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Che M, Fresno AH, Calvo-Fernandez C, Hasman H, Kurittu PE, Heikinheimo A, Hansen LT. Comparison of IncK- blaCMY-2 Plasmids in Extended-Spectrum Cephalosporin-Resistant Escherichia coli Isolated from Poultry and Humans in Denmark, Finland, and Germany. Antibiotics (Basel) 2024; 13:349. [PMID: 38667025 PMCID: PMC11047599 DOI: 10.3390/antibiotics13040349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/29/2024] Open
Abstract
Escherichia coli carrying IncK-blaCMY-2 plasmids mediating resistance to extended-spectrum cephalosporins (ESC) has been frequently described in food-producing animals and in humans. This study aimed to characterize IncK-blaCMY-2-positive ESC-resistant E. coli isolates from poultry production systems in Denmark, Finland, and Germany, as well as from Danish human blood infections, and further compare their plasmids. Whole-genome sequencing (Illumina) of all isolates (n = 46) confirmed the presence of the blaCMY-2 gene. Minimum inhibitory concentration (MIC) testing revealed a resistant phenotype to cefotaxime as well as resistance to ≥3 antibiotic classes. Conjugative transfer of the blaCMY-2 gene confirmed the resistance being on mobile plasmids. Pangenome analysis showed only one-third of the genes being in the core with the remainder being in the large accessory gene pool. Single nucleotide polymorphism (SNP) analysis on sequence type (ST) 429 and 1286 isolates showed between 0-60 and 13-90 SNP differences, respectively, indicating vertical transmission of closely related clones in the poultry production, including among Danish, Finnish, and German ST429 isolates. A comparison of 22 ST429 isolates from this study with 80 ST429 isolates in Enterobase revealed the widespread geographical occurrence of related isolates associated with poultry production. Long-read sequencing of a representative subset of isolates (n = 28) allowed further characterization and comparison of the IncK-blaCMY-2 plasmids with publicly available plasmid sequences. This analysis revealed the presence of highly similar plasmids in ESC-resistant E. coli from Denmark, Finland, and Germany pointing to the existence of common sources. Moreover, the analysis presented evidence of global plasmid transmission and evolution. Lastly, our results indicate that IncK-blaCMY-2 plasmids and their carriers had been circulating in the Danish production chain with an associated risk of spreading to humans, as exemplified by the similarity of the clinical ST429 isolate to poultry isolates. Its persistence may be driven by co-selection since most IncK-blaCMY-2 plasmids harbor resistance factors to drugs used in veterinary medicine.
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Affiliation(s)
- Meiyao Che
- National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (M.C.); (C.C.-F.)
| | - Ana Herrero Fresno
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Campus Terra, Universidade da Santiago de Compostela (USC), 27002 Lugo, Spain;
| | - Cristina Calvo-Fernandez
- National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (M.C.); (C.C.-F.)
| | - Henrik Hasman
- Reference Laboratory for Antibiotic Resistance, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark;
| | - Paula E. Kurittu
- Department of Food Health and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland; (P.E.K.); (A.H.)
| | - Annamari Heikinheimo
- Department of Food Health and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland; (P.E.K.); (A.H.)
- Microbiology Unit, Finnish Food Authority, Mustialankatu 3, 00790 Helsinki, Finland
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Woyda R, Oladeinde A, Endale D, Strickland T, Plumblee Lawrence J, Abdo Z. Genetic Characteristics of Salmonella Isolates Recovered From Reused Broiler Litter Over Three Successive Flocks. J Food Prot 2024; 87:100236. [PMID: 38307462 PMCID: PMC11000695 DOI: 10.1016/j.jfp.2024.100236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
Salmonella infections are a leading cause of bacterial food-borne illness worldwide. Infections are highly associated with the consumption of contaminated food, and in particular, chicken meat. The severity of Salmonella infections depends on the presence of antimicrobial resistance genes and virulence factors. While there are many studies which have investigated Salmonella strains isolated from postharvest chicken samples, there is a gap in our understanding of the genetic properties that influence the persistence of Salmonella in preharvest and in particular their makeup of antimicrobial resistance genes and virulence factors. We used whole genome sequencing and hierarchical clustering to characterize and classify the genetic diversity of Salmonella enterica isolates (n = 55) recovered from the litter of commercial broiler chicken raised in four colocated broiler houses of one integrated farm over three consecutive flocks. The chicken were raised under a newly adopted "No Antibiotics Ever" program, and copper sulfate was administered via drinking water. In-silico serovar prediction identified three S. enterica serovars: Enteritidis (n = 12), Kentucky (n = 40), and Senftenberg (n = 3). Antimicrobial susceptibility testing revealed that only one S. Kentucky isolate was resistant to streptomycin, while the remaining isolates were susceptible to all antibiotics tested. Metal resistance operons, including copper and silver, were identified chromosomally and on plasmids in serovar Senftenberg and Kentucky isolates, respectively, while serovar Enteritidis carried several virulence factors on plasmids. Serovar Kentucky isolates harboring metal resistance operons were the only Salmonella isolates recovered from the litter of third flock cohort. These results suggest that there might be environmental selection for Salmonella strains carrying plasmid-associated metal resistance and virulence genes, which could play a role in their persistence in litter.
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Affiliation(s)
- Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA; Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Dinku Endale
- Southeast Watershed Research, USDA, Tifton, Georgia, USA
| | | | | | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA; Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.
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Haley BJ, Salaheen S, Kim SW, Van Kessel JA. Virulome analysis of Escherichia coli ST117 from bovine sources identifies similarities and differences with strains isolated from other food animals. PLoS One 2024; 19:e0296514. [PMID: 38175844 PMCID: PMC10766182 DOI: 10.1371/journal.pone.0296514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
Escherichia coli ST117 is a pandemic extraintestinal pathogenic E. coli (ExPEC) causing significant morbidity globally. Poultry are a known reservoir of this pathogen, but the characteristics of ST117 strains from other animal sources have not been adequately investigated. Here we characterize the genomes of 36 ST117 strains recovered primarily from preweaned dairy calves, but also from older postweaned calves and lactating cows, in the context of other bovine-associated strains and strains from poultry, swine, and humans. Results of this study demonstrate that bovine-associated ST117 genomes encode virulence factors (VFs) known to be involved in extraintestinal infections, but also occasionally encode the Shiga toxin, a virulence factor (VF) involved in severe gastrointestinal infections and more frequently identified in E. coli from ruminants than other animals. Bovine-associated ST117 genomes were also more likely to encode afa-VIII (adhesins), pap (P-fimbriae), cdt (cytolethal distending toxin), and stx (Shiga toxins) than were poultry and swine-associated genomes. All of the ST117 genomes were grouped into seven virulence clusters, with bovine-associated genomes grouping into Clusters 1, 2, 4, 5, but not 3, 6, or 7. Major differences in the presence of virulence factors between clusters were observed as well. Antimicrobial resistance genes were detected in 112 of 122 (91%) bovine-associated genomes, with 103 of these being multidrug-resistant (MDR). Inclusion of genomes that differed from ST117 by one multi-locus sequence type (MLST) allele identified 31 STs, four of these among the bovine-associated genomes. These non-ST117 genomes clustered with the ST117 genomes suggesting that they may cause similar disease as ST117. Results of this study identify cattle as a reservoir of ST117 strains, some of which are highly similar to those isolated from other food animals and some of which have unique bovine-specific characteristics.
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Affiliation(s)
- Bradd J. Haley
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Serajus Salaheen
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Jo Ann Van Kessel
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
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Shoaib M, He Z, Geng X, Tang M, Hao R, Wang S, Shang R, Wang X, Zhang H, Pu W. The emergence of multi-drug resistant and virulence gene carrying Escherichia coli strains in the dairy environment: a rising threat to the environment, animal, and public health. Front Microbiol 2023; 14:1197579. [PMID: 37520353 PMCID: PMC10382034 DOI: 10.3389/fmicb.2023.1197579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/08/2023] [Indexed: 08/01/2023] Open
Abstract
Escherichia coli is a common inhabitant of the intestinal microbiota and is responsible for udder infection in dairy cattle and gastro-urinary tract infections in humans. We isolated E. coli strains from a dairy farm environment in Xinjiang, China, and investigated their epidemiological characteristics, phenotypic and genotypic resistance to antimicrobials, virulence-associated genes, and phylogenetic relationship. A total of 209 samples were collected from different sources (feces, slurry, water, milk, soil) and cultured on differential and selective agar media (MAC and EMB). The presumptive identification was done by the VITEK2 system and confirmed by 16S rRNA gene amplification by PCR. Antimicrobial susceptibility testing was done by micro-dilution assay, and genomic characterization was done by simple and multiplex polymerase chain reaction (PCR). A total of 338 E. coli strains were identified from 141/209 (67.5%) of the samples. Most of the E. coli strains were resistant to sulfamethoxazole/trimethoprim (62.43%), followed by cefotaxime (44.08%), ampicillin (33.73%), ciprofloxacin (31.36%), tetracycline (28.99%), and a lesser extent to florfenicol (7.99%), gentamicin (4.44%), amikacin (1.77%), and fosfomycin (1.18%). All of the strains were susceptible to meropenem, tigecycline, and colistin sulfate. Among the resistant strains, 44.4% were identified as multi-drug resistant (MDR) showing resistance to at least one antibiotic from ≥3 classes of antibiotics. Eighteen out of 20 antibiotic-resistance genes (ARGs) were detected with sul2 (67.3%), blaTEM (56.3%), gyrA (73.6%), tet(B) (70.4%), aph(3)-I (85.7%), floR (44.4%), and fosA3 (100%, 1/1) being the predominant genes among different classes of antibiotics. Among the virulence-associated genes (VAGs), ompA was the most prevalent (86.69%) followed by ibeB (85.0%), traT (84.91%), ompT (73.96%), fyuA (23.1%), iroN (23.1%), and irp2 gene (21.9%). Most of the E. coli strains were classified under phylogenetic group B1 (75.45%), followed by A (18.34%), C (2.96%), D (1.18%), E (1.18%), and F (0.30%). The present study identified MDR E. coli strains carrying widely distributed ARGs and VAGs from the dairy environment. The findings suggested that the dairy farm environment may serve as a source of mastitis-causing pathogens in animals and horizontal transfer of antibiotic resistance and virulence genes carrying bacterial strains to humans via contaminated milk and meat, surface water and agricultural crops.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Wanxia Pu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, China
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Zhou K, Sun L, Zhang X, Xu X, Mi K, Ma W, Zhang L, Huang L. Salmonella antimicrobials inherited and the non-inherited resistance: mechanisms and alternative therapeutic strategies. Front Microbiol 2023; 14:1176317. [PMID: 37303797 PMCID: PMC10249997 DOI: 10.3389/fmicb.2023.1176317] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/24/2023] [Indexed: 06/13/2023] Open
Abstract
Salmonella spp. is one of the most important foodborne pathogens. Typhoid fever and enteritis caused by Salmonella enterica are associated with 16-33 million infections and 500,000 to 600,000 deaths annually worldwide. The eradication of Salmonella is becoming increasingly difficult because of its remarkable capacity to counter antimicrobial agents. In addition to the intrinsic and acquired resistance of Salmonella, increasing studies indicated that its non-inherited resistance, which commonly mentioned as biofilms and persister cells, plays a critical role in refractory infections and resistance evolution. These remind the urgent demand for new therapeutic strategies against Salmonella. This review starts with escape mechanisms of Salmonella against antimicrobial agents, with particular emphasis on the roles of the non-inherited resistance in antibiotic failure and resistance evolution. Then, drug design or therapeutic strategies that show impressive effects in overcoming Salmonella resistance and tolerance are summarized completely, such as overcoming the barrier of outer membrane by targeting MlaABC system, reducing persister cells by limiting hydrogen sulfide, and applying probiotics or predatory bacteria. Meanwhile, according to the clinical practice, the advantages and disadvantages of above strategies are discussed. Finally, we further analyze how to deal with this tricky problems, thus can promote above novel strategies to be applied in the clinic as soon as possible. We believed that this review will be helpful in understanding the relationships between tolerance phenotype and resistance of Salmonella as well as the efficient control of antibiotic resistance.
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Affiliation(s)
- Kaixiang Zhou
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Lei Sun
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Xuehua Zhang
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Xiangyue Xu
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Kun Mi
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Wenjin Ma
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Lan Zhang
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Lingli Huang
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
- MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, Hubei, China
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Zwirzitz B, Oladeinde A, Johnson J, Zock G, Milfort MC, Fuller AL, Ghareeb AFA, Foutz JC, Teran JA, Woyda R, Abdo Z, Looft T, Lawrence JP, Cudnik D, Aggrey SE. Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses. Front Physiol 2023; 14:1083192. [PMID: 36935743 PMCID: PMC10018173 DOI: 10.3389/fphys.2023.1083192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
In this study, we investigated the dynamics of the ceca and litter microbiome of chickens from post-hatch through pre-harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of Escherichia coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and correlated with some of the environmental parameters measured (p < 0.05). We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (p < 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (p < 0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (p < 0.05).
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Affiliation(s)
- Benjamin Zwirzitz
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | | | - Jasmine Johnson
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Gregory Zock
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Marie C. Milfort
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | | | - Ahmed F. A. Ghareeb
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - James C. Foutz
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Jose Alexis Teran
- College of Engineering, University of Georgia, Athens, GA, United States
| | - Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Torey Looft
- USDA-ARS, National Animal Disease Center, Ames, IA, United States
| | | | - Denice Cudnik
- USDA-ARS, U.S. National Poultry Research Center, Athens, GA, United States
| | - Samuel E. Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA, United States
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Schnizlein MK, Young VB. Capturing the environment of the Clostridioides difficile infection cycle. Nat Rev Gastroenterol Hepatol 2022; 19:508-520. [PMID: 35468953 DOI: 10.1038/s41575-022-00610-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/11/2022]
Abstract
Clostridioides difficile (formerly Clostridium difficile) infection is a substantial health and economic burden worldwide. Great strides have been made over the past several years in characterizing the physiology of C. difficile infection, particularly regarding how gut microorganisms and their host work together to provide colonization resistance. As mammalian hosts and their indigenous gut microbiota have co-evolved, they have formed a complex yet stable relationship that prevents invading microorganisms from establishing themselves. In this Review, we discuss the latest advances in our understanding of C. difficile physiology that have contributed to its success as a pathogen, including its versatile survival factors and ability to adapt to unique niches. Using discoveries regarding microorganism-host and microorganism-microorganism interactions that constitute colonization resistance, we place C. difficile within the fiercely competitive gut environment. A comprehensive understanding of these relationships is required to continue the development of precision medicine-based treatments for C. difficile infection.
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Affiliation(s)
- Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, USA.
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Ott LC, Mellata M. Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation. Front Microbiol 2022; 13:891548. [PMID: 35847067 PMCID: PMC9280185 DOI: 10.3389/fmicb.2022.891548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.
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Affiliation(s)
- Logan C. Ott
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Melha Mellata
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Melha Mellata,
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Pławińska-Czarnak J, Wódz K, Kizerwetter-Świda M, Bogdan J, Kwieciński P, Nowak T, Strzałkowska Z, Anusz K. Multi-Drug Resistance to Salmonella spp. When Isolated from Raw Meat Products. Antibiotics (Basel) 2022; 11:antibiotics11070876. [PMID: 35884130 PMCID: PMC9311972 DOI: 10.3390/antibiotics11070876] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 12/10/2022] Open
Abstract
Salmonella spp. is the most frequent cause of foodborne diseases, and the increasing occurrence of MDR strains is an additional and increasing problem. We collected Salmonella spp. strains isolated from meat (poultry and pork) and analysed their antibiotic susceptibility profiles and the occurrence of resistance genes. To determine the susceptibility profiles and identify MDR strains, we used two MIC methods (MICRONAUT and VITEC2 Compact) and 25 antibiotics. Phenotypic tests showed that 53.84% strains were MDR. Finally, molecular analysis strains revealed the presence of blaSHV, blaPSE-1, blaTEM, but not blaCTX-M genes. Moreover, several genes were associated with resistance to aminoglycosides, cephalosporins, fluorochinolones, sulfonamides, and tetracyclines. This suggests that further research on the prevalence of antibiotic resistance genes (ARGs) in foodborne strains is needed, especially from a One Health perspective.
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Affiliation(s)
- Joanna Pławińska-Czarnak
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (J.B.); (Z.S.); (K.A.)
- Correspondence:
| | - Karolina Wódz
- Laboratory of Molecular Biology, Vet-Lab Brudzew, Ul. Turkowska 58c, 62-720 Brudzew, Poland; (K.W.); (P.K.); (T.N.)
| | - Magdalena Kizerwetter-Świda
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego Str. 8, 02-786 Warsaw, Poland;
| | - Janusz Bogdan
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (J.B.); (Z.S.); (K.A.)
| | - Piotr Kwieciński
- Laboratory of Molecular Biology, Vet-Lab Brudzew, Ul. Turkowska 58c, 62-720 Brudzew, Poland; (K.W.); (P.K.); (T.N.)
| | - Tomasz Nowak
- Laboratory of Molecular Biology, Vet-Lab Brudzew, Ul. Turkowska 58c, 62-720 Brudzew, Poland; (K.W.); (P.K.); (T.N.)
| | - Zuzanna Strzałkowska
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (J.B.); (Z.S.); (K.A.)
| | - Krzysztof Anusz
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (J.B.); (Z.S.); (K.A.)
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Vinayamohan PG, Pellissery AJ, Venkitanarayanan K. Role of Horizontal Gene Transfer in the Dissemination of Antimicrobial Resistance in Food Animal Production. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Wang Y, Ge H, Wei X, Zhao X. Research progress on antibiotic resistance of Salmonella. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Antibiotic abuse results in various antibiotic resistance among a number of foodborne bacteria, posing a severe threat to food safety. Antibiotic resistance genes are commonly detected in foodborne pathogens, which has sparked much interest in finding solutions to these issues. Various strategies against these drug-resistant pathogens have been studied, including new antibiotics and phages. Recently, a powerful tool has been introduced in the fight against drug-resistant pathogens, namely, clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) system aggregated by a prokaryotic defense mechanism. This review summarized the mechanism of antibiotic resistance in Salmonella and resistance to common antibiotics, analysed the relationship between Salmonella CRISPR-Cas and antibiotic resistance, discussed the changes in antibiotic resistance on the structure and function of CRISPR-Cas, and finally predicted the mechanism of CRISPR-Cas intervention in Salmonella antibiotic resistance. In the future, CRISPR-Cas is expected to become an important tool to reduce the threat of antibiotic-resistant pathogens in food safety.
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Affiliation(s)
- Yizhe Wang
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Hengwei Ge
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xinyue Wei
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
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12
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Bloomfield S, Duong VT, Tuyen HT, Campbell JI, Thomson NR, Parkhill J, Le Phuc H, Chau TTH, Maskell DJ, Perron GG, Ngoc NM, Vi LL, Adriaenssens EM, Baker S, Mather AE. Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam. Microb Genom 2022; 8. [PMID: 35511231 PMCID: PMC9465066 DOI: 10.1099/mgen.0.000798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Non-typhoidal Salmonella (NTS) is a major cause of bacterial enterocolitis globally but also causes invasive bloodstream infections. Antimicrobial resistance (AMR) hampers the treatment of these infections and understanding how AMR spreads between NTS may help in developing effective strategies. We investigated NTS isolates associated with invasive disease, diarrhoeal disease and asymptomatic carriage in animals and humans from Vietnam. Isolates included multiple serovars and both common and rare phenotypic AMR profiles; long- and short-read sequencing was used to investigate the genetic mechanisms and genomic backgrounds associated with phenotypic AMR profiles. We demonstrate concordance between most AMR genotypes and phenotypes but identified large genotypic diversity in clinically relevant phenotypes and the high mobility potential of AMR genes (ARGs) in this setting. We found that 84 % of ARGs identified were located on plasmids, most commonly those containing IncHI1A_1 and IncHI1B(R27)_1_R27 replicons (33%), and those containing IncHI2_1 and IncHI2A_1 replicons (31%). The vast majority (95%) of ARGS were found within 10 kbp of IS6/IS26 elements, which provide plasmids with a mechanism to exchange ARGs between plasmids and other parts of the genome. Whole genome sequencing with targeted long-read sequencing applied in a One Health context identified a comparatively limited number of insertion sequences and plasmid replicons associated with AMR. Therefore, in the context of NTS from Vietnam and likely for other settings as well, the mechanisms by which ARGs move contribute to a more successful AMR profile than the specific ARGs, facilitating the adaptation of bacteria to different environments or selection pressures.
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Affiliation(s)
| | | | - Ha Thanh Tuyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - James I Campbell
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Tran Thi Hong Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Gabriel G Perron
- Department of Biology, Bard College, Annandale-on-Hudson, New York, USA
| | | | - Lu Lan Vi
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.,University of East Anglia, Norwich, UK
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13
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Dorr M, Silver A, Smurlick D, Arukha A, Kariyawasam S, Oladeinde A, Cook K, Denagamage T. Transferability of ESBL-encoding IncN and IncI1 plasmids among field strains of different Salmonella serovars and Escherichia coli. J Glob Antimicrob Resist 2022; 30:88-95. [PMID: 35489678 DOI: 10.1016/j.jgar.2022.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/12/2022] [Accepted: 04/14/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES This study aimed to sequence, assemble and annotate three plasmids (two IncN and one IncI1) carrying the blaCTX-M-1 gene and assess their transmissibility rates between homologous and heterologous serovars and/or species of bacteria. METHODS First, the plasmids were sequenced, assembled, and annotated. They were then transferred from three donor strains (E. coli/IncN, S. Heidelberg/IncN, and S. Heidelberg/IncI1) into nine recipient strains (S. Enteritidis, S. Heidelberg, S. Saint Paul, S. Cero, S. Infantis, S. Braenderup, E. coli 50, and E. coli 2010). The blaCTX-M-1 gene PCR, plasmid isolation, and antimicrobial susceptibility testing were used on the transconjugants to confirm the successful transfer of ESBL plasmids into the recipient strains. RESULTS Both IncN plasmids were 42,407 bp in size and showed >99.4% similarity to the S. Bredeney pET1.2-IncN (GenBank accession CP043224.1) whereas the IncI1 plasmid was 107,635 bp in size and demonstrated >99.9% similarity to the E. coli pCOV33 plasmid (GenBank accession MG649046.1). Successful plasmid transfer was observed between donor E. coli (IncN) and all recipient strains except for E. coli 50 and between donor S. Heidelberg (IncN) and all recipient strains. Successful plasmid transfer was also observed between S. Heidelberg (IncI1) and E. coli 50. CONCLUSIONS Transfer of the bla CTX-M-1 encoding IncN and IncI1 plasmids via conjugation is possible yet occurs at different frequencies depending on the donor strain of bacteria with S. Heidelberg (IncN) having the highest donor-dependent transfer frequency, followed by E. coli 9079 (IncN) and S. Heidelberg (IncI1).
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Affiliation(s)
- Mackenzie Dorr
- University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | - Aryeh Silver
- University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | - Dylan Smurlick
- University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | - Ananta Arukha
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | - Subhashinie Kariyawasam
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA
| | | | - Kimberly Cook
- U.S. National Poultry Research Center, Athens, GA, 30605, USA
| | - Thomas Denagamage
- Department of Large Animal Clinical Sciences, University of Florida College of Veterinary Medicine, 1945 SW 16th Ave. Gainesville, FL 32608, USA.
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14
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Haley BJ, Kim SW, Salaheen S, Hovingh E, Van Kessel JAS. Virulome and genome analyses identify associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves. PLoS One 2022; 17:e0265445. [PMID: 35298535 PMCID: PMC8929554 DOI: 10.1371/journal.pone.0265445] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022] Open
Abstract
Food animals are known reservoirs of multidrug-resistant (MDR) Escherichia coli, but information regarding the factors influencing colonization by these organisms is lacking. Here we report the genomic analysis of 66 MDR E. coli isolates from non-redundant veal calf fecal samples. Genes conferring resistance to aminoglycosides, β-lactams, sulfonamides, and tetracyclines were the most frequent antimicrobial resistance genes (ARGs) detected and included those that confer resistance to clinically significant antibiotics (blaCMY-2, blaCTX-M, mph(A), erm(B), aac(6’)Ib-cr, and qnrS1). Co-occurrence analyses indicated that multiple ARGs significantly co-occurred with each other, and with metal and biocide resistance genes (MRGs and BRGs). Genomic analysis also indicated that the MDR E. coli isolated from veal calves were highly diverse. The most frequently detected genotype was phylogroup A-ST Cplx 10. A high percentage of isolates (50%) were identified as sequence types that are the causative agents of extra-intestinal infections (ExPECs), such as ST69, ST410, ST117, ST88, ST617, ST648, ST10, ST58, and ST167, and an appreciable number of these isolates encoded virulence factors involved in the colonization and infection of the human urinary tract. There was a significant difference in the presence of multiple accessory virulence factors (VFs) between MDR and susceptible strains. VFs associated with enterohemorrhagic infections, such as stx, tir, and eae, were more likely to be harbored by antimicrobial-susceptible strains, while factors associated with extraintestinal infections such as the sit system, aerobactin, and pap fimbriae genes were more likely to be encoded in resistant strains. A comparative analysis of SNPs between strains indicated that several closely related strains were recovered from animals on different farms indicating the potential for resistant strains to circulate among farms. These results indicate that veal calves are a reservoir for a diverse group of MDR E. coli that harbor various resistance genes and virulence factors associated with human infections. Evidence of co-occurrence of ARGs with MRGs, BRGs, and iron-scavenging genes (sit and aerobactin) may lead to management strategies for reducing colonization of resistant bacteria in the calf gut.
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Affiliation(s)
- Bradd J. Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
- * E-mail:
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Serajus Salaheen
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Ernest Hovingh
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States of America
| | - Jo Ann S. Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
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15
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Feng Y, Wang Y, Zhu B, Gao GF, Guo Y, Hu Y. Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes. Commun Biol 2021; 4:1305. [PMID: 34795385 PMCID: PMC8602611 DOI: 10.1038/s42003-021-02827-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
Gut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut, Lactobacillus aviarius and Lactobacillus crispatus were the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes. Feng et al. include genome recovery and data analysis of large number of chicken gut metagenomic datasets which significantly expands the reference genomes available from the chicken gut microbial communities, and catalog the genes prevalent in the gut systems. They further depict the countryspecific chicken gut antibiotic resistomes and the effects of geography and host species on the gut resistome.
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Affiliation(s)
- Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Yanan Wang
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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16
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Beaudry MS, Thomas JC, Baptista RP, Sullivan AH, Norfolk W, Devault A, Enk J, Kieran TJ, Rhodes OE, Perry-Dow KA, Rose LJ, Bayona-Vásquez NJ, Oladeinde A, Lipp EK, Sanchez S, Glenn TC. Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture. Environ Microbiol 2021; 23:7523-7537. [PMID: 34519156 DOI: 10.1111/1462-2920.15767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.
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Affiliation(s)
- Megan S Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Jesse C Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Center for Tropical and Emerging Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Amanda H Sullivan
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - William Norfolk
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Alison Devault
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Olin E Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA.,Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
| | - K Allison Perry-Dow
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura J Rose
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Division of Natural Science and Mathematics, Oxford College, Emory University, Oxford, GA, 30054, USA
| | - Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Erin K Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Susan Sanchez
- Department of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
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17
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Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the Southeastern United States. Microbiol Spectr 2021; 9:e0009721. [PMID: 34431703 PMCID: PMC8552609 DOI: 10.1128/spectrum.00097-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The prevalence of antibiotic resistance genes (ARGs) can be driven by direct selection from antibiotic use and indirect selection from substances such as heavy metals (HMs). While significant progress has been made to characterize the influence of HMs on the enrichment and dissemination of ARGs in the environment, there is still much we do not know. To fill this knowledge gap, we present a comprehensive analysis of gut bacteria associated with wild cotton mice (Peromyscus gossypinus) trapped from several areas affected by legacies of HM and radionuclide contamination. We explore how these contaminants affect gut microbial community (GMC) composition and diversity and the enrichment of antibiotic, biocide, and metal resistance genes. Although we were able to identify that a myriad of co-occurring antimicrobial and HM resistance genes appear in mice from all areas, including those without a history of contamination, the proportions of co-occurring ARGs and metal resistance genes (MRGs) are higher in sites with radionuclide contamination. These results support those from several previous studies and enhance our understanding of the coselection process, while providing new insights into the ubiquity of antimicrobial resistance in the resistome of wild animals. IMPORTANCE Antimicrobial resistance is a serious global public health concern because of its prevalence and ubiquitous distribution. The rapid dissemination of antibiotic resistance genes is thought to be the result of the massive overuse of antibiotics in agriculture and therapeutics. However, previous studies have demonstrated that the spread of antibiotic resistance genes can also be influenced by heavy metal contamination. This coselection phenomenon, whereby different resistance determinants are genetically linked on the same genetic element (coresistance) or a single genetic element provides resistance to multiple antimicrobial agents (cross-resistance), has profound clinical and environmental implications. In contrast to antibiotics, heavy metals can persist in the environment as a selection pressure for long periods of time. Thus, it is important to understand how antibiotic resistance genes are distributed in the environment and to what extent heavy metal contaminants may be driving their selection, which we have done in one environmental setting.
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18
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Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg. mSystems 2021; 6:e0072921. [PMID: 34427525 PMCID: PMC8409728 DOI: 10.1128/msystems.00729-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg, a model food pathogen, to test if chicks raised antibiotic free harbor transferable AR. We challenged chicks with an antibiotic-susceptible S. Heidelberg strain using various routes of inoculation and determined if S. Heidelberg isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole-genome sequencing (WGS) to show that chicks grown without antibiotics harbored an antimicrobial resistant S. Heidelberg population at 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing, we found that S. Heidelberg infection perturbed the microbiota of broiler chicks, and we used metagenomics and WGS to confirm that a commensal Escherichia coli population was the main reservoir of an IncI1 plasmid acquired by S. Heidelberg. The carriage of this IncI1 plasmid posed no fitness cost to S. Heidelberg but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of S. Heidelberg and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella enterica. IMPORTANCE The reported increase in antibiotic-resistant bacteria in humans has resulted in a major shift away from antibiotic use in food animal production. This shift has been driven by the assumption that removing antibiotics will select for antibiotic susceptible bacterial taxa, which in turn will allow the currently available antibiotic arsenal to be more effective. This change in practice has highlighted new questions that need to be answered to assess the effectiveness of antibiotic removal in reducing the spread of antibiotic resistance bacteria. This research demonstrates that antibiotic-susceptible Salmonella enterica serovar Heidelberg strains can acquire multidrug resistance from commensal bacteria present in the gut of neonatal broiler chicks, even in the absence of antibiotic selection. We demonstrate that exposure to acidic pH drove the horizontal transfer of antimicrobial resistance plasmids and suggest that simply removing antibiotics from food animal production might not be sufficient to limit the spread of antimicrobial resistance.
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19
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Kern L, Abdeen SK, Kolodziejczyk AA, Elinav E. Commensal inter-bacterial interactions shaping the microbiota. Curr Opin Microbiol 2021; 63:158-171. [PMID: 34365152 DOI: 10.1016/j.mib.2021.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022]
Abstract
The gut microbiota, a complex ecosystem of microorganisms of different kingdoms, impacts host physiology and disease. Within this ecosystem, inter-bacterial interactions and their impacts on microbiota community structure and the eukaryotic host remain insufficiently explored. Microbiota-related inter-bacterial interactions range from symbiotic interactions, involving exchange of nutrients, enzymes, and genetic material; competition for nutrients and space, mediated by biophysical alterations and secretion of toxins and anti-microbials; to predation of overpopulating bacteria. Collectively, these understudied interactions hold important clues as to forces shaping microbiota diversity, niche formation, and responses to signals perceived from the host, incoming pathogens and the environment. In this review, we highlight the roles and mechanisms of selected inter-bacterial interactions in the microbiota, and their potential impacts on the host and pathogenic infection. We discuss challenges in mechanistically decoding these complex interactions, and prospects of harnessing them as future targets for rational microbiota modification in a variety of diseases.
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Affiliation(s)
- Lara Kern
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Suhaib K Abdeen
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | | | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel; Cancer-Microbiota Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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20
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Melo RT, Galvão NN, Guidotti-Takeuchi M, Peres PABM, Fonseca BB, Profeta R, Azevedo VAC, Monteiro GP, Brenig B, Rossi DA. Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil. Front Microbiol 2021; 12:674147. [PMID: 34220757 PMCID: PMC8253257 DOI: 10.3389/fmicb.2021.674147] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/12/2021] [Indexed: 12/02/2022] Open
Abstract
The aim of the study was to evaluate the genotypic and phenotypic characteristics of 20 strains of S. Heidelberg (SH) isolated from broilers produced in southern Brazil. The similarity and presence of genetic determinants linked to virulence, antimicrobial resistance, biofilm formation, and in silico-predicted metabolic interactions revealed this serovar as a threat to public health. The presence of the ompC, invA, sodC, avrA, lpfA, and agfA genes was detected in 100% of the strains and the luxS gene in 70% of them. None of the strains carries the blaSHV, mcr-1, qnrA, qnrB, and qnrS genes. All strains showed a multidrug-resistant profile to at least three non-β-lactam drugs, which include colistin, sulfamethoxazole, and tetracycline. Resistance to penicillin, ceftriaxone (90%), meropenem (25%), and cefoxitin (25%) were associated with the presence of blaCTX–M and blaCMY–2 genes. Biofilm formation reached a mature stage at 25 and 37°C, especially with chicken juice (CJ) addition. The sodium hypochlorite 1% was the least efficient in controlling the sessile cells. Genomic analysis of two strains identified more than 100 virulence genes and the presence of resistance to 24 classes of antibiotics correlated to phenotypic tests. Protein-protein interaction (PPI) prediction shows two metabolic pathways correlation with biofilm formation. Virulence, resistance, and biofilm determinants must be constant monitoring in SH, due to the possibility of occurring infections extremely difficult to cure and due risk of the maintenance of the bacterium in production environments.
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Affiliation(s)
- Roberta T Melo
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Newton N Galvão
- Ministry of Agriculture, Livestock and Supply, Rio de Janeiro, Brazil
| | | | - Phelipe A B M Peres
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Belchiolina B Fonseca
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme P Monteiro
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Daise A Rossi
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
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21
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Abstract
Antimicrobial resistance (AMR) is an important global health threat that impacts millions of people worldwide each year. Developing methods that can detect and predict AMR phenotypes can help to mitigate the spread of AMR by informing clinical decision making and appropriate mitigation strategies. Many bioinformatic methods have been developed for predicting AMR phenotypes from whole-genome sequences and AMR genes, but recent studies have indicated that predictions can be made from incomplete genome sequence data. In order to more systematically understand this, we built random forest-based machine learning classifiers for predicting susceptible and resistant phenotypes for Klebsiella pneumoniae (1,640 strains), Mycobacterium tuberculosis (2,497 strains), and Salmonella enterica (1,981 strains). We started by building models from alignments that were based on a reference chromosome for each species. We then subsampled each chromosomal alignment and built models for the resulting subalignments, finding that very small regions, representing approximately 0.1 to 0.2% of the chromosome, are predictive. In K. pneumoniae, M. tuberculosis, and S. enterica, the subalignments are able to predict multiple AMR phenotypes with at least 70% accuracy, even though most do not encode an AMR-related function. We used these models to identify regions of the chromosome with high and low predictive signals. Finally, subalignments that retain high accuracy across larger phylogenetic distances were examined in greater detail, revealing genes and intergenic regions with potential links to AMR, virulence, transport, and survival under stress conditions. IMPORTANCE Antimicrobial resistance causes thousands of deaths annually worldwide. Understanding the regions of the genome that are involved in antimicrobial resistance is important for developing mitigation strategies and preventing transmission. Machine learning models are capable of predicting antimicrobial resistance phenotypes from bacterial genome sequence data by identifying resistance genes, mutations, and other correlated features. They are also capable of implicating regions of the genome that have not been previously characterized as being involved in resistance. In this study, we generated global chromosomal alignments for Klebsiella pneumoniae, Mycobacterium tuberculosis, and Salmonella enterica and systematically searched them for small conserved regions of the genome that enable the prediction of antimicrobial resistance phenotypes. In addition to known antimicrobial resistance genes, this analysis identified genes involved in virulence and transport functions, as well as many genes with no previous implication in antimicrobial resistance.
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22
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Lone A, Mottawea W, Mehdi Y, Hammami R. Bacteriocinogenic probiotics as an integrated alternative to antibiotics in chicken production - why and how? Crit Rev Food Sci Nutr 2021; 62:8744-8760. [PMID: 34060404 DOI: 10.1080/10408398.2021.1932722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The misuse of antibiotics in the livestock industry has played an important role in the spread of resistant superbugs with severe health implications for humans. With the recent ban on the use of antibiotics in poultry and poultry feed in Canada and the USA, poultry farmers will have to rely on the use of alternatives to antibiotics (such as feed acidifiers, antibodies, bacteriophages, antimicrobial peptides, prebiotics, and probiotics) to maintain the same productivity and health of their livestock. Of particular interest are bacteriocinogenic probiotics, that is, bacterial strains capable of producing bacteriocins that confer health benefits on the host. These bacterial strains have multiple promising features, such as the ability to attach to the host mucosa, colonize, proliferate, and produce advantageous products such as bacteriocins and short-chain fatty acids. These not only affect pathogenic colonization but improve poultry phenotype as well. Bacteriocins are antimicrobial peptides with multiple promising features such as being non-harmful for human and animal consumption, non-disruptive to the host microbiota eubiosis, non-cytotoxic, and non-carcinogenic. Therefore, bacteriocinogenic probiotics are at the forefront to be excellent candidates for effective replacements to antibiotics. While evidence of their safety and effectiveness is accumulating in vitro and in vivo in inhibiting pathogens while promoting animal health, their safety and history of use in livestock remains unclear and requires additional investigations. In the present paper, we review the safety assessment regulations and commercialization policies on existing and novel bacteriocinogenic and bacteriocin products intended to be used in poultry feed as an alternative to antibiotics.
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Affiliation(s)
- Ayesha Lone
- GUT Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Walid Mottawea
- GUT Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada.,Faculty of Pharmacy, Department of Microbiology and Immunology, Mansoura University, Mansoura, Egypt
| | - Youcef Mehdi
- Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, Canada
| | - Riadh Hammami
- GUT Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
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23
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Ibekwe A, Durso L, Ducey TF, Oladeinde A, Jackson CR, Frye JG, Dungan R, Moorman T, Brooks JP, Obayiuwana A, Karathia H, Fanelli B, Hasan N. Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum β-Lactamase in Escherichia coli from Different Animal Sources. Microorganisms 2021; 9:microorganisms9051057. [PMID: 34068339 PMCID: PMC8153348 DOI: 10.3390/microorganisms9051057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 12/25/2022] Open
Abstract
Antimicrobial resistance associated with the spread of plasmid-encoded extended-spectrum β-lactamase (ESBL) genes conferring resistance to third generation cephalosporins is increasing worldwide. However, data on the population of ESBL producing E. coli in different animal sources and their antimicrobial characteristics are limited. The purpose of this study was to investigate potential reservoirs of ESBL-encoded genes in E. coli isolated from swine, beef, dairy, and poultry collected from different regions of the United States using whole-genome sequencing (WGS). Three hundred isolates were typed into different phylogroups, characterized by BOX AIR-1 PCR and tested for resistance to antimicrobials. Of the 300 isolates, 59.7% were resistant to sulfisoxazole, 49.3% to tetracycline, 32.3% to cephalothin, 22.3% to ampicillin, 20% to streptomycin, 16% to ticarcillin; resistance to the remaining 12 antimicrobials was less than 10%. Phylogroups A and B1 were most prevalent with A (n = 92, 30%) and B1 (87 = 29%). A total of nine E. coli isolates were confirmed as ESBL producers by double-disk synergy testing and multidrug resistant (MDR) to at least three antimicrobial drug classes. Using WGS, significantly higher numbers of ESBL-E. coli were detected in swine and dairy manure than from any other animal sources, suggesting that these may be the primary animal sources for ESBL producing E. coli. These isolates carry plasmids, such as IncFIA(B), IncFII, IncX1, IncX4, IncQ1, CollRNAI, Col440I, and acquired ARGs aph(6)-Id, aph(3″)-Ib, aadA5, aph(3')-Ia, blaCTX-M-15, blaTEM-1B, mphA, ermB, catA1, sul1, sul2, tetB, dfrA17. One of the E. coli isolates from swine with ST 410 was resistant to nine antibiotics and carried more than 28 virulence factors, and this ST has been shown to belong to an international high-risk clone. Our data suggests that ESBL producing E. coli are widely distributed in different animal sources, but swine and dairy cattle may be their main reservoir.
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Affiliation(s)
- Abasiofiok Ibekwe
- US Salinity Laboratory, Agricultural Research Service, United States Department of Agriculture, Riverside, CA 92507, USA
- Correspondence:
| | - Lisa Durso
- Agricultural Research Service, United States Department of Agriculture, Lincoln, NE 68583, USA;
| | - Thomas F. Ducey
- Agricultural Research Service, United States Department of Agriculture, Florence, SC 29501, USA;
| | - Adelumola Oladeinde
- Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, USA; (A.O.); (C.R.J.); (J.G.F.)
| | - Charlene R. Jackson
- Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, USA; (A.O.); (C.R.J.); (J.G.F.)
| | - Jonathan G. Frye
- Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, USA; (A.O.); (C.R.J.); (J.G.F.)
| | - Robert Dungan
- Agricultural Research Service, United States Department of Agriculture, Kimberly, ID 83341, USA;
| | - Tom Moorman
- Agricultural Research Service, United States Department of Agriculture, Ames, IA 50011, USA;
| | - John P. Brooks
- Agricultural Research Service, United States Department of Agriculture, Mississippi State, MS 39762, USA;
| | - Amarachukwu Obayiuwana
- Department of Biological Sciences (Microbiology Option), Augustine University Ilara (AUI), Epe 106101, Lagos State, Nigeria;
| | - Hiren Karathia
- CosmosID Inc., Rockville, MD 20850, USA; (H.K.); (B.F.); (N.H.)
| | - Brian Fanelli
- CosmosID Inc., Rockville, MD 20850, USA; (H.K.); (B.F.); (N.H.)
| | - Nur Hasan
- CosmosID Inc., Rockville, MD 20850, USA; (H.K.); (B.F.); (N.H.)
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20878, USA
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24
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Taviani E, Muchongo A, Kim SW, Van Kessel JAS, Haley BJ. Genomic Analysis of Antibiotic-Resistant and -Susceptible Escherichia coli Isolated from Bovine Sources in Maputo, Mozambique. Foodborne Pathog Dis 2021; 18:426-435. [PMID: 33978455 DOI: 10.1089/fpd.2020.2901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
This study reports a genomic analysis of Escherichia coli isolates recovered from 25 bovine fecal composite samples collected from four different production units in Maputo city and around Maputo Province, Mozambique. The genomes were analyzed to determine the presence of antibiotic resistance genes (ARGs), genetic relatedness, and virulence factors known to cause diseases in humans. Whole-genome sequencing was conducted on 28 isolates using an Illumina NextSeq 500 sequencing platform. The genomes were analyzed using BLASTN for the presence of resistance genes and virulence factors, as well as to determine their phylogenetic groups, sequence types (ST), and ST complexes (ST Cplxs). The majority of the isolates (85%) were identified as members of phylogenetic groups B1, with fewer isolates identified as members of group A, and a single isolate identified as group "E/Clade I." The ST analysis demonstrated a higher level of diversity than the phylogenetic group analysis. Sixteen different STs, five ST Cplxs, and seven singleton complexes were identified. A strain identified as a novel ST (ST9215) showed a high level of similarity with an isolate recovered from a wild animal in the Gambia. Seven different ARGs were identified, with tet(B) being the most frequently detected, followed by aph(3″)-Ib, aph(6)-Id, sul2, blaTEM-1B, and dfrA1. Three isolates encoded β-lactam-conferring point mutations in the ampC promoter (-42C>T). In total, 51 different virulence factors were identified among the genomes. This study demonstrates that E. coli from bovine sources in Mozambique encoded multiple antibiotic resistance elements, plasmids, and virulence factors. To the best of our knowledge, this is the first genomic description of antibiotic-resistant E. coli isolated from bovine sources in Mozambique.
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Affiliation(s)
- Elisa Taviani
- Center of Biotechnology, University Eduardo Mondlane, Maputo, Mozambique.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Arsenio Muchongo
- Center of Biotechnology, University Eduardo Mondlane, Maputo, Mozambique
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland, USA
| | - Jo Ann S Van Kessel
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland, USA
| | - Bradd J Haley
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland, USA
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25
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Lin Z, Yuan T, Zhou L, Cheng S, Qu X, Lu P, Feng Q. Impact factors of the accumulation, migration and spread of antibiotic resistance in the environment. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:1741-1758. [PMID: 33123928 DOI: 10.1007/s10653-020-00759-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance is a great concern, which leads to global public health risks and ecological and environmental risks. The presence of antibiotic-resistant genes and antibiotic-resistant bacteria in the environment exacerbates the risk of spreading antibiotic resistance. Among them, horizontal gene transfer is an important mode in the spread of antibiotic resistance genes, and it is one of the reasons that the antibiotic resistance pollution has become increasingly serious. At the same time, free antibiotic resistance genes and resistance gene host bacterial also exist in the natural environment. They can not only affect horizontal gene transfer, but can also migrate and aggregate among environmental media in many ways and then continue to affect the proliferate and transfer of antibiotic resistance genes. All this shows the seriousness of antibiotic resistance pollution. Therefore, in this review, we reveal the sensitive factors affecting the distribution and spread of antibiotic resistance through three aspects: the influencing factors of horizontal gene transfer, the host bacteria of resistance genes and the migration of antibiotic resistance between environmental media. This review reveals the huge role of environmental migration in the spread of antibiotic resistance, and the environmental behavior of antibiotic resistance deserves wider attention. Meanwhile, extracellular antibiotic resistance genes and intracellular antibiotic resistance genes play different roles, so they should be studied separately.
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Affiliation(s)
- Zibo Lin
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Tao Yuan
- Department of Construction Equipment and Municipal Engineering, Jiangsu Vocational Institute of Architectural Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
- Jiangsu Collaborative Innovation Center for Building Energy Saving and Construct Technology, Xuzhou, 221116, China
| | - Lai Zhou
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Sen Cheng
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Xu Qu
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Ping Lu
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China.
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China.
| | - Qiyan Feng
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
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26
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Beaudry MS, Wang J, Kieran TJ, Thomas J, Bayona-Vásquez NJ, Gao B, Devault A, Brunelle B, Lu K, Wang JS, Rhodes OE, Glenn TC. Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment. Front Microbiol 2021; 12:644662. [PMID: 33986735 PMCID: PMC8110821 DOI: 10.3389/fmicb.2021.644662] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases, but are much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having <78% sequence identity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average > 400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely due in part to the extent and curation of the reference databases considered. Thus, enriching existing aliquots of shotgun metagenomic libraries and obtaining modest numbers of reads from them offers an efficient orthogonal method for assessment of bacterial community composition.
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Affiliation(s)
- Megan S. Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jincheng Wang
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jesse Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | | | | | - Kun Lu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jia-Sheng Wang
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
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27
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Szmolka A, Wami H, Dobrindt U. Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli. Front Microbiol 2021; 12:642125. [PMID: 33717039 PMCID: PMC7947892 DOI: 10.3389/fmicb.2021.642125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/03/2021] [Indexed: 01/06/2023] Open
Abstract
Introduction Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants. Objectives In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources. Results The core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers. Conclusion This is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.
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Affiliation(s)
- Ama Szmolka
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Haleluya Wami
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
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28
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Park CJ, Li J, Zhang X, Gao F, Benton CS, Andam CP. Diverse lineages of multidrug resistant clinical Salmonella enterica and a cryptic outbreak in New Hampshire, USA revealed from a year-long genomic surveillance. INFECTION GENETICS AND EVOLUTION 2020; 87:104645. [PMID: 33246085 DOI: 10.1016/j.meegid.2020.104645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/11/2020] [Accepted: 11/22/2020] [Indexed: 01/02/2023]
Abstract
Salmonella enterica, the causative agent of gastrointestinal diseases and typhoid fever, is a human and animal pathogen that causes significant mortality and morbidity worldwide. In this study, we examine the genomic diversity and phylogenetic relationships of 63 S. enterica isolates from human-derived clinical specimens submitted to the Department of Health and Human Services (DHHS) in the state of New Hampshire, USA in 2017. We found a remarkably large genomic, phylogenetic and serotype variation among the S. enterica isolates, dominated by serotypes Enteritidis (sequence type [ST] 11), Heidelberg (ST 15) and Typhimurium (ST 19). Analysis of the distribution of single nucleotide polymorphisms in the core genome suggests that the ST 15 cluster is likely a previously undetected or cryptic outbreak event that occurred in the south/southeastern part of New Hampshire in August-September. We found that nearly all of the clinical S. enterica isolates carried horizontally acquired genes that confer resistance to multiple classes of antimicrobials, most notably aminoglycosides, fluoroquinolones and macrolides. Majority of the isolates (76.2%) carry at least four resistance determinants per genome. We also detected the genes mdtK and mdsABC that encode multidrug efflux pumps and the gene sdiA that encodes a regulator for a third multidrug resistance pump. Our results indicate rapid microevolution and geographical dissemination of multidrug resistant lineages over a short time span. These findings are critical to aid the DHHS and similar public health laboratories in the development of effective disease control measures, epidemiological studies and treatment options for serious Salmonella infections.
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Affiliation(s)
- Cooper J Park
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Jinfeng Li
- New Hampshire Department of Health and Human Services, 29 Hazen Drive, Concord, NH, USA
| | - Xinglu Zhang
- New Hampshire Department of Health and Human Services, 29 Hazen Drive, Concord, NH, USA
| | - Fengxiang Gao
- New Hampshire Department of Health and Human Services, 29 Hazen Drive, Concord, NH, USA
| | - Christopher S Benton
- New Hampshire Department of Health and Human Services, 29 Hazen Drive, Concord, NH, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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29
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Aljahdali NH, Sanad YM, Han J, Foley SL. Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota. BMC Microbiol 2020; 20:353. [PMID: 33203384 PMCID: PMC7673091 DOI: 10.1186/s12866-020-02008-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/12/2020] [Indexed: 12/27/2022] Open
Abstract
In the past decade, the initial studies of the gut microbiota started focusing on the correlation of the composition of the gut microbiota and the health or diseases of the host, and there are extensive literature reviews pertaining to this theme. However, little is known about the association between the microbiota, the host, and pathogenic bacteria, such as Salmonella enterica, which is among the most important foodborne pathogens and identified as the source of multiple outbreaks linked to contaminated foods causing salmonellosis. Secretion systems, flagella, fimbriae, endotoxins, and exotoxins are factors that play the most important roles in the successful infection of the host cell by Salmonella. Infections with S. enterica, which is a threat to human health, can alter the genomic, taxonomic, and functional traits of the gut microbiota. The purpose of this review is to outline the state of knowledge on the impacts of S. enterica on the intestinal microbiota and highlight the need to identify the gut bacteria that could contribute to salmonellosis.
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Affiliation(s)
- Nesreen H Aljahdali
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.,Biological Science Department, College of Science, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Yasser M Sanad
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.,Department of Agriculture, University of Arkansas, Pine Bluff, AR, USA.,Department of Parasitology and Animal Diseases, Veterinary Research Division, National Research Centre, Giza, Egypt
| | - Jing Han
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Steven L Foley
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
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30
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Kleiner M, Bushnell B, Sanderson KE, Hooper LV, Duerkop BA. Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities. MICROBIOME 2020; 8:158. [PMID: 33190645 PMCID: PMC7667829 DOI: 10.1186/s40168-020-00935-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range of HGT in polymicrobial environments is limited, as we currently rely on historical HGT events inferred from genome sequencing and studies involving cultured microorganisms. We lack approaches to observe ongoing HGT in microbial communities. RESULTS To address this knowledge gap, we developed a DNA sequencing-based "transductomics" approach that detects and characterizes microbial DNA transferred via transduction. We validated our approach using model systems representing a range of transduction modes and show that we can detect numerous classes of transducing DNA. Additionally, we show that we can use this methodology to obtain insights into DNA transduction among all major taxonomic groups of the intestinal microbiome. CONCLUSIONS The transductomics approach that we present here allows for the detection and characterization of genes that are potentially transferred between microbes in complex microbial communities at the time of measurement and thus provides insights into real-time ongoing horizontal gene transfer. This work extends the genomic toolkit for the broader study of mobile DNA within microbial communities and could be used to understand how phenotypes spread within microbiomes. Video Abstract.
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Affiliation(s)
- Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
| | - Brian Bushnell
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kenneth E Sanderson
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA.
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31
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Herrera-Sánchez MP, Rodríguez-Hernández R, Rondón-Barragán IS. Molecular characterization of antimicrobial resistance and enterobacterial repetitive intergenic consensus-PCR as a molecular typing tool for Salmonella spp. isolated from poultry and humans. Vet World 2020; 13:1771-1779. [PMID: 33132588 PMCID: PMC7566269 DOI: 10.14202/vetworld.2020.1771-1779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/14/2020] [Indexed: 01/01/2023] Open
Abstract
Background and Aim: Salmonella spp. are one of the most important food-borne pathogens in the world, emerging as a major public health concern. Moreover, multidrug-resistant (MDR) strains have been isolated from salmonellosis outbreaks, which compromise its treatment success. This study was conducted to characterize the phenotypic and genotypic antibiotic resistance profile of Salmonella strains isolated from broilers and humans from the regions of Tolima and Santander (Colombia). Materials and Methods: Salmonella spp. strains (n=49) were confirmed through molecular detection by amplification of the invA gene. Phenotypic antibiotic resistance was determined by the automated method and the agar diffusion method, and the presence of resistance genes was evaluated by PCR. Genotypic characterization was conducted using the enterobacterial repetitive intergenic consensus (ERIC)-PCR method, from which a dendrogram was generated and the possible phylogenetic relationships were established. Results: Salmonella isolates were classified as MDR strains exhibiting resistance to four antibiotic classes, penicillins, aminoglycosides, sulfonamides, and cephalosporins, and the human strains were resistant to gentamicin. At the genotypic level, the isolates contained the genes blaCMY2, blaCTX-M, blaPSE-1, blaTEM, aadA1, srtB, dfrA1, sul2, and floR. The genotyping results obtained by ERIC-PCR allowed the grouping of strains according to the source of isolation. Conclusion: The Salmonella spp. strains exhibited resistance to multiple antibiotics, as well as multiple genes associated with them, and the ERIC-PCR method was a technique that was helpful in generating clusters with biological significance.
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Affiliation(s)
- María Paula Herrera-Sánchez
- Research Group in Immunology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
| | - Roy Rodríguez-Hernández
- Poultry Research Group, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
| | - Iang Schroniltgen Rondón-Barragán
- Research Group in Immunology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia.,Poultry Research Group, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué, Tolima, Colombia
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Martins AF, Rabinowitz P. The impact of antimicrobial resistance in the environment on public health. Future Microbiol 2020; 15:699-702. [DOI: 10.2217/fmb-2019-0331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Andreza Francisco Martins
- Department of Microbiology, Immunology & Parasitology, Federal University of Rio Grande do Sul, Sarmento Leite 500, Porto Alegre, 90050 170, RS, Brazil
| | - Peter Rabinowitz
- Department of Environmental & Occupational Health Sciences, Center of One Health Research, University of Washington, Seattle, WA 98195, USA
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