scholarly journals Melioidosis fatalities in captive slender-tailed meerkats (Suricata suricatta): combining epidemiology, pathology and whole-genome sequencing supports variable mechanisms of transmission with one health implications

2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Audrey Rachlin ◽  
Cathy Shilton ◽  
Jessica R. Webb ◽  
Mark Mayo ◽  
Mirjam Kaestli ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
One Health ◽  
Whole Genome ◽  
Direct Transmission ◽  
Health Implications ◽  
Suricata Suricatta ◽  
Environmental Bacterium ◽  
Direct Exposure ◽  
Genome Level

Abstract Background Melioidosis is a tropical infectious disease which is being increasingly recognised throughout the globe. Infection occurs in humans and animals, typically through direct exposure to soil or water containing the environmental bacterium Burkholderia pseudomallei. Case clusters of melioidosis have been described in humans following severe weather events and in exotic animals imported into melioidosis endemic zones. Direct transmission of B. pseudomallei between animals and/or humans has been documented but is considered extremely rare. Between March 2015 and October 2016 eight fatal cases of melioidosis were reported in slender-tailed meerkats (Suricata suricatta) on display at a Wildlife Park in Northern Australia. To further investigate the melioidosis case cluster we sampled the meerkat enclosure and adjacent park areas and performed whole-genome sequencing (WGS) on all culture-positive B. pseudomallei environmental and clinical isolates. Results WGS confirmed that the fatalities were caused by two different B. pseudomallei sequence types (STs) but that seven of the meerkat isolates were highly similar on the whole-genome level. Used concurrently with detailed pathology data, our results demonstrate that the seven cases originated from a single original source, but routes of infection varied amongst meerkats belonging to the clonal outbreak cluster. Moreover, in some instances direct transmission may have transpired through wounds inflicted while fighting. Conclusions Collectively, this study supports the use of high-resolution WGS to enhance epidemiological investigations into transmission modalities and pathogenesis of melioidosis, especially in the instance of a possible clonal outbreak scenario in exotic zoological collections. Such findings from an animal outbreak have important One Health implications.

scholarly journals 740. Elucidation of the Mode of Clostridioides difficile Transmission Based on One Health Approach

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S468-S468
Author(s):  
Sadako Yoshizawa ◽  
Tomoka Sawa ◽  
Kohji Komori ◽  
Masakazu Sasaki ◽  
Nobuaki Mori ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
One Health ◽  
Companion Animals ◽  
Living Environment ◽  
Animal Origin ◽  
Toxin Gene ◽  
Whole Genome ◽  
Mlst Analysis ◽  
Clostridioides Difficile

Abstract Background Community-onset Clostridioides difficile (C. difficile) infection (CACDI) has been increasing in recent years. To explore the transmission route of CACDI, we performed the whole-genome sequencing of C. difficile isolated from CACDI patients and compared it to the isolates from livestock, companion animals, and soil. Methods From October 2020 until April 2021, fecal specimens of cattle, poultry, swine, felines, canines, CACDI patients, their families, and soil from the CACDI patients' living environment were applied for isolation of C.difficile. Whole-genome sequencing of C. difficile was performed on the MiSeq system (Illumina). Using the draft genome obtained from these analyses, the house-keeping gene (tpi), MLST, toxin genes (tcdA, tcdB, cdtA, cdtB), and resistance genes (gyrA, gyrB, rpoA, rpoB, rpoC) were comprehensively analyzed. Results As of March 31, 2021, 275 specimens were collected. Forty-five fecal specimens of companion animal origin (23 feline and 22 canines) were collected and the positive rate of C.difficile was 28.9% (2 felines, 11 canines). In MLST analysis, ST 15 (4 strains), ST 26 (2 strains), ST 42, ST 3, ST 28, ST 100, and ST 185 were detected in canines, and ST 203 and ST 297 strains were detected in felines. Samples of livestock origin were collected from 135 cattle, 41 poultries, and 20 swine. The detection rate in cattle was 11%, toxin-gene positivity was 60%. MLST analysis of 9 strains revealed ST 11 (5 strains), ST 2, ST 15, ST 58, and ST 101. No isolates were found from poultry or swine. Patient-derived strains of CACDI were collected from 14 patients at 2 sites. MLST analysis revealed ST42, ST37, ST100, and ST203(two isolates, respectively), ST 224, ST 81, ST 28, and ST 47. 2 isolates were unclassifiable. One case was a healthy 1-year-old girl, whose family revealed no isolation of C.difficile. Impressively, the soil in the parks (A and B) related to the child detected C.difficile from 4/4 samples (toxin-gene positivity; 75%) in Park A and 1/4 samples (toxin-gene positive) in Park B. MLST analysis demonstrated ST 42, the same as that in the affected child and core-genome single-nucleotide polymorphisms(SNPs) analysis suggested closely related strain. Conclusion Our results suggest one health approach is fundamental to prevent the transmission of C.difficile. Disclosures All Authors: No reported disclosures

scholarly journals Corrigendum: Whole Genome Sequencing: Bridging One-Health Surveillance of Foodborne Diseases

2019 ◽  
Vol 7 ◽  
Author(s):  
Peter Gerner-Smidt ◽  
John Besser ◽  
Jeniffer Concepción-Acevedo ◽  
Jason P. Folster ◽  
Jasmine Huffman ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
One Health ◽  
Health Surveillance ◽  
Foodborne Diseases ◽  
Whole Genome

Reactive Infection Control Strategy for Control of New Delhi Metallo-β-Lactamase (NDM)-Producing Enterobacteriaceae Analyzed Using Whole-Genome Sequencing: Hits and Misses

2016 ◽  
Vol 37 (8) ◽  
pp. 987-990 ◽  
Author(s):  
Kalisvar Marimuthu ◽  
Oon Tek Ng ◽  
Wei Xin Khong ◽  
Eryu Xia ◽  
Yik-Ying Teo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Infection Control ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Control Strategy ◽  
Infect Control Hosp ◽  
The Other ◽  
New Delhi ◽  
Whole Genome ◽  
Direct Transmission

Genetically distinct isolates of New Delhi metallo-β-lactamase (NDM)–producing Enterobacteriaceae were identified from the clinical cultures of 6 patients. Screening of shared-ward contacts identified 2 additional NDM-positive patients. Phylogenetic analysis proved that 1 contact was a direct transmission while the other was unrelated to the index, suggesting hidden routes of transmission.Infect Control Hosp Epidemiol 2016;37:987–990

scholarly journals Tracing the environmental footprint of theBurkholderia pseudomalleilipopolysaccharide genotypes in the tropical “Top End” of the Northern Territory, Australia

2019 ◽  
Author(s):  
Jessica R. Webb ◽  
Audrey Rachlin ◽  
Vanessa Rigas ◽  
Derek S. Sarovich ◽  
Erin P. Price ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Burkholderia Pseudomallei ◽  
Northern Territory ◽  
Whole Genome ◽  
Endemic Region ◽  
Tropical Regions ◽  
Motility Factor ◽  
Environmental Bacterium

AbstractThe Tier 1 select agentBurkholderia pseudomalleiis an environmental bacterium that causes melioidosis, a high mortality disease. Variably present genetic markers used to elucidate strain origin, relatedness and virulence inB. pseudomalleiinclude theBurkholderiaintracellular motility factor A (bimA) and filamentous hemagglutinin 3 (fhaB3) gene variants. Three lipopolysaccharide (LPS) O-antigen types inB. pseudomalleihave been described, which vary in proportion between Australian and Asian isolates. However, it remains unknown if these LPS types can be used as genetic markers for geospatial analysis within a contiguous melioidosis-endemic region. Using a combination of whole-genome sequencing (WGS), statistical analysis and geographical mapping, we examined if the LPS types can be used as geographical markers in the Northern Territory, Australia. The clinical isolates revealed that LPS A prevalence was highest in the Darwin and surrounds (n = 660; 96% being LPS A and 4% LPS B) and LPS B in the Katherine and Katherine remote and East Arnhem regions (n = 79; 60% being LPS A and 40% LPS B). Bivariate logistics regression of 999 clinicalB. pseudomalleiisolates revealed that the odds of getting a clinical isolate with LPS B was highest in East Arnhem in comparison to Darwin and surrounds (OR 19.5, 95% CI 9.1 – 42.0;p<0.001). This geospatial correlation was subsequently confirmed by geographically mapping the LPS type from 340 environmental Top End strains. We also found that in the Top End, the minoritybimAgenotypebimABmhas a similar remote region geographical footprint to that of LPS B. In addition, correlation of LPS type with multi-locus sequence typing (MLST) was strong, and where multiple LPS types were identified within a single sequence type, WGS confirmed homoplasy of the MLST loci. The clinical, sero-diagnostic and vaccine implications of geographically-basedB. pseudomalleiLPS types, and their relationships to regional and global dispersal of melioidosis, require global collaborations with further analysis of larger clinically and geospatially-linked datasets.Author SummaryBurkholderia pseudomalleiis a pathogenic soil bacterium that causes the disease melioidosis, which occurs in many tropical regions globally and in recent years has emerged in non-tropical regions. Melioidosis has been predicted to affect 165,000 people every year resulting in an estimated 89,000 deaths. Person to person transmission is rare with most cases linked to exposure to the bacterium from the environment. The genetic background ofB. pseudomalleihas been well studied and variably present genes have been linked to distinct melioidosis disease states and geographic regions, however we still need a stronger understanding of the association of genes with geography. Three lipopolysaccharide types exist inB. pseudomalleiand the prevalence of the lipopolysaccharide genes vary between melioidosis endemic regions, but it is unknown if the lipopolysaccharide genes can be used as geographical markers in a single melioidosis-endemic region. In this study, we used a combination of whole-genome sequencing, statistics and geographical mapping to elucidate if the three lipopolysaccharide genes can be used as geographical markers within the Northern Territory, Australia. We show that the three LPS types have distinct but overlapping geographical footprints within a single melioidosis region and can be used as geographic markers alongside a number of other important variably presentB. pseudomalleigenes.

scholarly journals Comprehensive Characterization of Transgene Integration in a Similar Intragenesis Rice Event Using Paired-end Whole-genome Sequencing Approach

2021 ◽  
Author(s):  
Wenting Xu ◽  
Hanwen Zhang ◽  
Yuchen Zhang ◽  
Rong Li ◽  
Litao Yang
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Rice Chromosome ◽  
Whole Genome ◽  
Transgene Integration ◽  
Gm Rice ◽  
Genome Level ◽  
Comprehensive Characterization

Abstract Efficient, accurate molecular characterization of genetically modified (GM) organisms is challenging, especially for novel transgenic products of cisgenesis/intragenesis transferred with genes/elements of recipient species. Herein, GM rice event G281, involving transfer with native promoters and an RNA interference (RNAi) expression cassette in a process similar to intragenesis, was subjected to molecular characterization using paired-end whole genome sequencing (PE-WGS). The results showed that transgenes integrated at rice chromosome 3 locus 16,439,674 included a 36 bp deletion of rice genomic DNA, and the whole integration contained two copies of the complete transfer DNA (T-DNA) in a head-to-head arrangement. No unintended insertion or backbone sequence of the transformed plasmid were observed at the whole genome level. Molecular characterization of the G281 event will assist risk assessment and application for a commercial license. Additionally, the findings demonstrate the applicability of PE-WGS for molecular characterization of cisgenesis/intragenesis crops.

scholarly journals Whole Genome Sequencing: Bridging One-Health Surveillance of Foodborne Diseases

2019 ◽  
Vol 7 ◽  
Author(s):  
Peter Gerner-Smidt ◽  
John Besser ◽  
Jeniffer Concepción-Acevedo ◽  
Jason P. Folster ◽  
Jasmine Huffman ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
One Health ◽  
Health Surveillance ◽  
Foodborne Diseases ◽  
Whole Genome

scholarly journals Molecular Characteristics of Extraintestinal Pathogenic E. coli (ExPEC), Uropathogenic E. coli (UPEC), and Multidrug Resistant E. coli Isolated from Healthy Dogs in Spain. Whole Genome Sequencing of Canine ST372 Isolates and Comparison with Human Isolates Causing Extraintestinal Infections

2020 ◽  
Vol 8 (11) ◽  
pp. 1712
Author(s):  
Saskia-Camille Flament-Simon ◽  
María de Toro ◽  
Vanesa García ◽  
Jesús E. Blanco ◽  
Miguel Blanco ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
One Health ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
E Coli ◽  
Healthy Dogs ◽  
The One

Under a one health perspective and the worldwide antimicrobial resistance concern, we investigated extraintestinal pathogenic Escherichia coli (ExPEC), uropathogenic E. coli (UPEC), and multidrug resistant (MDR) E. coli from 197 isolates recovered from healthy dogs in Spain between 2013 and 2017. A total of 91 (46.2%) isolates were molecularly classified as ExPEC and/or UPEC, including 50 clones, among which (i) four clones were dominant (B2-CH14-180-ST127, B2-CH52-14-ST141, B2-CH103-9-ST372 and F-CH4-58-ST648) and (ii) 15 had been identified among isolates causing extraintestinal infections in Spanish and French humans in 2015 and 2016. A total of 28 (14.2%) isolates were classified as MDR, associated with B1, D, and E phylogroups, and included 24 clones, of which eight had also been identified among the human clinical isolates. We selected 23 ST372 strains, 21 from healthy dogs, and two from human clinical isolates for whole genome sequencing and built an SNP-tree with these 23 genomes and 174 genomes (128 from canine strains and 46 from human strains) obtained from public databases. These 197 genomes were segregated into six clusters. Cluster 1 comprised 74.6% of the strain genomes, mostly composed of canine strain genomes (p < 0.00001). Clusters 4 and 6 also included canine strain genomes, while clusters 2, 3, and 5 were significantly associated with human strain genomes. Finding several common clones and clone-related serotypes in dogs and humans suggests a potentially bidirectional clone transfer that argues for the one health perspective.

scholarly journals Molecular Characteristics of Extraintestinal Pathogenic E. coli (ExPEC), Uropathogenic E. coli (UPEC), and Multidrug Resistant E. coli Isolated from Healthy Dogs in Spain. Whole Genome Sequencing of Canine ST372 Isolates and Comparison with Human Isolates

2020 ◽  
Author(s):  
Saskia-Camille Flament-Simon ◽  
María de Toro ◽  
Vanesa García ◽  
Jesús Eulogio Blanco ◽  
Miguel Blanco ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
One Health ◽  
Multidrug Resistant ◽  
Molecular Characteristics ◽  
Zoonotic Potential ◽  
Whole Genome ◽  
E Coli ◽  
Pathogenic Escherichia Coli ◽  
Healthy Dogs

Under one-health perspective and the worldwide antimicrobial resistance concern, we investigate extraintestinal pathogenic Escherichia coli (ExPEC), uropathogenic E. coli (UPEC), and multidrug resistant (MDR) E. coli from 197 isolates recovered from healthy dogs in Spain between 2013 and 2017. Ninety-one (46.2%) isolates were classified as ExPEC and/or UPEC including 50 clones, among which (i) four clones were dominant (B2-CH14-180-ST127, B2-CH52-14-ST141, B2-CH103-9-ST372 and F-CH4-58-ST64815) and (ii) 15 had been shown to be displayed by previously published isolates causing extraintestinal infections in humans. Twenty-eight (14.2%) isolates were classified as MDR, associated with B1, D and E phylogroups and included 24 clones, of which eight had also been identified among human isolates causing infections. We selected 23 ST372 strains, 21 healthy dogs faecal isolates and two human clinical isolates for whole genome sequencing and built a SNP-tree with these 23 genomes and 174 genomes (128 from canine strains and 46 from human strains) obtained from public databases. The analysis of these 197 genomes allowed to identify six clusters. Cluster 1 comprised 74.6% of the strain genomes that were mostly composed of canine strain genomes (P &amp;lt; 0.00001). Clusters 4 and 6 also included canine strain genomes, while clusters 2, 3 and 5 were significantly associated with human strain genomes. All these findings suggest that dogs are reservoirs of ExPEC, UPEC and MDR E. coli isolates with zoonotic potential.

scholarly journals Outbreak of invasive wound mucormycosis in a burn unit due to multiple strains of Mucor circinelloides f. circinelloides resolved by whole genome sequencing

2017 ◽  
Author(s):  
Dea Garcia-Hermoso ◽  
Alexis Criscuolo ◽  
Soo chan Lee ◽  
Matthieu Legrand ◽  
Marc Chaouat ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Mucor Circinelloides ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Direct Transmission ◽  
Burn Unit ◽  
Environmental Reservoir ◽  
Multiple Strains

AbstractMucorales are ubiquitous environmental molds responsible for mucormycosis in diabetic, immunocompromised, and severely burned patients. Small outbreaks of invasive wound mucormycosis (IWM) have already been reported in burn units without extensive microbiological investigations. We faced an outbreak of IWM in our center and investigated the clinical isolates with whole genome sequencing (WGS) analysis.We analyzed M. circinelloides isolates from patients in our burn unit (BU1) together with non-outbreak isolates from burn unit 2 (BU2, Paris area) and from France over a two-year period (2013-2015). For each isolate, WGS and a de novo genome assembly was performed from read data extracted from the aligned contig sequences of the reference genome (1006PhL).A total of 21 isolates were sequenced including 14 isolates from six BU1 patients. Phylogenetic classification showed that the clinical isolates clustered in four highly divergent clades. Clade1 contained at least one of the strains from the six epidemiologically-linked BU1 patients. The clinical isolates seemed specific to each patient. Two patients were infected with more than two strains from different clades suggesting that an environmental reservoir of clonally unrelated isolates was the source of contamination. Only two patients shared one strain in BU1, suggesting direct transmission or contamination with the same environmental source.WGS coupled with precise epidemiological data and analysis of several isolates per patients revealed in our study a complex situation with both potential cross-transmission and multiple contaminations with a heterogeneous pool of strains from a cryptic environmental reservoir.ImportanceInvasive wound mucormycosis (IWM) is a severe infection due to the environmental molds belonging to the order Mucorales. Severely burned patients are particularly at risk for IWM. Here, we used Whole Genome Sequencing (WGS) analysis to resolve an outbreak of IWM due to Mucor circinelloides that occurred in our hospital (BU1). We sequenced 21 clinical isolates, including 14 from BU1 and 7 unrelated isolates, and compared them to the reference genome (1006PhL). This analysis revealed that the outbreak was mainly due to multiple strains that seemed patient-specific, suggesting that the patients were more likely infected from a pool of diverse strains from the environment rather than from direct transmission between the patients. This study revealed the complexity of a Mucorales outbreak in the settings of IWM in burn patients, which has been highlighted based on whole genome sequencing and careful sampling.

Sign in / Sign up

Export Citation Format

Share Document