| Literature DB >> 35783410 |
Daniel F M Monte1,2, Matthew A Nethery3,4, Hanna Berman5, Shivaramu Keelara5, Nilton Lincopan6,7, Paula J Fedorka-Cray5, Rodolphe Barrangou3,4, Mariza Landgraf1.
Abstract
Salmonella enterica subsp. enterica serovar Heidelberg has been associated with a broad host range, such as poultry, dairy calves, swine, wild birds, environment, and humans. The continuous evolution of S. Heidelberg raises a public health concern since there is a global dispersal of lineages harboring a wide resistome and virulome on a global scale. Here, we characterized the resistome, phylogenetic structure and clustered regularly interspaced short palindromic repeats (CRISPR) array composition of 81 S. Heidelberg strains isolated from broiler farms (n = 16), transport and lairage (n = 5), slaughterhouse (n = 22), and retail market (n = 38) of the poultry production chain in Brazil, between 2015 and 2016 using high-resolution approaches including whole-genome sequencing (WGS) and WGS-derived CRISPR genotyping. More than 91% of the S. Heidelberg strains were multidrug-resistant. The total antimicrobial resistance (AMR) gene abundances did not vary significantly across regions and sources suggesting the widespread distribution of antibiotic-resistant strains from farm to market. The highest AMR gene abundance was observed for fosA7, aac(6')-Iaa, sul2, tet(A), gyrA, and parC for 100% of the isolates, followed by 88.8% for bla CMY-2. The β-lactam resistance was essentially driven by the presence of the plasmid-mediated AmpC (pAmpC) bla CMY-2 gene, given the isolates which did not carry this gene were susceptible to cefoxitin (FOX). Most S. Heidelberg strains were classified within international lineages, which were phylogenetically nested with Salmonella strains from European countries; while CRISPR genotyping analysis revealed that the spacer content was overall highly conserved, but distributed into 13 distinct groups. In summary, our findings underscore the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork in Brazil and reinforce the importance of CRISPR-based genotyping for salmonellae. Hence, we emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen.Entities:
Keywords: CRISPR; Salmonella Heidelberg; WGS; antibiotic resistance; foodborne disease; phylogeny
Year: 2022 PMID: 35783410 PMCID: PMC9248969 DOI: 10.3389/fmicb.2022.867278
Source DB: PubMed Journal: Front Microbiol ISSN: 1664-302X Impact factor: 6.064
Features of S. Heidelberg strains (n = 81) isolated from different sources.
| Strain ID | Location*/year | Origin | Source | Resistance profile | Resistance genes | Sequence type |
| SH018 | SP/2016 | Farm | Broiler chicken | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH019 | SP/2016 | Farm | Broiler chicken | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH10211124 | SC/2016 | Farm | Broiler chicken | TET-CIP-NAL | ST15 | |
| SH10227492 | SC/2016 | Farm | Broiler chicken | TET-CIP-NAL-STR | ST15 | |
| SH10230633 | MS/2016 | Farm | Broiler chicken | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH10190712 | PR/2016 | Farm | Broiler chicken | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH10201911 | SC/2016 | Farm | Broiler chicken | TET-CIP-NAL | ST15 | |
| SH10206799 | SC/2016 | Farm | Broiler chicken | TET-CIP-NAL | ST15 | |
| SH10225532 | SC/2016 | Farm | Broiler chicken | TET-CIP-NAL | ST15 | |
| STy012 | SP/2015 | Farm | Broiler chicken | TET-CIP-NAL | ST15 | |
| SI015 | SP/2015 | Farm | Broiler chicken | TET-CIP-NAL | ST15 | |
| SH134 | SP/2016 | Farm | Chicken cage after cleaning | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH159 | MG/2016 | Farm | Chicken cage after cleaning | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH415 | SC/2016 | Farm | Chicken cage after cleaning | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH434 | SC/2016 | Farm | Chicken cage after cleaning | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH715 | SP/2016 | Farm | Chicken cage after cleaning | TET-CIP-GEN-NAL-STR |
| ST15 |
| SH264 | PR/2016 | Transport and lairage | Truck after cleaning | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH265 | PR/2016 | Transport and lairage | Truck after cleaning | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH414 | SC/2016 | Transport and lairage | Truck after cleaning | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH433 | SC/2016 | Transport and lairage | Truck after cleaning | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH435 | SC/2016 | Transport and lairage | Truck after cleaning | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH122 | SP/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH125 | SP/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH128 | SP/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH129 | SP/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH258 | PR/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH266 | ||||||
|
| PR/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH283 | SP/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH284 | SP/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH285 | SP/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SSc148 | DF/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SSc155 | DF/2016 | Slaughterhouse | Chicken carcass | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH268 | PR/2016 | Slaughterhouse | Chicken carcass after chiller | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH269 | PR/2016 | Slaughterhouse | Chicken carcass after chiller | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH270 | PR/2016 | Slaughterhouse | Chicken carcass after chiller | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH1 | SP/2016 | Slaughterhouse | Mechanically recovered chicken meat | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH131 | SP/2016 | Slaughterhouse | Mechanically recovered chicken meat | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH296 | SP/2016 | Slaughterhouse | Mechanically recovered | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH297 | SP/2016 | Slaughterhouse | Mechanically recovered chicken meat | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH697 | SC/2016 | Slaughterhouse | Mechanically recovered chicken meat | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH700 | SC/2016 | Slaughterhouse | Mechanically recovered chicken meat | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH712 | SP/2016 | Slaughterhouse | Mechanically recovered chicken meat | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH164 | ||||||
|
| SP/2016 | Slaughterhouse | Viscera | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH118 | SP/2016 | Retail market | Chicken breast | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP |
| ST15 |
| SH276 | SP/2016 | Retail market | Salted chicken breast | TET-CIP-NAL | ST15 | |
| SH405 | SC/2016 | Retail market | Chicken breast fillet | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH410 | SC/2016 | Retail market | Chicken breast fillet | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH694 | ||||||
|
| SC/2016 | Retail market | Chicken breast fillet | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH120 | SP/2016 | Retail market | Chicken thigh and drumstick | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP |
| ST15 |
| SH286 | SP/2016 | Retail market | Chicken thigh and drumstick | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH411 | SC/2016 | Retail market | Chicken thigh and drumstick | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH692 | SC/2016 | Retail market | Chicken thigh and drumstick | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH121 | SP/2016 | Retail market | Chicken fillet sassami | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP |
| ST15 |
| SH127 | SP/2016 | Retail market | Chicken fillet sassami | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP |
| ST15 |
| SH135 | SP/2016 | Retail market | Whole chicken | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH427 | SC/2016 | Retail market | Whole chicken | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH138 | SC/2016 | Retail market | Leg quarter | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH158 | MG/2016 | Retail market | Fiesta boneless | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR |
| ST15 |
| SH287 | SP/2016 | Retail market | Chicken skin | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH289 | SP/2016 | Retail market | Seasoned chicken fillet | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH403 | SC/2016 | Retail market | Seasoned chicken fillet | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH290 | SP/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH402 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH408 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH422 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH423 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH429 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH430 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH431 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH674 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH687 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH707 | SC/2016 | Retail market | Chicken liver | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH412 | SC/2016 | Retail market | Chicken wing | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH680 | SC/2016 | Retail market | Retail meat | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH681 | SC/2016 | Retail market | Chicken wing | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SH685 | SC/2016 | Retail market | Chicken neck | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH691 | SC/2016 | Retail market | Chicken wing | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH693 | SC/2016 | Retail market | Chicken wing | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SSc139 | SP/2016 | Retail market | Chicken wing | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP-STR | ST15 | |
| SH716 | SC/2016 | Retail market | Chicken wing paddle | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 | |
| SSC136 | SP/2016 | Retail market | Chicken wing | FOX-TET-AXO-AUG2-CIP-NAL-XNL-AMP | ST15 |
Minimum inhibitory concentration values for Salmonella Heidelberg strains (n = 81).
| Antimicrobials | Resistance (%) | Intermediate resistance (%) | Distribution of | |||||||||||||||
|
| ||||||||||||||||||
| 0.015 | 0.03 | 0.06 | 0.12 | 0.25 | 0.5 | 1 | 2 | 4 | 8 | 16 | 32 | 64 | 128 | 256 | ≥512 | |||
| Cefoxitin | 88.8 | 0 | 6 | 2 | 1 |
| ||||||||||||
| Azithromycin | 12.3 | 0 | 22 | 49 | 10 | |||||||||||||
| Chloramphenicol | 1.23 | 12.3 | 7 | 63 | 10 |
| ||||||||||||
| Tetracycline | 100 | 0 |
| |||||||||||||||
| Ceftriaxone | 88.8 | 0 | 9 |
|
|
|
| |||||||||||
| Amoxicillin/clavulanic acid | 88.8 | 0 | 6 | 3 |
| |||||||||||||
| Ciprofloxacin | 100 | 0 |
|
|
| |||||||||||||
| Gentamicin | 1.23 | 0 | 64 | 16 |
| |||||||||||||
| Nalidixic acid | 100 | 0 |
| |||||||||||||||
| Ceftiofur | 88.8 | 0 | 1 | 8 |
| |||||||||||||
| Sulfisoxazole | 100 | 0 |
| |||||||||||||||
| Trimethoprim/sulfamethoxazole | 1.23 | 0 | 72 | 7 | 1 |
| ||||||||||||
| Ampicillin | 88.8 | 0 | 2 | 1 | 5 | 1 |
| |||||||||||
| Streptomycin | 16.0 | 0 | 68 |
|
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FIGURE 1(A) Reconstructed phylogeny based on the core genome (4,139 genes) of the 81 S. Heidelberg strains. The percentage of bootstrap samples in which nodes appeared is shown. The location of isolation of each strain is labeled on its respective branch. Color strips depict the year (Y) and source (S) of isolation, respectively. (B) The presence and absence of selected antimicrobial resistance genes are shown, with black indicating presence. The drug classes impacted by these genes are: (a) aminoglycosides, (b) beta-lactams, (c) chloramphenicol, (d) fosfomycin, (e) lincosamide, (f) quaternary ammonium compounds, (g) quinolones, (h) streptomycin, (i) sulfonamides, (j) tetracylines. (C) Presence and absence of plasmid incompatibility groups, with black indicating presence. Brazilian States: PR, Paraná; SC, Santa Catarina; SP, São Paulo; MG, Minas Gerais; DF, Distrito Federal; MS, Mato Grosso do Sul.
Clustered regularly interspaced short palindromic repeats (CRISPR) patterns obtained from 81 Salmonella Heidelberg strains.
| CRISPR profile | Location | Source | Year of isolation |
| P1 | SC ( | Retail market ( | 2015 ( |
| P2 | SC ( | Retail market ( | 2016 ( |
| P3 | SC ( | Slaughterhouse ( | 2016 ( |
| P4 | SC ( | Retail market ( | 2016 ( |
| P5 | SC ( | Retail market ( | 2016 ( |
| P6 | SP ( | Broiler farm ( | 2016 ( |
| P7 | SC ( | Retail market ( | 2015 ( |
| P8 | SP ( | Retail market ( | 2016 ( |
| P9 | PR ( | Slaughterhouse ( | 2016 ( |
| P10 | SP ( | Retail market ( | 2016 ( |
| P11 | SP ( | Retail market ( | 2016 ( |
| P12 | PR ( | Transport and lairage ( | 2016 ( |
| P13 | SC ( | Broiler farm ( | 2016 ( |
*Brazilian States: PR, Paraná; SC, Santa Catarina; SP, São Paulo; MG, Minas Gerais; DF, Distrito Federal; MS, Mato Grosso do Sul.
FIGURE 2Reconstructed phylogeny based on the core genome, distribution of spacers composition, clustered regularly interspaced short palindromic repeats (CRISPR) loci, and CRISPR profiles among Salmonella Heidelberg strains. The location of isolation of each strain is labeled on its respective branch. Color strips depict the year (Y) and source (S) of isolation, respectively. Brazilian States: PR, Paraná; SC, Santa Catarina; SP, São Paulo; MG, Minas Gerais; DF, Distrito Federal; MS, Mato Grosso do Sul.
FIGURE 3Salmonella enterica subsp. enterica serovar Heidelberg type I-E CRISPR locus architecture. This system contains two distinct CRISPR arrays—one associated with the cas genes and one disparate locus upstream (5′) from the cas genes.