RESUMEN
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.
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Enfermedades Transmitidas por los Alimentos , Vigilancia de la Población , Humanos , Incidencia , Enfermedades Transmitidas por los Alimentos/epidemiología , Enfermedades Transmitidas por los Alimentos/diagnóstico , Enfermedades Transmitidas por los Alimentos/parasitología , Estados Unidos/epidemiología , Pruebas Diagnósticas de Rutina , Microbiología de AlimentosRESUMEN
Multidrug-resistant Salmonella enterica subspecies enterica 4,[5],12:i:- sequence type 34 represents a worldwide public health risk. To determine its origin in the United States, we reconstructed a time-scaled phylogeny with a discrete trait geospatial model. The clone in the United States was introduced from Europe on multiple occasions in the early 2000s.
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Salmonelosis Animal , Salmonella enterica , Animales , Antibacterianos/farmacología , Farmacorresistencia Bacteriana Múltiple/genética , Europa (Continente)/epidemiología , Pruebas de Sensibilidad Microbiana , Salmonella enterica/genética , Estados Unidos/epidemiologíaRESUMEN
BACKGROUND: Enteroaggregative Escherichia coli (EAEC) is increasingly recognized as an enteric pathogen as clinical laboratories transition to culture-independent diagnostic tests that detect EAEC. To date, epidemiological studies have focused on children aged <5 years, and information on EAEC incidence, illness outcomes, and transmission avenues is limited. METHODS: Enteric disease surveillance data in Minnesota were used to describe EAEC illnesses reported to the Minnesota Department of Health from September 2016 through August 2017. We determined laboratory characteristics of EAEC using pulsed-field gel electrophoresis and next-generation sequencing. Frequency of EAEC illness, demographic profile of cases, clinical characteristics of illness, and plausible food or environmental exposures leading to EAEC transmission were assessed. RESULTS: During the study period, 329 EAEC cases were reported. Among a subset of health systems able to detect EAEC over the entire study, EAEC was the second most common reportable enteric pathogen detected after Campylobacter and the most detected diarrheagenic E. coli pathotype. No other reportable enteric pathogens were detected among 75.3% of EAEC cases, and 68% of cases reported no international travel before onset. Several virulence genes were associated with clinical characteristics. CONCLUSIONS: We provide evidence that EAEC is a likely causative agent of diarrheal illness in the United States. Our study contributes to criteria development for identification of pathogenic EAEC and proposes potential exposure avenues.
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Diarrea/epidemiología , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/transmisión , Escherichia coli/patogenicidad , Enfermedades Transmitidas por los Alimentos/epidemiología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Preescolar , Diarrea/microbiología , Brotes de Enfermedades/estadística & datos numéricos , Electroforesis en Gel de Campo Pulsado , Monitoreo Epidemiológico , Escherichia coli/genética , Femenino , Enfermedades Transmitidas por los Alimentos/microbiología , Humanos , Masculino , Persona de Mediana Edad , Minnesota/epidemiología , Virulencia , Factores de Virulencia/genética , Adulto JovenRESUMEN
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.
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Staphylococcus aureus Resistente a Meticilina/genética , Infecciones Estafilocócicas/microbiología , Staphylococcus aureus/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Antibacterianos/farmacología , Niño , Preescolar , Monitoreo Epidemiológico , Femenino , Humanos , Lactante , Masculino , Meticilina/farmacología , Resistencia a la Meticilina , Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , Persona de Mediana Edad , Minnesota/epidemiología , Infecciones Estafilocócicas/epidemiología , Staphylococcus aureus/aislamiento & purificación , Adulto JovenRESUMEN
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.
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Enfermedades Transmitidas por los Alimentos/epidemiología , Infecciones por Salmonella/epidemiología , Salmonella typhimurium/genética , Animales , Estudios de Casos y Controles , Brotes de Enfermedades , Monitoreo Epidemiológico , Enfermedades Transmitidas por los Alimentos/microbiología , Genómica , Humanos , Ganado/microbiología , Filogenia , Estudios Retrospectivos , Infecciones por Salmonella/microbiología , Salmonella typhimurium/aislamiento & purificación , Estados Unidos/epidemiología , Secuenciación Completa del Genoma , ZoonosisRESUMEN
Nontyphoidal Salmonella enterica (NTS) poses a major public health risk worldwide that is amplified by the existence of antimicrobial-resistant strains, especially those resistant to quinolones and extended-spectrum cephalosporins (ESC). Little is known on the dissemination of plasmids harboring the acquired genetic determinants that confer resistance to these antimicrobials across NTS serotypes from livestock in the United States. NTS isolates (n = 183) from U.S. swine clinical cases retrieved during 2014 to 2016 were selected for sequencing based on their phenotypic resistance to enrofloxacin (quinolone) or ceftiofur (3rd-generation cephalosporin). De novo assemblies were used to identify chromosomal mutations and acquired antimicrobial resistance genes (AARGs). In addition, plasmids harboring AARGs were identified using short-read assemblies and characterized using a multistep approach that was validated by long-read sequencing. AARGs to quinolones [qnrB15, qnrB19, qnrB2, qnrD, qnrS1, qnrS2, and aac(6')Ib-cr] and ESC (blaCMY-2, blaCTX-M-1, blaCTX-M-27, and blaSHV-12) were distributed across serotypes and were harbored by several plasmids. In addition, chromosomal mutations associated with resistance to quinolones were identified in the target enzyme and efflux pump regulation genes. The predominant plasmid harboring the prevalent qnrB19 gene was distributed across serotypes. It was identical to a plasmid previously reported in S. enterica serovar Anatum from swine in the United States (GenBank accession number KY991369.1) and similar to Escherichia coli plasmids from humans in South America (GenBank accession numbers GQ374157.1 and JN979787.1). Our findings suggest that plasmids harboring AARGs encoding mechanisms of resistance to critically important antimicrobials are present in multiple NTS serotypes circulating in swine in the United States and can contribute to resistance expansion through horizontal transmission.
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Resistencia a las Cefalosporinas/genética , Cefalosporinas/farmacología , Plásmidos/genética , Quinolonas/farmacología , Salmonella enterica/genética , Animales , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Farmacorresistencia Bacteriana Múltiple/genética , Enrofloxacina/farmacología , Escherichia coli/efectos de los fármacos , Escherichia coli/genética , Pruebas de Sensibilidad Microbiana/métodos , Salmonella enterica/efectos de los fármacos , Serogrupo , América del Sur , Porcinos , Estados UnidosRESUMEN
Background: Salmonella 4,[5],12:i:-, a worldwide emerging pathogen that causes many food-borne outbreaks mostly attributed to pig and pig products, is expanding in the United States. Methods: Whole-genome sequencing was applied to conduct multiple comparisons of 659 S. 4,[5],12:i:- and 325 Salmonella Typhimurium from different sources and locations (ie, the United States and Europe) to assess their genetic heterogeneity, with a focus on strains recovered from swine in the US Midwest. In addition, the presence of resistance genes and other virulence factors was detected and the antimicrobial resistance phenotypes of 50 and 22 isolates of livestock and human origin, respectively, was determined. Results: The S. 4,5,12:i:- strains formed two main clades regardless of their source and geographic origin. Most (84%) of the US isolates recovered in 2014-2016, including those (48 of 51) recovered from swine in the US Midwest, were part of an emerging clade. In this clade, multiple genotypic resistance determinants were predominant, including resistance against ampicillin, streptomycin, sulfonamides, and tetracyclines. Phenotypic resistance to enrofloxacin (11 of 50) and ceftiofur (9 of 50) was found in conjunction with the presence of plasmid-mediated resistance genes (qnrB19/qnrB2/qnrS1 and blaCMY-2/blaSHV-12, respectively). Higher similarity was also found between S. 4,[5],12:i:- from the emerging clade and S. Typhimurium from Europe than with S. Typhimurium from the United States. Conclusions: Salmonella 4,[5],12:i:- currently circulating in swine in the US Midwest are likely to be part of an emerging multidrug-resistant clade first reported in Europe, and can carry plasmid-mediated resistance genes that may be transmitted horizontally to other bacteria, and thus may represent a public health concern.
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Farmacorresistencia Bacteriana Múltiple/genética , Salmonelosis Animal/epidemiología , Salmonella enterica/genética , Serogrupo , Animales , Antibacterianos/farmacología , Europa (Continente)/epidemiología , Variación Genética , Genotipo , Pruebas de Sensibilidad Microbiana , Medio Oeste de Estados Unidos/epidemiología , Fenotipo , Quinolonas/farmacología , Salmonella enterica/efectos de los fármacos , Salmonella enterica/aislamiento & purificación , Salmonella typhimurium/genética , Salmonella typhimurium/aislamiento & purificación , Porcinos/microbiología , Factores de Virulencia/genética , Secuenciación Completa del GenomaRESUMEN
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.
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Bacterias/genética , Genoma Bacteriano , Meningitis Bacterianas/diagnóstico , Programas Informáticos , Bacterias/aislamiento & purificación , Escherichia coli/genética , Escherichia coli/aislamiento & purificación , Genómica , Haemophilus influenzae/genética , Haemophilus influenzae/aislamiento & purificación , Humanos , Meningitis Bacterianas/microbiología , Neisseria meningitidis/genética , Neisseria meningitidis/aislamiento & purificación , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/aislamiento & purificaciónRESUMEN
Whole-genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of Staphylococcus aureus outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typing S. aureus Forty-two S. aureus isolates from three outbreaks and 12 reference isolates were studied. Near-complete genomes, assembled de novo with paired-end and long-mate-pair (8 kb) libraries were first assembled and analyzed utilizing an in-house assembly and analytical informatics pipeline. In addition, paired-end data were assembled and analyzed using a commercial software package. Single nucleotide variant (SNP) analysis was performed using the in-house pipeline. Two assembly strategies were used to generate core genome multilocus sequence typing (cgMLST) data. First, the near-complete genome data generated with the in-house pipeline were imported into the commercial software and used to perform cgMLST analysis. Second, the commercial software was used to assemble paired-end data, and resolved assemblies were used to perform cgMLST. Similar isolate clustering was observed using SNP calling and cgMLST, regardless of data assembly strategy. All methods provided more discrimination between outbreaks than did PFGE. Overall, all of the evaluated WGS strategies yielded statistically similar results for S. aureus typing.
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Brotes de Enfermedades , Staphylococcus aureus Resistente a Meticilina/clasificación , Staphylococcus aureus Resistente a Meticilina/genética , Epidemiología Molecular/métodos , Tipificación Molecular/métodos , Infecciones Estafilocócicas/epidemiología , Secuenciación Completa del Genoma/métodos , Análisis por Conglomerados , Biología Computacional/métodos , Humanos , Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , Infecciones Estafilocócicas/microbiologíaRESUMEN
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.
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Control de Enfermedades Transmisibles/métodos , Enfermedades Transmisibles Emergentes/diagnóstico , Pruebas Diagnósticas de Rutina/tendencias , Técnicas Bacteriológicas , Centers for Disease Control and Prevention, U.S. , Enfermedades Transmisibles Emergentes/epidemiología , Técnicas de Cultivo , Predicción , Humanos , Vigilancia en Salud Pública , Estados Unidos/epidemiologíaRESUMEN
Carbapenemase-producing, carbapenem-resistant Enterobacteriaceae, or CP-CRE, are an emerging threat to human and animal health, because they are resistant to many of the last-line antimicrobials available for disease treatment. Carbapenemase-producing Enterobacter cloacae harboring blaKPC-3 recently was reported in the upper midwestern United States and implicated in a hospital outbreak in Fargo, North Dakota (L. M. Kiedrowski, D. M. Guerrero, F. Perez, R. A. Viau, L. J. Rojas, M. F. Mojica, S. D. Rudin, A. M. Hujer, S. H. Marshall, and R. A. Bonomo, Emerg Infect Dis 20:1583-1585, 2014, http://dx.doi.org/10.3201/eid2009.140344). In early 2009, the Minnesota Department of Health began collecting and screening CP-CRE from patients throughout Minnesota. Here, we analyzed a retrospective group of CP-E. cloacae isolates (n = 34) collected between 2009 and 2013. Whole-genome sequencing and analysis revealed that 32 of the strains were clonal, belonging to the ST171 clonal complex and differing collectively by 211 single-nucleotide polymorphisms, and it revealed a dynamic clone under positive selection. The phylogeography of these strains suggests that this clone existed in eastern North Dakota and western Minnesota prior to 2009 and subsequently was identified in the Minneapolis and St. Paul metropolitan area. All strains harbored identical IncFIA-like plasmids conferring a CP-CRE phenotype and an additional IncX3 plasmid. In a single patient with multiple isolates submitted over several months, we found evidence that these plasmids had transferred from the E. cloacae clone to an Escherichia coli ST131 bacterium, rendering it as a CP-CRE. The spread of this clone throughout the upper midwestern United States is unprecedented for E. cloacae and highlights the importance of continued surveillance to identify such threats to human health.
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Enterobacter cloacae/efectos de los fármacos , Enterobacter cloacae/genética , Infecciones por Enterobacteriaceae/microbiología , beta-Lactamasas/genética , ADN Bacteriano/genética , Farmacorresistencia Bacteriana , Infecciones por Enterobacteriaceae/transmisión , Genoma Bacteriano , Geografía , Humanos , Pruebas de Sensibilidad Microbiana , Medio Oeste de Estados Unidos , Minnesota , North Dakota , Plásmidos/genética , Polimorfismo de Nucleótido Simple , Estudios RetrospectivosRESUMEN
Widespread infections with community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) have occurred in the United States with the dissemination of the USA300 strain beginning in 2000. We examined 105 isolates obtained from children treated at the University of Chicago from 1994 to 1997 (75 methicillin-susceptible S. aureus [MSSA] and 30 MRSA isolates) in order to investigate for possible evidence of USA300 during this period. Infections were defined epidemiologically based on medical record review. The isolates underwent multilocus sequence typing (MLST), as well as assays for the Panton-Valentine leukocidin (PVL) genes, the protein A gene (spa), and arcA and opp3, proxy markers for the arginine catabolic mobile element (ACME), characteristic of USA300 MRSA. MRSA isolates also underwent staphylococcal cassette chromosome mec (SCCmec) typing and pulsed-field gel electrophoresis (PFGE) subtyping. MSSA isolates belonged to 17 sequence type (ST) groups. The 12 epidemiologically defined CA-MRSA infection isolates were either ST1 (n = 4) or ST8 (n = 8). They belonged to 3 different PFGE types: USA100 (n = 1), USA400 (n = 5), and USA500 (n = 6). Among the CA-MRSA infection isolates, 8 (67%) were PVL(+). None of the MRSA or MSSA isolates contained arcA or opp3. Only one MRSA isolate was USA300 by PFGE. This was a health care-associated (HA) MRSA isolate, negative for PVL, that carried SCCmec type II. USA300 with its characteristic features was not identified in the collection from the years 1994 to 1997.
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Infecciones Comunitarias Adquiridas/epidemiología , Infecciones Comunitarias Adquiridas/microbiología , Genotipo , Staphylococcus aureus Resistente a Meticilina/clasificación , Staphylococcus aureus Resistente a Meticilina/genética , Infecciones Estafilocócicas/epidemiología , Infecciones Estafilocócicas/microbiología , Adolescente , Chicago/epidemiología , Niño , Preescolar , ADN Bacteriano/química , ADN Bacteriano/genética , Epidemias , Femenino , Humanos , Lactante , Recién Nacido , Masculino , Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , Epidemiología Molecular , Tipificación Molecular , Factores de Virulencia/genéticaRESUMEN
Methicillin-resistant Staphylococcus aureus (MRSA) has become a common cause of skin infections and invasive infections in community dwellers in the United States since the late 1990s. Isolates characterized as USA300 by pulsed-field gel electrophoresis (PFGE) are the predominant strain type in these infections. USA100 and USA500 strains commonly cause health care-associated infections. We compared PFGE with a number of other methods of genotyping in a sample of 149 clinical MRSA isolates from the University of Chicago Medical Center. The 5 USA500 isolates yielded 3 spa types and 2 multilocus sequence types (MLSTs). Among the 24 USA100 isolates, 21 (88%) were of spa type t002, 19 (79%) were of ST5, 2 carried arcA and opp3, and 1 was Panton-Valentine leukocidin positive (PVL(+)). Among the 102 USA300 isolates, 96 (94%) were of ST8 and 94 (92%) were of spa type t008. The combination of traits that provided the best sensitivity (98%), specificity (97%), positive predictive value (PPV) (99%), and negative predictive value (NPV) (95%) for identifying USA300 isolates were the presence of the arcA gene and the presence of the PVL genes (area under the curve, 0.980; 95% confidence interval [CI], 0.955 to 1.0). PFGE did not delineate a homogeneous group of MRSA genetic backgrounds, as documented for other typing methods, particularly for USA500 and USA100 pulsotypes. Documenting the presence of arcA and PVL genes by PCR was an efficient and accurate means of identifying USA300 in a collection of MRSA isolates in which USA300 is common. None of the tested genotyping methods provided an accurate means of identifying the next most common PFGE-based backgrounds, USA100 and USA500.
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Staphylococcus aureus Resistente a Meticilina/clasificación , Staphylococcus aureus Resistente a Meticilina/genética , Tipificación Molecular/métodos , Infecciones Estafilocócicas/microbiología , Factores de Virulencia/genética , Centros Médicos Académicos , Chicago , Genotipo , Humanos , Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , Epidemiología Molecular/métodos , Valor Predictivo de las Pruebas , Sensibilidad y EspecificidadRESUMEN
Listeria monocytogenes is a foodborne pathogen that can develop serious invasive infections. Among foodborne pathogens, L. monocytogenes exhibits the highest case fatality despite antibiotic treatment, suggesting the current therapy should be improved. Although ampicillin and gentamicin are used as a combination therapy to treat listeriosis, our results showed there is no synergy between the two antibiotics. We discovered that aqueous extract of licorice generated significant antimicrobial synergy when combined with aminoglycosides, such as gentamicin, in L. monocytogenes. In the presence of 1 mg/mL licorice extract, for instance, the minimum inhibitory concentration (MIC) of gentamicin was reduced by 32-fold. Moreover, antimicrobial synergy with licorice extract made gentamicin-resistant clinical isolates of L. monocytogenes susceptible to gentamicin. Given the common use of licorice as a food sweetener in Western countries and a herb in Oriental medicine, our findings suggest that licorice extract can be potentially used as an antibiotic adjuvant to improve the efficacy of antimicrobial treatment of listeriosis.
RESUMEN
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.
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Salmonelosis Animal/transmisión , Infecciones por Salmonella/epidemiología , Infecciones por Salmonella/microbiología , Salmonella enterica/genética , Pavos/microbiología , Animales , Canadá/epidemiología , Brotes de Enfermedades , Industria de Alimentos , Genoma Bacteriano , Humanos , Filogenia , Salmonelosis Animal/epidemiología , Salmonella enterica/clasificación , Serogrupo , Estados Unidos/epidemiología , Secuenciación Completa del GenomaRESUMEN
BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) cause significant diarrheal morbidity and mortality in children of resource-limited regions, warranting development of effective vaccine strategies. Genetic diversity of the ETEC pathovar has impeded development of broadly protective vaccines centered on the classical canonical antigens, the colonization factors and heat-labile toxin. Two non-canonical ETEC antigens, the EtpA adhesin, and the EatA mucinase are immunogenic in humans and protective in animal models. To foster rational vaccine design that complements existing strategies, we examined the distribution and molecular conservation of these antigens in a diverse population of ETEC isolates. METHODS: Geographically diverse ETEC isolates (n = 1159) were interrogated by PCR, immunoblotting, and/or whole genome sequencing (n = 46) to examine antigen conservation. The most divergent proteins were purified and their core functions assessed in vitro. RESULTS: EatA and EtpA or their coding sequences were present in 57.0% and 51.5% of the ETEC isolates overall, respectively; and were globally dispersed without significant regional differences in antigen distribution. These antigens also exhibited >93% amino acid sequence identity with even the most divergent proteins retaining the core adhesin and mucinase activity assigned to the prototype molecules. CONCLUSIONS: EtpA and EatA are well-conserved molecules in the ETEC pathovar, suggesting that they serve important roles in virulence and that they could be exploited for rational vaccine design.
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Antígenos Bacterianos/genética , Escherichia coli Enterotoxigénica/genética , Infecciones por Escherichia coli/microbiología , Proteínas de Escherichia coli/genética , Variación Genética , Glicoproteínas de Membrana/genética , Péptido Hidrolasas/genética , Antígenos Bacterianos/análisis , Escherichia coli Enterotoxigénica/química , Escherichia coli Enterotoxigénica/clasificación , Escherichia coli Enterotoxigénica/aislamiento & purificación , Infecciones por Escherichia coli/inmunología , Proteínas de Escherichia coli/análisis , Salud Global , Humanos , Immunoblotting , Glicoproteínas de Membrana/análisis , Péptido Hidrolasas/análisis , Reacción en Cadena de la Polimerasa , Secuenciación Completa del GenomaRESUMEN
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.
RESUMEN
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.
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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).
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Antígenos de Protozoos/análisis , Bioensayo/métodos , Técnicas de Laboratorio Clínico/métodos , Criptosporidiosis/diagnóstico , Cryptosporidium/aislamiento & purificación , Heces/parasitología , Técnica del Anticuerpo Fluorescente Directa/métodos , Adolescente , Adulto , Niño , Preescolar , Criptosporidiosis/parasitología , Femenino , Humanos , Lactante , Recién Nacido , Masculino , Persona de Mediana Edad , Vigilancia en Salud Pública , Adulto JovenRESUMEN
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 needed, and implementation of cryptococcal diagnostics is critical.