Last data update: Jan 13, 2025. (Total: 48570 publications since 2009)
Records 1-25 (of 25 Records) |
Query Trace: Fields PI[original query] |
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Genomic perspective on the bacillus causing paratyphoid B fever
Hawkey J , Frézal L , Tran Dien A , Zhukova A , Brown D , Chattaway MA , Simon S , Izumiya H , Fields PI , De Lappe N , Kaftyreva L , Xu X , Isobe J , Clermont D , Njamkepo E , Akeda Y , Issenhuth-Jeanjean S , Makarova M , Wang Y , Hunt M , Jenkins BM , Ravel M , Guibert V , Serre E , Matveeva Z , Fabre L , Cormican M , Yue M , Zhu B , Morita M , Iqbal Z , Silva Nodari C , Pardos de la Gandara M , Weill FX . Nat Commun 2024 15 (1) 10143 Paratyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). However, little was known about the global population structure, geographic distribution, and evolution of this pathogen. Here, we report a whole-genome analysis of 568 historical and contemporary SPB PG1 isolates, obtained globally, between 1898 and 2021. We show that this pathogen existed in the 13th century, subsequently diversifying into 11 lineages and 38 genotypes with strong phylogeographic patterns. Following its discovery in 1896, it circulated across Europe until the 1970s, after which it was mostly reimported into Europe from South America, the Middle East, South Asia, and North Africa. Antimicrobial resistance recently emerged in various genotypes of SPB PG1, mostly through mutations of the quinolone-resistance-determining regions of gyrA and gyrB. This study provides an unprecedented insight into SPB PG1 and essential genomic tools for identifying and tracking this pathogen, thereby facilitating the global genomic surveillance of PTB. |
A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia
Cuypers WL , Meysman P , Weill FX , Hendriksen RS , Beyene G , Wain J , Nair S , Chattaway MA , Perez-Sepulveda BM , Ceyssens PJ , de Block T , Lee WWY , Pardos de la Gandara M , Kornschober C , Moran-Gilad J , Veldman KT , Cormican M , Torpdahl M , Fields PI , Černý T , Hardy L , Tack B , Mellor KC , Thomson N , Dougan G , Deborggraeve S , Jacobs J , Laukens K , Van Puyvelde S . Nat Commun 2023 14 (1) 3517 Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance. |
Epidemiology of salmonellosis among infants in the United States: 1968-2015
Self JL , Judd MC , Huang J , Fields PI , Griffin PM , Wong KK . Pediatrics 2023 151 (6) OBJECTIVES: Describe characteristics of gastroenteritis, bacteremia, and meningitis caused by nontyphoidal Salmonella among US infants. METHODS: We analyze national surveillance data during 1968-2015 and active, sentinel surveillance data during 1996-2015 for culture-confirmed Salmonella infections by syndrome, year, serotype, age, and race. RESULTS: During 1968-2015, 190 627 culture-confirmed Salmonella infections among infants were reported, including 165 236 (86.7%) cases of gastroenteritis, 6767 (3.5%) bacteremia, 371 (0.2%) meningitis, and 18 253 (9.7%) with other or unknown specimen sources. Incidence increased during the late 1970s-1980s, declined during the 1990s-early 2000s, and has gradually increased since the mid-2000s. Infants' median age was 4 months for gastroenteritis and bacteremia and 2 months for meningitis. The most frequently reported serotypes were Typhimurium (35 468; 22%) for gastroenteritis and Heidelberg for bacteremia (1954; 29%) and meningitis (65; 18%). During 1996-2015 in sentinel site surveillance, median annual incidence of gastroenteritis was 120, bacteremia 6.2, and meningitis 0.25 per 100 000 infants. Boys had a higher incidence of each syndrome than girls in both surveillance systems, but most differences were not statistically significant. Overall, hospitalization and fatality rates were 26% and 0.1% for gastroenteritis, 70% and 1.6% for bacteremia, and 96% and 4% for meningitis. During 2004-2015, invasive salmonellosis incidence was higher for Black (incident rate ratio, 2.7; 95% confidence interval, 2.6-2.8) and Asian (incident rate ratio, 1.8; 95% confidence interval, 1.7-1.8) than white infants. CONCLUSIONS: Salmonellosis causes substantial infant morbidity and mortality; serotype heidelberg caused the most invasive infections. Infants with meningitis were younger than those with bacteremia or gastroenteritis. Research into risk factors for infection and invasive illness could inform prevention efforts. |
Exploration of risk factors for ceftriaxone resistance in invasive non-typhoidal Salmonella infections in western Kenya
Luvsansharav UO , Wakhungu J , Grass J , Oneko M , Nguyen V , Bigogo G , Ogola E , Audi A , Onyango D , Hamel MJ , Montgomery JM , Fields PI , Mahon BE . PLoS One 2020 15 (3) e0229581 Multidrug-resistant non-typhoidal Salmonella (NTS) infection has emerged as a prominent cause of invasive infections in Africa. We investigated the prevalence of ceftriaxone-resistant invasive NTS infections, conducted exploratory analysis of risk factors for resistance, and described antimicrobial use in western Kenya. We conducted a secondary analysis of existing laboratory, epidemiology, and clinical data from three independent projects, a malaria vaccine trial, a central nervous system (CNS) study, and the International Emerging Infections Program morbidity surveillance (surveillance program) during 2009-2014. We calculated odds ratios (OR) with 95% confidence intervals (CI) for ceftriaxone-resistant NTS infections compared with ceftriaxone-susceptible infections. We surveyed hospitals, pharmacies, and animal drug retailers about the availability and use of antimicrobials. In total, 286 invasive NTS infections were identified in the three projects; 43 NTS isolates were ceftriaxone-resistant. The absolute prevalence of ceftriaxone resistance varied among these methodologically diverse projects, with 18% (16/90) of isolates resistant to ceftriaxone in the vaccine trial, 89% (16/18) in the CNS study, and 6% (11/178) in the surveillance program. Invasive ceftriaxone-resistant infections increased over time. Most ceftriaxone-resistant isolates were co-resistant to multiple other antimicrobials. Having an HIV-positive mother (OR = 3.7; CI = 1.2-11.4) and taking trimethoprim-sulfamethoxazole for the current illness (OR = 9.6, CI = 1.2-78.9) were significantly associated with acquiring ceftriaxone-resistant invasive NTS infection. Ceftriaxone and other antibiotics were widely prescribed; multiple issues related to prescription practices and misuse were identified. In summary, ceftriaxone-resistant invasive NTS infection is increasing and limiting treatment options for serious infections. Efforts are ongoing to address the urgent need for improved microbiologic diagnostic capacity and an antimicrobial surveillance system in Kenya. |
Evaluation of a Bead-Based Salmonella Molecular Serotyping Method for Salmonella Isolated from Food and Environmental Samples.
Moore MM , Nucci MJ , Madson SM , Wagley GS , Keys CE , Brown EW , McQuiston JR , Fields PI . J Food Prot 2019 82 (11) 1973-1987 Salmonella is a leading cause of foodborne illness worldwide, and foods containing Salmonella (except raw meat and poultry products) are considered adulterated. Serotyping of Salmonella is an essential part of surveillance and investigation of outbreaks. This study evaluated a bead-based Salmonella molecular serotyping (SMS) method, which included the O-group 1, H-antigen, alternate target, and O-group 2 assays, compared with traditional serotyping. Salmonella was isolated from food, pet food, and environmental samples or were reference strains. A total of 572 isolates were analyzed by using two formats of the SMS method in comparison with traditional methods: 485 were analyzed by using Radix SMS (a custom user-mixed format), 218 were analyzed by using Luminex SMS (a commercial kit format), and 131 of the total isolates were analyzed by both formats for comparison. The SMS method was evaluated on the basis of the successful identification of antigens by the probes included in the method. The method identified 550 (96.2%) isolates as expected, 6 (1.0%) isolates were not identified as initially expected but were shown to be correctly identified by SMS after reanalysis by traditional serotyping, and 16 (2.8%) isolates not identified as expected possessed an antigen that should have been detected by the method but was not. Among the isolates considered correctly identified, 255 (44.6%) were identified to a single serovar, 44 (7.7%) required additional biochemical testing to differentiate variants or subspecies, and 251 (43.9%) were partially serotyped because probes for some antigens were not in the assay or had allelic variation for known serovars. Whole genome sequencing, SeqSero, and the Salmonella In Silico Typing Resource gave added confirmation for three isolates. Addition of the O-group 2 assay enabled the identification of 55 (9.6%) of 572 isolates. The SMS method could fully or partially serotype most isolates within a day. The SMS method should be a valuable tool when faster screening methods are needed, such as outbreaks and screening large numbers of environmental isolates. |
SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data.
Zhang S , Den-Bakker HC , Li S , Chen J , Dinsmore BA , Lane C , Lauer AC , Fields PI , Deng X . Appl Environ Microbiol 2019 85 (23) SeqSero, launched in 2015, is a software tool for Salmonella serotype determination from whole genome sequencing (WGS) data. Despite its routine use in public health and food safety laboratories in the United States and other countries, the original SeqSero pipeline is relatively slow (minutes per genome using sequencing reads), is not optimized for draft genome assemblies, and may assign multiple serotypes for a strain. Here we present SeqSero2 (github.com/denglab/SeqSero2; denglab.info/SeqSero2), an algorithmic transformation and functional update of the original SeqSero. Major improvements include: 1) additional sequence markers for identification of Salmonella species and subspecies and certain serotypes; 2) a k-mer based algorithm for rapid serotype prediction from raw reads (seconds per genome) and improved serotype prediction from assemblies; and 3) a targeted assembly approach for specific retrieval of serotype determinants from WGS for serotype prediction, new allele discovery, and prediction troubleshooting. Evaluated using 5,794 genomes representing 364 common US serotypes, including 2,280 human isolates of 117 serotypes from the National Antimicrobial Resistance Monitoring System, SeqSero2 is up to 50 times faster than the original SeqSero while maintaining equivalent accuracy for raw reads and substantially improving accuracy for assemblies. SeqSero2 further suggested that 3% of the tested genomes contained reads from multiple serotypes, indicating a use for contamination detection. In addition to short reads, SeqSero2 demonstrated potential for accurate and rapid serotype prediction directly from long nanopore reads despite base call errors. Testing of 40 nanopore-sequenced genomes of 17 serotypes yielded a single H antigen misidentification.IMPORTANCE: Serotyping is the basis of public health surveillance of Salmonella It remains a first-line subtyping method even as surveillance continues to be transformed by whole genome sequencing. SeqSero allows the integration of Salmonella serotyping into a whole genome sequencing-based laboratory workflow while maintaining continuity with the classic serotyping scheme. SeqSero2, informed by extensive testing and application of SeqSero in the United States and other countries, incorporates important improvements and updates that further strengthen its application in routine and large scale surveillance of Salmonella by whole genome sequencing. |
Epidemiologic patterns of human Salmonella serotype diversity in the USA, 1996-2016
Judd MC , Hoekstra RM , Mahon BE , Fields PI , Wong KK . Epidemiol Infect 2019 147 e187 Although researchers have described numerous risk factors for salmonellosis and for infection with specific common serotypes, the drivers of Salmonella serotype diversity among human populations remain poorly understood. In this retrospective observational study, we partition records of serotyped non-typhoidal Salmonella isolates from human clinical specimens reported to CDC national surveillance by demographic, geographic and seasonal characteristics and adapt sample-based rarefaction methods from the field of community ecology to study how Salmonella serotype diversity varied within and among these populations in the USA during 1996-2016. We observed substantially higher serotype richness in children <2 years old than in older children and adults and steadily increasing richness with age among older adults. Whereas seasonal and regional variation in serotype diversity was highest among infants and young children, variation by specimen source was highest in adults. Our findings suggest that the risk for infection from uncommon serotypes is associated with host and environmental factors, particularly among infants, young children and older adults. These populations may have a higher proportion of illness acquired through environmental transmission pathways than published source attribution models estimate. |
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. |
Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association.
Nguyen SV , Harhay DM , Bono JL , Smith TPL , Fields PI , Dinsmore BA , Santovenia M , Wang R , Bosilevac JM , Harhay GP . Microb Genom 2018 4 (8) Salmonella enterica serovar Montevideo has been linked to recent foodborne illness outbreaks resulting from contamination of products such as fruits, vegetables, seeds and spices. Studies have shown that Montevideo also is frequently associated with healthy cattle and can be isolated from ground beef, yet human salmonellosis outbreaks of Montevideo associated with ground beef contamination are rare. This disparity fuelled our interest in characterizing the genomic differences between Montevideo strains isolated from healthy cattle and beef products, and those isolated from human patients and outbreak sources. To that end, we sequenced 13 Montevideo strains to completion, producing high-quality genome assemblies of isolates from human patients (n=8) or from healthy cattle at slaughter (n=5). Comparative analysis of sequence data from this study and publicly available sequences (n=72) shows that Montevideo falls into four previously established clades, differentially occupied by cattle and human strains. The results of these analyses reveal differences in metabolic islands, environmental adhesion determinants and virulence factors within each clade, and suggest explanations for the infrequent association between bovine isolates and human illnesses. |
Invasive infections with nontyphoidal Salmonella in sub-Saharan Africa
Mahon BE , Fields PI . Microbiol Spectr 2016 4 (3) Invasive nontyphoidal Salmonella (NTS) infections in Africa cause an enormous burden of illness. These infections are often devastating, with mortality estimated at 20%, even with appropriate antimicrobial therapy. Two major groups-young children and HIV-infected adults-suffer the great majority of these infections. In children, younger age itself, as well as malaria, malnutrition, and HIV infection, are prominent risk factors. In adults, HIV infection is by far the most important risk factor. The most common serotypes in invasive infections are Salmonella enterica serotypes Typhimurium and Enteritidis. In recent years, a specific strain of Salmonella Typhimurium, multilocus sequence type 313, has caused epidemics of invasive disease. Little is known about risk factors for exposure to NTS, making the design of rational interventions to decrease exposure difficult. Antimicrobial therapy is critically important for treatment of invasive NTS infections. Thus, the emergence and spread of resistance to agents commonly used for treatment of invasive NTS infection, now including third-generation cephalosporins, is an ominous development. Already, many invasive NTS infections are essentially untreatable in many health care facilities in sub-Saharan Africa. Several candidate vaccines are in early development and, if safe and effective, could be promising. Interventions to prevent exposure to NTS (e.g., improved sanitation), to prevent the occurrence of disease if exposure does occur (e.g., vaccination, malaria control), and to prevent severe disease and death in those who become ill (e.g., preserving antimicrobial effectiveness) are all important in reducing the toll of invasive NTS disease in sub-Saharan Africa. |
Complete, Closed Genome Sequences of 10 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Human and Bovine Sources.
Nguyen SV , Harhay DM , Bono JL , Smith TP , Fields PI , Dinsmore BA , Santovenia M , Kelley CM , Wang R , Bosilevac JM , Harhay GP . Genome Announc 2016 4 (6) Salmonella enterica is a leading cause of enterocolitis for humans and animals. S. enterica subsp. enterica serovar Typhimurium infects a broad range of hosts. To facilitate genomic comparisons among isolates from different sources, we present the complete genome sequences of 10 S Typhimurium strains, 5 each isolated from human and bovine sources. |
Complete and Closed Genome Sequences of 10 Salmonella enterica subsp. enterica Serovar Anatum Isolates from Human and Bovine Sources.
Nguyen SV , Harhay DM , Bono JL , Smith TP , Fields PI , Dinsmore BA , Santovenia M , Kelley CM , Wang R , Bosilevac JM , Harhay GP . Genome Announc 2016 4 (3) Salmonella enterica is an important pathogen transmitted by numerous vectors. Genomic comparisons of Salmonella strains from disparate hosts have the potential to further our understanding of mechanisms underlying host specificities and virulence. Here, we present the closed genome and plasmid sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolates from bovine and human sources. |
Complete Closed Genome Sequences of Salmonella enterica subsp. enterica Serotypes Anatum, Montevideo, Typhimurium, and Newport, Isolated from Beef, Cattle, and Humans.
Harhay DM , Bono JL , Smith TP , Fields PI , Dinsmore BA , Santovenia M , Kelley CM , Wang R , Harhay GP . Genome Announc 2016 4 (1) Salmonella enterica spp. are a diverse group of bacteria with a wide range of virulence potential. To facilitate genome comparisons across this virulence spectrum, we present eight complete closed genome sequences of four S. enterica serotypes (Anatum, Montevideo, Typhimurium, and Newport), isolated from various cattle samples and from humans. |
Antimicrobial resistance in Salmonella in the United States: 1948 - 1995
Tadesse DA , Singh A , Zhao S , Bartholomew M , Womack N , Ayers S , Fields PI , McDermott PF . Antimicrob Agents Chemother 2016 60 (4) 2567-71 We conducted a retrospective study of 2,149 clinical Salmonella strains to help document the historical emergence of antimicrobial resistance. There were significant increases in resistance to older drugs including ampicillin, chloramphenicol, streptomycin, sulfamethoxazole and tetracycline, which was most common in serotype Typhimurium. An increase in multidrug-resistance was observed for each decade since the 1950s. These data help show how Salmonella has evolved over the past six decades following the introduction of new antimicrobial agents. |
Salmonella enterica infections in the United States and assessment of coefficients of variation: a novel approach to identify epidemiologic characteristics of individual serotypes, 1996-2011
Boore AL , Hoekstra RM , Iwamoto M , Fields PI , Bishop RD , Swerdlow DL . PLoS One 2015 10 (12) e0145416 BACKGROUND: Despite control efforts, salmonellosis continues to cause an estimated 1.2 million infections in the United States (US) annually. We describe the incidence of salmonellosis in the US and introduce a novel approach to examine the epidemiologic similarities and differences of individual serotypes. METHODS: Cases of salmonellosis in humans reported to the laboratory-based National Salmonella Surveillance System during 1996-2011 from US states were included. Coefficients of variation were used to describe distribution of incidence rates of common Salmonella serotypes by geographic region, age group and sex of patient, and month of sample isolation. RESULTS: During 1996-2011, more than 600,000 Salmonella isolates from humans were reported, with an average annual incidence of 13.1 cases/100,000 persons. The annual reported rate of Salmonella infections did not decrease during the study period. The top five most commonly reported serotypes, Typhimurium, Enteritidis, Newport, Heidelberg, and Javiana, accounted for 62% of fully serotyped isolates. Coefficients of variation showed the most geographically concentrated serotypes were often clustered in Gulf Coast states and were also more frequently found to be increasing in incidence. Serotypes clustered in particular months, age groups, and sex were also identified and described. CONCLUSIONS: Although overall incidence rates of Salmonella did not change over time, trends and epidemiological factors differed remarkably by serotype. A better understanding of Salmonella, facilitated by this comprehensive description of overall trends and unique characteristics of individual serotypes, will assist in responding to this disease and in planning and implementing prevention activities. |
Salmonella serotype determination utilizing high-throughput genome sequencing data.
Zhang S , Yin Y , Jones MB , Zhang Z , Deatherage Kaiser BL , Dinsmore BA , Fitzgerald C , Fields PI , Deng X . J Clin Microbiol 2015 53 (5) 1685-92 Serotyping forms the basis of national and international surveillance networks for Salmonella, one of the most prevalent foodborne pathogens worldwide (1-3). Public health microbiology is currently being transformed by whole genome sequencing (WGS) which opens the door to serotype determination using WGS data. SeqSero (www.denglab.info/SeqSero) is a novel web-based tool for determining Salmonella serotypes using high-throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing: 1) raw reads from genomes of 308 Salmonella isolates of known serotype; 2) raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and 3) 354 other publicly available draft or complete Salmonella genomes. We also demonstrated Salmonella serotype determination from raw sequencing reads of fecal metagenomes from mice orally infected with this pathogen. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization. |
Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica serotype Enteritidis.
Deng X , Shariat N , Driebe EM , Roe CC , Tolar B , Trees E , Keim P , Zhang W , Dudley EG , Fields PI , Engelthaler DM . J Clin Microbiol 2014 53 (1) 212-8 A retrospective investigation was performed to evaluate whole genome sequencing as a benchmark for comparing molecular subtyping methods for Salmonella enterica serotype Enteritidis (SE) and survey the population structure of commonly encountered SE outbreak isolates in the United States. A total of 52 SE isolates representing 16 major outbreaks and three sporadic cases between 2001 and 2012 were sequenced and subjected to subtyping by four different methods: 1) whole genome single nucleotide polymorphism typing (WGST), 2) multiple loci VNTR (variable-number tandem repeat) analysis (MLVA), 3) clustered regularly interspaced short palindromic repeats combined with multi-virulence-locus sequence typing (CRISPR-MVLST) and 4) pulsed-field gel electrophoresis (PFGE). WGST resolved all outbreak clusters and provided useful robust phylogenetic inference with high epidemiological correlation. While both MLVA and CRISPR-MVLST yielded higher discriminatory power than PFGE, MLVA outperformed in delineating outbreak clusters whereas CRISPR-MVLST showed the potential to trace major lineages and ecological origins of SE. Our results suggested that whole genome sequencing makes a viable platform for the evaluation and benchmarking molecular subtyping methods. |
Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages.
Deng X , Desai PT , den Bakker HC , Mikoleit M , Tolar B , Trees E , Hendriksen RS , Frye JG , Porwollik S , Weimer BC , Wiedmann M , Weinstock GM , Fields PI , McClelland M . Emerg Infect Dis 2014 20 (9) 1481-9 Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th-18th centuries and diversified during the 1920s and 1950s. |
Supplement 2008-2010 (no. 48) to the White-Kauffmann-Le Minor scheme
Issenhuth-Jeanjean S , Roggentin P , Mikoleit M , Guibourdenche M , de Pinna E , Nair S , Fields PI , Weill FX . Res Microbiol 2014 165 (7) 526-30 This supplement (no. 48) of the White-Kauffmann-Le Minor scheme reports on the characterization of 63 new Salmonella serovars and 25 new variants of previously described Salmonella serovars recognized by the WHO Collaborating Centre for Reference and Research on Salmonella between 2008 and 2010. Forty-four new serovars were assigned to Salmonella enterica subspecies enterica, 12 to subspecies salamae, two to subspecies arizonae, two to subspecies diarizonae and three to subspecies houtenae. All these new serovars or new variants are described with their multilocus sequence type. |
Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles.
Fitzgerald C , Tu ZC , Patrick M , Stiles T , Lawson AJ , Santovenia M , Gilbert MJ , van Bergen M , Joyce K , Pruckler J , Stroika S , Duim B , Miller WG , Loparev VL , Sinnige JC , Fields PI , Tauxe RV , Blaser MJ , Wagenaar JA . Int J Syst Evol Microbiol 2014 64 2944-2948 A polyphasic study was undertaken to determine the taxonomic position of 13 Campylobacter fetus-like strains from humans (n=8) and reptiles (n=5). The results of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and genomic data from sap analysis, 16S rRNA and hsp60 sequence comparison, pulsed- field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP) analysis, DNA-DNA hybridization and whole genome sequencing demonstrate that these strains are closely related to C. fetus but clearly differentiated from the present C. fetus subspecies. Therefore this unique cluster of 13 strains represents a novel subspecies within the species C. fetus, for which the name Campylobacter fetus subsp. testudinum subsp. nov. is proposed, with strain 03-427T (=ATCC BAA-2539T = LMG 27499T) as the type strain. Although this novel taxon cannot be differentiated from C. fetus subsp. fetus and C. fetus subsp. venerealis using conventional phenotypic tests, MALDI-TOF MS analysis revealed the presence of multiple phenotypic biomarkers which distinguish C. fetus subsp. testudinum from the present C. fetus subspecies. |
Multilocus sequence typing confirms wild birds as the source of a Campylobacter outbreak associated with the consumption of raw peas.
Kwan PS , Xavier C , Santovenia M , Pruckler J , Stroika S , Joyce K , Gardner T , Fields PI , McLaughlin J , Tauxe RV , Fitzgerald C . Appl Environ Microbiol 2014 80 (15) 4540-6 From August to September 2008, the Centers for Disease Control and Prevention (CDC) assisted the Alaska Division of Public Health with an outbreak investigation of campylobacteriosis occurring among the residents of Southcentral Alaska. During the investigation, pulsed-field gel electrophoresis (PFGE) of Campylobacter jejuni isolates from human, raw pea and wild bird fecal samples confirmed the epidemiologic link between illness and the consumption of raw peas contaminated by Sandhill cranes from 15 of 43 epidemiologically-linked human isolates. However, an association between the remaining epidemiologically-linked human infections and the pea and wild bird isolates was not established. To better understand the molecular epidemiology of the outbreak, C. jejuni isolates (n=130; 59 humans, 40 peas and 31 wild birds) were further characterized by multi-locus sequence typing (MLST). Here, we present the molecular evidence to demonstrate the association of many more human C. jejuni infections associated with the outbreak with raw peas and wild bird feces. Among all sequence types (STs) identified, 26 (67%) of 39 were novel and exclusive to the outbreak. Five clusters of overlapping STs (n=32 isolates; 17 humans, 2 peas and 13 wild birds) were identified. In particular, Cluster E (n=7 isolates, ST-5049) consisted of isolates from humans, peas and wild birds. Novel STs clustered closely with isolates typically associated with wild birds and the environment, but distinct from lineages commonly seen in human infections. Novel STs and alleles recovered from human outbreak isolates allowed additional infections caused by these rare genotypes to be attributed to the contaminated raw peas. |
Genome Sequence of Salmonella enterica Serotype Tennessee Strain CDC07-0191, Implicated in the 2006-2007 Multistate Food-Borne Outbreak Linked to Peanut Butter in the United States.
Deng X , Salazar JK , Frezet S , Maccannell D , Ribot EM , Fields PI , Fricke WF , Zhang W . Genome Announc 2013 1 (3) Salmonella enterica serotype Tennessee strain CDC07-0191 was isolated from the 2006-2007 multistate food-borne outbreak linked to peanut butter in the United States. Here we report a high-quality draft assembly of the genome sequence of this strain, derived from a patient. This is the first reported high-quality draft genome sequence for S. enterica serotype Tennessee, which will enable in-depth studies of its transmission and virulence. |
Variable expression of O:61 in Salmonella group C2
Mikoleit M , Van Duyne MS , Halpin J , McGlinchey B , Fields PI . J Clin Microbiol 2012 50 (12) 4098-9 According to the Kauffmann-White scheme, 39 pairs of serovars in Salmonella serogroup C2 differ only by the minor antigen O:6(1). We characterized strains from 10 serovars representing five Salmonella serogroup C2 pairs. All strains demonstrated variable expression of O:6. These results indicate that these pairs are not distinct serovars. |
Molecular determination of H antigens of Salmonella by use of a microsphere-based liquid array.
McQuiston JR , Waters RJ , Dinsmore BA , Mikoleit ML , Fields PI . J Clin Microbiol 2010 49 (2) 565-573 Serotyping of Salmonella has been an invaluable subtyping method for epidemiologic studies for more than 70 years. Technical difficulties of serotyping, primarily in antisera production and quality control, can be overcome with modern molecular methods. We developed a DNA based assay targeting the genes encoding the flagellar antigens (fliC and fljB) of the Kauffmann-White serotyping scheme. Fifteen H antigens (H:a; b; c; d; d/j; e,h; i; k; r; y; z; z10; z29;z35 and z6), five complex major antigens (H:G; EN; Z4; 1 and L) and 16 complex secondary antigens (H:2; 5; 6; 7; f; m/g,m; m/m,t; p; s; t/m,t; v; x; z15; z24; z28 and z51) were targeted in the assay. DNA probes targeting these antigens were designed and evaluated on 500 isolates tested in parallel with traditional serotyping methods. The assay correctly identified 461 (92.2%) isolates based on the 36 antigens detected in the assay. Among the isolates considered correctly identified, 47 (9.4%) were partially serotyped because probes corresponding to some antigens in the strains were not in the assay, and 13 (2.6%) were monophasic or nonmotile strains that possessed flagellar antigen genes that were not expressed but were detected in the assay. The 39 (7.8%) strains that were not correctly identified possessed an antigen that should have been detected by the assay, but was not. Apparent false negative results may be attributed to allelic divergence. The molecular assay provided results that paralleled traditional methods with a much greater throughput, while maintaining the integrity of the Kauffmann White serotyping scheme, thus providing backwards compatible epidemiologic data. This assay should greatly enhance the ability of clinical and public health laboratories to serotype of Salmonella. |
Supplement 2003-2007 (No. 47) to the White-Kauffmann-Le Minor scheme
Guibourdenche M , Roggentin P , Mikoleit M , Fields PI , Bockemuhl J , Grimont PA , Weill FX . Res Microbiol 2010 161 (1) 26-9 This supplement reports the characterization of 70 new Salmonella serovars recognized between 2003 and 2007 by the WHO Collaborating Center for Reference and Research on Salmonella: 44 were assigned to Salmonella enterica subspecies enterica, 11 to subspecies salamae, 5 to subspecies arizonae, 8 to subspecies diarizonae, one to subspecies houtenae and one to Salmonella bongori. One new serovar, Mygdal, displayed a new H factor, H:z(91). |
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