. These findings emphasize the need for improvements to testing platform specificity and the importance of combining clinical and exposure information when diagnosing an infection. This study underscores the importance of maintaining the ability to culture Vibrio species to aid in accurate diagnoses. |
Epidemiology of enterotoxigenic Escherichia coli infection in Minnesota, 2016-2017
Buuck S , Smith K , Fowler RC , Cebelinski E , Lappi V , Boxrud D , Medus C . Epidemiol Infect 2020 148 1-26 Enterotoxigenic Escherichia coli (ETEC) is a well-established cause of traveller's diarrhoea and occasional domestic foodborne illness outbreaks in the USA. Although ETEC are not detected by conventional stool culture methods used in clinical laboratories, syndromic culture-independent diagnostic tests (CIDTs) capable of detecting ETEC have become increasingly prevalent in the last decade. This study describes the epidemiology of ETEC infections reported to the Minnesota Department of Health (MDH) during 2016-2017. ETEC-positive stool specimens were submitted to MDH to confirm the presence of ETEC DNA by polymerase chain reaction (PCR). Cases were interviewed to ascertain illness and exposures. Contemporaneous Salmonella cases were used as a comparison group in a case-case comparison analysis of risk factors. Of 222 ETEC-positive specimens received by MDH, 108 (49%) were concordant by PCR. ETEC was the sixth most frequently reported bacterial enteric pathogen among a subset of CIDT-positive specimens. Sixty-nine (64%) laboratory-confirmed cases had an additional pathogen codetected with ETEC, including enteroaggregative E. coli (n = 40) and enteropathogenic E. coli (n = 39). Although travel is a risk factor for ETEC infection, only 43% of cases travelled internationally, providing evidence for ETEC as an underestimated source of domestically acquired enteric illness in the USA. |
Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America.
Miller EA , Elnekave E , Flores-Figueroa C , Johnson A , Kearney A , Munoz-Aguayo J , Tagg KA , Tschetter L , Weber BP , Nadon CA , Boxrud D , Singer RS , Folster JP , Johnson TJ . mSphere 2020 5 (2) Two separate human outbreaks of Salmonella enterica serotype Reading occurred between 2017 and 2019 in the United States and Canada, and both outbreaks were linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys and to determine the genomic context of outbreaks involving this infrequently isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole-genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade, isolates clustered into three subclades, including an "emergent" clade that contained only isolates dated 2016 or later, with many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades, suggesting that the apparent success of currently circulating subclades is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source.IMPORTANCE Increasingly, outbreak investigations involving foodborne pathogens are difficult due to the interconnectedness of food animal production and distribution, and homogeneous nature of industry integration, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole-genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincided with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in commercial turkeys and ability to cause illness in humans. |
Genetic Characterization of Mumps Viruses Associated with the Resurgence of Mumps in the United States: 2015-2017.
McNall RJ , Wharton AK , Anderson R , Clemmons N , Lopareva EN , Gonzalez C , Espinosa A , Probert WS , Hacker JK , Liu G , Garfin J , Strain A , Boxrud D , Bryant PW , George KS , Davis T , Griesser RH , Shult P , Bankamp B , Hickman CJ , Wroblewski K , Rota PA . Virus Res 2020 281 197935 Despite high coverage with measles, mumps, and rubella vaccine in the United States, outbreaks of mumps occur in close contact settings such as schools, colleges, and camps. Starting in late 2015, outbreaks were reported from several universities, and by the end of 2017, greater than 13,800 cases had been reported nation-wide. In 2013, the CDC and the Association of Public Health Laboratories contracted four Vaccine Preventable Diseases Reference Centers (VPD-RCs) to perform real-time reverse transcription PCR (RT-qPCR) to detect mumps RNA in clinical samples and to determine the genotype. Twelve genotypes of mumps virus are currently recognized by the World Health Organization, and the standard protocol for genotyping requires sequencing the entire gene coding for the small hydrophobic (SH) protein. Phylogenetic analysis of the 1862 mumps samples genotyped from 2015 through 2017 showed that the overall diversity of genotypes detected was low. Only 0.8% of the sequences were identified as genotypes C, H, J, or K, and 0.5% were identified as vaccine strains in genotypes A or N, while most sequences (98.7%) were genotype G. The majority of the genotype G sequences could be included into one of two large groups with identical SH sequences. Within genotype G, a small number of phylogenetically significant outlier sequences were associated with epidemiologically distinct chains of transmission. These results demonstrate that molecular and epidemiologic data can be used to track transmission pathways of mumps virus; however, the limited diversity of the SH sequences may be insufficient for resolving transmission in all outbreaks. |
PulseNet and the Changing Paradigm of Laboratory-Based Surveillance for Foodborne Diseases.
Kubota KA , Wolfgang WJ , Baker DJ , Boxrud D , Turner L , Trees E , Carleton HA , Gerner-Smidt P . Public Health Rep 2019 134 22s-28s PulseNet, the National Molecular Subtyping Network for Foodborne Disease Surveillance, was established in 1996 through a collaboration with the Centers for Disease Control and Prevention; the US Department of Agriculture, Food Safety and Inspection Service; the US Food and Drug Administration; 4 state public health laboratories; and the Association of Public Health Laboratories. The network has since expanded to include 83 state, local, and food regulatory public health laboratories. In 2016, PulseNet was estimated to be helping prevent an estimated 270 000 foodborne illnesses annually. PulseNet is undergoing a transformation toward whole-genome sequencing (WGS), which provides better discriminatory power and precision than pulsed-field gel electrophoresis (PFGE). WGS improves the detection of outbreak clusters and could replace many traditional reference identification and characterization methods. This article highlights the contributions made by public health laboratories in transforming PulseNet's surveillance and describes how the transformation is changing local and national surveillance practices. Our data show that WGS is better at identifying clusters than PFGE, especially for clonal organisms such as Salmonella Enteritidis. The need to develop prioritization schemes for cluster follow-up and additional resources for both public health laboratory and epidemiology departments will be critical as PulseNet implements WGS for foodborne disease surveillance in the United States. |
Burdens of invasive methicillin-susceptible and methicillin-resistant Staphylococcus aureus disease, Minnesota, USA
Koeck M , Como-Sabetti K , Boxrud D , Dobbins G , Glennen A , Anacker M , Jawahir S , See I , Lynfield R . Emerg Infect Dis 2019 25 (1) 171-174 During August 1, 2014-July 31, 2015, in 2 counties in Minnesota, USA, incidence of invasive methicillin-susceptible Staphylococcus aureus (MSSA) (27.1 cases/100,000 persons) was twice that of invasive methicillin-resistant S. aureus (13.1 cases/100,000 persons). MSSA isolates were more genetically diverse and susceptible to more antimicrobial drugs than methicillin-resistant S. aureus isolates. |
Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States.
Zhang S , Li S , Gu W , den Bakker H , Boxrud D , Taylor A , Roe C , Driebe E , Engelthaler DM , Allard M , Brown E , McDermott P , Zhao S , Bruce BB , Trees E , Fields PI , Deng X . Emerg Infect Dis 2019 25 (1) 82-91 Increasingly, routine surveillance and monitoring of foodborne pathogens using whole-genome sequencing is creating opportunities to study foodborne illness epidemiology beyond routine outbreak investigations and case-control studies. Using a global phylogeny of Salmonella enterica serotype Typhimurium, we found that major livestock sources of the pathogen in the United States can be predicted through whole-genome sequencing data. Relatively steady rates of sequence divergence in livestock lineages enabled the inference of their recent origins. Elevated accumulation of lineage-specific pseudogenes after divergence from generalist populations and possible metabolic acclimation in a representative swine isolate indicates possible emergence of host adaptation. We developed and retrospectively applied a machine learning Random Forest classifier for genomic source prediction of Salmonella Typhimurium that correctly attributed 7 of 8 major zoonotic outbreaks in the United States during 1998-2013. We further identified 50 key genetic features that were sufficient for robust livestock source prediction. |
Draft Genome Sequences for a Diverse Set of Seven Haemophilus and Aggregatibacter Species.
Nichols M , Topaz N , Wang X , Wang X , Boxrud D . Microbiol Resour Announc 2018 7 (16) Haemophilus is a complex genus that includes commensal and pathogenic species that pose a public health threat to humans. While the pathogenic species have been studied extensively, many commensals have limited genomic information available. Here, we present 24 draft genomes for a diverse set of 7 Haemophilus and Aggregatibacter species. Copyright © 2018 Microbiology Resource Announcements.All right reserved. |
Prevalence and Molecular Characteristics of Clostridium difficile in Retail Meats, Food-Producing and Companion Animals, and Humans in Minnesota.
Shaughnessy MK , Snider T , Sepulveda R , Boxrud D , Cebelinski E , Jawahir S , Holzbauer S , Johnston BD , Smith K , Bender JB , Thuras P , Diez-Gonzalez F , Johnson JR . J Food Prot 2018 81 (10) 1635-1642 Community-associated Clostridium difficile infection (CA-CDI) now accounts for approximately 50% of CDI cases in central Minnesota; animals and meat products are potential sources. From November 2011 to July 2013, we cultured retail meat products and fecal samples from food-producing and companion animals in central Minnesota for C. difficile by using standard methods. The resulting 51 C. difficile isolates, plus 30 archived local veterinary C. difficile isolates and 208 human CA-CDI case isolates from central Minnesota (from 2012) from the Minnesota Department of Health, were characterized molecularly, and source groups were compared using discriminant analysis. C. difficile was recovered from 0 (0%) of 342 retail meat samples and 51 (9%) of 559 animal fecal samples. Overall, the 81 animal source isolates and 208 human source isolates were highly diverse genetically. Molecular traits segregated extensively in relation to animal versus human origin. Discriminant analysis classified 95% of isolates correctly by source group; only five (2.5%) human source isolates were classified as animal source. These data do not support meat products or food-producing and companion animals as important sources of CA-CDI in the central Minnesota study region. |
BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species.
Topaz N , Boxrud D , Retchless AC , Nichols M , Chang HY , Hu F , Wang X . BMC Infect Dis 2018 18 (1) 405 BACKGROUND: Bacterial meningitis is a life-threatening infection that remains a public health concern. Bacterial meningitis is commonly caused by the following species: Neisseria meningitidis, Streptococcus pneumoniae, Listeria monocytogenes, Haemophilus influenzae and Escherichia coli. Here, we describe BMScan (Bacterial Meningitis Scan), a whole-genome analysis tool for the species identification of bacterial meningitis-causing and closely-related pathogens, an essential step for case management and disease surveillance. BMScan relies on a reference collection that contains genomes for 17 focal species to scan against to identify a given species. We established this reference collection by supplementing publically available genomes from RefSeq with genomes from the isolate collections of the Centers for Disease Control Bacterial Meningitis Laboratory and the Minnesota Department of Health Public Health Laboratory, and then filtered them down to a representative set of genomes which capture the diversity for each species. Using this reference collection, we evaluated two genomic comparison algorithms, Mash and Average Nucleotide Identity, for their ability to accurately and rapidly identify our focal species. RESULTS: We found that the results of Mash were strongly correlated with the results of ANI for species identification, while providing a significant reduction in run-time. This drastic difference in run-time enabled the rapid scanning of large reference genome collections, which, when combined with species-specific threshold values, facilitated the development of BMScan. Using a validation set of 15,503 genomes of our species of interest, BMScan accurately identified 99.97% of the species within 16 min 47 s. CONCLUSIONS: Identification of the bacterial meningitis pathogenic species is a critical step for case confirmation and further strain characterization. BMScan employs species-specific thresholds for previously-validated, genome-wide similarity statistics compiled from a curated reference genome collection to rapidly and accurately identify the species of uncharacterized bacterial meningitis pathogens and closely related pathogens. BMScan will facilitate the transition in public health laboratories from traditional phenotypic detection methods to whole genome sequencing based methods for species identification. |
Draft Genome Sequences for a Diverse Set of Isolates from 10 Neisseria Species.
Nichols M , Topaz N , Wang X , Wang X , Boxrud D . Genome Announc 2018 6 (20) Neisseria is a diverse genus that includes commensal and pathogenic species that pose a public health threat. While the pathogenic species have been studied extensively, many of the commensals have limited genomic information available. Here, we present draft genome sequences for a diverse set of 37 isolates from 10 Neisseria species. |
Detection of Influenza C Viruses Among Outpatients and Patients Hospitalized for Severe Acute Respiratory Infection, Minnesota, 2013-2016.
Thielen BK , Friedlander H , Bistodeau S , Shu B , Lynch B , Martin K , Bye E , Como-Sabetti K , Boxrud D , Strain AK , Chaves SS , Steffens A , Fowlkes AL , Lindstrom S , Lynfield R . Clin Infect Dis 2018 66 (7) 1092-1098 Background: Existing literature suggests that influenza C typically causes mild respiratory tract disease. However, clinical and epidemiological data are limited. Methods: Four outpatient clinics and 3 hospitals submitted clinical data and respiratory specimens through a surveillance network for acute respiratory infection (ARI) from May 2013 through December 2016. Specimens were tested using multitarget nucleic acid amplification for 19-22 respiratory pathogens, including influenza C. Results: Influenza C virus was detected among 59 of 10 202 (0.58%) hospitalized severe ARI cases and 11 of 2282 (0.48%) outpatients. Most detections occurred from December to March, 73% during the 2014-2015 season. Influenza C detections occurred among patients of all ages, with rates being similar between inpatients and outpatients. The highest rate of detection occurred among children aged 6-24 months (1.2%). Among hospitalized cases, 7 required intensive care. Medical comorbidities were reported in 58% of hospitalized cases and all who required intensive care. At least 1 other respiratory pathogen was detected in 40 (66%) cases, most commonly rhinovirus/enterovirus (25%) and respiratory syncytial virus (20%). The hemagglutinin-esterase-fusion gene was sequenced in 37 specimens, and both C/Kanagawa and C/Sao Paulo lineages were detected in inpatients and outpatients. Conclusions: We found seasonal circulation of influenza C with year-to-year variability. Detection was most frequent among young children but occurred in all ages. Some cases that were positive for influenza C, particularly those with comorbid conditions, had severe disease, suggesting a need for further study of the role of influenza C virus in the pathogenesis of respiratory disease. |
Surveillance for and Discovery of Borrelia Species in US Patients Suspected of Tickborne Illness.
Kingry LC , Anacker M , Pritt B , Bjork J , Respicio-Kingry L , Liu G , Sheldon S , Boxrud D , Strain A , Oatman S , Berry J , Sloan L , Mead P , Neitzel D , Kugeler KJ , Petersen JM . Clin Infect Dis 2017 66 (12) 1864-1871 Background: Tick-transmitted Borrelia species fall into two heterogeneous bacterial complexes comprised of multiple species, the relapsing fever (RF) group and the Borrelia burgdorferi sensu lato group, which are the causative agents of Lyme borreliosis (LB), the most common tickborne disease in the northern hemisphere. Geographic expansion of human LB in the United States and discovery of emerging Borrelia pathogens underscores the importance of surveillance for disease causing Borrelia. Methods: De-identified clinical specimens, submitted by providers throughout the United States, for patients suspected of LB, anaplasmosis, ehrlichiosis, or babesiosis, were screened using a Borrelia genus level TaqMan PCR. Borrelia species and sequence types (STs) were characterized by multi-locus sequence typing (MLST) utilizing next generation sequencing. Results: Among the 7,292 tested specimens tested, five different Borrelia species were identified: two causing LB, B. burgdorferi (n=25) and B. mayonii (n=9), and three RF borreliae, B. hermsii (n=1), B. miyamotoi (n=8), and CandidatusB. johnsonii (n=1), a species previously detected only in the bat tick, Carios kelleyi. ST diversity was greatest for B. burgdorferi positive specimens, with new STs identified primarily among synovial fluids. Conclusion: These results demonstrate broad PCR screening followed by MLST is a powerful surveillance tool for uncovering the spectrum of Borrelia species causing human disease, improving understanding of their geographic distribution, and investigating the correlation between B. burgdorferi STs and joint involvement. Detection of CandidatusB. johnsonii in a patient with suspected tickborne disease suggests this species may be a previously undetected cause of illness in humans with exposure to bat ticks. |
Community laboratory testing for cryptosporidium: Multicenter study retesting public health surveillance stool samples positive for cryptosporidium by rapid cartridge assay with direct fluorescent antibody testing
Roellig DM , Yoder JS , Madison-Antenucci S , Robinson TJ , Van TT , Collier SA , Boxrud D , Monson T , Bates LA , Blackstock AJ , Shea S , Larson K , Xiao L , Beach M . PLoS One 2017 12 (1) e0169915 Cryptosporidium is a common cause of sporadic diarrheal disease and outbreaks in the United States. Increasingly, immunochromatography-based rapid cartridge assays (RCAs) are providing community laboratories with a quick cryptosporidiosis diagnostic method. In the current study, the Centers for Disease Control and Prevention (CDC), the Association of Public Health Laboratories (APHL), and four state health departments evaluated RCA-positive samples obtained during routine Cryptosporidium testing. All samples underwent "head to head" re-testing using both RCA and direct fluorescence assay (DFA). Community level results from three sites indicated that 54.4% (166/305) of Meridian ImmunoCard STAT! positives and 87.0% (67/77) of Remel Xpect positives were confirmed by DFA. When samples were retested by RCA at state laboratories and compared with DFA, 83.3% (155/186) of Meridian ImmunoCard STAT! positives and 95.2% (60/63) of Remel Xpect positives were confirmed. The percentage of confirmed community results varied by site: Minnesota, 39.0%; New York, 63.9%; and Wisconsin, 72.1%. The percentage of confirmed community results decreased with patient age; 12.5% of community positive tests could be confirmed by DFA for patients 60 years of age or older. The percentage of confirmed results did not differ significantly by sex, storage temperature, time between sample collection and testing, or season. Findings from this study demonstrate a lower confirmation rate of community RCA positives when compared to RCA positives identified at state laboratories. Elucidating the causes of decreased test performance in order to improve overall community laboratory performance of these tests is critical for understanding the epidemiology of cryptosporidiosis in the United States (US). |
Borrelia mayonii sp. nov., a member of the Borrelia burgdorferi sensu lato complex, detected in patients and ticks in the upper midwestern United States
Pritt BS , Respicio-Kingry LB , Sloan LM , Schriefer ME , Replogle AJ , Bjork J , Liu G , Kingry LC , Mead PS , Neitzel DF , Schiffman E , Hoang Johnson DK , Davis JP , Paskewitz SM , Boxrud D , Deedon A , Lee X , Miller TK , Feist MA , Steward CR , Theel ES , Patel R , Irish CL , Petersen JM . Int J Syst Evol Microbiol 2016 66 (11) 4878-4880 Lyme borreliosis (LB) is a multisystem disease caused by spirochetes in the Borrelia burgdorferisensu lato (Bbsl) genospecies complex. We previously described a novel Bbsl genospecies (type strain MN14-1420T) that causes LB among patients with exposures to ticks in the upper midwestern USA. Patients infected with the novel Bbsl genospecies demonstrated higher levels of spirochetemia and somewhat differing clinical symptoms as compared with those infected with other Bbsl genospecies. The organism was detected from human specimens using PCR, microscopy, serology and culture. The taxonomic status was determined using an eight-housekeeping-gene (uvrA, rplB, recG, pyrG, pepX, clpX, clpA and nifS) multi-locus sequence analysis (MLSA) and comparison of 16S rRNA gene, flaB, rrf-rrl, ospC and oppA2 nucleotide sequences. Using a system threshold of 98.3 % similarity for delineation of Bbsl genospecies by MLSA, we demonstrated that the novel species is a member of the Bbsl genospecies complex, most closely related to B. burgdorferisensu stricto (94.7-94.9 % similarity). This same species was identified in Ixodes scapularis ticks collected in Minnesota and Wisconsin. This novel species, Borrelia mayonii sp. nov, is formally described here. The type strain, MN14-1420, is available through the Deutsche Sammlung von Mikroorganismen und Zelkulturen GmbH (DSM 102811) and the American Type Culture Collection (ATCC BAA-2743). |
Effect of Culture-Independent Diagnostic Tests on Future Emerging Infections Program Surveillance.
Langley G , Besser J , Iwamoto M , Lessa FC , Cronquist A , Skoff TH , Chaves S , Boxrud D , Pinner RW , Harrison LH . Emerg Infect Dis 2015 21 (9) 1582-8 The Centers for Disease Control and Prevention Emerging Infections Program (EIP) network conducts population-based surveillance for pathogens of public health importance. Central to obtaining estimates of disease burden and tracking microbiological characteristics of these infections is accurate laboratory detection of pathogens. The use of culture-independent diagnostic tests (CIDTs) in clinical settings presents both opportunities and challenges to EIP surveillance. Because CIDTs offer better sensitivity than culture and are relatively easy to perform, their use could potentially improve estimates of disease burden. However, changes in clinical testing practices, use of tests with different sensitivities and specificities, and changes to case definitions make it challenging to monitor trends. Isolates are still needed for performing strain typing, antimicrobial resistance testing, and identifying other molecular characteristics of organisms. In this article, we outline current and future EIP activities to address issues associated with adoption of CIDTs, which may apply to other public health surveillance. |
Live animal markets in Minnesota: a potential source for emergence of novel influenza A viruses and interspecies transmission.
Choi MJ , Torremorell M , Bender JB , Smith K , Boxrud D , Ertl JR , Yang M , Suwannakarn K , Her D , Nguyen J , Uyeki TM , Levine M , Lindstrom S , Katz JM , Jhung M , Vetter S , Wong KK , Sreevatsan S , Lynfield R . Clin Infect Dis 2015 61 (9) 1355-62 BACKGROUND: Live animal markets have been implicated in transmission of influenza A viruses (IAVs) from animals to people. We sought to characterize IAVs at two live animal markets in Minnesota to assess potential routes of occupational exposure and risk for interspecies transmission. METHODS: We implemented surveillance for IAVs among employees, swine, and environment (air and surfaces) during a 12-week period (October 2012-January 2013) at two markets epidemiologically associated with persons with swine-origin IAV (variant) infections. Real-time reverse transcription polymerase chain reaction (rRT-PCR), viral culture, and whole genome sequencing were performed on respiratory and environmental specimens, and serology on sera from employees at beginning and end of surveillance. RESULTS: Nasal swabs from 11 (65%) of 17 employees tested positive for IAVs by rRT-PCR; seven employees tested positive on multiple occasions and one employee reported influenza-like illness. Eleven (73%) of 15 employees had baseline hemagglutination-inhibition antibody titers ≥40 to swine-origin IAVs, but only one demonstrated a 4-fold titer increase to both swine-origin, and pandemic A/Mexico/4108/2009 IAVs. IAVs were isolated from swine (72/84), air (30/45) and pen railings (5/21). Whole genome sequencing of 122 IAVs isolated from swine and environmental specimens revealed multiple strains and subtype codetections. Multiple gene segment exchanges among and within subtypes were observed, resulting in new genetic constellations and reassortant viruses. Genetic sequence similarities of 99%-100% among IAVs of one market customer and swine indicated interspecies transmission. CONCLUSIONS: At markets where swine and persons are in close contact, swine-origin IAVs are prevalent and potentially provide conditions for novel IAV emergence. |
Epidemiology of meningitis in an HIV-infected Ugandan cohort
Rajasingham R , Rhein J , Klammer K , Musubire A , Nabeta H , Akampurira A , Mossel EC , Williams DA , Boxrud DJ , Crabtree MB , Miller BR , Rolfes MA , Tengsupakul S , Andama AO , Meya DB , Boulware DR . Am J Trop Med Hyg 2014 92 (2) 274-9 There is limited understanding of the epidemiology of meningitis among human immunodeficiency virus (HIV)-infected populations in sub-Saharan Africa. We conducted a prospective cohort study of HIV-infected adults with suspected meningitis in Uganda, to comprehensively evaluate the etiologies of meningitis. Intensive cerebrospiral fluid (CSF) testing was performed to evaluate for bacterial, viral, fungal, and mycobacterial etiologies, including neurosyphilis,16s ribosomal DNA (rDNA) polymerase chain reaction (PCR) for bacteria, Plex-ID broad viral assay, quantitative-PCR for HSV-1/2, cytomegalovirus (CMV), Epstein-Barr virus (EBV), and Toxoplasma gondii; reverse transcription-PCR (RT-PCR) for Enteroviruses and arboviruses, and Xpert MTB/RIF assay. Cryptococcal meningitis accounted for 60% (188 of 314) of all causes of meningitis. Of 117 samples sent for viral PCR, 36% were EBV positive. Among cryptococcal antigen negative patients, the yield of Xpert MTB/RIF assay was 22% (8 of 36). After exclusion of cryptococcosis and bacterial meningitis, 61% (43 of 71) with an abnormal CSF profile had no definitive diagnosis. Exploration of new TB diagnostics and diagnostic algorithms for evaluation of meningitis in resource-limited settings remains critical. |
An outbreak of measles in an undervaccinated community
Gahr P , DeVries AS , Wallace G , Miller C , Kenyon C , Sweet K , Martin K , White K , Bagstad E , Hooker C , Krawczynski G , Boxrud D , Liu G , Stinchfield P , LeBlanc J , Hickman C , Bahta L , Barskey A , Lynfield R . Pediatrics 2014 134 (1) e220-8 Measles is readily spread to susceptible individuals, but is no longer endemic in the United States. In March 2011, measles was confirmed in a Minnesota child without travel abroad. This was the first identified case-patient of an outbreak. An investigation was initiated to determine the source, prevent transmission, and examine measles-mumps-rubella (MMR) vaccine coverage in the affected community. Investigation and response included case-patient follow-up, post-exposure prophylaxis, voluntary isolation and quarantine, and early MMR vaccine for non-immune shelter residents >6 months and <12 months of age. Vaccine coverage was assessed by using immunization information system records. Outreach to the affected community included education and support from public health, health care, and community and spiritual leaders. Twenty-one measles cases were identified. The median age was 12 months (range, 4 months to 51 years) and 14 (67%) were hospitalized (range of stay, 2-7 days). The source was a 30-month-old US-born child of Somali descent infected while visiting Kenya. Measles spread in several settings, and over 3000 individuals were exposed. Sixteen case-patients were unvaccinated; 9 of the 16 were age-eligible: 7 of the 9 had safety concerns and 6 were of Somali descent. MMR vaccine coverage among Somali children declined significantly from 2004 through 2010 starting at 91.1% in 2004 and reaching 54.0% in 2010 (chi2 for linear trend 553.79; P < .001). This was the largest measles outbreak in Minnesota in 20 years, and aggressive response likely prevented additional transmission. Measles outbreaks can occur if undervaccinated subpopulations exist. Misunderstandings about vaccine safety must be effectively addressed. |
Neuraminidase H275Y and hemagglutinin D222G mutations in a fatal case of 2009 pandemic influenza A (H1N1) virus infection.
Devries A , Wotton J , Lees C , Boxrud D , Uyeki T , Lynfield R . Influenza Other Respir Viruses 2012 6 (6) e85-8 Oseltamivir-resistant 2009 H1N1 influenza virus infections associated with neuraminidase (NA) H275Y have been identified sporadically. Strains possessing the hemagglutinin (HA) D222G mutation have been detected in small numbers of fatal 2009 H1N1 cases. We report the first clinical description of 2009 H1N1 virus infection with both NA-H275Y and HA-D222G mutations detected by pyrosequencing of bronchioalveolar lavage fluid obtained on symptom day 19. The 59-year-old immunosuppressed patient had multiple conditions conferring higher risk of prolonged viral replication and severe illness and died on symptom day 34. Further investigations are needed to determine the significance of infection with strains possessing NA-H275Y and HA-D222G. |
Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans
Garten RJ , Davis CT , Russell CA , Shu B , Lindstrom S , Balish A , Sessions WM , Xu X , Skepner E , Deyde V , Okomo-Adhiambo M , Gubareva L , Barnes J , Smith CB , Emery SL , Hillman MJ , Rivailler P , Smagala J , de Graaf M , Burke DF , Fouchier RA , Pappas C , Alpuche-Aranda CM , Lopez-Gatell H , Olivera H , Lopez I , Myers CA , Faix D , Blair PJ , Yu C , Keene KM , Dotson PD Jr , Boxrud D , Sambol AR , Abid SH , St George K , Bannerman T , Moore AL , Stringer DJ , Blevins P , Demmler-Harrison GJ , Ginsberg M , Kriner P , Waterman S , Smole S , Guevara HF , Belongia EA , Clark PA , Beatrice ST , Donis R , Katz J , Finelli L , Bridges CB , Shaw M , Jernigan DB , Uyeki TM , Smith DJ , Klimov AI , Cox NJ . Science 2009 325 (5937) 197-201 Since its identification in April 2009, an A(H1N1) virus containing a unique combination of gene segments from both North American and Eurasian swine lineages has continued to circulate in humans. The lack of similarity between the 2009 A(H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Its low genetic diversity suggests that the introduction into humans was a single event or multiple events of similar viruses. Molecular markers predictive of adaptation to humans are not currently present in 2009 A(H1N1) viruses, suggesting that previously unrecognized molecular determinants could be responsible for the transmission among humans. Antigenically the viruses are homogeneous and similar to North American swine A(H1N1) viruses but distinct from seasonal human A(H1N1). |
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