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 Whole Genome Sequencing and Antimicrobial Resistance of Staphylococcus aureus from Surgical Site Infections in Ghana

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 196
Author(s):  
Beverly Egyir ◽  
Jeannette Bentum ◽  
Naiki Attram ◽  
Anne Fox ◽  
Noah Obeng-Nkrumah ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Meca Gene ◽  
Surgical Site Infections ◽  
Illumina Miseq ◽  
Multi Drug Resistance ◽  
Toxin Gene ◽  
Whole Genome ◽  
Flight Mass Spectrometry

Staphylococcus aureus (S. aureus) is a common cause of surgical site infections (SSIs) globally. Data on the occurrence of methicillin-susceptible S. aureus (MSSA) as well as methicillin-resistant S. aureus (MRSA) among patients with surgical site infections (SSIs) in sub-Saharan African are scarce. We characterized S. aureus from SSIs in Ghana using molecular methods and antimicrobial susceptibility testing (AST). Wound swabs or aspirate samples were collected from subjects with SSIs. S. aureus was identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF-MS); AST was performed by Kirby-Bauer disk diffusion, and results were interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guideline. Detection of spa, mecA, and pvl genes was performed by polymerase chain reaction (PCR). Whole-genome sequencing (WGS) was done using the Illumina MiSeq platform. Samples were collected from 112 subjects, with 13 S. aureus isolates recovered. Of these, 92% were sensitive to co-trimoxazole, 77% to clindamycin, and 54% to erythromycin. Multi-drug resistance was detected in 5 (38%) isolates. The four mecA gene-positive MRSA isolates detected belonged to ST152 (n = 3) and ST5 (n = 1). In total, 62% of the isolates were positive for the Panton-Valentine leukocidin (pvl) toxin gene. This study reports, for the first time, a pvl-positive ST152-t355 MRSA clone from SSIs in Ghana. The occurrence of multi-drug-resistant S. aureus epidemic clones suggests that continuous surveillance is required to monitor the spread and resistance trends of S. aureus in hospital settings in the country.

scholarly journals Clinical Characteristics of Patients and Whole Genome Sequencing-Based Surveillance of Escherichia coli Community-Onset Bloodstream Infections at a Non-tertiary Hospital in CHINA

2021 ◽  
Vol 12 ◽  
Author(s):  
Fenghong Chen ◽  
Tao Lv ◽  
Yupeng Xiao ◽  
Aizhi Chen ◽  
Yonghong Xiao ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Mortality Rate ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Agents ◽  
Bloodstream Infections ◽  
Tertiary Hospital ◽  
Living Environment ◽  
Whole Genome ◽  
Community Onset

Background:Escherichia coli is the most common pathogens in patients with community-onset blood stream infections (COBSI). Knowledge of the epidemiology of this disease is crucial to improve allocation of health resources, formulate isolation strategies that prevent transmission, and guide empirical antibiotic therapy.Methods: This retrospective observational study examined patients with E. coli COBSI (EC-COBSI) at a non-tertiary hospital in China. Whole-genome sequencing and analysis of the isolates was performed. The relationships of clinical variables with antimicrobial resistance and the genetic background of the isolates were examined.Results: There were 148 isolates in patients with EC-COBSI. All isolates were susceptible to ceftazidime/avibactam, carbapenems, and tigecycline; 35.1% were positive for extended spectrum β-lactamase (ESBL+); and blaCTX–M–14 was the most common ESBL gene. Patients with ESBL- isolates were more likely to receive appropriate empiric treatment than those with ESBL+ isolates (61.5% vs. 91.4%, p < 0.001), but these two groups had similar mortality rates. The overall 30-day mortality rate was 9.5%. Phylogenetic analysis showed that the isolates were diverse, and that the main sequence types (STs) were ST95, ST131, and ST69. Intra-abdominal infection was the primary source of disease, and isolates from these patients had lower frequencies of virulence genes.Conclusion: The mortality rate of patients with EC-COBSI was unrelated to ESBL status of the isolates. Most isolates had low resistance to most of the tested antimicrobial agents. The isolates were diverse, and multiple strains were related. Prevention and control of EC-COBSI should target prevention of patient colonization and the living environment.

scholarly journals Enterobacter cloacae Complex Sequence Type 171 Isolates Expressing KPC-4 Carbapenemase Recovered from Canine Patients in Ohio

2018 ◽  
Vol 62 (12) ◽  
Author(s):  
Joshua B. Daniels ◽  
Liang Chen ◽  
Susan V. Grooters ◽  
Dixie F. Mollenkopf ◽  
Dimitria A. Mathys ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Companion Animals ◽  
Enterobacter Cloacae ◽  
Sequence Type ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Content Type ◽  
Complex Sequence ◽  
Enterobacter Cloacae Complex

ABSTRACT Companion animals are likely relevant in the transmission of antimicrobial-resistant bacteria. Enterobacter xiangfangensis sequence type 171 (ST171), a clone that has been implicated in clusters of infections in humans, was isolated from two dogs with clinical disease in Ohio. The canine isolates contained IncHI2 plasmids encoding blaKPC-4. Whole-genome sequencing was used to put the canine isolates in phylogenetic context with available human ST171 sequences, as well as to characterize their blaKPC-4 plasmids.

scholarly journals Are Many Patients Diagnosed With Healthcare-associated Clostridioides difficile Infections Colonized With the Infecting Strain on Admission?

2019 ◽  
Vol 69 (10) ◽  
pp. 1801-1804 ◽  
Author(s):  
Melany Gonzalez-Orta ◽  
Carlos Saldana ◽  
Yilen Ng-Wong ◽  
Jennifer Cadnum ◽  
Annette Jencson ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acute Care ◽  
Genome Sequencing ◽  
Acute Care Hospital ◽  
Whole Genome ◽  
Care Hospital ◽  
Clostridioides Difficile ◽  
Healthcare Associated

Abstract In a cohort of 480 patients admitted to an acute care hospital, 68 (14%) had positive perirectal cultures for toxigenic Clostridioides difficile on admission. Of the 11 patients (2%) diagnosed with healthcare-associated C. difficile infections, 3 (27%) had genetically related admission and infection isolates, based on whole-genome sequencing.

scholarly journals Assessing the Genetic Diversity of Austrian Corynebacterium diphtheriae Clinical Isolates, 2011-2019

2020 ◽  
Author(s):  
Justine Schaeffer ◽  
Steliana Huhulescu ◽  
Anna Stoeger ◽  
Franz Allerberger ◽  
Werner Ruppitsch
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Diphtheria Toxin ◽  
Corynebacterium Diphtheriae ◽  
Toxin Gene ◽  
Whole Genome ◽  
Skin Infections ◽  
Antimicrobial Resistance Genes

Background: Diphtheria is a vaccine preventable disease with a high potential for re-emergence. One of its causative agent is Corynebacterium diphtheriae, some strains producing the diphtheria toxin. From 2011 to 2019, 57 clinical C. diphtheriae strains were isolated in Austria, either from the respiratory track or from skin infections. Objectives: The aim of the study was to investigate the genetic diversity of these C. diphtheriae isolates using whole genome sequencing. Methods: Isolates were characterized by genome wide comparison using single nucleotide polymorphism or core genome multilocus sequence typing, and by searching sequence data for antimicrobial resistance genes and genes involved in diphtheria toxin production. Results: Genetic diversity between the isolates was high, with no clear distribution over time or place. C. belfantii isolates were separated from other strains, and were strongly associated with respiratory infections (OR = 57). Two clusters, limited in time and space, were identified. Almost 40% of strains carried resistance genes against tetracycline or sulfonamides, mostly from skin infections. Microbiological tests showed that 55% of isolates were resistant to penicillin, but did not carry genes conferring β-lactam resistance. Diphtheria toxin gene with no non-synonymous mutation was found in three isolates only. Conclusion: This study showed that sequencing can provide valuable information complementing routine microbiological and epidemiological investigations. It allowed us to identify unknown clusters, evaluate antimicrobial resistances more broadly and support toxigenicity results obtained by PCR. For these reasons, C. diphtheriae surveillance could strongly benefit from the routine implementation of whole genome sequencing.

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

scholarly journals Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains

2019 ◽  
Vol 6 (2) ◽  
Author(s):  
Bradley T Endres ◽  
Khurshida Begum ◽  
Hua Sun ◽  
Seth T Walk ◽  
Ali Memariani ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
The United States ◽  
Whole Genome Sequence ◽  
Snp Analysis ◽  
Whole Genome ◽  
Ribotype 027 ◽  
Clostridioides Difficile

Abstract Background The epidemic Clostridioides difficile ribotype 027 strain resulted from the dissemination of 2 separate fluoroquinolone-resistant lineages: FQR1 and FQR2. Both lineages were reported to originate in North America; however, confirmatory large-scale investigations of C difficile ribotype 027 epidemiology using whole genome sequencing has not been undertaken in the United States. Methods Whole genome sequencing and single-nucleotide polymorphism (SNP) analysis was performed on 76 clinical ribotype 027 isolates obtained from hospitalized patients in Texas with C difficile infection and compared with 32 previously sequenced worldwide strains. Maximum-likelihood phylogeny based on a set of core genome SNPs was used to construct phylogenetic trees investigating strain macro- and microevolution. Bayesian phylogenetic and phylogeographic analyses were used to incorporate temporal and geographic variables with the SNP strain analysis. Results Whole genome sequence analysis identified 2841 SNPs including 900 nonsynonymous mutations, 1404 synonymous substitutions, and 537 intergenic changes. Phylogenetic analysis separated the strains into 2 prominent groups, which grossly differed by 28 SNPs: the FQR1 and FQR2 lineages. Five isolates were identified as pre-epidemic strains. Phylogeny demonstrated unique clustering and resistance genes in Texas strains indicating that spatiotemporal bias has defined the microevolution of ribotype 027 genetics. Conclusions Clostridioides difficile ribotype 027 lineages emerged earlier than previously reported, coinciding with increased use of fluoroquinolones. Both FQR1 and FQR2 ribotype 027 epidemic lineages are present in Texas, but they have evolved geographically to represent region-specific public health threats.

scholarly journals Method comparison of targeted influenza A virus typing and whole-genome sequencing from respiratory specimens of companion animals

2020 ◽  
pp. 104063872093387
Author(s):  
Patrick K. Mitchell ◽  
Brittany D. Cronk ◽  
Ian E. H. Voorhees ◽  
Derek Rothenheber ◽  
Renee R. Anderson ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Influenza A ◽  
Sequence Data ◽  
Companion Animals ◽  
The United States ◽  
Quality Data ◽  
Whole Genome ◽  
Influenza A Viruses ◽  
Respiratory Specimens

Epidemics of H3N8 and H3N2 influenza A viruses (IAVs) in dogs, along with recognition of spillover infections from IAV strains typically found in humans or other animals, have emphasized the importance of efficient laboratory testing. Given the lack of active IAV surveillance or immunization requirements for dogs, cats, or horses imported into the United States, serotype prediction and whole-genome sequencing of positive specimens detected at veterinary diagnostic laboratories are also needed. The conserved sequences at the ends of the viral genome segments facilitate universal amplification of all segments of viral genomes directly from respiratory specimens. Although several methods for genomic analysis have been reported, no optimization focusing on companion animal strains has been described, to our knowledge. We compared 2 sets of published universal amplification primers using 26 IAV-positive specimens from dogs, horses, and a cat. Libraries prepared from the resulting amplicons were sequenced using Illumina chemistry, and reference-based assemblies were generated from the data produced by both methods. Although both methods produced high-quality data, coverage profiles and base calling differed between the 2 methods. The sequence data were also used to identify the subtype of the IAV strains sequenced and then compared to standard PCR assays for neuraminidase types N2 and N8.

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