Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-11 (of 11 Records) |
Query Trace: Brown EW[original query] |
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A multinational listeriosis outbreak and the importance of sharing genomic data
Pettengill JB , Markell A , Conrad A , Carleton HA , Beal J , Rand H , Musser S , Brown EW , Allard MW , Huffman J , Harris S , Wise M , Locas A . Lancet Microbe 2020 1 (6) e233-e234 Our globalised food supply presents immense challenges to ensuring food safety, as shown by outbreaks of foodborne illnesses associated with imported foods.1 The speed with which such outbreaks are resolved often depends on how rapidly public health scientists communicate and disseminate actionable data. One such data source is whole-genome sequencing, which is the newest method of molecular subtyping and has superior discriminatory power compared with previous methods.2 Consequently, whole-genome sequencing has been and continues to be adopted by countries across the world as a tool to combat foodborne pathogens.3 Sequence data can be made publicly available through numerous databases (eg, the European Nucleotide Archive, the National Center for Biotechnology Information [NCBI] Sequence Read Archive, and the DNA Data Bank of Japan Sequence Read Archive). Laboratories are encouraged to share the genomes they have sequenced4 and, as new genomes are made public, isolates can be clustered into genetically similar groups to facilitate the detection of potential outbreaks and sources of contamination. |
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. |
Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers
Llewellyn AC , Lucas CE , Roberts SE , Brown EW , Nayak BS , Raphael BH , Winchell JM . PLoS One 2017 12 (12) e0189937 Cooling towers (CTs) are a leading source of outbreaks of Legionnaires' disease (LD), a severe form of pneumonia caused by inhalation of aerosols containing Legionella bacteria. Accordingly, proper maintenance of CTs is vital for the prevention of LD. The aim of this study was to determine the distribution of Legionella in a subset of regionally diverse US CTs and characterize the associated microbial communities. Between July and September of 2016, we obtained aliquots from water samples collected for routine Legionella testing from 196 CTs located in eight of the nine continental US climate regions. After screening for Legionella by PCR, positive samples were cultured and the resulting Legionella isolates were further characterized. Overall, 84% (164) were PCR-positive, including samples from every region studied. Of the PCR-positive samples, Legionella spp were isolated from 47% (78), L. pneumophila was isolated from 32% (53), and L. pneumophila serogroup 1 (Lp1) was isolated from 24% (40). Overall, 144 unique Legionella isolates were identified; 53% (76) of these were Legionella pneumophila. Of the 76 L. pneumophila isolates, 51% (39) were Lp1. Legionella were isolated from CTs in seven of the eight US regions examined. 16S rRNA amplicon sequencing was used to compare the bacterial communities of CT waters with and without detectable Legionella as well as the microbiomes of waters from different climate regions. Interestingly, the microbial communities were homogenous across climate regions. When a subset of seven CTs sampled in April and July were compared, there was no association with changes in corresponding CT microbiomes over time in the samples that became culture-positive for Legionella. Legionella species and Lp1 were detected frequently among the samples examined in this first large-scale study of Legionella in US CTs. Our findings highlight that, under the right conditions, there is the potential for CT-related LD outbreaks to occur throughout the US. |
Whole genome and core genome multilocus sequence typing and single nucleotide polymorphism analyses of Listeria monocytogenes associated with an outbreak linked to cheese, United States, 2013.
Chen Y , Luo Y , Carleton H , Timme R , Melka D , Muruvanda T , Wang C , Kastanis G , Katz LS , Turner L , Fritzinger A , Moore T , Stones R , Blankenship J , Salter M , Parish M , Hammack TS , Evans PS , Tarr CL , Allard MW , Strain EA , Brown EW . Appl Environ Microbiol 2017 83 (15) Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by Company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from Company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS three months later revealed that the equipment purchased by Company B from Company A yielded an environmental isolate highly similar to all outbreak isolates. The whole genome and core genome multilocus sequence typing and single nucleotide polymorphism (SNP) analyses were compared to demonstrate the maximum discriminatory power obtained by using multiple analyses, which were needed to differentiate outbreak-associated isolates from a PFGE-indistinguishable isolate collected in a non-implicated food source in 2012. This unrelated isolate differed from the outbreak isolates by only 7 to 14 SNPs, and as a result, minimum spanning tree by the whole genome analyses and certain variant calling approach and phylogenetic algorithm for core genome-based analyses could not provide the differentiation between unrelated isolates. Our data also suggest that SNP/allele counts should always be combined with WGS clustering generated by phylogenetically meaningful algorithms on sufficient number of isolates, and SNP/allele threshold alone is not sufficient evidence to delineate an outbreak. The putative prophages were conserved across all the outbreak isolates. All outbreak isolates belonged to clonal complex 5 and serotype 1/2b, had an identical inlA sequence, which did not have premature stop codons.IMPORTANCE In this outbreak, multiple analytical approaches were used for maximum discriminatory power. A PFGE-matched, epidemiologically unrelated isolate had high genetic similarity to the outbreak-associated isolates, with as few as only 7 SNP differences. Therefore, the SNP/allele threshold should not be used as the only evidence to define the scope of an outbreak. It is critical that the SNP/allele counts be complemented by WGS clustering generated by phylogenetically meaningful algorithms to distinguish outbreak-associated isolates from epidemiologically unrelated isolates. Careful selection of a variant calling approach and phylogenetic algorithm is critical for core genome-based analyses. The whole genome-based analyses were able to construct the highly resolved phylogeny needed to support the findings of the outbreak investigation. Ultimately, epidemiologic evidence and multiple WGS analyses should be combined to increase the confidence in outbreak investigations. |
Genome Sequences of Multidrug-Resistant, Colistin-Susceptible and -Resistant Klebsiella pneumoniae Clinical Isolates from Pakistan.
Crawford MA , Timme R , Lomonaco S , Lascols C , Fisher DJ , Sharma SK , Strain E , Allard MW , Brown EW , McFarland MA , Croley T , Hammack TS , Weigel LM , Anderson K , Hodge DR , Pillai SP , Morse SA , Khan E , Hughes MA . Genome Announc 2016 4 (6) The emergence and spread of colistin resistance among multidrug-resistant (MDR) Klebsiella pneumoniae represent a critical threat to global health. Here, we report the complete genome sequences of 10 MDR, colistin-susceptible and -resistant K. pneumoniae clinical isolates obtained in Pakistan between 2010 and 2013. |
Simultaneous detection of Legionella species and L. anisa, L. bozemanii, L. longbeachae and L. micdadei using conserved primers and multiple probes in a multiplex real-time PCR assay
Cross KE , Mercante JW , Benitez AJ , Brown EW , Diaz MH , Winchell JM . Diagn Microbiol Infect Dis 2016 85 (3) 295-301 Legionnaires' disease is a severe respiratory disease that is estimated to cause between 8,000 and 18,000 hospitalizations each year, though the exact burden is unknown due to under-utilization of diagnostic testing. Although Legionella pneumophila is the most common species detected in clinical cases (80-90%), other species have also been reported to cause disease. However, little is known about Legionnaires' disease caused by these non-pneumophila species. We designed a multiplex real-time PCR assay for detection of all Legionella spp. and simultaneous specific identification of four clinically-relevant Legionella species, L. anisa, L. bozemanii, L. longbeachae, and L. micdadei, using 5'-hydrolysis probe real-time PCR. The analytical sensitivity for detection of nucleic acid from each target species was ≤50fg per reaction. We demonstrated the utility of this assay in spiked human sputum specimens. This assay could serve as a tool for understanding the scope and impact of non-pneumophila Legionella species in human disease. |
The importance of clinical surveillance in detecting Legionnaires' disease outbreaks: a large outbreak in a hospital with a Legionella disinfection system, Pennsylvania, 2011-2012
Demirjian A , Lucas CE , Garrison LE , Kozak-Muiznieks NA , States S , Brown EW , Wortham JM , Beaudoin A , Casey ML , Marriott C , Ludwig AM , Sonel AF , Muder RR , Hicks LA . Clin Infect Dis 2015 60 (11) 1596-602 BACKGROUND: Healthcare-associated Legionnaires' disease (LD) is a preventable pneumonia with a 30% case-fatality rate. The Centers for Disease Control and Prevention guidelines recommend a high index of suspicion for the diagnosis of healthcare-associated LD. We characterized an outbreak and evaluated contributing factors in a hospital using copper-silver ionization for prevention of Legionella growth in water. METHODS: Through medical chart review at a large, urban tertiary care hospital in November 2012, we identified patients diagnosed with LD during 2011-2012. Laboratory-confirmed cases were categorized as definite, probable, and not healthcare-associated based on time spent in the hospital during the incubation period. We performed an environmental assessment of the hospital, including collection of samples for Legionella culture. Clinical and environmental isolates were compared by genotyping. Copper and silver ion concentrations were measured in 11 water samples. RESULTS: We identified five definite and 17 probable healthcare-associated LD cases; six case-patients died. Of 25 locations (mostly potable water) where environmental samples were obtained for Legionella-specific culture, all but two showed Legionella growth; eleven isolates were identical to three clinical isolates by sequence-based typing. Mean copper and silver concentrations were at or above the manufacturer's recommended target for Legionella control. Despite this, all samples where copper and silver concentrations were tested showed Legionella growth. CONCLUSIONS: This outbreak was linked to the hospital's potable water system and highlights the importance of maintaining a high index of suspicion for healthcare-associated LD, even in the setting of a long-term disinfection program. |
Comparative genomic analysis and virulence differences in closely related salmonella enterica serotype heidelberg isolates from humans, retail meats, and animals.
Hoffmann M , Zhao S , Pettengill J , Luo Y , Monday SR , Abbott J , Ayers SL , Cinar HN , Muruvanda T , Li C , Allard MW , Whichard J , Meng J , Brown EW , McDermott PF . Genome Biol Evol 2014 6 (5) 1046-68 Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. Recently, an antibiotic-resistant strain of this serovar was implicated in a large 2011 multistate outbreak resulting from consumption of contaminated ground turkey that involved 136 confirmed cases, with one death. In this study, we assessed the evolutionary diversity of 44 S. Heidelberg isolates using whole-genome sequencing (WGS) generated by the 454 GS FLX (Roche) platform. The isolates, including 30 with nearly indistinguishable (one band difference) Xbal pulsed-field gel electrophoresis patterns (JF6X01.0032, JF6X01.0058), were collected from various sources between 1982 and 2011 and included nine isolates associated with the 2011 outbreak. Additionally, we determined the complete sequence for the chromosome and three plasmids from a clinical isolate associated with the 2011 outbreak using the Pacific Biosciences (PacBio) system. Using single-nucleotide polymorphism (SNP) analyses, we were able to distinguish highly clonal isolates, including strains isolated at different times in the same year. The isolates from the recent 2011 outbreak clustered together with a mean SNP variation of only 17 SNPs. The S. Heidelberg isolates carried a variety of phages, such as prophage P22, P4, lambda-like prophage Gifsy-2, and the P2-like phage which carries the sopE1 gene, virulence genes including 62 pathogenicity, and 13 fimbrial markers and resistance plasmids of the incompatibility (Inc)I1, IncA/C, and IncHI2 groups. Twenty-one strains contained an IncX plasmid carrying a type IV secretion system. On the basis of the recent and historical isolates used in this study, our results demonstrated that, in addition to providing detailed genetic information for the isolates, WGS can identify SNP targets that can be utilized for differentiating highly clonal S. Heidelberg isolates. |
Survey of Legionella species found in Thai soil
Travis TC , Brown EW , Peruski LF , Siludjai D , Jorakate P , Salika P , Yang G , Kozak NA , Kodani M , Warner AK , Lucas CE , Thurman KA , Winchell JM , Thamthitiwat S , Fields BS . Int J Microbiol 2012 2012 218791 Members of the Gram-negative genus Legionella are typically found in freshwater environments, with the exception of L. longbeachae, which is present in composts and potting mixes. When contaminated aerosols are inhaled, legionellosis may result, typically as either the more serious pneumonia Legionnaires' disease or the less severe flu-like illness Pontiac fever. It is presumed that all species of the genus Legionella are capable of causing disease in humans. As a followup to a prior clinical study of legionellosis in rural Thailand, indigenous soil samples were collected proximal to cases' homes and workplaces and tested for the presence of legionellae by culture. We obtained 115 isolates from 22/39 soil samples and used sequence-based methods to identify 12 known species of Legionella represented by 87 isolates. |
Eight years of Legionnaires' disease transmission in travellers to a condominium complex in Las Vegas, Nevada
Silk BJ , Moore MR , Bergtholdt M , Gorwitz RJ , Kozak NA , Tha MM , Brown EW , Winchester JL , Labus BJ , Rowley P , Middaugh JP , Fields BS , Hicks LA . Epidemiol Infect 2012 140 (11) 1-10 SUMMARY: Travel is a risk factor for Legionnaires' disease. In 2008, two cases were reported in condominium guests where we investigated a 2001 outbreak. We reinvestigated to identify additional cases and determine whether ongoing transmission resulted from persistent colonization of potable water. Exposures were assessed by matched case-control analyses (2001) and case-series interviews (2008). We sampled potable water and other water sources. Isolates were compared using sequence-based typing. From 2001 to 2008, 35 cases were identified. Confirmed cases reported after the cluster in 2001-2002 were initially considered sporadic, but retrospective case-finding identified five additional cases. Cases were more likely than controls to stay in tower 2 of the condominium [matched odds ratio (mOR) 6.1, 95% confidence interval (CI) 1.6-22.9]; transmission was associated with showering duration (mOR 23.0, 95% CI 1.4-384). We characterized a clinical isolate as sequence type 35 (ST35) and detected ST35 in samples of tower 2's potable water in 2001, 2002, and 2008. This prolonged outbreak illustrates the importance of striving for permanent Legionella eradication from potable water. |
Legionella nagasakiensis sp. nov., isolated from water samples in Japan and Australia and from a patient with pneumonia in the United States
Yang PG , Benson RF , Ratcliff R , Brown EW , Steigerwalt AG , Thacker LW , Daneshvar M , Morey RE , Saito A , Fields BS . Int J Syst Evol Microbiol 2011 62 284-288 A novel Legionella species was identified based on 16S rRNA and mip (macrophage infectivity potentiator) gene sequencing analysis, cellular fatty acids, isoprenoid quinones, biochemical reactions, antigens, and quantitative DNA-DNA hybridization. The strain CDC-1796-JAP-E(T) was isolated from well water at the Nagassaki Municipal Medical Center, Japan. Two strains, CDC-3041-AUS-E and CDC-3558-AUS-E, were isolated from water samples during an outbreak of legionellosis in South Australia. The strain CDC-5427-OH-H was isolated from a 66-year-old female patient diagnosed with Legionnaires' disease in the U.S. The cells from these four strains were gram-negative, non-fluorescent, rod-shaped, and positive for alkaline phosphatase, esterase, leucine arylamidase, catalase, gelatinase, beta-lactamase, and tyrosine browning assay. Phylogenetic analysis of 16S rRNA and mip genes revealed that the four strains formed a distinct cluster within the genus Legionella. The bacteria contained branched-chain fatty acids and quinones that are typical of the genus Legionella. Slide agglutination tests demonstrated no cross-reaction with 52 previously described Legionellaceae. DNA hybridization studies indicated DNAs from the four strains were highly related (78-84%) but showed 29% relatedness to L. oakridgensis (ATCC 33761(T)) and less than 10% to other Legionella species tested. These characterizations suggest that the isolates represent a novel species, for which the name Legionella nagasakiensis sp. nov is proposed, for the type strain CDC-1796-JAP-E(T) (=ATCC BAA-1557(T)=JCM 15315(T)). |
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