scholarly journals Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260234
Author(s):  
Nadine A. Vogt ◽  
Benjamin M. Hetman ◽  
David L. Pearl ◽  
Adam A. Vogt ◽  
Richard J. Reid-Smith ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Sequence Data ◽  
Swine Manure ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Southern Ontario ◽  
Swine Farms ◽  
Source Type

To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.

scholarly journals Genomically Informed Strain-Specific Recovery of Shiga Toxin–Producing Escherichia coli during Foodborne Illness Outbreak Investigations

2018 ◽  
Vol 82 (1) ◽  
pp. 39-44 ◽  
Author(s):  
BURTON W. BLAIS ◽  
KYLE TAPP ◽  
MARTINE DIXON ◽  
CATHERINE D. CARRILLO
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Shiga Toxin ◽  
Sequence Data ◽  
Food Samples ◽  
Foodborne Illness ◽  
Whole Genome Sequence ◽  
Source Attribution ◽  
Selective Enrichment ◽  
Food Testing

ABSTRACT Next-generation sequencing plays an important role in the characterization of clinical bacterial isolates for source attribution purposes during investigations of foodborne illness outbreaks. Once an illness cluster and a suspect food vehicle have been identified, food testing is initiated for confirmation and to determine the scope of a contamination event so that the implicated lots may be removed from the marketplace. For biochemically diverse families of pathogens such as Shiga toxin–producing Escherichia coli (STEC), the ability to detect specific strains may be hampered by the lack of a universal selective enrichment approach for their recovery against high levels of background microbiota. The availability of whole genome sequence data for a given outbreak STEC strain prior to commencement of food testing may provide food microbiologists an opportunity to customize selective enrichment techniques favoring the recovery of the outbreak strain. Here we demonstrate the advantages of using the publicly available ResFinder tool in the analysis of STEC model strains belonging to serotypes O111 and O157 to determine antimicrobial resistance traits that can be used in formulating strain-specific enrichment media to enhance recovery of these strains from microbiologically complex food samples. The improved recovery from ground beef of model STEC strains with various antimicrobial resistance profiles was demonstrated using three classes of antibiotics as selective agents, suggesting the universal applicability of this new approach in supporting foodborne illness investigations.

scholarly journals Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection

2019 ◽  
Vol 20 (S15) ◽  
Author(s):  
Jinhong Shi ◽  
Yan Yan ◽  
Matthew G. Links ◽  
Longhai Li ◽  
Jo-Anne R. Dillon ◽  
...  
Keyword(s):  
Feature Selection ◽  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Sequence Data ◽  
Bacterial Species ◽  
Clinical Diagnostics ◽  
New Drugs ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

Abstract Background Antimicrobial resistance (AMR) is a major threat to global public health because it makes standard treatments ineffective and contributes to the spread of infections. It is important to understand AMR’s biological mechanisms for the development of new drugs and more rapid and accurate clinical diagnostics. The increasing availability of whole-genome SNP (single nucleotide polymorphism) information, obtained from whole-genome sequence data, along with AMR profiles provides an opportunity to use feature selection in machine learning to find AMR-associated mutations. This work describes the use of a supervised feature selection approach using deep neural networks to detect AMR-associated genetic factors from whole-genome SNP data. Results The proposed method, DNP-AAP (deep neural pursuit – average activation potential), was tested on a Neisseria gonorrhoeae dataset with paired whole-genome sequence data and resistance profiles to five commonly used antibiotics including penicillin, tetracycline, azithromycin, ciprofloxacin, and cefixime. The results show that DNP-AAP can effectively identify known AMR-associated genes in N. gonorrhoeae, and also provide a list of candidate genomic features (SNPs) that might lead to the discovery of novel AMR determinants. Logistic regression classifiers were built with the identified SNPs and the prediction AUCs (area under the curve) for penicillin, tetracycline, azithromycin, ciprofloxacin, and cefixime were 0.974, 0.969, 0.949, 0.994, and 0.976, respectively. Conclusions DNP-AAP can effectively identify known AMR-associated genes in N. gonorrhoeae. It also provides a list of candidate genes and intergenic regions that might lead to novel AMR factor discovery. More generally, DNP-AAP can be applied to AMR analysis of any bacterial species with genomic variants and phenotype data. It can serve as a useful screening tool for microbiologists to generate genetic candidates for further lab experiments.

scholarly journals Conjugal Transfer, Whole-Genome Sequencing, and Plasmid Analysis of Four mcr-1-Bearing Isolates from U.S. Patients

2019 ◽  
Vol 63 (4) ◽  
Author(s):  
Wenming Zhu ◽  
Adrian Lawsin ◽  
Rebecca L. Lindsey ◽  
Dhwani Batra ◽  
Kristen Knipe ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Whole Genome ◽  
Colistin Resistance ◽  
Content Type ◽  
Plasmid Analysis ◽  
Antimicrobial Resistance Genes

ABSTRACT Four Enterobacteriaceae clinical isolates bearing mcr-1 gene-harboring plasmids were characterized. All isolates demonstrated the ability to transfer colistin resistance to Escherichia coli; plasmids were stable in conjugants after multiple passages on nonselective media. mcr-1 was located on an IncX4 (n = 3) or IncN (n = 1) plasmid. The IncN plasmid harbored 13 additional antimicrobial resistance genes. Results indicate that the mcr-1-bearing plasmids in this study were highly transferable in vitro and stable in the recipients.

scholarly journals Discerning the Antimicrobial Resistance, Virulence, and Phylogenetic Relatedness of Salmonella Isolates Across the Human, Poultry, and Food Materials Sources in Malaysia

2021 ◽  
Vol 12 ◽  
Author(s):  
Zunita Zakaria ◽  
Latiffah Hassan ◽  
Norazah Ahmad ◽  
Suraya Amir Husin ◽  
Rohaya Mohd Ali ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Sequence Data ◽  
Food Samples ◽  
Peninsular Malaysia ◽  
Resistance Rate ◽  
Food Sources ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Aminoglycoside Resistance ◽  
Genetic Traits

Salmonella enterica subspecies enterica serovar Enteritidis is one of the major foodborne zoonotic pathogens globally. It has significantly impacted human health and global trade. In this investigation, whole-genome sequencing was employed to determine the antimicrobial resistance (AMR) pattern of a collection of Salmonella Enteritidis isolated from humans, poultry, and food sources. The study also investigated the virulence genes profile of the isolates as well as the phylogenetic relationships among strains. Illumina NextSeq technology was used to sequence the genome of 82 Salmonella Enteritidis strains isolated over 3 years (2016–2018) in Peninsular Malaysia. The pattern of resistance showed that tetracycline had the highest frequency (37/82, 45.12%), and isolates from food samples showed the highest rate of 9/18 (50.00%), followed by human 17/35 (48.57%) and then poultry 11/29 (37.93%). The second drug with the highest resistance rate is ampicillin with 5/29 (17.24%) for poultry, 4/35 (11.43%) for human, and 0/18 (0.00%) for food isolates respectively. Similarly, a total of 19 antimicrobial resistance (AMR) genes corresponding to the nine drugs used in the disc diffusion assay were evaluated from the whole genome sequence data. The aminoglycoside resistance gene aac(6′)-ly was detected in 79 of the 82 isolates (96.34%). While the phylogenetic analysis revealed distinct lineages isolated, the three sources indicating possible cross-contamination. In conclusion, the results showed that the genomic profile of Salmonella Enteritidis isolated from humans, poultry, and food samples share genetic traits, hence the need to institute measures at controlling the continuous spread of these resistant pathogens.

scholarly journals Antimicrobial Resistance in GenericEscherichia coliIsolates from Wild Small Mammals Living in Swine Farm, Residential, Landfill, and Natural Environments in Southern Ontario, Canada

2010 ◽  
Vol 77 (3) ◽  
pp. 882-888 ◽  
Author(s):  
Samantha E. Allen ◽  
Patrick Boerlin ◽  
Nicol Janecko ◽  
John S. Lumsden ◽  
Ian K. Barker ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Small Mammals ◽  
Resistance Genes ◽  
Resistant Bacteria ◽  
Residential Areas ◽  
Swine Farm ◽  
Natural Habitats ◽  
Southern Ontario ◽  
E Coli ◽  
Swine Farms

ABSTRACTTo assess the impacts of different types of human activity on the development of resistant bacteria in the feces of wild small mammals, we compared the prevalences and patterns of antimicrobial resistance and resistance genes in genericEscherichia coliandSalmonella entericaisolates from fecal samples collected from wild small mammals living in four environments: swine farms, residential areas, landfills, and natural habitats. Resistance to antimicrobials was observed inE. coliisolates from animals in all environments: 25/52 (48%) animals trapped at swine farms, 6/69 (9%) animals trapped in residential areas, 3/20 (15%) animals trapped at landfills, and 1/22 (5%) animals trapped in natural habitats. Animals trapped on farms were significantly more likely to carryE. coliisolates with resistance to tetracycline, ampicillin, sulfisoxazole, and streptomycin than animals trapped in residential areas. The resistance genessul2,aadA, andtet(A) were significantly more likely to be detected inE. coliisolates from animals trapped on farms than from those trapped in residential areas. ThreeS. entericaserotypes (Give, Typhimurium, and Newport) were recovered from the feces of 4/302 (1%) wild small mammals. AllSalmonellaisolates were pansusceptible. Our results show that swine farm origin is significantly associated with the presence of resistant bacteria and resistance genes in wild small mammals in southern Ontario, Canada. However, resistant fecal bacteria were found in small mammals living in all environments studied, indicating that environmental exposure to antimicrobials, antimicrobial residues, resistant bacteria, or resistance genes is widespread.

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