scholarly journals Genomic Characterization of Salmonella typhimurium DT104 Strains Associated with Cattle and Beef Products

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 529
Author(s):  
Craig T. Parker ◽  
Steven Huynh ◽  
Aaron Alexander ◽  
Andrew S. Oliver ◽  
Kerry K. Cooper
Keyword(s):  
Phage Type ◽  
Ground Beef ◽  
Multidrug Resistant ◽  
Snp Analysis ◽  
Nucleotide Polymorphisms ◽  
Deletion Event ◽  
Genomic Epidemiology ◽  
Serovar Typhimurium ◽  
Beef Products ◽  
Utilization Pathway

Salmonella enterica subsp. enterica serovar Typhimurium DT104, a multidrug-resistant phage type, has emerged globally as a major cause of foodborne outbreaks particularly associated with contaminated beef products. In this study, we sequenced three S. Typhimurium DT104 strains associated with a 2009 outbreak caused by ground beef, including the outbreak source strain and two clinical strains. The goal of the study was to gain a stronger understanding of the genomics and genomic epidemiology of highly clonal S. typhimurium DT104 strains associated with bovine sources. Our study found no single nucleotide polymorphisms (SNPs) between the ground beef source strain and the clinical isolates from the 2009 outbreak. SNP analysis including twelve other S. typhimurium strains from bovine and clinical sources, including both DT104 and non-DT104, determined DT104 strains averaged 55.0 SNPs between strains compared to 474.5 SNPs among non-DT104 strains. Phylogenetic analysis separated the DT104 strains from the non-DT104 strains, but strains did not cluster together based on source of isolation even within the DT104 phage type. Pangenome analysis of the strains confirmed previous studies showing that DT104 strains are missing the genes for the allantoin utilization pathway, but this study confirmed that the genes were part of a deletion event and not substituted or disrupted by the insertion of another genomic element. Additionally, cgMLST analysis revealed that DT104 strains with cattle as the source of isolation were quite diverse as a group and did not cluster together, even among strains from the same country. Expansion of the analysis to 775 S. typhimurium ST19 strains associated with cattle from North America revealed diversity between strains, not limited to just among DT104 strains, which suggests that the cattle environment is favorable for a diverse group of S. typhimurium strains and not just DT104 strains.

scholarly journals Molecular epidemiology and diversity ofSalmonellaserovar Typhimurium in pigs using phenotypic and genotypic approaches

2005 ◽  
Vol 134 (1) ◽  
pp. 187-198 ◽  
Author(s):  
W. A. GEBREYES ◽  
C. ALTIER ◽  
S. THAKUR
Keyword(s):  
Production Systems ◽  
Phage Type ◽  
Geographical Area ◽  
Multidrug Resistant ◽  
Resistance Pattern ◽  
Public Health Importance ◽  
Pig Production ◽  
Phage Types ◽  
Serovar Typhimurium ◽  
Discriminatory Index

SUMMARYFor epidemiological investigations of the most common and non-host-adaptedSalmonellaserotypes, such as Typhimurium, highly discriminatory approaches are essential. In the present study, we evaluated three genotyping methods; amplified fragment length polymorphism (AFLP), pulsed-field gel electrophoresis (PFGE) and repetitive palindromic extragenic–PCR (Rep–PCR) using 40 isolates. AFLP showed the highest discriminatory index (0·939), resolution and throughput. To determine clonality ofSalmonellaTyphimurium isolates and epidemiological relatedness in different commercial pig production units, we employed AFLP in combination with antimicrobial resistance pattern and phage typing.Salmonellaserovar Typhimurium isolates (n=196) obtained from a longitudinal study of 18 pig farms over a 3-year period were studied. Using this approach, 16 distinct clonal types were identified. We found two common multidrug- resistant patterns including AmCmStSuTe and AmKmStSuTe. Two commonly multidrug- resistant phage types that are of known public health importance, DT104 and DT193, were also common. AFLP differentiated distinct clones within DT104, a phage type previously reported to be clonal. Fourteen of the clonal types were unique to one of the two production systems, showing diversity between independent commercial pig production systems located in the same geographical area. Clonal types obtained from nursery farms and corresponding finishing units were, however, similar.

scholarly journals In Vitro and In Vivo Assessment of Salmonella enterica Serovar Typhimurium DT104 Virulence

2001 ◽  
Vol 69 (7) ◽  
pp. 4673-4677 ◽  
Author(s):  
Chris A. Allen ◽  
Paula J. Fedorka-Cray ◽  
Andrés Vazquez-Torres ◽  
Mitsu Suyemoto ◽  
Craig Altier ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Phage Type ◽  
Multidrug Resistant ◽  
Peritoneal Macrophages ◽  
Lethal Infection ◽  
Animal Infection ◽  
Serovar Typhimurium ◽  
Clinical Illness

ABSTRACT Multidrug-resistant Salmonella enterica serovar Typhimurium phage type DT104 has become a widespread cause of human and other animal infection worldwide. The severity of clinical illness inS. enterica serovar Typhimurium DT104 outbreaks has led to the suggestion that this strain possesses enhanced virulence. In the present study, in vitro and in vivo virulence-associated phenotypes of several clinical isolates of S. enterica serovar Typhimurium DT104 were examined and compared to S. entericaserovar Typhimurium ATCC 14028s. The ability of these DT104 isolates to survive within murine peritoneal macrophages, invade cultured epithelial cells, resist antimicrobial actions of reactive oxygen and nitrogen compounds, and cause lethal infection in mice were assessed. Our results failed to demonstrate that S. enterica serovar Typhimurium DT104 isolates are more virulent than S. enterica serovar Typhimurium ATCC 14028s.

Multistate Outbreak of Multidrug-Resistant Salmonella Newport Infections Associated with Ground Beef, October to December 2007

2011 ◽  
Vol 74 (8) ◽  
pp. 1315-1319 ◽  
Author(s):  
J. L. SCHNEIDER ◽  
P. L. WHITE ◽  
J. WEISS ◽  
D. NORTON ◽  
J. LIDGARD ◽  
...  
Keyword(s):  
Case Control Study ◽  
Ground Beef ◽  
Multidrug Resistant ◽  
Chain Store ◽  
Department Of Agriculture ◽  
California Department ◽  
Salmonella Newport ◽  
Beef Products ◽  
Inspection Service ◽  
Control Study

In late October 2007, an outbreak of multidrug-resistant Salmonella Newport infections affected 42 case patients in California, Arizona, Idaho, and Nevada. A case-control study implicated ground beef from one chain store. Despite detailed ground beef purchase histories—including shopper card information for several case patients—traceback efforts by both the U.S. Department of Agriculture, Food Safety and Inspection Service and the California Department of Public Health were unable to identify the source of contamination. Case patients consumed multiple types of ground beef products purchased at numerous chain store A retail locations. These stores had received beef products for grinding from multiple beef slaughter–processing establishments. Detailed retail grinding logs and grinding policies that prevent cross-contamination between batches of ground beef products are crucial in the identification of contaminated beef products associated with foodborne illness.

scholarly journals Diffusion and Persistence of Multidrug ResistantSalmonellaTyphimurium Strains Phage Type DT120 in Southern Italy

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Danila De Vito ◽  
Rosa Monno ◽  
Federica Nuccio ◽  
Marilisa Legretto ◽  
Marta Oliva ◽  
...  
Keyword(s):  
Genomic Island ◽  
Southern Italy ◽  
Phage Type ◽  
Multidrug Resistant ◽  
Clinical Strains ◽  
Pork Products ◽  
Antimicrobial Resistance Genes ◽  
Serovar Typhimurium ◽  
Resistance Patterns ◽  
Type Shifting

Sixty-two multidrug resistantSalmonella entericaserovar Typhimurium strains isolated from 255 clinical strains collected in Southern Italy in 2006–2008 were characterised for antimicrobial resistance genes, pulsotype, and phage type. Most strains (83.9%) were resistant to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (ACSSuT) encoded in 88.5% by theSalmonellagenomic island (SGI1) and in 11.5% by the InH-like integron (blaOXA-30–aadA1) andcatA1,sul1, andtet(B) genes. STYMXB.0061 (75%) and DT120 (84.6%) were the prevalent pulsotype and phage type identified in these strains, respectively. Five other resistance patterns were found either in single or in a low number of isolates. The pandemic clone DT104 (ACSSuT encoded by SGI1) has been identified in Italy since 1992, while strains DT120 (ACSSuT encoded by SGI1) have never been previously reported in Italy. In Europe, clinical strains DT120 have been reported from sporadic outbreaks linked to the consumption of pork products. However, none of these strains were STYMXB.0061 and SGI1 positive. The prevalent identification and persistence of DT120 isolates would suggest, in Southern Italy, a phage type shifting of the pandemic DT104 clone pulsotype STYMXB.0061. Additionally, these findings raise epidemiological concern about the potential diffusion of these emerging multidrug resistant (SGI linked) DT120 strains.

scholarly journals Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

2016 ◽  
Vol 82 (8) ◽  
pp. 2516-2526 ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Rene S. Hendriksen ◽  
Simon Le Hello ◽  
François-Xavier Weill ◽  
Dorte Lau Baggesen ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Phylogenetic Trees ◽  
Demographic History ◽  
Credible Interval ◽  
The United States ◽  
Multidrug Resistant ◽  
Content Type ◽  
Genomic Epidemiology ◽  
Serovar Typhimurium ◽  
History Of

ABSTRACTIt has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistantSalmonella entericaserovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. We used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315S. Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ∼1948 (95% credible interval [CI], 1934 to 1962) and later became MDR DT104 in ∼1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kbSalmonellagenomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ∼1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicateSalmonellafrom pig herds in Denmark from 1996 to 2000. The results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention ofSalmonellainfections.

scholarly journals Molecular Epidemiology ofSalmonella entericaSerovar Typhimurium Isolates from Cattle in Hokkaido, Japan: Evidence of Clonal Replacement and Characterization of the Disseminated Clone

2011 ◽  
Vol 77 (5) ◽  
pp. 1739-1750 ◽  
Author(s):  
Yukino Tamamura ◽  
Ikuo Uchida ◽  
Kiyoshi Tanaka ◽  
Hizuru Okazaki ◽  
Satoru Tezuka ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Phage Type ◽  
Variable Number Tandem Repeat ◽  
Genomic Analysis ◽  
Subtractive Hybridization ◽  
Multidrug Resistant ◽  
Variable Number ◽  
Virulence Plasmid ◽  
Plasmid Analysis ◽  
Serovar Typhimurium

ABSTRACTThe molecular epidemiology of 545Salmonella entericaserovar Typhimurium isolates collected between 1977 and 2009 from cattle in Hokkaido, Japan, was investigated using pulsed-field gel electrophoresis (PFGE). Nine main clusters were identified from 116 PFGE patterns. Cluster I comprised 248 isolates, 243 of which possessed a sequence specific to definitive phage type 104 (DT104) or U302. The cluster I isolates were dominant in 1993 to 2003, but their numbers declined beginning in 2004. Beginning in 2002, an increase was observed in the number of cluster VII isolates, consisting of 21 PFGE patterns comprising 165 isolates. A total of 116 isolates representative of the 116 PFGE profiles were analyzed by multilocus variable-number tandem-repeat analysis (MLVA). Other than two drug-sensitive isolates, 19 isolates within cluster VII were classified in the same cluster by MLVA. Among the cluster VII isolates, an antibiotic resistance type showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, tetracycline, kanamycin, cefazolin, and sulfamethoxazole-trimethoprim and a resistance type showing resistance to ampicillin, streptomycin, sulfonamides, tetracycline, and kanamycin were found in 23 and 125 isolates, respectively. In the 19 isolates representative of cluster VII, theblaTEM-1gene was found on aSalmonellaserotype Typhimurium virulence plasmid, which was transferred toEscherichia coliby electroporation along with resistance to two to four other antimicrobials. Genomic analysis by subtractive hybridization and plasmid analysis suggested that theblaTEM-1-carrying virulence plasmid has a mosaic structure composed of elements of different origin. These results indicate an emerging multidrug-resistantS. Typhimurium clone carrying a virulence-resistance plasmid among cattle in Hokkaido, Japan.

scholarly journals Genomic Epidemiology of Candida auris in Qatar Reveals Hospital Transmission Dynamics and a South Asian Origin

2021 ◽  
Vol 7 (3) ◽  
pp. 240
Author(s):  
Husam Salah ◽  
Sathyavathi Sundararaju ◽  
Lamya Dalil ◽  
Sarah Salameh ◽  
Walid Al-Wali ◽  
...  
Keyword(s):  
South Asian ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Nucleotide Polymorphisms ◽  
Resistance Mutations ◽  
Candida Auris ◽  
Single Nucleotide ◽  
Genomic Epidemiology ◽  
East Region ◽  
Middle East Region

Candida auris is an emerging, multidrug-resistant fungal pathogen that has become a public health threat with an increasing incidence of infections worldwide. Candida auris spreads easily among patients within and between hospitals. Infections and outbreaks caused by C. auris have been reported in the Middle East region including Oman, Kuwait, Saudi Arabia, and Qatar; however, the origin of these isolates is largely unknown. Pathogen whole genome sequencing (WGS) was used to determine the epidemiology and drug resistance mutations of C. auris in Qatar. Forty-four samples isolated from patients in three hospitals and the hospital environment were sequenced by Illumina NextSeq. Core genome single nucleotide polymorphisms (SNPs) revealed that all isolates belonged to the South Asian lineage with genetic heterogeneity that suggests previous acquisition from foreign healthcare. The genetic variability among the outbreak isolates in the two hospitals (A and B) was low. Four environmental isolates clustered with the related clinical isolates, and epidemiologically linked isolates clustered together, suggesting that the ongoing transmission of C. auris could be linked to infected/colonized patients and the hospital environment. Prominent mutations Y132F and K143R in ERG11 linked to increased fluconazole resistance were detected.

scholarly journals Complete Nucleotide Sequence of a 43-Kilobase Genomic Island Associated with the Multidrug Resistance Region of Salmonella enterica Serovar Typhimurium DT104 and Its Identification in Phage Type DT120 and Serovar Agona

2001 ◽  
Vol 183 (19) ◽  
pp. 5725-5732 ◽  
Author(s):  
David Boyd ◽  
Geoffrey A. Peters ◽  
Axel Cloeckaert ◽  
Karim Sidi Boumedine ◽  
Elisabeth Chaslus-Dancla ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Genomic Island ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Phage Type ◽  
Multidrug Resistant ◽  
Open Reading Frames ◽  
Antibiotic Resistant ◽  
Canadian Isolate ◽  
Significant Homology ◽  
Serovar Typhimurium

ABSTRACT This study describes the characterization of the recently describedSalmonella genomic island 1 (SGI1) (D. A. Boyd, G. A. Peters, L.-K. Ng, and M. R. Mulvey, FEMS Microbiol. Lett. 189:285–291, 2000), which harbors the genes associated with the ACSSuT phenotype in a Canadian isolate of Salmonella enterica serovar Typhimurium DT104. A 43-kb region has been completely sequenced and found to contain 44 predicted open reading frames (ORFs) which comprised ∼87% of the total sequence. Fifteen ORFs did not show any significant homology to known gene sequences. A number of ORFs show significant homology to plasmid-related genes, suggesting, at least in part, a plasmid origin for the SGI1, although some with homology to phage-related genes were identified. The SGI1 was identified in a number of multidrug-resistant DT120 and S. enterica serovar Agona strains with similar antibiotic-resistant phenotypes. The G+C content suggests a potential mosaic structure for the SGI1. Emergence of the SGI1 in serovar Agona strains is discussed.

scholarly journals AcrAB-TolC Directs Efflux-Mediated Multidrug Resistance in Salmonella enterica Serovar Typhimurium DT104

2004 ◽  
Vol 48 (10) ◽  
pp. 3729-3735 ◽  
Author(s):  
Sylvie Baucheron ◽  
Shaun Tyler ◽  
David Boyd ◽  
Michael R. Mulvey ◽  
Elisabeth Chaslus-Dancla ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Salmonella Enterica ◽  
Genomic Island ◽  
Phage Type ◽  
Efflux Pumps ◽  
Multidrug Resistant ◽  
Quinolone Resistance ◽  
Efflux System ◽  
Serovar Typhimurium

ABSTRACT Multidrug-resistant Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) strains harbor a genomic island, called Salmonella genomic island 1 (SGI1), which contains an antibiotic resistance gene cluster conferring resistance to ampicillin, chloramphenicol, florfenicol, streptomycin, sulfonamides, and tetracyclines. They may be additionally resistant to quinolones. Among the antibiotic resistance genes there are two, i.e., floR and tet(G), which code for efflux pumps of the major facilitator superfamily with 12 transmembrane segments that confer resistance to chloramphenicol-florfenicol and the tetracyclines, respectively. In the present study we determined, by constructing acrB and tolC mutants, the role of the AcrAB-TolC multidrug efflux system in the multidrug resistance of several DT104 strains displaying additional quinolone resistance or not displaying quinolone resistance. This study shows that the quinolone resistance and the decreased fluoroquinolone susceptibilities of the strains are highly dependent on the AcrAB-TolC efflux system and that single mutations in the quinolone resistance-determining region of gyrA are of little relevance in mediating this resistance. Overproduction of the AcrAB efflux pump, as determined by Western blotting with an anti-AcrA polyclonal antibody, appeared to be the major mechanism of resistance to quinolones. Moreover, chloramphenicol-florfenicol and tetracycline resistance also appeared to be highly dependent on the presence of AcrAB-TolC, since the introduction of mutations in the respective acrB and tolC genes resulted in a susceptible or intermediate resistance phenotype, according to clinical MIC breakpoints, despite the presence of the FloR and Tet(G) efflux pumps. Resistance to other antibiotics, ampicillin, streptomycin, and sulfonamides, was not affected in the acrB and tolC mutants of DT104 strains harboring SGI1. Therefore, AcrAB-TolC appears to direct efflux-mediated resistance to quinolones, chloramphenicol-florfenicol, and tetracyclines in multidrug-resistant S. enterica serovar Typhimurium DT104 strains.

Importation, Mitigation, and Genomic Epidemiology of Candida auris at a Large Teaching Hospital

2017 ◽  
Vol 39 (1) ◽  
pp. 53-57 ◽  
Author(s):  
Emil P. Lesho ◽  
Melissa Z. Bronstein ◽  
Patrick McGann ◽  
Jason Stam ◽  
Yoon Kwak ◽  
...  
Keyword(s):  
New York ◽  
Teaching Hospital ◽  
Index Case ◽  
Index Patient ◽  
Multidrug Resistant ◽  
Multidisciplinary Teams ◽  
Nucleotide Polymorphisms ◽  
Case Patient ◽  
Candida Auris ◽  
Genomic Epidemiology

OBJECTIVECandida auris (CA) is an emerging multidrug-resistant pathogen associated with increased mortality. The environment may play a role, but transmission dynamics remain poorly understood. We sought to limit environmental and patient CA contamination following a sustained unsuspected exposure.DESIGNQuasi-experimental observation.SETTINGA 528-bed teaching hospital.PATIENTSThe index case patient and 17 collocated ward mates.INTERVENTIONImmediately after confirmation of CA in the bloodstream and urine of a patient admitted 6 days previously, active surveillance, enhanced transmission-based precautions, environmental cleaning with peracetic acid-hydrogen peroxide and ultraviolet light, and patient relocation were undertaken. Pre-existing agreements and foundational relationships among internal multidisciplinary teams and external partners were leveraged to bolster detection and mitigation efforts and to provide genomic epidemiology.RESULTSCandida auris was isolated from 3 of 132 surface samples on days 8, 9, and 15 of ward occupancy, and from no patient samples (0 of 48). Environmental and patient isolates were genetically identical (4–8 single-nucleotide polymorphisms [SNPs]) and most closely related to the 2013 India CA-6684 strain (~200 SNPs), supporting the epidemiological hypothesis that the source of environmental contamination was the index case patient, who probably acquired the South Asian strain from another New York hospital. All isolates contained a mutation associated with azole resistance (K163R) found in the India 2105 VPCI strain but not in CA-6684. The index patient remained colonized until death. No surfaces were CA-positive 1 month later.CONCLUSIONCompared to previous descriptions, CA dissemination was minimal. Immediate access to rapid CA diagnostics facilitates early containment strategies and outbreak investigations.Infect Control Hosp Epidemiol 2018;39:53–57

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