scholarly journals High-Resolution Comparative Genomics of Salmonella Kentucky Aids Source Tracing and Detection of ST198 and ST152 Lineage-Specific Mutations

2021 ◽  
Vol 5 ◽  
Author(s):  
Rachel C. Soltys ◽  
Carson K. Sakomoto ◽  
Hanna N. Oltean ◽  
Jean Guard ◽  
Bradd J. Haley ◽  
...  
Keyword(s):  
Epidemiological Studies ◽  
Metabolic Adaptation ◽  
Nucleotide Polymorphisms ◽  
Global Database ◽  
Source Tracing ◽  
Whole Genomes ◽  
Report Data ◽  
Human Illness ◽  
Human Infections ◽  
Sequence Types

Non-typhoidal Salmonella (NTS) is a major cause of foodborne illness globally. Salmonella Kentucky is a polyphyletic NTS serovar comprised of two predominant multilocus sequence types (STs): ST152 and ST198. Epidemiological studies have revealed that ST152 is most prevalent in US poultry whereas ST198 is more prevalent in international poultry. Interestingly, ST152 is sporadically associated with human illness, whereas ST198 is more commonly associated with human disease. The goal of this study was to develop a better understanding of the epidemiology of ST198 and ST152 in WA State. We compared the antimicrobial resistance phenotypes and genetic relationship, using pulsed-field gel electrophoresis, of 26 clinical strains of S. Kentucky isolated in Washington State between 2004 and 2014, and 140 poultry-associated strains of S. Kentucky mostly recovered from the northwestern USA between 2004 and 2014. We also sequenced whole genomes of representative human clinical and poultry isolates from the northwestern USA. Genome sequences of these isolates were compared with a global database of S. Kentucky genomes representing 400 ST198 and 50 ST152 strains. The results of the phenotypic, genotypic, and case report data on food consumption and travel show that human infections caused by fluoroquinolone-resistant (FluR) S. Kentucky ST198 in WA State originated from outside of North America. In contrast, fluoroquinolone-susceptible (FluS) S. Kentucky ST198 and S. Kentucky ST152 infection have a likely domestic origin, with domestic cattle and poultry being the potential sources. We also identified lineage-specific non-synonymous single nucleotide polymorphisms (SNPs) that distinguish ST198 and ST152. These SNPs may provide good targets for further investigations on lineage-specific traits such as variation in virulence, metabolic adaptation to different environments, and potential for the development of intervention strategies to improve the safety of food.

scholarly journals Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

2014 ◽  
Vol 53 (1) ◽  
pp. 191-200 ◽  
Author(s):  
Walter Demczuk ◽  
Tarah Lynch ◽  
Irene Martin ◽  
Gary Van Domselaar ◽  
Morag Graham ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Large Scale ◽  
Epidemiological Studies ◽  
23S Rrna ◽  
Genome Comparison ◽  
Whole Genome ◽  
Content Type ◽  
Genomic Epidemiology ◽  
High Level ◽  
Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

scholarly journals Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources

Foods ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2454
Author(s):  
Rebecca N. Bland ◽  
Jared D. Johnson ◽  
Joy G. Waite-Cusic ◽  
Alexandra J. Weisberg ◽  
Elizabeth R. Riutta ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Phenotype Screening ◽  
Screening Assays ◽  
Contamination Events ◽  
Sequence Types ◽  
Potential Use

Recent listeriosis outbreaks linked to fresh produce suggest the need to better understand and mitigate L. monocytogenes contamination in packing and processing environments. Using whole genome sequencing (WGS) and phenotype screening assays for sanitizer tolerance, we characterized 48 L. monocytogenes isolates previously recovered from environmental samples in five produce handling facilities. Within the studied population there were 10 sequence types (STs) and 16 cgMLST types (CTs). Pairwise single nucleotide polymorphisms (SNPs) ranged from 0 to 3047 SNPs within a CT, revealing closely and distantly related isolates indicative of both sporadic and continuous contamination events within the facility. Within Facility 1, we identified a closely related cluster (0–2 SNPs) of isolates belonging to clonal complex 37 (CC37; CT9492), with isolates recovered during sampling events 1-year apart and in various locations inside and outside the facility. The accessory genome of these CC37 isolates varied from 94 to 210 genes. Notable genetic elements and mutations amongst the isolates included the bcrABC cassette (2/48), associated with QAC tolerance; mutations in the actA gene on the Listeria pathogenicity island (LIPI) 1 (20/48); presence of LIPI-3 (21/48) and LIPI-4 (23/48). This work highlights the potential use of WGS in tracing the pathogen within a facility and understanding properties of L. monocytogenes in produce settings.

scholarly journals Molecular characterization of Anaplasma phagocytophilum infection in the cervids and feeding ticks from Lithuania

Biologija ◽  
2020 ◽  
Vol 66 (3) ◽  
Author(s):  
Jana Radzijevskaja ◽  
Justina Snegiriovaitė ◽  
Artūras Kibiša ◽  
Irma Ražanskė ◽  
Algimantas Paulauskas
Keyword(s):  
Sequence Analysis ◽  
Anaplasma Phagocytophilum ◽  
Red Deer ◽  
Roe Deer ◽  
Bacterial Pathogen ◽  
Epidemiological Studies ◽  
Msp4 Gene ◽  
Ixodes Ticks ◽  
High Degree ◽  
Sequence Types

Anaplasma phagocytophilum is a bacterial pathogen, which is a major cause of zoonotic disease, anaplasmosis. The main vectors of A. phagocytophilum are ticks of the Ixodes ricinus complex. A. phagocytophilum has a broad geographic distribution and a high degree of biological and clinical diversity. Epidemiological studies in multiple countries have shown that the prevalence of A. phagocytophilum highly depends on the density of ticks and their potential hosts such as the cervids, which are one of the main sources of nutrition for Ixodes ticks. In Lithuania, the cervids are important game animals but their contribution as reservoirs for A. phagocytophilum remains unknown. The objectives of the study were to investigate the prevalence of A. phagocytophilum infections in the cervids and feeding ticks and to characterize the A. phagocytophilum strains obtained from the cervids and ticks based on sequence analysis of msp4 gene. A total of 187 ticks were collected from 44 cervids (roe deer, red deer, and moose) harvested by professional hunters during the hunting seasons of 2010–2013 and 2016–2017 in Lithuania. Blood and spleen samples were collected from 29 animals (27 roe deer and two red deer). A. phagocytophilum DNA was identified in ten (37.04%) of the 27 roe deer. The overall prevalence of A. phagocytophilum in I. ricinus and D. reticulatus ticks was 39.3% (70/178) and 22.2% (2/9) respectively. The sequence analysis of the msp4 gene of A. phagocytophilum revealed nine different sequence types: five msp4 sequence types were detected in ticks and seven in roe deer.

scholarly journals Population Structure and Antimicrobial Resistance of Canine UropathogenicEscherichia coli

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Tessa E. LeCuyer ◽  
Barbara A. Byrne ◽  
Joshua B. Daniels ◽  
Dubraska V. Diaz-Campos ◽  
G. Kenitra Hammac ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Companion Animals ◽  
Sequence Type ◽  
Content Type ◽  
E Coli ◽  
Extraintestinal Disease ◽  
Human Infections ◽  
Sequence Types

ABSTRACTEscherichia coliis the most common cause of human and canine urinary tract infection (UTI). Clonal groups, often with high levels of antimicrobial resistance, are a major component of theE. colipopulation that causes human UTI. While little is known about the population structure ofE. colithat causes UTI in dogs, there is evidence that dogs and humans can share fecal strains ofE. coliand that human-associated strains can cause disease in dogs. In order to better characterize theE. colistrains that cause canine UTI, we analyzed 295E. coliisolates obtained from canine urine samples from five veterinary diagnostic laboratories and analyzed their multilocus sequence types, phenotypic and genotypic antimicrobial resistance profiles, and virulence-associated gene repertoires. Sequence type 372 (ST372), an infrequent human pathogen, was the predominant sequence type in dogs at all locations. Extended-spectrum β-lactamase-producing isolates withblaCTX-Mgenes were uncommon in canine isolates but when present were often associated with sequence types that have been described in human infections. This provides support for occasional cross-host-species sharing of strains that cause extraintestinal disease and highlights the importance of understanding the role of companion animals in the overall transmission patterns of extraintestinal pathogenicE. coli.

scholarly journals Two cases of septic shock with different outcomes caused by non-O1/non-O139 Vibrio cholerae isolates

2020 ◽  
Vol 48 (6) ◽  
pp. 030006052093345
Author(s):  
Jie Chen ◽  
Jian Huang ◽  
Meirong Huang ◽  
Zehui Chen ◽  
Anlin Chen ◽  
...  
Keyword(s):  
Septic Shock ◽  
Vibrio Cholerae ◽  
High Mortality ◽  
Virulence Genes ◽  
Antibiotic Sensitivity ◽  
Sporadic Cases ◽  
Human Infections ◽  
Sequence Types

In recent decades, increasing numbers of human infections have been linked to non-O1/non-O139 Vibrio cholerae. Septicemia resulting from non-O1/non-O139 V. cholerae infection is rare but has high mortality. The pathogenesis of non-O1/non-O139 V. cholerae septicemia is poorly understood. Here, we report two sporadic cases of septicemia following non-O1/non-O139 V. cholerae infection from an inland area of China. Patient 1 died rapidly within 24 hours, while patient 2 gradually recovered from septic shock. To explore the reasons for these divergent outcomes, we compared the two cases, tested the antibiotic sensitivity of the two isolates, and investigated their virulence genes and sequence types.

Development of a diagnostic assay for race differentiation of Podosphaera macularis

Plant Disease ◽  
2020 ◽  
Author(s):  
Mary Block ◽  
Brian Knaus ◽  
Michele S. Wiseman ◽  
Niklaus J. Grünwald ◽  
David H. Gent
Keyword(s):  
Powdery Mildew ◽  
Pacific Northwest ◽  
The United States ◽  
Epidemiological Studies ◽  
Locked Nucleic Acid ◽  
Nucleotide Polymorphisms ◽  
Practical Applications ◽  
Powdery Mildew Fungi ◽  
Perfect Discrimination ◽  
Podosphaera Macularis

Hop powdery mildew (caused by Podosphaera macularis) was confirmed in the Pacific Northwest in 1996. Before 2012, the most common race of P. macularis was able to infect plants that possessed powdery mildew resistance based on the R-genes Rb, R3, and R5. After 2012, two additional races of P. macularis were discovered that can overcome the resistance gene R6 and the partial resistance found in the cultivar Cascade. These three races now occur throughout the region, which can complicate management and research efforts because of uncertainty on which race(s) may be present in the region and able to infect susceptible hop genotypes. Current methods for determining the races of P. macularis are labor intensive, costly, and typically require more than 14 days to obtain results. We sought to develop a molecular assay to differentiate races of the fungus possessing virulence on plants with R6, referred to as V6-virulent, from other races. The transcriptomes of 46 isolates of P. macularis were sequenced to identify loci and variants unique to V6-isolates. Fourteen primer pairs were designed for 10 candidate loci that contained single nucleotide polymorphisms (SNP) and short insertion-deletion polymorphisms. Two differentially-labeled locked nucleic acid probes were designed for a contig that contained a conserved SNP associated with V6-virulence. The resulting duplexed real-time PCR assay was validated against 46 V6 and 54 non-V6 P. macularis isolates collected from the United States and Europe. The assay had perfect discrimination of V6-virulence among isolates of P. macularis originating from the western U.S. but failed to predict V6-virulence in three isolates collected from Europe. The specificity of the assay was tested with different species of powdery mildew fungi and other microorganisms associated with hop. Weak non-specific amplification occurred with powdery mildew fungi collected from Vitis vinifera, Fragaria sp., and Zinnia sp.; however, non-specification amplification is not a concern when differentiating pathogen race from colonies on hop. The assay has practical applications in hop breeding, epidemiological studies, and other settings where rapid confirmation of pathogen race is needed.

Association study of CRP gene polymorphisms with serum CRP level and cardiovascular risk in the NHLBI Family Heart Study

2006 ◽  
Vol 291 (6) ◽  
pp. H2752-H2757 ◽  
Author(s):  
Qingwei Wang ◽  
Steven C. Hunt ◽  
Qin Xu ◽  
Yuqing E. Chen ◽  
Michael A. Province ◽  
...  
Keyword(s):  
Cardiovascular Risk ◽  
Intima Media Thickness ◽  
Epidemiological Studies ◽  
Study Cohort ◽  
Strong Impact ◽  
Snp Analysis ◽  
Nucleotide Polymorphisms ◽  
Family Heart Study ◽  
Heart Study ◽  
Nhlbi Family Heart Study

Recent epidemiological studies have indicated that baseline C-reactive protein (CRP) levels may have value in prediction of cardiovascular risk. Using six tag single-nucleotide polymorphisms (SNPs) selected from our complete list of SNPs on the CRP gene, we investigated the association of CRP genotypes with plasma CRP levels and cardiovascular risk in the National Heart, Lung, and Blood Institute (NHLBI) Family Heart Study cohort (1,296 Caucasians, 48.5% male, 54.7 ± 12.8 yr old). There was a significant trend toward association of CRP haplotypes with CRP levels ( P = 0.045). SNP analysis indicated a highly significant association of SNP −757 (rs3093059, P = 0.0004) and SNP −286 (rs3091244, P = 0.0065) and a borderline association of SNP −7180 (rs1341665, P = 0.06) with CRP levels. Neither CRP haplotypes nor individual SNP genotypes were associated with intima-media thickness of the common carotid or internal carotid artery or the bifurcation of the carotid arteries. These results indicated a strong impact of local SNPs of the CRP gene on plasma CRP levels, but there was no direct evidence that these genetically controlled CRP elevations by local CRP SNPs contributed to cardiovascular disease phenotypes.

scholarly journals Mating Type Locus-Specific Polymerase Chain Reaction Markers for Differentiation of Pyrenophora teres f. teres and P. teres f. maculata, the Causal Agents of Barley Net Blotch

2010 ◽  
Vol 100 (12) ◽  
pp. 1298-1306 ◽  
Author(s):  
Shunwen Lu ◽  
Gregory J. Platz ◽  
Michael C. Edwards ◽  
Timothy L. Friesen
Keyword(s):  
Polymerase Chain Reaction ◽  
Mating Type ◽  
Pathogen Detection ◽  
Epidemiological Studies ◽  
Pyrenophora Teres ◽  
Nucleotide Polymorphisms ◽  
Net Blotch ◽  
Chain Reaction ◽  
Type Locus ◽  
Polymerase Chain

Fourteen single nucleotide polymorphisms (SNPs) were identified at the mating type (MAT) loci of Pyrenophora teres f. teres (Ptt), which causes net form (NF) net blotch, and P. teres f. maculata (Ptm), which causes spot form (SF) net blotch of barley. MAT-specific SNP primers were developed for polymerase chain reaction (PCR) and the two forms were differentiated by distinct PCR products: PttMAT1-1 (1,143 bp) and PttMAT1-2 (1,421 bp) for NF MAT1-1 and MAT1-2 isolates; PtmMAT1-1 (194 bp) and PtmMAT1-2 (939 bp) for SF MAT1-1 and MAT1-2 isolates, respectively. Specificity was validated using 37 NF and 17 SF isolates collected from different geographic regions. Both MAT1-1 and MAT1-2 SNP primers retained respective specificity when used in duplex PCR. No cross-reactions were observed with DNA from P. graminea, P. tritici-repentis, or other ascomycetes, or barley. Single or mixed infections of the two different forms were also differentiated. This study provides the first evidence that the limited SNPs at the MAT locus are sufficient for distinguishing closely related heterothallic ascomycetes at subspecies levels, thus allowing pathogenicity and mating type characteristics of the fungus to be determined simultaneously. Methods presented will facilitate pathogen detection, disease management, and epidemiological studies.

scholarly journals Whole genome sequencing reveals extensive community-level transmission of group AStreptococcusin remote communities

2016 ◽  
Vol 144 (9) ◽  
pp. 1991-1998 ◽  
Author(s):  
A. C. BOWEN ◽  
T. HARRIS ◽  
D. C. HOLT ◽  
P. M. GIFFARD ◽  
J. R. CARAPETIS ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Remote Communities ◽  
Single Nucleotide ◽  
Indigenous Children ◽  
Primary Driver ◽  
Group A ◽  
Sequence Types

SUMMARYImpetigo is common in remote Indigenous children of northern Australia, with the primary driver in this context beingStreptococcus pyogenes[or group AStreptococcus(GAS)]. To reduce the high burden of impetigo, the transmission dynamics of GAS must be more clearly elucidated. We performed whole genome sequencing on 31 GAS isolates collected in a single community from children in 11 households with ⩾2 GAS-infected children. We aimed to determine whether transmission was occurring principally within households or across the community. The 31 isolates were represented by nine multilocus sequence types and isolates within each sequence type differed from one another by only 0–3 single nucleotide polymorphisms. There was evidence of extensive transmission both within households and across the community. Our findings suggest that strategies to reduce the burden of impetigo in this setting will need to extend beyond individual households, and incorporate multi-faceted, community-wide approaches.

scholarly journals Protocol for Specific Isolation of Virulent Strains of Vibrio vulnificus Serovar E (Biotype 2) from Environmental Samples

2004 ◽  
Vol 70 (12) ◽  
pp. 7024-7032 ◽  
Author(s):  
Eva Sanjuán ◽  
Carmen Amaro
Keyword(s):  
Environmental Samples ◽  
Vibrio Vulnificus ◽  
Growth Yield ◽  
Field Studies ◽  
Epidemiological Studies ◽  
Alkaline Peptone Water ◽  
Virulent Strains ◽  
Peptone Water ◽  
Human Sera ◽  
Human Infections

ABSTRACT The eel pathogen Vibrio vulnificus biotype 2 comprises at least three serovars, with serovar E being the only one involved in both epizootics of eel vibriosis and sporadic cases of human infections. The virulent strains of this serovar (VSE) have only been recovered from clinical (mainly eel tissue) sources. The main objective of this work was to design and validate a new protocol for VSE-specific isolation from environmental samples. The key element of the new protocol is the broth used for the first step (saline eel serum broth [SEB]), which contains eel serum as a nutritive and selective component. This approach takes advantage of the ability of VSE cells to grow in eel serum and thus to separate themselves from the pool of competitors. The growth yield in SEB after 8 h of incubation was 1,000 times higher for VSE strains than for their putative competitors (including biotype 1 strains of the species). The selective and differential agar Vibrio vulnificus medium (VVM) was selected from five selective media for the second step because it gave the highest plating efficiency not only for the VSE group but also for other V. vulnificus groups, including biotype 3. The entire protocol was validated by field studies, with alkaline peptone water plus VVM as a control. V. vulnificus was isolated by both protocols, but serovar E was only recovered by the new method described here. All selected serovar E isolates were identified as VSE since they were virulent for both eels and iron-overloaded mice and resisted the bactericidal action of eel and iron-overloaded human sera. In conclusion, this new protocol is a suitable method for the isolation of VSE strains from environmental samples and is recommended for epidemiological studies of the pathogenic serovar E.

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