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Lee KY, Schlesener CL, Aly SS, Huang BC, Li X, Atwill ER, Weimer BC. Whole genome sequence analysis reveals high genomic diversity and potential host-driven adaptations among multidrug-resistant Escherichia coli from pre-weaned dairy calves. Front Microbiol 2024; 15:1420300. [PMID: 39296303 PMCID: PMC11409426 DOI: 10.3389/fmicb.2024.1420300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/16/2024] [Indexed: 09/21/2024] Open
Abstract
Food-producing animals such as dairy cattle are potential reservoirs of antimicrobial resistance (AMR), with multidrug-resistant (MDR) organisms such as Escherichia coli observed in higher frequency in young calves compared to older cattle. In this study, we characterized the genomes of enteric MDR E. coli from pre-weaned dairy calves with and without diarrhea and evaluated the influence of host-level factors on genomic composition. Whole genome sequence comparative analysis of E. coli (n = 43) revealed substantial genomic diversity that primarily clustered by sequence type and was minimally driven by calf diarrheal disease status (healthy, diarrheic, or recovered), antimicrobial exposure, and dietary zinc supplementation. Diverse AMR genes (ARGs)-including extended-spectrum beta-lactamase genes and quinolone resistance determinants-were identified (n = 40), with unique sets of ARGs co-occurring in gene clusters with large AMR plasmids IncA/C2 and IncFIB(AP001918). Zinc supplementation was not significantly associated with the selection of individual ARGs in E. coli, however analysis of ARG and metal resistance gene pairs identified positive associations between certain aminoglycoside, beta-lactam, sulfonamide, and trimethoprim ARGs with acid, tellurium and mercury resistance genes. Although E. coli in this study lacked the typical virulence factors of diarrheagenic strains, virulence genes overlapping with those in major pathotypes were identified. Among the 103 virulence genes detected, the highest abundance and diversity of genes corresponded to iron acquisition (siderophores and heme uptake). Our findings indicate that the host-level factors evaluated in this study were not key drivers of genomic variability, but that certain accessory genes in enteric MDR E. coli may be enriched. Collectively, this work provides insight into the genomic diversity and host-microbe interface of MDR E. coli from pre-weaned dairy calves.
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Affiliation(s)
- Katie Y Lee
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Cory L Schlesener
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Sharif S Aly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
| | - Bihua C Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Xunde Li
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Edward R Atwill
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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Trinh P, Teichman S, Roberts MC, Rabinowitz PM, Willis AD. A cross-sectional comparison of gut metagenomes between dairy workers and community controls. BMC Genomics 2024; 25:708. [PMID: 39033279 DOI: 10.1186/s12864-024-10562-1] [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: 08/22/2023] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. RESULTS Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). CONCLUSIONS This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.
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Affiliation(s)
- Pauline Trinh
- Department of Biostatistics, University of Washington, Seattle, USA
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Sarah Teichman
- Department of Statistics, University of Washington, Seattle, USA
| | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Peter M Rabinowitz
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, USA.
- Department of Statistics, University of Washington, Seattle, USA.
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Garzon A, Basbas C, Schlesener C, Silva-del-Rio N, Karle BM, Lima FS, Weimer BC, Pereira RV. WGS of intrauterine E. coli from cows with early postpartum uterine infection reveals a non-uterine specific genotype and virulence factors. mBio 2024; 15:e0102724. [PMID: 38742889 PMCID: PMC11237492 DOI: 10.1128/mbio.01027-24] [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: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Escherichia coli has been attributed to playing a major role in a cascade of events that affect the prevalence and severity of uterine disease in cattle. The objectives of this project were to (i) define the association between the prevalence of specific antimicrobial resistance and virulence factor genes in E. coli with the clinical status related to uterine infection, (ii) identify the genetic relationship between E. coli isolates from cows with diarrhea, with mastitis, and with and without metritis, and (iii) determine the association between the phenotypic and genotypic antimicrobial resistance identified on the E. coli isolated from postpartum cattle. Bacterial isolates (n = 148) were obtained from a larger cross-sectional study. Cows were categorized into one of three clinical groups before enrollment: metritis, cows with purulent discharge, and control cows. For genomic comparison, public genomes (n = 130) from cows with diarrhea, mastitis, and metritis were included in a genome-wide association study, to evaluate differences between the drug classes or the virulence factor category among clinical groups. A distinct E. coli genotype associated with metritis could not be identified. Instead, a high genetic diversity among the isolates from uterine sources was present. A virulence factor previously associated with metritis (fimH) using PCR was not associated with metritis. There was moderate accuracy for whole-genome sequencing to predict phenotypic resistance, which varied depending on the antimicrobial tested. Findings from this study contradict the traditional pathotype classification and the unique intrauterine E. coli genotype associated with metritis in dairy cows.IMPORTANCEMetritis is a common infectious disease in dairy cattle and the second most common reason for treating a cow with antimicrobials. The pathophysiology of the disease is complex and is not completely understood. Specific endometrial pathogenic Escherichia coli have been reported to be adapted to the endometrium and sometimes lead to uterine disease. Unfortunately, the specific genomic details of the endometrial-adapted isolates have not been investigated using enough genomes to represent the genomic diversity of this organism to identify specific virulence genes that are consistently associated with disease development and severity. Results from this study provide key microbial ecological advances by elucidating and challenging accepted concepts for the role of Intrauterine E. coli in metritis in dairy cattle, especially contradicting the existence of a unique intrauterine E. coli genotype associated with metritis in dairy cows, which was not found in our study.
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Affiliation(s)
- Adriana Garzon
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Carl Basbas
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Cory Schlesener
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Noelia Silva-del-Rio
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Tulare, California, USA
| | - Betsy M. Karle
- Cooperative Extension, Division of Agriculture and Natural Resources, University of California, Orland, California, USA
| | - Fabio S. Lima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Richard V. Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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Romanò A, Ivanovic I, Segessemann T, Vazquez Rojo L, Widmer J, Egger L, Dreier M, Sesso L, Vaccani M, Schuler M, Frei D, Frey J, Ahrens CH, Steiner A, Graber HU. Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin. Front Microbiol 2023; 14:1183018. [PMID: 37583512 PMCID: PMC10425240 DOI: 10.3389/fmicb.2023.1183018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 08/17/2023] Open
Abstract
Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.
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Affiliation(s)
- Alicia Romanò
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ivana Ivanovic
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
| | - Tina Segessemann
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Laura Vazquez Rojo
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
| | - Jérôme Widmer
- Method Development and Analytics, Group Biochemistry of Milk, Agroscope, Bern, Switzerland
| | - Lotti Egger
- Method Development and Analytics, Group Biochemistry of Milk, Agroscope, Bern, Switzerland
| | - Matthias Dreier
- Food Microbial Systems, Group Cultures, Biodiversity, and Terroir, Agroscope, Bern, Switzerland
| | - Lorenzo Sesso
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michael Vaccani
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Martin Schuler
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Daniel Frei
- Method Development and Analytics, Group Molecular Diagnostics, Genomics, and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Juerg Frey
- Method Development and Analytics, Group Molecular Diagnostics, Genomics, and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Christian H. Ahrens
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Adrian Steiner
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hans Ulrich Graber
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
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Uzairue LI, Shittu OB, Ojo OE, Obuotor TM, Olanipekun G, Ajose T, Arogbonlo R, Medugu N, Ebruke B, Obaro SK. Antimicrobial resistance and virulence genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria. SAGE Open Med 2023; 11:20503121231175322. [PMID: 37223673 PMCID: PMC10201152 DOI: 10.1177/20503121231175322] [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] [Received: 12/27/2022] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Objectives Bacteremia due to invasive Salmonella enterica has been reported earlier in children in Nigeria. This study aimed to detect the virulence and antibiotic resistance genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria. Method From June 2015 to June 2018, 4163 blood cultures yielded 83 Salmonella isolates. This is a secondary cross-sectional analysis of the Salmonella isolates. The Salmonella enterica were isolated and identified using standard bacteriology protocol. Biochemical identifications of the Salmonella enterica were made by Phoenix MD 50 identification system. Further identification and confirmation were done with polyvalent antisera O and invA gene. Antimicrobial susceptibility testing was done following clinical and laboratory standard institute guidelines. Resistant genes and virulence genes were determined using a real-time polymerase chain reaction. Result Salmonella typhi 51 (61.4%) was the most prevalent serovar, followed by Salmonella species 13 (15.7%), choleraesuis 8 (9.6%), enteritidis 6 (7.2%), and typhimurium 5 (6.1%). Fifty-one (61.4%) of 83 Salmonella enterica were typhoidal, while 32 (38.6%) were not. Sixty-five (78.3%) of the 83 Salmonella enterica isolates were resistant to ampicillin and trimethoprim-sulfamethoxazole, followed by chloramphenicol 39 (46.7%), tetracycline 41 (41.4%), piperacillin 33 (33.9%), amoxicillin-clavulanate, and streptomycin 21 (25.3%), while cephalothin was 19 (22.9%). Thirty-nine (46.9%) of the 83 Salmonella enterica isolates were multi-drug resistant, and none were extensive drug resistant or pan-drug resistant. A blaTEM 42 (50.6%), floR 32 (38.6%), qnrA 24 (28.9%), tetB 20 (20.1%), tetA 10 (10.0%), and tetG 5 (6.0%) were the antibiotic resistance genes detected. There were perfect agreement between phenotypic and genotypic detection of antimicrobial resistance in tetracycline, ciprofloxacin, and chloramphenicol, while beta-lactam showed κ = 0.60 agreement. All of the Salmonella enterica isolates had the virulence genes invA, sopB, mgtC, and sip4D, while 33 (39.8%), 45 (51.8%), and 2 (2.4%) had ssaQ, spvC, and ljsGI-1, respectively. Conclusion Our findings showed multi-drug resistant Salmonella enterica in children with bacteremia in northern Nigeria. In addition, significant virulence and antimicrobial resistance genes were found in invasive Salmonella enterica in northern Nigeria. Thus, our study emphasizes the need to monitor antimicrobial resistance in Salmonella enterica from invasive sources in Nigeria and supports antibiotic prudence.
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Affiliation(s)
- Leonard I Uzairue
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Department of Medical Laboratory
Sciences, Federal University Oye Ekiti, Ekiti State, Nigeria
| | - Olufunke B Shittu
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Olufemi E Ojo
- Department of Veterinary Microbiology
and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Tolulope M Obuotor
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Grace Olanipekun
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Theresa Ajose
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Ronke Arogbonlo
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Nubwa Medugu
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Department of Microbiology and
Parasitology, National Hospital, Abuja, FCT, Nigeria
| | - Bernard Ebruke
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Stephen K Obaro
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Pediatric Infectious Division, the
University of Nebraska Medical Center, Omaha, NE, USA
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Trinh P, Roberts MC, Rabinowitz PM, Willis AD. Differences in gut metagenomes between dairy workers and community controls: a cross-sectional study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540270. [PMID: 37215025 PMCID: PMC10197731 DOI: 10.1101/2023.05.10.540270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens as they undergo evolution prior to a spillover event. In light of this, we are interested in characterizing the microbiome and resistome of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. Results Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of the human gut microbiome of 10 dairy farm workers and 6 community controls, supplementing these samples with additional publicly available gut metagenomes. We observed greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes in dairy workers' metagenomes, and lower average gene diversity. We also found evidence of commensal organism association with plasmid-mediated tetracycline resistance genes in both dairy workers and community controls (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). However, we did not find significant differences in the prevalence of resistance genes or virulence factors overall, nor differences in the taxonomic composition of dairy worker and community control metagenomes. Conclusions This study presents the first metagenomics analysis of United States dairy workers, providing insights into potential risks of exposure to antibiotics and pathogens in animal farming environments. Previous metagenomic studies of livestock workers in China and Europe have reported increased abundance and carriage of antibiotic resistance genes in livestock workers. While our investigation found no strong evidence for differences in the abundance or carriage of antibiotic resistance genes and virulence factors between dairy worker and community control gut metagenomes, we did observe patterns in the abundance of tetracycline resistance genes and the prevalence of cephamycin resistance genes that is consistent with previous work.
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Affiliation(s)
- Pauline Trinh
- Department of Environmental & Occupational Health Sciences, University of Washington
- Department of Biostatistics, University of Washington
| | - Marilyn C Roberts
- Department of Environmental & Occupational Health Sciences, University of Washington
| | - Peter M Rabinowitz
- Department of Environmental & Occupational Health Sciences, University of Washington
| | - Amy D Willis
- Department of Biostatistics, University of Washington
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Lee KY, Lavelle K, Huang A, Atwill ER, Pitesky M, Li X. Assessment of Prevalence and Diversity of Antimicrobial Resistant Escherichia coli from Retail Meats in Southern California. Antibiotics (Basel) 2023; 12:antibiotics12040782. [PMID: 37107144 PMCID: PMC10135137 DOI: 10.3390/antibiotics12040782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Retail meat products may serve as reservoirs and conduits for antimicrobial resistance, which is frequently monitored using Escherichia coli as indicator bacteria. In this study, E. coli isolation was conducted on 221 retail meat samples (56 chicken, 54 ground turkey, 55 ground beef, and 56 pork chops) collected over a one-year period from grocery stores in southern California. The overall prevalence of E. coli in retail meat samples was 47.51% (105/221), with E. coli contamination found to be significantly associated with meat type and season of sampling. From antimicrobial susceptibility testing, 51 isolates (48.57%) were susceptible to all antimicrobials tested, 54 (51.34%) were resistant to at least 1 drug, 39 (37.14%) to 2 or more drugs, and 21 (20.00%) to 3 or more drugs. Resistance to ampicillin, gentamicin, streptomycin, and tetracycline were significantly associated with meat type, with poultry counterparts (chicken or ground turkey) exhibiting higher odds for resistance to these drugs compared to non-poultry meats (beef and pork). From the 52 E. coli isolates selected to undergo whole-genome sequencing (WGS), 27 antimicrobial resistance genes (ARGs) were identified and predicted phenotypic AMR profiles with an overall sensitivity and specificity of 93.33% and 99.84%, respectively. Clustering assessment and co-occurrence networks revealed that the genomic AMR determinants of E. coli from retail meat were highly heterogeneous, with a sparsity of shared gene networks.
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Affiliation(s)
- Katie Yen Lee
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
- Western Institute for Food Safety and Security, University of California, Davis, Davis, CA 95616, USA
| | - Kurtis Lavelle
- Western Institute for Food Safety and Security, University of California, Davis, Davis, CA 95616, USA
| | - Anny Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Edward Robert Atwill
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Maurice Pitesky
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Xunde Li
- Western Institute for Food Safety and Security, University of California, Davis, Davis, CA 95616, USA
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Osman M, Altier C, Cazer C. Antimicrobial resistance among canine enterococci in the northeastern United States, 2007-2020. Front Microbiol 2023; 13:1025242. [PMID: 36687655 PMCID: PMC9849698 DOI: 10.3389/fmicb.2022.1025242] [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: 08/22/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Antimicrobial resistance (AMR) is a growing and complex One Health concern worldwide, threatening the practice of human and veterinary medicine. Although dogs are a potential reservoir of multidrug-resistant bacteria, there are very few surveillance studies on AMR from the canine population in the United States. Here, we assessed the antimicrobial susceptibility patterns, identified temporal resistance and minimum inhibitory concentration trends, and described associations between resistance phenotypes among canine clinical enterococci in the northeastern United States. Methods Through a large-scale retrospective study design, we collected species identification, minimum inhibitory concentration, and clinical data from 3,659 canine enterococci isolated at the Cornell University Animal Health Diagnostic Center between 2007 and 2020. We used the Mann-Kendall test, Sen's slope, multivariable logistic regression, and survival analysis models to detect the presence of a significant trend in resistance over the study period. Results Enterococcus faecalis was the most prevalent species (67.1% of isolates), followed by Enterococcus faecium (20.4%). We found high levels of AMR among enterococci to almost all the tested antimicrobials, particularly E. faecium. The lowest percentage of resistance was to vancomycin and chloramphenicol. Multidrug resistance was common (80% of E. faecium and 33% of E. faecalis) and 31 isolates were extensively drug resistant. Multidrug resistance among E. faecium increased over time, but not in E. faecalis. Resistance to penicillins, enrofloxacin, and rifampin increased during the study period, but resistance to tetracyclines is on a downward trajectory compared to AMR data from the last decade. Emerging vancomycin-resistant E. faecalis (0.3%) and E. faecium (0.8%) infections in the canine population are of great concern to both human and animal health. One E. faecium isolate with acquired vancomycin resistance was identified in 2017 and four vancomycin-resistant enterococci isolates were identified in 2020. Conclusion There is a crucial need to make rational prescribing decisions on the prudent use of antimicrobials and improve the quality of care for patients, especially when empirical antimicrobial treatment for enterococcal infection is common.
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Affiliation(s)
- Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY, United States,Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States,*Correspondence: Marwan Osman,
| | - Craig Altier
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Casey Cazer
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
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9
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Cui Q, Yu HD, Xu QJ, Liu Y, Wang YT, Li PH, Kong LC, Zhang HP, Jiang XY, Giuliodori AM, Fabbretti A, He CG, Ma HX. Antibiotic synergist OM19r reverses aminoglycoside resistance in multidrug-resistant Escherichia coli. Front Microbiol 2023; 14:1144946. [PMID: 37143537 PMCID: PMC10151501 DOI: 10.3389/fmicb.2023.1144946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/24/2023] [Indexed: 05/06/2023] Open
Abstract
Introduction The continued emergence and spread of multidrug-resistant (MDR) bacterial pathogens require a new strategy to improve the efficacy of existing antibiotics. Proline-rich antimicrobial peptides (PrAMPs) could also be used as antibacterial synergists due to their unique mechanism of action. Methods Utilizing a series of experiments on membrane permeability, In vitro protein synthesis, In vitro transcription and mRNA translation, to further elucidate the synergistic mechanism of OM19r combined with gentamicin. Results A proline-rich antimicrobial peptide OM19r was identified in this study and its efficacy against Escherichia coli B2 (E. coli B2) was evaluated on multiple aspects. OM19r increased antibacterial activity of gentamicin against multidrug-resistance E. coli B2 by 64 folds, when used in combination with aminoglycoside antibiotics. Mechanistically, OM19r induced change of inner membrane permeability and inhibited translational elongation of protein synthesis by entering to E. coli B2 via intimal transporter SbmA. OM19r also facilitated the accumulation of intracellular reactive oxygen species (ROS). In animal models, OM19r significantly improved the efficacy of gentamicin against E. coli B2. Discussion Our study reveals that OM19r combined with GEN had a strong synergistic inhibitory effect against multi-drug resistant E. coli B2. OM19r and GEN inhibited translation elongation and initiation, respectively, and ultimately affected the normal protein synthesis of bacteria. These findings provide a potential therapeutic option against multidrug-resistant E. coli.
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Affiliation(s)
- Qi Cui
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Han-Dong Yu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Qi-Jun Xu
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Yue Liu
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Yu-Ting Wang
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Peng-Hui Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Ling-Cong Kong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Hai-Peng Zhang
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Xiu-Yun Jiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Anna Maria Giuliodori
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Attilio Fabbretti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Cheng-Guang He
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
- Cheng-Guang He,
| | - Hong-Xia Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
- *Correspondence: Hong-Xia Ma,
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dos Santos RL, Davanzo EFA, Palma JM, Castro VHDL, da Costa HMB, Dallago BSL, Perecmanis S, Santana ÂP. Molecular characterization and biofilm-formation analysis of Listeria monocytogenes, Salmonella spp., and Escherichia coli isolated from Brazilian swine slaughterhouses. PLoS One 2022; 17:e0274636. [PMID: 36126071 PMCID: PMC9488830 DOI: 10.1371/journal.pone.0274636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
This study aimed to verify the presence of Listeria monocytogenes, Salmonella spp., and Escherichia coli in two Brazilian swine slaughterhouses, as well as to perform antibiograms, detect virulence and antimicrobial resistance genes, and evaluate the in vitro biofilm-forming capability of bacterial isolates from these environments. One Salmonella Typhi isolate and 21 E. coli isolates were detected, while L. monocytogenes was not detected. S. Typhi was isolated from the carcass cooling chamber’s floor, resistant to several antimicrobials, including nalidixic acid, cefazolin, chloramphenicol, doxycycline, streptomycin, gentamicin, tetracycline, and sulfonamide, and contained resistance genes, such as tet(B), tet(C), tet(M), and ampC. It also showed moderate biofilm-forming capacity at 37°C after incubating for 72 h. The prevalence of the 21 E. coli isolates was also the highest on the carcass cooling chamber floor (three of the four samplings [75%]). The E. coli isolates were resistant to 12 of the 13 tested antimicrobials, and none showed sensitivity to chloramphenicol, an antimicrobial prohibited in animal feed since 2003 in Brazil. The resistance genes MCR-1, MCR-3, sul1, ampC, clmA, cat1, tet(A), tet(B), and blaSHV, as well as the virulence genes stx-1, hlyA, eae, tir α, tir β, tir γ, and saa were detected in the E. coli isolates. Moreover, 5 (23.8%) and 15 (71.4%) E. coli isolates presented strong and moderate biofilm-forming capacity, respectively. In general, the biofilm-forming capacity increased after incubating for 72 h at 10°C. The biofilm-forming capacity was the lowest after incubating for 24 h at 37°C. Due to the presence of resistance and virulence genes, multi-antimicrobial resistance, and biofilm-forming capacity, the results of this study suggest a risk to the public health as these pathogens are associated with foodborne diseases, which emphasizes the hazard of resistance gene propagation in the environment.
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Affiliation(s)
- Rebecca Lavarini dos Santos
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, Federal District, Brazil
- * E-mail:
| | | | - Joana Marchesini Palma
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, Federal District, Brazil
| | | | | | - Bruno Stéfano Lima Dallago
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Simone Perecmanis
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, Federal District, Brazil
| | - Ângela Patrícia Santana
- Faculty of Agronomy and Veterinary Medicine, University of Brasília (UnB), Brasília, Federal District, Brazil
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11
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Turner A, Schubert H, Puddy EF, Sealey JE, Gould VC, Cogan TA, Avison MB, Reyher KK. Factors influencing the detection of antibacterial-resistant Escherichia coli in faecal samples from individual cattle. J Appl Microbiol 2021; 132:2633-2641. [PMID: 34923720 DOI: 10.1111/jam.15419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/14/2021] [Accepted: 12/15/2021] [Indexed: 11/26/2022]
Abstract
AIMS To investigate whether on-farm antibacterial usage (ABU), environmental antibacterial-resistant (ABR) Escherichia coli prevalence, sampling and sample handling methodologies are associated with ABR E. coli positivity in individual faecal samples from dairy heifers. METHODS AND RESULTS Three hundred and sixty-four heifers from 37 farms were sampled via rectal or faecal pat sampling. Samples were stored at -80°C for variable periods before microbiological analysis. Data analysis was done through a multilevel, multivariable logistic regression approach. Individual rectal samples had increased odds of positivity for amoxicillin-, cefalexin- and tetracycline-resistant E. coli. Sample storage for 6-12 months was associated with decreased odds of finding amoxicillin- and tetracycline-resistant E. coli. On-farm ABU had little influence, and environmental ABR E. coli prevalence had no significant influence on the odds of sample-level positivity for ABR E. coli. CONCLUSIONS Sampling methodology and sample handling have a greater association than on-farm factors with the detection of ABR E. coli in individual faecal samples from dairy heifers. SIGNIFICANCE AND IMPACT OF THE STUDY Sampling and storage methodologies should be considered carefully at the point of designing ABR surveillance studies in livestock and their environments and, where possible, these methodologies should be standardized between and within future studies.
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Affiliation(s)
| | | | | | - Jordan E Sealey
- University of Bristol School of Cellular and Molecular Medicine, Bristol, UK
| | - Virginia C Gould
- University of Bristol Vet School, Bristol, UK.,University of Bristol School of Cellular and Molecular Medicine, Bristol, UK
| | | | - Matthew B Avison
- University of Bristol School of Cellular and Molecular Medicine, Bristol, UK
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