1
|
Sivasankaran SK, Bearson BL, Trachsel JM, Nielsen DW, Looft T, Bearson SMD. Genomic and phenotypic characterization of multidrug-resistant Salmonella enterica serovar Reading isolates involved in a turkey-associated foodborne outbreak. Front Microbiol 2024; 14:1304029. [PMID: 38304860 PMCID: PMC10830755 DOI: 10.3389/fmicb.2023.1304029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 02/03/2024] Open
Abstract
Salmonella is a global bacterial foodborne pathogen associated with a variety of contaminated food products. Poultry products are a common source of Salmonella-associated foodborne illness, and an estimated 7% of human illnesses in the United States are attributed to turkey products. From November 2017 to March 2019, the Centers for Disease Control and Prevention reported a turkey-associated outbreak of multidrug-resistant (MDR; resistant to ≥3 antimicrobial classes) Salmonella enterica serovar Reading (S. Reading) linked to 358 human infections in 42 US states and Canada. Since S. Reading was seldom linked to human illness prior to this outbreak, the current study compared genomic sequences of S. Reading isolates prior to the outbreak (pre-outbreak) to isolates identified during the outbreak period, focusing on genes that were different between the two groups but common within a group. Following whole-genome sequence analysis of five pre-outbreak and five outbreak-associated turkey/turkey product isolates of S. Reading, 37 genes located within two distinct chromosomal regions were identified only in the pre-outbreak isolates: (1) an ~5 kb region containing four protein-coding genes including uidA which encodes beta-glucuronidase, pgdA encoding peptidoglycan deacetylase, and two hypothetical proteins and (2) an ~28 kb region comprised of 32 phage-like genes and the xerC gene, which encodes tyrosine recombinase (frequently associated with phage genes). The five outbreak isolates also had a deletional event within the cirA gene, introducing a translational frame shift and premature stop codon. The cirA gene encodes a protein with dual receptor functions: a siderophore receptor for transport of dihydroxybenzoylserine as well as a colicin Ia/b receptor. Significant differences for the identified genetic variations were also detected in 75 S. Reading human isolates. Of the 41 S. Reading isolates collected before or in 2017, 81 and 90% of the isolates contained the uidA and pgdA genes, respectively, but only 24% of the isolates collected after 2017 harbored the uidA and pgdA genes. The truncation event within the cirA gene was also significantly higher in isolates collected after 2017 (74%) compared to before or in 2017 (5%). Phenotypic analysis of the S. Reading isolates for colicin and cefiderocol sensitivities (CirA) and β-methyl-D-glucuronic acid utilization (UidA and accessory proteins) supported the genomic data. Overall, a similar genome reduction pattern was generally observed in both the turkey and human isolates of S. Reading during the outbreak period, and the genetic differences were present in genes that could potentially promote pathogen dissemination due to variation in Salmonella colonization, fitness, and/or virulence.
Collapse
Affiliation(s)
- Sathesh K. Sivasankaran
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA, United States
- Genome Informatics Facility, Iowa State University, Ames, IA, United States
| | - Bradley L. Bearson
- Agroecosystems Management Research Unit, USDA, ARS, National Laboratory for Agriculture and the Environment, Ames, IA, United States
| | - Julian M. Trachsel
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA, United States
| | - Daniel W. Nielsen
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA, United States
- ARS Research Participation Program, Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
| | - Torey Looft
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA, United States
| | - Shawn M. D. Bearson
- USDA, ARS, National Animal Disease Center, Food Safety and Enteric Pathogens, Ames, IA, United States
| |
Collapse
|
2
|
Wang Q, Jin L, Sun S, Yin Y, Wang R, Chen F, Wang X, Zhang Y, Hou J, Zhang Y, Zhang Z, Luo L, Guo Z, Li Z, Lin X, Bi L, Wang H. Occurrence of High Levels of Cefiderocol Resistance in Carbapenem-Resistant Escherichia coli before Its Approval in China: a Report from China CRE-Network. Microbiol Spectr 2022; 10:e0267021. [PMID: 35481835 PMCID: PMC9241927 DOI: 10.1128/spectrum.02670-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/14/2022] [Indexed: 12/14/2022] Open
Abstract
Cefiderocol has been approved in the United States and Europe but not in China. We aim to evaluate carbapenem-resistant Enterobacterales (CRE) susceptibility to cefiderocol to provide baseline data and investigate the resistance mechanism. From 2018 to 2019, 1,158 CRE isolates were collected from 23 provinces and municipalities across China. The MICs of antimicrobials were determined via the agar dilution and broth microdilution methods. Whole-genome sequencing was performed for 26 cefiderocol-resistant Escherichia coli isolates to investigate the resistance mechanism. Clone transformations were used to explore the function of cirA, pbp3, and blaNDM-5 in resistance. Among the 21 antimicrobials tested, aztreonam-avibactam had the highest antibacterial activity (98.3%), followed by cefiderocol (97.3%) and colistin (95.3%). A total of 26 E. coli isolates harboring New Delhi metallo-beta-lactamase 5 (NDM-5) showed high levels of cefiderocol resistance, of which sequence type 167 (ST167) accounted for 76.9% (20/26). We found 4 amino-acid insertions (YRIN/YRIK) at position 333 of penicillin-binding protein 3 (PBP3) in the 26 E. coli isolates, and 22 isolates had a siderophore receptor cirA premature stop codon. After obtaining the wild-type cirA supplementation, the MIC of the transformants decreased by 8 to 16 times in two cefiderocol-resistant isolates. A cefiderocol-susceptible isolate harboring NDM-5 has an MIC increased from 1 μg/mL to 64 μg/mL after cirA deletion, and the MIC decreased from 64 μg/mL to 0.5 μg/mL after blaNDM-5 deletion. The MIC of the E. coli DH5α, from which the pbp3 mutant was obtained, increased from 0.064 μg/mL to 0.25 μg/mL. Cefiderocol showed activity against most CRE in China. The resistance of ST167 E. coli to cefiderocol is a combination of the premature stop codon of cirA, pbp3 mutation, and blaNDM-5 existence. IMPORTANCE Cefiderocol, a new siderophore cephalosporin, has been approved in the United States and Europe but not in China. At present, there are almost no antimicrobial susceptibility evaluation data on cefiderocol in China. We evaluated the in vitro susceptibility of 1,158 strains of carbapenem-resistant Enterobacterales to cefiderocol and other antibiotics. We found that a high proportion of Escherichia coli showed high-level resistance to cefiderocol. Whole-genome sequencing (WGS) and molecular cloning experiments confirmed that the synergistic effect of the cirA gene premature stop codon, blaNDM-5 existence, and the pbp3 mutation is associated with high levels of cefiderocol resistance.
Collapse
Affiliation(s)
- Qi Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Longyang Jin
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Fengning Chen
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Xiaojuan Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Yawei Zhang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Jun Hou
- Department of Clinical Laboratory, The Third Hospital of Mianyang, Sichuan, China
| | - Yumei Zhang
- Department of Clinical Laboratory, People’s Hospital of Zunhua, Hebei, China
| | - Zhijie Zhang
- Department of Clinical Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Liuchun Luo
- Department of Clinical Laboratory, Liuzhou People’s Hospital, Guangxi, China
| | - Zhusheng Guo
- Department of Clinical Laboratory, Dongguan Donghua Hospital, Guangdong, China
| | - Zhenpeng Li
- Department of Clinical Laboratory, Wanbei Coal-Electricity Group General Hospital, Anhui, China
| | - Xin Lin
- Department of Clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lei Bi
- Department of Clinical Laboratory, Zibo Central Hospital, Shandong, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| |
Collapse
|
3
|
Zárate-Bonilla LJ, Del Portillo P, Sáenz-Suárez H, Gonzáles-Santos J, Barreto-Sampaio GE, Poutou-Piñales RA, Rey AF, Rey JG. Computational modeling and preliminary iroN, fepA, and cirA gene expression in Salmonella Enteritidis under iron-deficiency-induced conditions. Poult Sci 2014; 93:221-30. [PMID: 24570443 DOI: 10.3382/ps.2012-02993] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonellosis outbreaks in Europe, the United States, and Latin America have been associated with contaminated food derivatives including meat from the poultry industry. Salmonella grown under iron-limiting conditions has the capability to increase concentration of several iron-regulated outer-membrane proteins to augment the acquisition of the metal. These proteins have been proved to have immunogenic properties. Our aim was to increase the relative expression of iroN, fepA, and cirA in Salmonella Enteritidis domestic strain. Furthermore, we proposed a 3-dimensional structure model for each protein to predict and locate antigenic peptides. Our eventual objective is to produce an effective vaccine against regional avian salmonellosis. Two simple factorial designs were carried out to discriminate between 2 nitrogen sources and determine chelating-agent addition timing to augment relative gene expression. Two antigenic peptides located at the external face of each protein and 2 typical domains of iron-regulated outer-membrane proteins, plug and TonB-dep-Rec, were identified from the 3-dimensional models. Tryptone was selected as the best nitrogen source based on growth rate (μx = 0.36 h(-1)) and biomass productivity (Px = 0.9 g•h(-1)•L(-1)) as determined by a general factorial design. Optimum timing for chelating agent addition was in the middle of the log phase, which allowed relative expressions at 4 h of culture. Increase in iroN, fepA, and cirA relative expression was favored by the length of log phase and the addition of chelating agent, which decreased chelating toxicity and enhanced cell growth rate.
Collapse
|