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Wang C, Wu S, Zhou W, Hu L, Hu Q, Cao Y, Wang L, Chen X, Zhang Q. Effects of Neolamarckia cadamba leaves extract on microbial community and antibiotic resistance genes in cecal contents and feces of broilers challenged with lipopolysaccharides. Appl Environ Microbiol 2024; 90:e0110723. [PMID: 38231769 PMCID: PMC10880616 DOI: 10.1128/aem.01107-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/20/2023] [Indexed: 01/19/2024] Open
Abstract
The effects of Neolamarckia cadamba leaves extract (NCLE), with effective ingredients of flavonoids, on antibiotic resistance genes (ARGs) and relevant microorganisms in cecal contents and feces of broilers treated with or without lipopolysaccharide stimulation (LPS) were investigated. LPS stimulation increased (P < 0.05) the relative abundance of ARGs and mobile genetic elements (MGEs), such as tet(W/N/W), APH(3')-IIIa, ErmB, tet (44), ANT (6)-Ia, tet(O), tet (32), Vang_ACT_CHL, myrA, ANT (6)-Ib, IncQ1, tniB, and rep2 in cecal contents. However, the difference disappeared (P > 0.05) when NCLE was added at the same time. These differential ARGs and MGEs were mainly correlated (P < 0.01) with Clostridiales bacterium, Lachnospiraceae bacterium, and Candidatus Woodwardibium gallinarum. These species increased in LPS-stimulated broilers and decreased when NCLE was applied at the same time. In feces, LPS stimulation decreased (P < 0.05) the relative abundance of tet(Q), adeF, ErmF, Mef(En2), OXA-347, tet (40), npmA, tmrB, CfxA3, and ISCrsp1, while the LPS + NCLE treated group showed no significant effect (P > 0.05) on these ARGs. These differential ARGs and MGEs in feces were mainly correlated (P < 0.01) with Clostridiales bacterium, Pseudoflavonifractor sp. An184, Flavonifractor sp. An10, Ruminococcaceae bacterium, etc. These species increased in LPS-stimulated broilers and increased when NCLE was applied at the same time. In conclusion, LPS stimulation and NCLE influenced microbial communities and associated ARGs in both cecal contents and feces of broilers. NCLE alleviated the change of ARGs and MGEs in LPS-induced broilers by maintaining the microbial balance.IMPORTANCEAntibiotics showed a positive effect on gut health regulation and growth performance improvement in livestock breeding, but the antimicrobial resistance threat and environment pollution problem are increasingly severe with antibiotics abuse. As alternatives, plant extract containing bioactive substances are increasingly used to improve immunity and promote productivity. However, little is known about their effects on diversity and abundance of ARGs. Here, we investigated the effects of NCLE, with effective ingredients of flavonoids, on ARGs and relevant microorganisms in cecal contents and feces of broilers treated with or without lipopolysaccharide stimulation. We found that NCLE reduced the abundance of ARGs in cecal contents of lipopolysaccharide-induced broilers by maintaining the microbial balance. This study provides a comprehensive view of cecal and fecal microbial community, ARGs, and MGEs of broiler following LPS stimulation and NCLE treatment. It might be used to understand and control ARGs dissemination in livestock production.
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Affiliation(s)
- Cheng Wang
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
- State key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shuo Wu
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
| | - Wei Zhou
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
| | - Lei Hu
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
| | - Qi Hu
- Bioinformation Center, NEOMICS Institute, Shenzhen, China
| | - Yong Cao
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Li Wang
- State key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoyang Chen
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
| | - Qing Zhang
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
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Ayoola MB, Das AR, Krishnan BS, Smith DR, Nanduri B, Ramkumar M. Predicting Salmonella MIC and Deciphering Genomic Determinants of Antibiotic Resistance and Susceptibility. Microorganisms 2024; 12:134. [PMID: 38257961 PMCID: PMC10819212 DOI: 10.3390/microorganisms12010134] [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: 11/29/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Salmonella spp., a leading cause of foodborne illness, is a formidable global menace due to escalating antimicrobial resistance (AMR). The evaluation of minimum inhibitory concentration (MIC) for antimicrobials is critical for characterizing AMR. The current whole genome sequencing (WGS)-based approaches for predicting MIC are hindered by both computational and feature identification constraints. We propose an innovative methodology called the "Genome Feature Extractor Pipeline" that integrates traditional machine learning (random forest, RF) with deep learning models (multilayer perceptron (MLP) and DeepLift) for WGS-based MIC prediction. We used a dataset from the National Antimicrobial Resistance Monitoring System (NARMS), comprising 4500 assembled genomes of nontyphoidal Salmonella, each annotated with MIC metadata for 15 antibiotics. Our pipeline involves the batch downloading of annotated genomes, the determination of feature importance using RF, Gini-index-based selection of crucial 10-mers, and their expansion to 20-mers. This is followed by an MLP network, with four hidden layers of 1024 neurons each, to predict MIC values. Using DeepLift, key 20-mers and associated genes influencing MIC are identified. The 10 most significant 20-mers for each antibiotic are listed, showcasing our ability to discern genomic features affecting Salmonella MIC prediction with enhanced precision. The methodology replaces binary indicators with k-mer counts, offering a more nuanced analysis. The combination of RF and MLP addresses the limitations of the existing WGS approach, providing a robust and efficient method for predicting MIC values in Salmonella that could potentially be applied to other pathogens.
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Affiliation(s)
- Moses B. Ayoola
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.B.A.); (A.R.D.); (B.S.K.); (B.N.)
| | - Athish Ram Das
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.B.A.); (A.R.D.); (B.S.K.); (B.N.)
| | - B. Santhana Krishnan
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.B.A.); (A.R.D.); (B.S.K.); (B.N.)
| | - David R. Smith
- Department of Population Medicine, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA;
| | - Bindu Nanduri
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.B.A.); (A.R.D.); (B.S.K.); (B.N.)
| | - Mahalingam Ramkumar
- Department of Computer Science and Engineering, Mississippi State University, Starkville, MS 39762, USA
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Gafen HB, Liu CC, Ineck NE, Scully CM, Mironovich MA, Taylor CM, Luo M, Leis ML, Scott EM, Carter RT, Hernke DM, Paul NC, Lewin AC. Alterations to the bovine bacterial ocular surface microbiome in the context of infectious bovine keratoconjunctivitis. Anim Microbiome 2023; 5:60. [PMID: 37996960 PMCID: PMC10668498 DOI: 10.1186/s42523-023-00282-4] [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: 07/05/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Infectious bovine keratoconjunctivitis (IBK) is a common cause of morbidity in cattle, resulting in significant economic losses. This study aimed to characterize the bovine bacterial ocular surface microbiome (OSM) through conjunctival swab samples from Normal eyes and eyes with naturally acquired, active IBK across populations of cattle using a three-part approach, including bacterial culture, relative abundance (RA, 16 S rRNA gene sequencing), and semi-quantitative random forest modeling (real-time polymerase chain reaction (RT-PCR)). RESULTS Conjunctival swab samples were obtained from eyes individually classified as Normal (n = 376) or IBK (n = 228) based on clinical signs. Cattle unaffected by IBK and the unaffected eye in cattle with contralateral IBK were used to obtain Normal eye samples. Moraxella bovis was cultured from similar proportions of IBK (7/228, 3.07%) and Normal eyes (1/159, 0.63%) (p = 0.1481). Moraxella bovoculi was cultured more frequently (p < 0.0001) in IBK (59/228, 25.88%) than Normal (7/159, 4.40%) eyes. RA (via 16 S rRNA gene sequencing) of Actinobacteriota was significantly higher in Normal eyes (p = 0.0045). Corynebacterium variabile and Corynebacterium stationis (Actinobacteriota) were detected at significantly higher RA (p = 0.0008, p = 0.0025 respectively) in Normal eyes. Rothia nasimurium (Actinobacteriota) was detected at significantly higher RA in IBK eyes (p < 0.0001). Alpha-diversity index was not significantly different between IBK and Normal eyes (p > 0.05). Alpha-diversity indices for geographic location (p < 0.001), age (p < 0.0001), sex (p < 0.05) and breed (p < 0.01) and beta-diversity indices for geographic location (p < 0.001), disease status (p < 0.01), age (p < 0.001), sex (p < 0.001) and breed (p < 0.001) were significantly different between groups. Modeling of RT-PCR values reliably categorized the microbiome of IBK and Normal eyes; primers for Moraxella bovoculi, Moraxella bovis, and Staphylococcus spp. were consistently the most significant canonical variables in these models. CONCLUSIONS The results provide further evidence that multiple elements of the bovine bacterial OSM are altered in the context of IBK, indicating the involvement of a variety of bacteria in addition to Moraxella bovis, including Moraxella bovoculi and R. nasimurium, among others. Actinobacteriota RA is altered in IBK, providing possible opportunities for novel therapeutic interventions. While RT-PCR modeling provided limited further support for the involvement of Moraxella bovis in IBK, this was not overtly reflected in culture or RA results. Results also highlight the influence of geographic location and breed type (dairy or beef) on the bovine bacterial OSM. RT-PCR modeling reliably categorized samples as IBK or Normal.
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Affiliation(s)
- Hannah B Gafen
- Department of Veterinary Clinical Sciences, Louisiana State University, Skip Bertman Drive, Baton Rouge, LA, 70803, USA
| | - Chin-Chi Liu
- Department of Veterinary Clinical Sciences, Louisiana State University, Skip Bertman Drive, Baton Rouge, LA, 70803, USA
| | - Nikole E Ineck
- Department of Veterinary Clinical Sciences, Louisiana State University, Skip Bertman Drive, Baton Rouge, LA, 70803, USA
| | - Clare M Scully
- Department of Veterinary Clinical Sciences, Louisiana State University, Skip Bertman Drive, Baton Rouge, LA, 70803, USA
| | - Melanie A Mironovich
- Department of Veterinary Clinical Sciences, Louisiana State University, Skip Bertman Drive, Baton Rouge, LA, 70803, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, Louisiana State University, 2020 Gravier St, New Orleans, LA, 70112, USA
| | - Meng Luo
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, Louisiana State University, 2020 Gravier St, New Orleans, LA, 70112, USA
| | - Marina L Leis
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, 52 Campus Dr, Saskatoon, SK, S7N 5B4, Canada
| | - Erin M Scott
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd, Ithaca, NY, 14853, USA
| | - Renee T Carter
- Department of Veterinary Clinical Sciences, Louisiana State University, Skip Bertman Drive, Baton Rouge, LA, 70803, USA
| | - David M Hernke
- Department of Ambulatory Medicine and Theriogenology, Cummings School of Veterinary Medicine, Tufts University, 200 Westboro Rd, North Grafton, MA, 01536, USA
| | - Narayan C Paul
- Texas A&M Veterinary Medical Diagnostic Laboratory, Texas A&M University, 483 Agronomy Rd, College Station, TX, 77843, USA
| | - Andrew C Lewin
- Department of Veterinary Clinical Sciences, Louisiana State University, Skip Bertman Drive, Baton Rouge, LA, 70803, USA.
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Zhang S, Shu Y, Wang Y, Zhong Z, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Wu Y, Yang Q, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A. High rate of multidrug resistance and integrons in Escherichia coli isolates from diseased ducks in select regions of China. Poult Sci 2023; 102:102956. [PMID: 37586192 PMCID: PMC10450990 DOI: 10.1016/j.psj.2023.102956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023] Open
Abstract
With the increasing number of ducks being raised and consumed, it is crucial to monitor the presence of multidrug resistant (MDR) bacteria in duck farming. Waterfowl, such as ducks, can contribute to the rapid dissemination of antibiotic resistance genes (ARGs). The objective of this study was to investigate the antimicrobial resistance (AMR), ARGs, and mobile genetic elements (MGEs), such as IS26, tbrC, ISEcp1 in Escherichia coli(E. coli) isolated from the intestinal contents of diseased ducks between 2021 and 2022 in Sichuan, Chongqing and Anhui, China. The AMR phenotypes of 201 isolated E. coli strains were determined using the minimum inhibitory concentrations (MICs) method. Subsequently, polymerase chain reaction and sequencing techniques were employed to screen for integron-integrase genes (intI1, intI2, intI3 genes), gene cassettes (GCs), MGEs, and ARGs. The results demonstrated that 96.5% of the E. coli isolates were resistant to at least 1 antibiotic, with 88.1% of the strains displaying MDR phenotype. The highest AMR phenotype observed was for trimethoprim-sulfamethoxazole (88.1%). Furthermore, class 1 and class 2 integrons were detected in 68.2% and 3.0% of all the isolates, respectively, whereas no class 3 integrons were found. Ten types of GCs were identified in the variable regions of class 1 and class 2 integrons. Moreover, 10 MGEs were observed in 46 combinations, with IS26 exhibiting the highest detection rate (89.6%). Among the 22 types of ARGs, tetA (77.1%) was the most frequently detected. In the conjugational transfer experiment, transconjugants were found to carry specific ARGs and MGEs, with their MIC values were significantly higher than those of recipient E. coli J53, indicating their status as MDR bacteria. This study emphasizes the necessity of monitoring MGEs, ARGs, and integrons in duck farms. It provides valuable insights into the complex formation mechanisms of AMR and may aid in preventing and controlling the spread of MDR bacteria in waterfowl breeding farm.
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Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Yanxi Shu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Yuwei Wang
- Mianyang Academy of Agricultural Sciences, Mianyang, Sichuan 621023, P.R. China
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Ying Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Qiao Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Juan Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Xumin Ou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Sai Mao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Qun Gao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Di Sun
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu, Sichuan 611130, P.R. China.
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Tan MF, Li HQ, Yang Q, Zhang FF, Tan J, Zeng YB, Wei QP, Huang JN, Wu CC, Li N, Kang ZF. Prevalence and antimicrobial resistance profile of bacterial pathogens isolated from poultry in Jiangxi Province, China from 2020 to 2022. Poult Sci 2023; 102:102830. [PMID: 37343345 PMCID: PMC10404785 DOI: 10.1016/j.psj.2023.102830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/23/2023] Open
Abstract
Poultry is one of the most commonly farmed species and the most widespread meat industries. However, numerous poultry flocks have been long threatened by pathogenic bacterial infections, especially antimicrobial resistant pathogens. Here the prevalence and the antimicrobial resistance (AMR) profiles of bacterial pathogens isolated from poultry in Jiangxi Province, China were investigated. From 2020 to 2022, 283 tissue and liquid samples were collected from clinically diseased poultry, including duck, chicken, and goose, with an overall positive isolation rate of 62.90%. Among all the 219 bacterial isolates, 29 strains were gram-positive and 190 strains were gram-negative. Major bacteria species involved were avian pathogenic Escherichia coli (APEC; 57.53%; 126/219), followed by Salmonella spp. (11.87%, 26/219), Pasteurella multocida (6.39%, 14/219), and Staphylococcus spp. (1.22%, 11/219). Antimicrobial susceptibility testing showed the APEC isolates displayed considerably higher levels of AMR than the Salmonella and P. multocida isolates. The APEC isolates showed high resistance rate to amoxicillin (89.68%), ampicillin (89.68%), and florfenicol (83.33%), followed by streptomycin (75.40%), cefradine (65.87%), and enrofloxacin (64.29%). Multidrug-resistant isolates were observed in APEC (99.21%), Salmonella spp. (96.16%), and P. multocida (85.71%), and nearly 3 quarters of the APEC strains were resistant to 7 or more categories of antimicrobial drugs. Moreover, blaNDM genes associated with carbapenemase resistance and mcr-1 associated with colisitin resistance were detected in the APEC isolates. Our findings could provide evidence-based guidance for veterinarians to prevent and control bacterial diseases, and be helpful for monitoring the emerging and development of AMR in poultry bacterial pathogens.
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Affiliation(s)
- Mei-Fang Tan
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Hai-Qin Li
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Qun Yang
- Institute of Agricultural Engineering, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Fan-Fan Zhang
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jia Tan
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Yan-Bing Zeng
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Qi-Peng Wei
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jiang-Nan Huang
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Cheng-Cheng Wu
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Na Li
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Zhao-Feng Kang
- Institute of Animal Husbandry and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
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Zhang Y, Lv X, Cao W, Zhang H, Shi L, Bai W, Ye L. Survey of Colistin Resistance in Commensal Bacteria from Penaeus vannamei Farms in China. Foods 2023; 12:foods12112143. [PMID: 37297388 DOI: 10.3390/foods12112143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Aquatic environments are important reservoirs for drug resistance. Aquatic foods may act as carriers to lead antibiotic-resistant commensal bacteria into the human gastrointestinal system, then contacting gut microbiota and spreading antibiotic resistance. Here, several shrimp farms were investigated to identify colistin resistance among commensal bacteria of aquaculture. A total of 884 (41.6%) colistin-resistant isolates were identified among 2126 strains. Electroporation demonstrated that colistin-resistant fragments were present in some commensal bacteria that could be transferred to other bacteria. Most of the resistant bacteria were Bacillus spp., with 69.3% of the Bacillus species exhibiting multiple drug resistance. Bacillus licheniformis was prevalent, with 58 strains identified that comprised six sequence types (ST) based on multilocus sequence typing. Whole-genome sequencing and comparisons with previous B. licheniformis genomes revealed a high degree of genomic similarity among isolates from different regions. Thus, this species is widely distributed, and this study provides new insights into global antibiotic-resistant characteristics of B. licheniformis. Sequence analyses further revealed some of these strains are even pathogenic and virulent, suggesting the antibiotic resistance and hazards of commensal bacteria in aquaculture should be considered. Considering the "One Health" perspective, improved monitoring of aquatic food is needed to prevent the spread of drug-resistant commensal bacteria from food-associated bacteria to humans.
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Affiliation(s)
- Yilin Zhang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Xinrui Lv
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Weiwei Cao
- School of Food Science and Biology, Guangdong Polytechnic of Science and Trade, Guangzhou 510640, China
| | - Huang Zhang
- Guangzhou Double Helix Gene Technology Co., Ltd., Guangzhou International Bio Island Co., Ltd., Guangzhou 510320, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
- Shandong Yuwang Ecological Food Industry Co., Ltd., Yucheng 251200, China
| | - Weibin Bai
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lei Ye
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
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Yang JT, Xiao DY, Zhang LJ, Chen HX, Zheng XR, Xu XL, Jiang HX. Antimicrobial resistome during the transition from an integrated to a monoculture aquaculture farm in southern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163511. [PMID: 37080303 DOI: 10.1016/j.scitotenv.2023.163511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/10/2023] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
Integrated and monoculture freshwater aquaculture systems are often regarded as important reservoirs for antimicrobial resistance genes (ARGs) and antimicrobial resistance bacteria (ARBs), yet only a few studies have assessed differences in the antimicrobial resistome and antibiotic residues between aquaculture modes. In this study, a metagenomic approach was used to comprehensively explore the dynamic patterns and potential transmission mechanisms of ARGs in ducks, human workers, fish, water and sediments during the transition from an integrated to a monoculture freshwater aquaculture mode and to investigate the associations of ARGs with potential hosts in microbial communities using network analysis and a binning approach. The results showed that the abundance and diversity of ARGs were higher under integrated fish-duck farming than in single fish ponds. During the transition from an integrated to a monoculture aquaculture farm, ARGs in workers and sediments were not easily removed. However, ARGs in the aquatic environment underwent regular changes. In addition, duck manure was probably the most dominant source of ARGs in the duck farm environment. Network analysis indicated that Escherichia spp. were the most dominant hosts of ARGs. Variation partitioning analysis (VPA) showed that in water samples, the bacterial community played an important role in the ARG profile. In addition, we identified a potential risk of the presence of highly virulent and antimicrobial-resistant Klebsiella pneumoniae in workers. These results help assess the risk of ARG transmission in integrated and monoculture aquaculture farms and suggest that we should strengthen the monitoring of long-term resistance in integrated aquaculture environments.
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Affiliation(s)
- Jin-Tao Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Dan-Yu Xiao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Li-Juan Zhang
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526000, China
| | - Hai-Xin Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Run Zheng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Li Xu
- Instrumental Analysis & Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Hong-Xia Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
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Mitchell SW, Moran RA, Elbourne LDH, Chapman B, Bull M, Muscatello G, Coleman NV. Impacts of Domestication and Veterinary Treatment on Mobile Genetic Elements and Resistance Genes in Equine Fecal Bacteria. Appl Environ Microbiol 2023; 89:e0159022. [PMID: 36988354 PMCID: PMC10057962 DOI: 10.1128/aem.01590-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/05/2023] [Indexed: 03/09/2023] Open
Abstract
Antimicrobial resistance in bacteria is a threat to both human and animal health. We aimed to understand the impact of domestication and antimicrobial treatment on the types and numbers of resistant bacteria, antibiotic resistance genes (ARGs), and class 1 integrons (C1I) in the equine gut microbiome. Antibiotic-resistant fecal bacteria were isolated from wild horses, healthy farm horses, and horses undergoing veterinary treatment, and isolates (9,083 colonies) were screened by PCR for C1I; these were found at frequencies of 9.8% (vet horses), 0.31% (farm horses), and 0.05% (wild horses). A collection of 71 unique C1I+ isolates (17 Actinobacteria and 54 Proteobacteria) was subjected to resistance profiling and genome sequencing. Farm horses yielded mostly C1I+ Actinobacteria (Rhodococcus, Micrococcus, Microbacterium, Arthrobacter, Glutamicibacter, Kocuria), while vet horses primarily yielded C1I+ Proteobacteria (Escherichia, Klebsiella, Enterobacter, Pantoea, Acinetobacter, Leclercia, Ochrobactrum); the vet isolates had more extensive resistance and stronger PC promoters in the C1Is. All integrons in Actinobacteria were flanked by copies of IS6100, except in Micrococcus, where a novel IS5 family element (ISMcte1) was implicated in mobilization. In the Proteobacteria, C1Is were predominantly associated with IS26 and also IS1, Tn21, Tn1721, Tn512, and a putative formaldehyde-resistance transposon (Tn7489). Several large C1I-containing plasmid contigs were retrieved; two of these (plasmid types Y and F) also had extensive sets of metal resistance genes, including a novel copper-resistance transposon (Tn7519). Both veterinary treatment and domestication increase the frequency of C1Is in equine gut microflora, and each of these anthropogenic factors selects for a distinct group of integron-containing bacteria. IMPORTANCE There is increasing acknowledgment that a "one health" approach is required to tackle the growing problem of antimicrobial resistance. This requires that the issue is examined from not only the perspective of human medicine but also includes consideration of the roles of antimicrobials in veterinary medicine and agriculture and recognizes the importance of other ecological compartments in the dissemination of ARGs and mobile genetic elements such as C1I. We have shown that domestication and veterinary treatment increase the frequency of occurrence of C1Is in the equine gut microflora and that, in healthy farm horses, the C1I are unexpectedly found in Actinobacteria, while in horses receiving antimicrobial veterinary treatments, a taxonomic shift occurs, and the more typical integron-containing Proteobacteria are found. We identified several new mobile genetic elements (plasmids, insertion sequences [IS], and transposons) on genomic contigs from the integron-containing equine bacteria.
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Affiliation(s)
- Scott W. Mitchell
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Robert A. Moran
- Institute of Microbiology and Infection, School of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Liam D. H. Elbourne
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Belinda Chapman
- Quantal Bioscience Pty Ltd, Carlingford, New South Wales, Australia
| | - Michelle Bull
- Quantal Bioscience Pty Ltd, Carlingford, New South Wales, Australia
| | - Gary Muscatello
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nicholas V. Coleman
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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Rothia nasimurium as a Cause of Disease: First Isolation from Farmed Chickens. Vet Sci 2022; 9:vetsci9120653. [PMID: 36548814 PMCID: PMC9783258 DOI: 10.3390/vetsci9120653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Rothia nasimurium is a facultative anaerobic Gram-positive coccus belonging to the Rothia genus of the Micrococcaceae family. While Rothia nasimurium is considered an opportunistic pathogen, to date few studies have investigated its pathogenicity and drug resistance. In January 2022, chickens at a poultry farm in China's Xinjiang Uygur Autonomous Region became ill and died. Treatment with commonly used Chinese medicines and antibiotics was ineffective, causing economic losses to the poultry farm. In order to determine the cause of the disease in these poultry farm chickens, the isolation and identification of the pathogens in the livers and other internal organs of the sick and dead chickens were performed. Further, animal pathogenicity tests, antibiotic susceptibility tests, and the detection of antibiotic resistance genes were carried out to analyze the pathogenicity and drug resistance of the identified pathogens. A Gram-positive coccus was isolated from the livers of the diseased chickens. The isolate was resistant to 17 antibiotics, including ciprofloxacin, chloramphenicol, and florfenicol, and was only sensitive to penicillin, amikacin, and tigecycline, to varying degrees. The results of the drug resistance gene testing indicated that the isolated bacterium carried 13 kinds of resistance genes. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, morphological observations, biochemical tests, and 16S rRNA gene sequence analysis were performed on the isolated bacterium, and it was determined that the isolated bacterial strain was Rothia nasimurium. The animal pathogenicity tests showed that the isolate caused feather loss and death in chicks; the clinical symptoms and necropsy lesions of the test chicks were consistent with those observed in the farmed chickens. A review of the literature revealed that, to date, there are no reports of infection with Rothia nasimurium in chickens. Thus, in this study, Rothia nasimurium was isolated from chickens for the first time and an investigation of the biological characteristics of the bacterium was carried out in order to provide a reference for the clinical treatment, prevention, and control of Rothia nasimurium infection.
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Kang Y, Zhou H, Jin W. Rothia nasimurium as a Cause of Disease: First Isolation from Farmed Geese. Vet Sci 2022; 9:vetsci9050197. [PMID: 35622725 PMCID: PMC9145032 DOI: 10.3390/vetsci9050197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/29/2022] Open
Abstract
Rothia nasimurium was known previously as an opportunistic pathogen of animals. However, there are few reports regarding the pathogenicity of Rothia nasimurium. In September 2020, geese contracted a disease of unknown cause which brought economic losses to a farm in Jiangsu Province, China, prompting a series of investigations. The bacterium was isolated, cultured, and purified, and then identified using Gram staining, biochemical tests, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and 16S rRNA sequence analysis. After determining the obtained bacteria species, antibiotic susceptibility tests and animal regression experiments were carried out. A strain of bacterium was successfully isolated from the livers of the diseased geese, which was identified as a strain of the Gram-positive bacterium Rothia nasimurium according to the 16S rRNA sequencing results. By indexing references, no goose was reported to have been infected with Rothia nasimurium. The antibiotic susceptibility testing showed that only four antibiotics (amikacin, cefazolin, fosfomycin, and ampicillin/sulbactam) could effectively inhibit the growth of the Rothia nasimurium strain. The animal regression experiments showed that the novel isolated strain could infect goslings, and it also causes serious depilation of goslings. The results of the manuscript expanded the range of pathogenic microorganisms in geese, which is helpful to develop methods for avian endemic control.
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Affiliation(s)
- Yuhui Kang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.K.); (H.Z.)
| | - Hongshan Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.K.); (H.Z.)
| | - Wenjie Jin
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.K.); (H.Z.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou 225009, China
- Ministry of Education Key Laboratory of Poultry Preventive Medicine, Yangzhou 225009, China
- Correspondence:
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Characterization of the Bacterial Community of Rumen in Dairy Cows with Laminitis. Genes (Basel) 2021; 12:genes12121996. [PMID: 34946945 PMCID: PMC8700892 DOI: 10.3390/genes12121996] [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] [Received: 11/01/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Laminitis is the inflammation of the lamella, and it has caused great economic loss to the dairy industry and attracted wide attention around the world. In recent years, microbiota are considered to play a significant role in various diseases processes. Therefore, our study aimed to explore the characteristics of ruminal microbiota in laminitis cows. The serum of bovines with or without laminitis was collected to detect concentrations of lipopolysaccharide (LPS), lactic acid, and histamine, and ruminal fluid was collected for 16S rDNA sequence analysis. The results showed a significant increase in LPS and lactic acid levels in the laminitis group compared to the control group cows. In addition, a higher abundance of Candidatus Saccharimonas, Saccharofermentans, Erysipelotrichaceae UCG-009 genus, Acetobacter pasteurianus, Clostridium papyrosolvens, Ruminococcaceae bacterium AE2021, Porphyromonas crevioricanis, Pseudomonas boreopolis, Pseudomonas psychrotolerans, Rothia nasimurium, and Rothia pickettii was detected in the rumen fluid of laminitis bovines. In conclusion, this article confirms that there are differences in rumen microbiota between healthy and laminitis bovines. The elevated abundance of bacteria that enrich acid-enhancing metabolites, as well as increase the concentration of lactic acid and LPS, could be harmful factors to bovines and increase the risk of laminitis.
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Comprehensive Molecular Dissection of Dermatophilus congolensis Genome and First Observation of tet(Z) Tetracycline Resistance. Int J Mol Sci 2021; 22:ijms22137128. [PMID: 34281179 PMCID: PMC8267673 DOI: 10.3390/ijms22137128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
Dermatophilus congolensis is a bacterial pathogen mostly of ruminant livestock in the tropics/subtropics and certain temperate climate areas. It causes dermatophilosis, a skin disease that threatens food security by lowering animal productivity and compromising animal health and welfare. Since it is a prevalent infection in ruminants, dermatophilosis warrants more research. There is limited understanding of its pathogenicity, and as such, there is no registered vaccine against D. congolensis. To better understanding the genomics of D. congolensis, the primary aim of this work was to investigate this bacterium using whole-genome sequencing and bioinformatic analysis. D. congolensis is a high GC member of the Actinobacteria and encodes approximately 2527 genes. It has an open pan-genome, contains many potential virulence factors, secondary metabolites and encodes at least 23 housekeeping genes associated with antimicrobial susceptibility mechanisms and some isolates have an acquired antimicrobial resistance gene. Our isolates contain a single CRISPR array Cas type IE with classical 8 Cas genes. Although the isolates originate from the same geographical location there is some genomic diversity among them. In conclusion, we present the first detailed genomic study on D. congolensis, including the first observation of tet(Z), a tetracycline resistance-conferring gene.
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