scholarly journals Differences in Genotype and Antimicrobial Resistance between Campylobacter spp. Isolated from Organic and Conventionally Produced Chickens in Sweden

Pathogens ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1630
Author(s):  
Ingrid Hansson ◽  
Patrik Ellström ◽  
Oskar Nilsson ◽  
Matilda Chaba ◽  
Moa Skarin ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Production Systems ◽  
Whole Genome ◽  
Broiler Production ◽  
Outdoor Area ◽  
Sequence Types ◽  
Campylobacter Spp

Antibiotic resistance is a major challenge worldwide and increased resistance to quinolones in Campylobacter is being reported. Analysis of antibiotic resistance was performed on 157 Campylobacter strains (123 C. jejuni and 34 C. coli) from conventional and organic chickens produced in Sweden. Susceptibility for tetracycline, ciprofloxacin, erythromycin, nalidixic acid, streptomycin, and gentamycin was determined by microdilution. All 77 isolates from organic chickens were sensitive to all antibiotics, except two C. jejuni that were resistant to tetracycline. Of the 80 isolates from conventional chickens, 22.5% of C. jejuni and 11.1% of C. coli were resistant to quinolones and 5.6% of C. jejuni were resistant to tetracycline. Whole-genome sequencing resulted in 50 different sequence types of C. jejuni and six of C. coli. Nine sequence types were found in both organic and conventional chickens. Two of these (ST-19 and ST-257) included isolates from conventional broilers with different resistance phenotypes to the remaining isolates from conventional and organic broilers. There are management differences between the production systems, such as feed, breed, use of coccidiostats, and access to outdoor area. It is unlikely that quinolone resistance has arisen due to use of antimicrobials, since fluoroquinolones are not permitted in Swedish broiler production.

scholarly journals Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244358
Author(s):  
Rafika Indah Paramita ◽  
Erni Juwita Nelwan ◽  
Fadilah Fadilah ◽  
Editha Renesteen ◽  
Nelly Puspandari ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Bloodstream Infection ◽  
Genome Sequencing ◽  
Virulence Genes ◽  
Sequence Type ◽  
Whole Genome ◽  
National Hospital ◽  
Sequence Types

Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.

scholarly journals Detection of antimicrobial resistance, pathogenicity, and virulence potentials of non-typhoidal Salmonella isolates at the Yaounde abattoir using whole genome sequencing technique

2021 ◽  
Author(s):  
Chelea Matchawe ◽  
Eunice M Machuka ◽  
Martina Kyalo ◽  
Patrice Bonny ◽  
Nkeunen Gerard ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Pathogens ◽  
Critical Role ◽  
Multidrug Resistant ◽  
World Health ◽  
Whole Genome

One of the crucial public health problems today is emerging and re-emerging of multidrug-resistant bacterial pathogens coupled with a decline in the development of new antimicrobials. Non-typhoidal Salmonella is classified among the multidrug-resistant bacterial pathogens of international concern. To predict their multidrug resistance potentials, 19 assembled genomes (partial genomes) of 23 non-typhoidal Salmonella isolated at the Yaounde abattoir between December 2014 and November 2015 from live cattle (n=1), beef carcass (n=19), butchers' hands (n=1) and the beef processing environments (n=2) were explored using whole-genome sequencing. Phenotypically, while approximately 22% (n=5) of Salmonella isolates showed moderate resistance to streptomycin, 13.04 % (n=3) were multidrug-resistant. Genotypically, all the Salmonella isolates possessed high multidrug resistance potentials against several classes of antibiotics (third-generation cephalosporin and fluoroquinolone), which are assigned highest priority drugs by the World Health Organization. Moreover, more than 31% of the isolates exhibited resistance potentials to polymyxin, considered as the last resort drug with both clinical and veterinary relevance. Additionally, close to 80% of non-typhoidal Salmonella isolates in this study harbored "silent resistant genes" and thus constituted potential reservoirs of antibiotic resistance to other foodborne bacteria. Plasmids also appear to play a critical role in the horizontal transfer of antibiotic resistance genes of some isolates. The isolates showed a high degree of pathogenicity and possessed key effector proteins to establish infection in their hosts, including humans. The overall results demand prudent use of antibiotics and constant monitoring of antimicrobial resistance of non-typhoidal Salmonella in the Cameroonian abattoirs.

scholarly journals Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

2020 ◽  
Vol 58 (4) ◽  
Author(s):  
Ellen N. Kersh ◽  
Cau D. Pham ◽  
John R. Papp ◽  
Robert Myers ◽  
Richard Steece ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Whole Genome ◽  
Content Type ◽  
Laboratory Capacity

ABSTRACT U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae. AR-Ng testing, a subactivity of the CDC’s AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC’s national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

scholarly journals Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens

Antibiotics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1152
Author(s):  
Samuel M. Chekabab ◽  
John R. Lawrence ◽  
Alvin C. Alvarado ◽  
Bernardo Z. Predicala ◽  
Darren R. Korber
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Fecal Samples ◽  
Time Points ◽  
Conventional Farms ◽  
Production Practices ◽  
On Farm ◽  
The Impact

In response to new stringent regulations in Canada regarding the use of antibiotics in animal production, many farms have implemented practices to produce animals that are raised without antibiotics (RWA) from birth to slaughter. This study aims to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, the occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance of farms that adopted the RWA program and conventional farms using antibiotics in accordance with the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week-old pigs and composite manure from the barn over six time points and applying whole-genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug use records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced the frequency of AMR genes in piglet feces and in-barn manure. However, metagenomic analyses showed that RWA barns had a significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.

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 Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy

2014 ◽  
Vol 53 (1) ◽  
pp. 323-326 ◽  
Author(s):  
Birgit De Smet ◽  
Derek S. Sarovich ◽  
Erin P. Price ◽  
Mark Mayo ◽  
Vanessa Theobald ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Burkholderia Pseudomallei ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Sequence Types

Burkholderia pseudomalleiisolates with shared multilocus sequence types (STs) have not been isolated from different continents. We identified two STs shared between Australia and Cambodia. Whole-genome analysis revealed substantial diversity within STs, correctly identified the Asian or Australian origin, and confirmed that these shared STs were due to homoplasy.

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