A National Antimicrobial Resistance Monitoring System Survey of Antimicrobial-Resistant Foodborne Bacteria Isolated from Retail Veal in the United States

Tate, Heather; Li, Cong; Nyirabahizi, Epiphanie; Tyson, Gregory H.; Zhao, Shaohua; Rice-Trujillo, Crystal; Jones, S. B.; Ayers, Sherry; M’ikanatha, Nkuchia M.; Hanna, Simon; Ruesch, Laura; Cavanaugh, Marianna E; Laksanalamai, Pongpan; Mingle, Lisa A.; Matzinger, Shannon R.; McDermott, Patrick F.

doi:10.4315/jfp-21-005

Cited by 18 publications

(11 citation statements)

References 36 publications

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“…Out of 26 papers selected, 15 papers were from China [ 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ] and the rest (11 papers) were from the USA [ 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 ]. The data extracted contain 13,018 food samples, out of which 5000 samples were AMR positive (2276 and 2724 from China and the USA, respectively).…”

Section: Resultsmentioning

confidence: 99%

Systematic Surveillance and Meta-Analysis of Antimicrobial Resistance and Food Sources from China and the USA

et al. 2022

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Since the discovery of antibiotics in the 20th century, they have been used to fight against infections. The overuse of antibiotics in the wider environment has resulted in the emergence of multidrug-resistant bacteria. In developing countries such as China and developed countries such as the USA, there is evidence of the high pervasiveness of antibiotic-resistant infections. However, the studies on the spread of antibiotic-resistant microorganisms that inform about the consequences are limited. The aim of our study was to analyze and compare antimicrobial resistance (AMR) identified in published research papers from that found in different food sources, which were published between 2012 and December 2021, covering most retail food items. Out of 132 research papers identified, 26 papers have met our strict criteria and are included in the qualitative and quantitative analysis. The selected papers led to 13,018 food samples, out of which 5000 samples were contaminated, including 2276 and 2724 samples from China and the USA, respectively. Meat, aquatic products, milk, and eggs show high to medium potential for AMR exposure to Gram-positive bacteria such as Staphylococcus, Enterococci, etc. and Gram-negative foodborne pathogens such as Campylobacter, Salmonella, Vibrio, etc. Most of the food samples show antibiotic resistance to β-lactams, tetracycline, quinolones, and aminoglycosides. Retail food products such as meat, sea food, and some other food products, as well as AMR genetics and technically important bacteria, are proposed to be better merged with mitigation strategies and systematic One Health AMR surveillance to minimize the knowledge gaps and facilitate comprehensive AMR risk computation for the consumers.

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Section: Resultsmentioning

confidence: 99%

Systematic Surveillance and Meta-Analysis of Antimicrobial Resistance and Food Sources from China and the USA

et al. 2022

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“…Lineages S8 and SC2 harbour PMQR genes in Col(pHAD28) plasmid. Col(pHAD28) plasmids related to fluoroquinolone resistance were reported [ 82 ]. MCR-1 -carrying lncI2 and IncHI2 belong to the SC9 lineage.…”

Section: Discussionmentioning

confidence: 99%

WGS-Based Lineage and Antimicrobial Resistance Pattern of Salmonella Typhimurium Isolated during 2000–2017 in Peru

et al. 2022

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Salmonella Typhimurium is associated with foodborne diseases worldwide, including in Peru, and its emerging antibiotic resistance (AMR) is now a global public health problem. Therefore, country-specific monitoring of the AMR emergence is vital to control this pathogen, and in these aspects, whole genome sequence (WGS)—based approaches are better than gene-based analyses. Here, we performed the antimicrobial susceptibility test for ten widely used antibiotics and WGS-based various analyses of 90 S. Typhimurium isolates (human, animal, and environment) from 14 cities of Peru isolated from 2000 to 2017 to understand the lineage and antimicrobial resistance pattern of this pathogen in Peru. Our results suggest that the Peruvian isolates are of Typhimurium serovar and predominantly belong to sequence type ST19. Genomic diversity analyses indicate an open pan-genome, and at least ten lineages are circulating in Peru. A total of 48.8% and 31.0% of isolates are phenotypically and genotypically resistant to at least one antibiotic, while 12.0% are multi-drug resistant (MDR). Genotype–phenotype correlations for ten tested drugs show >80% accuracy, and >90% specificity. Sensitivity above 90% was only achieved for ciprofloxacin and ceftazidime. Two lineages exhibit the majority of the MDR isolates. A total of 63 different AMR genes are detected, of which 30 are found in 17 different plasmids. Transmissible plasmids such as lncI-gamma/k, IncI1-I(Alpha), Col(pHAD28), IncFIB, IncHI2, and lncI2 that carry AMR genes associated with third-generation antibiotics are also identified. Finally, three new non-synonymous single nucleotide variations (SNVs) for nalidixic acid and eight new SNVs for nitrofurantoin resistance are predicted using genome-wide association studies, comparative genomics, and functional annotation. Our analysis provides for the first time the WGS-based details of the circulating S. Typhimurium lineages and their antimicrobial resistance pattern in Peru.

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“…For long-read sequencing, DNA libraries were prepared using a 10 kb template preparation protocol with SMRTbell template prep kit v 1.0. Sequencing was performed using Pacific Biosciences technology on the Sequel platform with sequencing kit 3.0, as described previously (Tate et al, 2021)…”

Section: Isolate Sources and Pacbio Sequencingmentioning

confidence: 99%

Long-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in Salmonella enterica

et al. 2021

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Salmonella enterica is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on Salmonella isolated from retail meats and food animals. A collection of 134 multidrug-resistant isolates belonging to 33 serotypes were subjected to PacBio sequencing. One major locus of diversity among these isolates was the presence and orientation of Salmonella pathogenic islands (SPI), which varied across different serotypes but were largely conserved within individual serotypes. We also identified insertion of an IncQ resistance plasmid into the chromosome of fourteen strains of serotype I 4,[5],12:i:– and the Salmonella genomic island 1 (SGI-1) in five serotypes. The presence of various SPIs, SGI-1 and integrated plasmids contributed significantly to the genomic variability and resulted in chromosomal resistance in 55.2% (74/134) of the study isolates. A total of 93.3% (125/134) of isolates carried at least one plasmid, with isolates carrying up to seven plasmids. We closed 233 plasmid sequences of thirteen replicon types, along with twelve hybrid plasmids. Some associations between Salmonella isolate source, serotype, and plasmid type were seen. For instance, IncX plasmids were more common in serotype Kentucky from retail chicken. Plasmids IncC and IncHI had on average more than five antimicrobial resistance genes, whereas in IncX, it was less than one per plasmid. Overall, 60% of multidrug resistance (MDR) strains that carried >3 AMR genes also carried >3 heavy metal resistance genes, raising the possibility of co-selection of antimicrobial resistance in the presence of heavy metals. We also found nine isolates representing four serotypes that carried virulence plasmids with the spv operon. Together, these data demonstrate the power of long-read sequencing to reveal genomic arrangements and integrated plasmids with a high level of resolution for tracking and comparing resistant strains from different sources. Additionally, the findings from this study will help expand the reference set of closed Salmonella genomes that can be used to improve genome assembly from short-read data commonly used in One Health antimicrobial resistance surveillance.

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A National Antimicrobial Resistance Monitoring System Survey of Antimicrobial-Resistant Foodborne Bacteria Isolated from Retail Veal in the United States

Cited by 18 publications

References 36 publications

Systematic Surveillance and Meta-Analysis of Antimicrobial Resistance and Food Sources from China and the USA

Systematic Surveillance and Meta-Analysis of Antimicrobial Resistance and Food Sources from China and the USA

WGS-Based Lineage and Antimicrobial Resistance Pattern of Salmonella Typhimurium Isolated during 2000–2017 in Peru

Long-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in Salmonella enterica

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