scholarly journals Molecular Epidemiology of Novel Pathogen “Brachyspira hampsonii” Reveals Relationships between Diverse Genetic Groups, Regions, Host Species, and Other Pathogenic and Commensal Brachyspira Species

2015 ◽  
Vol 53 (9) ◽  
pp. 2908-2918 ◽  
Author(s):  
Nandita S. Mirajkar ◽  
Aschalew Z. Bekele ◽  
Yogesh Y. Chander ◽  
Connie J. Gebhart
Keyword(s):  
Population Structure ◽  
Host Species ◽  
Genetic Relatedness ◽  
Production Systems ◽  
Genetic Relationships ◽  
Single Species ◽  
The United States ◽  
Control Measures ◽  
Swine Production ◽  
Content Type

Outbreaks of bloody diarrhea in swine herds in the late 2000s signaled the reemergence of an economically significant disease, swine dysentery, in the United States. Investigations confirmed the emergence of a novel spirochete in swine, provisionally designated “Brachyspira hampsonii,” with two genetically distinct clades. Although it has since been detected in swine and migratory birds in Europe and North America, little is known about its genetic diversity or its relationships with otherBrachyspiraspecies. This study characterizesB. hampsoniiusing a newly developed multilocus sequence typing (MLST) approach and elucidates the diversity, distribution, population structure, and genetic relationships of this pathogen from diverse epidemiological sources globally. Genetic characterization of 81B. hampsoniiisolates, originating from six countries, with our newly established MLST scheme identified a total of 20 sequence types (STs) belonging to three clonal complexes (CCs).B. hampsoniishowed a heterogeneous population structure with evidence of microevolution locally in swine production systems, while its clustering patterns showed associations with its epidemiological origins (country, swine production system, and host species). The close genetic relatedness ofB. hampsoniiisolates from different countries and host species highlights the importance of strict biosecurity control measures. A comparative analysis of 430 isolates representing sevenBrachyspiraspecies (pathogens and commensals) from 19 countries and 10 host species depicted clustering by microbial species. It revealed the close genetic relatedness ofB. hampsoniiwith commensalBrachyspiraspecies and also provided support for the two clades ofB. hampsoniito be considered a single species.

scholarly journals Identifying Barriers to Implementing Pain Management for Piglet Castration: A Focus Group of Swine Veterinarians

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1202 ◽  
Author(s):  
Brooklyn Wagner ◽  
Kenneth Royal ◽  
Rachel Park ◽  
Monique Pairis-Garcia
Keyword(s):  
Decision Making ◽  
Pain Management ◽  
Focus Group ◽  
Production Systems ◽  
The United States ◽  
Swine Production ◽  
Factors Influencing ◽  
Audio Recordings ◽  
On Farm ◽  
And Training

Surgical castration is a painful husbandry procedure performed on piglets in the United States (US) to improve meat quality. Veterinarians play a crucial role in developing pain management protocols. However, providing pain management for castration is not common practice in US swine production systems. Therefore, the objective of the present study is to identify factors influencing swine veterinarian decision-making in regard to pain management protocols for piglet castration using focus group methodologies. Swine veterinarians (n = 21) were recruited to participate in one of three focus groups. Audio recordings were transcribed verbatim and analyzed by two independent coders who identified three areas of focus, including (1) the lack of approved products validated for efficacy, (2) economic limitations and challenges, and (3) deficient guidelines and training for veterinarians to develop protocols. Although participating veterinarians acknowledged the importance of pain management from an animal welfare standpoint, these barriers must be addressed to ensure that castration pain can be successfully mitigated on-farm.

scholarly journals Invasive Methicillin-ResistantStaphylococcus aureusUSA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages

mSphere ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
M. B. Frisch ◽  
S. Castillo-Ramírez ◽  
R. A. Petit ◽  
M. M. Farley ◽  
S. M. Ray ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Surface Protein ◽  
The United States ◽  
Recent Common Ancestor ◽  
Emerging Infections ◽  
Gene Encoding ◽  
Content Type ◽  
Insertion Elements ◽  
Mrsa Strains ◽  
The U.S

ABSTRACTUSA500 isolates are clonal complex 8 (CC8)Staphylococcus aureusstrains closely related to the prominent community- and hospital-associated USA300 group. Despite being relatively understudied, USA500 strains cause a significant burden of disease and are the third most common methicillin-resistantS. aureus(MRSA) strains identified in the U.S. Emerging Infections Program (EIP) invasiveS. aureussurveillance. To better understand the genetic relationships of the strains, we sequenced the genomes of 539 USA500 MRSA isolates from sterile site infections collected through the EIP between 2005 and 2013 in the United States. USA500 isolates fell into three major clades principally separated by their distribution across different U.S. regions. Clade C1 strains, found principally in the Northeast, were associated with multiple IS256insertion elements in their genomes and higher levels of antibiotic resistance. C2 was associated with Southern states, and E1 was associated with Western states. C1 and C2 strains all shared a frameshift in the gene encoding AdsA surface-attached surface protein. We propose that the term “USA500” should be used for CC8 strains sharing a recent common ancestor with the C1, C2, and E1 strains but not in the USA300 group.IMPORTANCEIn this work, we have removed some of the confusion surrounding the use of the name “USA500,” placed USA500 strains in the context of the CC8 group, and developed a strategy for assignment to subclades based on genome sequence. Our new phylogeny of USA300/USA500 will be a reference point for understanding the genetic adaptations that have allowed multiple highly virulent clonal strains to emerge from within CC8 over the past 50 years.

scholarly journals Carbapenemase-Producing Enterobacteriaceae in Swine Production in the United States: Impact and Opportunities

2016 ◽  
Vol 61 (2) ◽  
Author(s):  
Timothy J. Johnson
Keyword(s):  
United States ◽  
The United States ◽  
Swine Production ◽  
Content Type ◽  
Link Type

ABSTRACT The discovery of carbapenemase-producing Enterobacteriaceae in U.S. swine production is troubling and underscores a tumultuous period where the outlook on the battle against superbugs is bleak. However, all is not lost. This commentary highlights both the good and the bad that can come from such findings, including those of a recent study published by Mollenkopf et al. (Antimicrob Agents Chemother 61:e012198-16, 2017, https://doi.org/doi:10.1128/AAC.01298-16 ).

scholarly journals Serotype Distribution, Population Structure, and Antimicrobial Resistance of Group B Streptococcus Strains Recovered from Colonized Pregnant Women

2016 ◽  
Vol 55 (2) ◽  
pp. 412-422 ◽  
Author(s):  
Sarah Teatero ◽  
Patricia Ferrieri ◽  
Irene Martin ◽  
Walter Demczuk ◽  
Allison McGeer ◽  
...  
Keyword(s):  
Population Structure ◽  
Pregnant Women ◽  
Antimicrobial Agents ◽  
Vaccine Development ◽  
Group B Streptococcus ◽  
Tetracycline Resistance ◽  
The United States ◽  
High Rate ◽  
Content Type ◽  
Group B

ABSTRACTUsing serotyping, multilocus sequence typing, and whole-genome sequencing (WGS) of selected strains, we studied the population structure of 102 group BStreptococcus(GBS) isolates prospectively sampled in 2014 from vaginal/rectal swabs of healthy pregnant women in metropolitan Toronto, Canada. We also determined the susceptibilities of each of the colonizing isolates to penicillin, erythromycin, clindamycin, tetracycline, and other antimicrobial agents. Overall, we observed a high rate of tetracycline resistance (89%) among colonizing GBS isolates. We found resistance to erythromycin in 36% of the strains, and 33% were constitutively or inducibly resistant to clindamycin. The most frequently identified serotypes were III (25%), Ia (23%), and V (19%). Serotype IV accounted for 6% of the colonizing isolates, a rate consistent with that observed among patients with invasive GBS infections in metropolitan Toronto. The majority of serotype IV isolates belonged to sequence type (ST)459, a tetracycline-, erythromycin-, and clindamycin-resistant ST first identified in Minnesota, which is considered to be the main driver of serotype IV GBS expansion in North America. WGS revealed that ST459 isolates from Canada are clonally related to colonizing and invasive ST459 organisms circulating in regions of the United States. We also used WGS to study recombination in selected colonizing strains from metropolitan Toronto, which revealed multiple episodes of capsular switching. Present and future circulating GBS organisms and their genetic diversity may influence GBS vaccine development.

scholarly journals Pyricularia grisea Causing Gray Leaf Spot of Perennial Ryegrass Turf: Population Structure and Host Specificity

Plant Disease ◽  
2001 ◽  
Vol 85 (8) ◽  
pp. 817-826 ◽  
Author(s):  
G. Viji ◽  
B. Wu ◽  
S. Kang ◽  
W. Uddin ◽  
D. R. Huff
Keyword(s):  
United States ◽  
Population Structure ◽  
Winter Wheat ◽  
Perennial Ryegrass ◽  
Leaf Spot ◽  
Genetic Relationships ◽  
The United States ◽  
Gray Leaf Spot ◽  
Pyricularia Grisea ◽  
Highly Virulent

Gray leaf spot is a serious disease of perennial ryegrass (Lolium perenne) turf in the United States. Isolates of Pyricularia grisea causing the disease in perennial ryegrass were characterized using molecular markers and pathogenicity assays on various gramineous hosts. Genetic relationships among perennial ryegrass isolates were determined using different types of trans-posons as probes. Phylogenetic analysis using Pot2 and MGR586 probes, analyzed with AMOVA (analysis of molecular variance), showed that these isolates from perennial ryegrass consist of three closely related lineages. All the isolates belonged to a single mating type, MAT1-2. Among 20 isolates from 16 host species other than perennial ryegrass, only the isolates from wheat (Triticum aestivum) and triticale (× Triticosecale), showed notable similarity to the perennial ryegrass isolates based on their Pot2 fingerprints. The copy number and fingerprints of Pot2 and MGR586 in isolates of P. grisea from perennial ryegrass indicate that they are genetically distinct from the isolates derived from rice (Oryza sativa) in the United States. The perennial ryegrass isolates also had the same sequence in the internal transcribed spacer (ITS) region of the genes encoding ribosomal RNA as that of the wheat and triticale isolates, and exhibited rice isolate sequence polymorphisms. In pathogenicity assays, all the isolates of P. grisea from Legacy II perennial ryegrass caused characteristic blast symptoms on Marilee soft white winter wheat, Bennett hard red winter wheat, Era soft white spring wheat, and Presto triticale, and they were highly virulent on these hosts. An isolate from wheat and one from triticale (from Brazil) were also highly virulent on perennial ryegrass and Rebel III tall fescue (Festuca arundinacea). None of the isolates from perennial ryegrass caused the disease on Lagrue rice, and vice versa. Understanding the population structure of P. grisea isolates infecting perennial ryegrass and their relatedness to isolates from other gramineous hosts may aid in identifying alternate hosts for this pathogen.

scholarly journals Allelic Diversity and Population Structure in Oenococcus oeni as Determined from Sequence Analysis of Housekeeping Genes

2004 ◽  
Vol 70 (12) ◽  
pp. 7210-7219 ◽  
Author(s):  
Blanca de las Rivas ◽  
Ángela Marcobal ◽  
Rosario Muñoz
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Allelic Diversity ◽  
Rflp Analysis ◽  
The United States ◽  
Oenococcus Oeni ◽  
23S Rrna ◽  
Rrna Gene ◽  
Single Strain

ABSTRACT Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria.

scholarly journals A Prolonged Outbreak of KPC-3-Producing Enterobacter cloacae and Klebsiella pneumoniae Driven by Multiple Mechanisms of Resistance Transmission at a Large Academic Burn Center

2016 ◽  
Vol 61 (2) ◽  
Author(s):  
Hajime Kanamori ◽  
Christian M. Parobek ◽  
Jonathan J. Juliano ◽  
David van Duin ◽  
Bruce A. Cairns ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Molecular Mechanisms ◽  
Enterobacter Cloacae ◽  
The United States ◽  
Multidrug Resistant ◽  
Control Measures ◽  
Content Type ◽  
Burn Center ◽  
Infection Control Measures ◽  
Carbapenem Resistant

ABSTRACT Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacter cloacae has been recently recognized in the United States. Whole-genome sequencing (WGS) has become a useful tool for analysis of outbreaks and for determining transmission networks of multidrug-resistant organisms in health care settings, including carbapenem-resistant Enterobacteriaceae (CRE). We experienced a prolonged outbreak of CRE E. cloacae and K. pneumoniae over a 3-year period at a large academic burn center despite rigorous infection control measures. To understand the molecular mechanisms that sustained this outbreak, we investigated the CRE outbreak isolates by using WGS. Twenty-two clinical isolates of CRE, including E. cloacae (n = 15) and K. pneumoniae (n = 7), were sequenced and analyzed genetically. WGS revealed that this outbreak, which seemed epidemiologically unlinked, was in fact genetically linked over a prolonged period. Multiple mechanisms were found to account for the ongoing outbreak of KPC-3-producing E. cloacae and K. pneumoniae. This outbreak was primarily maintained by a clonal expansion of E. cloacae sequence type 114 (ST114) with distribution of multiple resistance determinants. Plasmid and transposon analyses suggested that the majority of bla KPC-3 was transmitted via an identical Tn4401b element on part of a common plasmid. WGS analysis demonstrated complex transmission dynamics within the burn center at levels of the strain and/or plasmid in association with a transposon, highlighting the versatility of KPC-producing Enterobacteriaceae in their ability to utilize multiple modes to resistance gene propagation.

scholarly journals Whole-Genome Sequencing Analysis of Salmonella enterica Serovar Enteritidis Isolates in Chile Provides Insights into Possible Transmission between Gulls, Poultry, and Humans

2016 ◽  
Vol 82 (20) ◽  
pp. 6223-6232 ◽  
Author(s):  
Magaly Toro ◽  
Patricio Retamal ◽  
Sherry Ayers ◽  
Marlen Barreto ◽  
Marc Allard ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Genetic Relationships ◽  
The United States ◽  
Interspecies Transmission ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Content Type ◽  
Published Evidence ◽  
Trace Back ◽  
The World

ABSTRACTSalmonella entericasubsp.entericaserotype Enteritidis is a major cause of human salmonellosis worldwide; however, little is known about the genetic relationships betweenS. Enteritidis clinical strains andS. Enteritidis strains from other sources in Chile. We compared the whole genomes of 30S. Enteritidis strains isolated from gulls, domestic chicken eggs, and humans in Chile, to investigate their phylogenetic relationships and to establish their relatedness to international strains. Core genome multilocus sequence typing (cgMLST) analysis showed that only 246/4,065 shared loci differed among these Chilean strains, separating them into two clusters (I and II), with cluster II being further divided into five subclusters. One subcluster (subcluster 2) contained strains from all surveyed sources that differed at 1 to 18 loci (of 4,065 loci) with 1 to 18 single-nucleotide polymorphisms (SNPs), suggesting interspecies transmission ofS. Enteritidis in Chile. Moreover, clusters were formed by strains that were distant geographically, which could imply that gulls might be spreading the pathogen throughout the country. Our cgMLST analysis, using otherS. Enteritidis genomes available in the National Center for Biotechnology Information (NCBI) database, showed thatS. Enteritidis strains from Chile and the United States belonged to different lineages, which suggests thatS. Enteritidis regional markers might exist and could be used for trace-back investigations.IMPORTANCEThis study highlights the importance of gulls in the spread ofSalmonellaEnteritidis in Chile. We revealed a close genetic relationship between some human and gullS. Enteritidis strains (with as few as 2 of 4,065 genes being different), and we also found that gull strains were present in clusters formed by strains isolated from other sources or distant locations. Together with previously published evidence, this suggests that gulls might be spreading this pathogen between different regions in Chile and that some of those strains have been transmitted to humans. Moreover, we discovered that ChileanS. Enteritidis strains clustered separately from most ofS. Enteritidis strains isolated throughout the world (in the GenBank database) and thus it might be possible to distinguish the geographical origins of strains based on specific genomic features. This could be useful for trace-back investigations of foodborne illnesses throughout the world.

scholarly journals Emergence of Multidrug-Resistant Salmonella enterica Serovar Goldcoast Strains in Taiwan and International Spread of the ST358 Clone

2019 ◽  
Vol 63 (10) ◽  
Author(s):  
Ying-Shu Liao ◽  
Bo-Han Chen ◽  
Yu-Ping Hong ◽  
Ru-Hsiou Teng ◽  
You-Wun Wang ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Genetic Relatedness ◽  
The United States ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Content Type ◽  
The United Kingdom ◽  
Routine Surveillance ◽  
Antimicrobial Resistance Genes ◽  
High Degree

ABSTRACT Salmonella enterica serovar Goldcoast infection was rare in Taiwan; it was not detected in routine surveillance from 2004 to 2013. This serovar was first identified in 2014, but the frequency of infection remained low until 2017. From 2014 to 2016, all but one isolate was pan-susceptible. S. Goldcoast infections abruptly increased in 2018, and all isolates were multidrug-resistant (MDR). All MDR isolates harbored an IncHI2 plasmid, and the majority carried 14 antimicrobial resistance genes, aac(3)-IId, aadA22, aph(3′)-Ia, aph(6)-Id, blaTEM-1B, blaCTX-M-55, lnu(F), floR, qnrS13, arr-2, sul2, sul3, tet(A), and dfrA14. S. Goldcoast strains recovered in Taiwan and 96 of 99 strains from Germany, the Netherlands, the United Kingdom, and the United States belonged to sequence type 358 (ST358). Whole-genome single-nucleotide polymorphism and core genome multilocus sequence type analyses revealed that all strains of the ST358 clone shared a high degree of genetic relatedness. The present study highlighted that a dramatic increase in S. Goldcoast infections followed the emergence of MDR strains and indicated that a genetically closely related S. Goldcoast ST358 clone may have widespread significance internationally.

scholarly journals Activities of Vancomycin, Ceftaroline, and Mupirocin against Staphylococcus aureus Isolates Collected in a 2011 National Surveillance Study in the United States

2013 ◽  
Vol 58 (2) ◽  
pp. 740-745 ◽  
Author(s):  
Sandra S. Richter ◽  
Daniel J. Diekema ◽  
Kristopher P. Heilmann ◽  
Cassie L. Dohrn ◽  
Emily K. Crispell ◽  
...  
Keyword(s):  
United States ◽  
Staphylococcus Aureus ◽  
Genetic Relatedness ◽  
Population Analysis ◽  
Brain Heart Infusion ◽  
The United States ◽  
Pcr Analysis ◽  
Surveillance Program ◽  
Content Type ◽  
Mupirocin Resistance

ABSTRACTForty-two medical centers from throughout the United States participating in a longitudinal surveillance program were asked to submit 100 consecutiveStaphylococcus aureusisolates during July to December 2011. Susceptibility testing using CLSI broth microdilution andmecAdetection by PCR analysis was performed on the 4,131 isolates collected. Methods employing Etest glycopeptide resistance detection (GRD; bioMérieux) and brain heart infusion agar containing 4 μg/ml vancomycin (BHIV) were used to screen methicillin-resistantS. aureus(MRSA) isolates for heterogeneous intermediate-level resistance to vancomycin (hVISA). Isolates with positive hVISA screen results were confirmed by population analysis profiling-area under the curve (PAP-AUC) determinations. The genetic relatedness of hVISA, ceftaroline-nonsusceptible, or high-level (HL) mupirocin resistance MRSA isolates was assessed by pulsed-field gel electrophoresis (PFGE). Among 2,093 MRSA isolates, the hVISA screen results were positive with 47 isolates by Etest GRD and 30 isolates by BHIV agar screen. Twenty-five of the GRD- or BHIV screen-positive isolates were confirmed as hVISA by PAP-AUC testing. Results of the current study were compared to results obtained from prior surveillance performed in 2009. The prevalence of hVISA among MRSA isolates was higher in 2011 than in 2009 (1.2% versus 0.4%,P= 0.003), especially for isolates with a vancomycin MIC of 2 (45.4% versus 14.3%,P= 0.01). The overall rate of ceftaroline susceptibility in the current study was 99.4% (one hVISA isolate had an intermediate ceftaroline MIC). HL mupirocin resistance increased from 2.2% in 2009 to 3.2% in 2011 (P= 0.006). Although overall rates of hVISA and HL mupirocin resistance are low, they have increased since 2009.

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