Comparison of Molecular Subtyping and Antimicrobial Resistance Detection Methods Used in a Large Multistate Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Linked to Pet Store Puppies Epidemiology

Campylobacter jejuni is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST), provided limited resolution to adequately identify C. jejuni outbreaks and separate out sporadic isolates during outbreak investigations. Whole-genome sequencing (WGS) has emerged as a powerful tool for C. jejuni outbreak detection. In this investigation, 45 human and 11 puppy isolates obtained during a 2016–2018 outbreak linked to pet store puppies were sequenced. Core genome multilocus sequence typing (cgMLST) and high-quality single nucleotide polymorphism (hqSNP) analysis of the sequence data separated the isolates into the same two clades containing minor within-clade differences; however, cgMLST analysis does not require selection of an appropriate reference genome, making the method preferable to hqSNP analysis for Campylobacter surveillance and cluster detection. The isolates were classified as sequence type 2109 (ST2109)—a rarely seen MLST sequence type. PFGE was performed on 38 human and 10 puppy isolates; PFGE patterns did not reliably predict clustering by cgMLST analysis. Genetic detection of antimicrobial resistance determinants predicted that all outbreak-associated isolates would be resistant to six drug classes. Traditional antimicrobial susceptibility testing (AST) confirmed a high correlation between genotypic and phenotypi...
Source: Journal of Clinical Microbiology - Category: Microbiology Authors: Tags: Epidemiology Source Type: research

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CONCLUSION: Prevalence of antibiotic use was high not only versus other hospitals in the region but globally including Africa, coupled with significant evidence of sub-optimal prescribing. Swift action is needed to improve future prescribing to reduce AMR. One or two areas should initially be targeted for quality improvement including development of local guidelines, documentation of antibiotic indications and/or stop/review dates. PMID: 33034234 [PubMed - as supplied by publisher]
Source: Expert Review of Anti-Infective Therapy - Category: Infectious Diseases Tags: Expert Rev Anti Infect Ther Source Type: research
CONCLUSIONS: Xyloglucan/gelose plus ORS was effective and safe in treating acute diarrhea in children. PMID: 33028102 [PubMed - as supplied by publisher]
Source: Expert Review of Gastroenterology and Hepatology - Category: Gastroenterology Tags: Expert Rev Gastroenterol Hepatol Source Type: research
Conclusions: (1) Data at our center suggests at least a regional implementation gap in GBS screening and IAP. (2) The decline in the resistance rate ofE. coli for all antimicrobial substances might indicate that the reduction of prenatal antibiotics use is beneficial and that neonatal antibiotic stewardship programs should include pregnant women as well.What is Known:• GBS screening and intrapartum antibiotic prophylaxis led to a 32%-reduction in GBS disease in Germany with a 0.75 (92:122) ratio of early-onset disease to late-onset disease in 2009–2010.• Prenatal antibiotic use might increase the risk of E....
Source: European Journal of Pediatrics - Category: Pediatrics Source Type: research
Abstract Trace metals concentrations of 25 elements were determined for 22 subcomponents of biodegradable and non-biodegradable waste samples representing the United States municipal solid waste (MSW) stream collected during three separate waste sorts. The subcomponent trace metal concentrations and estimated composition results were used to predict trace metal concentrations present in the overall MSW stream along with MSW compost and waste to energy (WTE) ash, which were compared to health-based standards (i.e., US EPA regional screening levels) and to values previously reported in the literature. These estimate...
Source: Chemosphere - Category: Chemistry Authors: Tags: Chemosphere Source Type: research
In conclusion, association rule mining is an effective tool for identifying patterns of multidrug resistance within antimicrobial susceptibility testing data and evaluating the statistical and biological significance of the patterns. Rule quality measures used to sort and differentiate rules should be tested using resampling procedures to minimize the false discovery rate. Rule mining identified consistent multidrug resistance patterns involving beta-lactams, sulfisoxazole, tetracycline, gentamicin, and streptomycin in E. coli isolated from chicken carcasses and meat between 2004 and 2012. The generally low rule overlap su...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
In this study, a BER homolog encoded by cj0595c (named nth) in C. jejuni was analyzed for endonuclease III activity and for its role in maintaining genomic stability. It was found that inactivation of nth resulted in elevated frequencies of spontaneous fluoroquinolone-resistant (FQR) and oxidative stress resistant (OXR) mutants, compared with the wild-type strain in C. jejuni. Sequencing analysis of the FQR and OXR mutants revealed that the elevated mutation rates were associated with C → T or G → A transition in gyrA (FQR mutants) or perR (for OXR mutants). In an in vitro assay, a purified recombinant C. jejuni ...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
In this study, we used the Illuminia MiSeq® to sequence 589 Campylobacter isolates obtained in 2015 from retail poultry meats as part of the National Antimicrobial Resistance Monitoring System (NARMS). WGS data were used to identify the Campylobacter species and to compare the concordance between resistance genotypes and phenotypes. WGS accurately identified 386 C. jejuni and 203 C. coli using gyrA sequence information. Ten resistance genes, including tetO, blaOXA-61, aph(2″)-Ic, aph(2″)-If, aph(2″)-Ig, aph(3')-III, ant(6)-1a, aadE, aph(3")-VIIa, and Inu(C), plus mutations in housekeeping ge...
Source: Food Microbiology - Category: Food Science Authors: Tags: Food Microbiol Source Type: research
Abstract Whole genome sequencing (WGS) has been broadly used to provide detailed characterization of foodborne pathogens. These genomes for diverse species including Salmonella, Escherichia coli, Listeria, Campylobacter and Vibrio have provided great insight into the genetic make-up of these pathogens. Numerous government agencies, industry and academia have developed new applications in food safety using WGS approaches such as outbreak detection and characterization, source tracking, determining the root cause of a contamination event, profiling of virulence and pathogenicity attributes, antimicrobial resistance ...
Source: Current Opinion in Biotechnology - Category: Biotechnology Authors: Tags: Curr Opin Biotechnol Source Type: research
Author Affiliations open 1Public Health Institute, Oakland, California, USA 2Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA 3Instituto de Microbiologia, Colegio de Ciencias Biologicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador 4Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA 5Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA 6Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, USA PDF Version (176 KB) Abstract ...
Source: EHP Research - Category: Environmental Health Authors: Tags: Brief Communication Source Type: research
Publication date: Available online 6 February 2017 Source:Genomics Data Author(s): Sandeep Ghatak, Yiping He, Sue Reed, Terence Strobaugh, Peter Irwin Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS) is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and detect...
Source: Genomics Data - Category: Genetics & Stem Cells Source Type: research
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