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Wang X, Dai Y, Kong N, Cao M, Zhang L, Wei Q. Screening Key Sites of Class 2 Integron Integrase that Impact Recombination Efficiency. Curr Microbiol 2024; 81:163. [PMID: 38710822 DOI: 10.1007/s00284-024-03674-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/19/2024] [Indexed: 05/08/2024]
Abstract
By capturing and expressing exogenous resistance gene cassettes through site-specific recombination, integrons play important roles in the horizontal transfer of antimicrobial resistant genes among bacteria. The characteristics of integron integrase make it to be a potential gene editing tool enzyme. In this study, a random mutation library using error-prone PCR was constructed, and amino acid residues mutants that impact on attI2 × attC or attC × attC recombination efficiency were screened and analyzed. Thirteen amino acid mutations were identified to be critical impacted on site-specific recombination of IntI2, including the predicted catalyzed site Y301. Nine of 13 mutated amino acid residues that have critically impacted on IntI2 activity were relative concentrated and near the predicted catalyzed site Y301 in the predicted three-dimensional structure indicated the importance of this area in maintain the activity of IntI2. No mutant with obviously increased recombination activity (more than four-fold as high as that of wild IntI2) was found in library screening, except P95S, R100K slightly increased (within two-fold) the excision activity of IntI2, and S243T slightly increased (within two-fold) both excision and integration activity of IntI2. These findings will provide clues for further specific modification of integron integrase to be a tool enzyme as well as establishing a new gene editing system and applied practically.
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Affiliation(s)
- Xiaotong Wang
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
- Clinical Laboratory, Songjiang Hospital Affiliated to Shanghai JiaoTong University School of Medicine, 748 Middle Zhongshan Road, Shanghai, 201602, China
| | - Yueru Dai
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Nana Kong
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Mei Cao
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Long Zhang
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Quhao Wei
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China.
- Department of Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China.
- Department of Laboratory Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 6600 Nanfeng Road, Shanghai, 201499, China.
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Zhang S, Guo X, 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. Implications of different waterfowl farming on cephalosporin resistance: Investigating the role of bla CTX-M-55. Poult Sci 2023; 102:102929. [PMID: 37562134 PMCID: PMC10432832 DOI: 10.1016/j.psj.2023.102929] [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: 05/08/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
We investigated the cephalosporin resistance of Escherichia coli from waterfowl among different breeding mode farms. In 2021, we isolated 200 strains of E. coli from waterfowl feces samples collected from Sichuan, Heilongjiang, and Anhui provinces. The key findings are: Out of the 200 strains, 80, 80, and 40 strains were isolated from waterfowl feces samples in intensive, courtyard, and outdoor breeding mode farms, respectively. The overall positive rate of the ESBL phenotype, detecting by the double disk diffusion method, was 68.00% (136/200). In particular, the rates for intensive, courtyard, and outdoor breeding modes were 98.75%, 36.25%, and 70.00%, respectively. Results of MIC test showed drug resistance rates in the intensive breeding mode: 100.00% for cephalothin, 38.75% for cefoxitin, 100.00% for cefotaxime, and 100.00% for cefepime. In courtyard breeding mode, the corresponding rates were 100.00%, 40.00%, 63.75%, and 45.00%, respectively. In outdoor breeding mode, the corresponding rates were 100.00%, 52.50%, 82.50%, and 77.50%, respectively. The PCR results for blaCTX-M, blaTEM, blaOXA, and blaSHV showed the detection rate of blaCTX-M was highest at 75.50%, with blaCTX-M-55 is the main subtype gene, followed by blaTEM at 73.50%. We screened 58 donor strains carrying blaCTX-M-55, including 52 strains from the intensive breeding mode. These donor bacteria can transfer different plasmids to recipient E. coli J53, resulting in recipient bacteria acquiring cephalosporin resistance, and the conjugational transfer frequency ranged from 1.01 × 10-5 to 6.56 × 10-2. The transferred plasmids remained stable in recipient bacteria for up to several days without significant adaptation costs observed. During molecular typing of E. coli with conjugational transfer ability, the blaCTX-M-55 was found to be widely present in different ST strains with several phylogenetic groups. In summary, cephalosporin resistance of E. coli carried by waterfowl birds in intensive breeding mode farm was significantly higher than in courtyard and outdoor mode farms. The blaCTX-M-55 subtype gene was the prevalent ARGs and can be horizontally transferred through plasmids, which plays a key role in the spread of cephalosporin drug resistance.
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Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Xiangyuan Guo
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yuwei Wang
- Mianyang Academy of Agricultural Sciences, Mianyang 621023, P.R. China
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Ying Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Qiao Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Juan Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Xumin Ou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Sai Mao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Qun Gao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Di Sun
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China.
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Zhu Y, Wang T, Zhu W, Wei Q. Influence of class 2 integron integrase concentration on gene cassette insertion and excision in vivo. Braz J Microbiol 2023; 54:645-653. [PMID: 36808308 PMCID: PMC10235263 DOI: 10.1007/s42770-023-00926-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/07/2023] [Indexed: 02/23/2023] Open
Abstract
Integron can capture and express antimicrobial resistance gene cassettes and plays important roles in horizontal gene transfer. The establishment of a complete in vitro reaction system will help to reveal integron integrase mediated site-specific recombination process and regulation mechanism. As an enzymatic reaction, the concentration of integrase is assumed to have a great influence on the reaction rate. To determine the influence of different concentrations of integrase on the reaction rate and to find the best range of enzyme concentration were essential to optimizing the in vitro reaction system. In this study, plasmids with gradient transcription levels of class 2 integron integrase gene intI2 under different promoters were constructed. Among plasmids pI2W16, pINTI2N, pI2W, and pI2NW, intI2 transcription levels ranged from about 0.61-fold to 49.65-fold of that in pINTI2N. And the frequencies of gene cassette sat2 integration and excision catalyzed by IntI2 were positively correlated with the transcription levels of intI2 within this range. Western blotting results indicated high expression of IntI2 partly existed in the form of an inclusion body. When compared with Pc of class 1 integron, the spacer sequence of PintI2 can increase the strength of PcW but decrease the strength of PcS. In conclusion, the frequencies of gene cassette integration and excision were positively correlated with the concentration of IntI2. intI2 driving by PcW with PintI2 spacer sequence can obtain the optimum IntI2 concentration required to achieve the maximum recombination efficiency in vivo in this study.
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Affiliation(s)
- Yu Zhu
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Tong Wang
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Wenwen Zhu
- Department of Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Quhao Wei
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China.
- Department of Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, 201499, China.
- Department of Laboratory Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 6600 Nanfeng Road, Shanghai, 201499, China.
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Patry A, Bothorel P, Labrunie A, Renesme L, Lehours P, Benard M, Dubois D, Ponthier L, Meyer S, Norbert K, Villeneuve L, Jouvencel P, Leysenne D, Chainier D, Luce S, Grélaud C, Ploy MC, Bedu A, Garnier F. Dynamics of the digestive acquisition of bacterial carriage and integron presence by French preterm newborns according to maternal colonization: The DAIR3N multicentric study. Front Microbiol 2023; 14:1148319. [PMID: 36998410 PMCID: PMC10043237 DOI: 10.3389/fmicb.2023.1148319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/21/2023] [Indexed: 03/15/2023] Open
Abstract
ObjectivesThe study aimed to describe the dynamics and risk factors of Gram-negative bacteria (GNB) acquisition in preterm infants.MethodsThis prospective multicenter French study included mothers hospitalized for preterm delivery and their newborns, followed until hospital discharge. Maternal feces and vaginal fluids at delivery, and neonatal feces from birth to discharge were tested for cultivable GNB, potential acquired resistance, and integrons. The primary outcome was the acquisition of GNB and integrons in neonatal feces, and their dynamics, evaluated by survival analysis using the actuarial method. Risk factors were analyzed using Cox models.ResultsTwo hundred thirty-eight evaluable preterm dyads were included by five different centers over 16 months. GNB were isolated in 32.6% of vaginal samples, with 15.4% of strains producing extended-spectrum beta-lactamase (ESBL) or hyperproducing cephalosporinase (HCase), and in 96.2% of maternal feces, with 7.8% ESBL-GNB or HCase-GNB. Integrons were detected in 40.2% of feces and 10.6% of GNB strains. The mean (SD) length of stay of newborns was 39.5 (15.9) days; 4 died in the hospital. At least one infection episode occurred in 36.1% of newborns. The acquisition of GNB and integrons was progressive from birth to discharge. At discharge, half of newborns had ESBL-GNB or HCase-GNB, independently favored by a premature rupture of membranes (Hazard Ratio (HR), 3.41, 95% confidence interval (CI), 1.71; 6.81), and 25.6% had integrons (protective factor: multiple gestation, HR, 0.367, 95% CI, 0.195; 0.693).ConclusionIn preterm newborns, the acquisitions of GNB, including resistant ones, and integrons are progressive from birth to discharge. A premature rupture of membranes favored the colonization by ESBL-GNB or Hcase-GNB.
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Affiliation(s)
- Alice Patry
- INSERM UMR, Limoges University, Limoges University Hospital, Limoges, France
| | - Philippe Bothorel
- Department of Pediatrics, Mother-Child Hospital, Limoges University Hospital, Limoges, France
| | - Anaïs Labrunie
- Epidemiology, Biostatistics, and Research Methodology Centre (CEBIMER), Limoges University Hospital, Limoges, France
| | - Laurent Renesme
- Department of Pediatrics, Neonatology and Maternity Unit, Pellegrin University Hospital, Bordeaux, France
| | - Philippe Lehours
- Bacteriology Laboratory, Pellegrin University Hospital, Bordeaux, France
| | - Melinda Benard
- Department of Pediatrics and Neonatology, CHU Toulouse, Toulouse, France
| | - Damien Dubois
- Bacteriology and Hygiene Department, Federative Institute of Biology, CHU Toulouse University Hospital, Toulouse, France
| | - Laure Ponthier
- Department of Pediatrics, Mother-Child Hospital, Limoges University Hospital, Limoges, France
| | - Sylvain Meyer
- INSERM UMR, Limoges University, Limoges University Hospital, Limoges, France
| | | | | | - Philippe Jouvencel
- Department of Pediatrics and Neonatology, « Côte Basque » Hospital, Bayonne, France
| | - David Leysenne
- Microbiology Laboratory, « Côte Basque » Hospital, Bayonne, France
| | - Delphine Chainier
- INSERM UMR, Limoges University, Limoges University Hospital, Limoges, France
| | - Sandrine Luce
- Epidemiology, Biostatistics, and Research Methodology Centre (CEBIMER), Limoges University Hospital, Limoges, France
| | - Carole Grélaud
- INSERM UMR, Limoges University, Limoges University Hospital, Limoges, France
| | - Marie-Cecile Ploy
- INSERM UMR, Limoges University, Limoges University Hospital, Limoges, France
| | - Antoine Bedu
- Department of Pediatrics, Mother-Child Hospital, Limoges University Hospital, Limoges, France
| | - Fabien Garnier
- INSERM UMR, Limoges University, Limoges University Hospital, Limoges, France
- *Correspondence: Fabien Garnier,
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Yang J, Shan G, Yu G, Wei J, Zhang Q, Su W, Lin Q, Zheng Z, Wu G, Li G, Chang Q, Yuan H, He Y, Chen Y, Zhang Y, Huang H, Hu W, Song R, Weng Y, Li X, Liu S. Whole genome sequencing of multidrug-resistant Proteus mirabilis strain PM1162 recovered from a urinary tract infection in China. J Glob Antimicrob Resist 2023; 33:44-50. [PMID: 36870531 DOI: 10.1016/j.jgar.2023.02.014] [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: 10/20/2022] [Revised: 01/26/2023] [Accepted: 02/19/2023] [Indexed: 03/06/2023] Open
Abstract
OBJECTIVES Proteus mirabilis is an important opportunistic Gram-negative pathogen. This study reports the whole genome sequence of multidrug-resistant (MDR) P. mirabilis PM1162 and explores its antibiotic resistance genes (ARGs) and their genetic environments. METHODS P. mirabilis PM1162 was isolated from a urinary tract infection in China. Antimicrobial susceptibility was determined, and whole genome sequencing (WGS) was performed. ARGs, insertion sequence (IS) elements, and prophages were identified using ResFinder, ISfinder, and PHASTER software, respectively. Sequence comparisons and map generation were performed using BLAST and Easyfig, respectively. RESULTS On its chromosome, P. mirabilis PM1162 harboured 15 ARGs, including cat, tet(J), blaCTX-M-14 (three copies), aph(3')-Ia, qnrB4, blaDHA-1, qacE, sul1, armA, msr(E), mph(E), aadA1, and dfrA1. We focused our analysis on the four related MDR regions: (1) genetic contexts associated with blaCTX-M-14; (2) the prophage containing blaDHA-1, qnrB4, and aph(3')-Ia; (3) genetic environments associated with mph(E), msr(E), armA, sul, and qacE; and (4) the class II integron harbouring dfrA1, sat2, and aadA1. CONCLUSION This study reported the whole genome sequence of MDR P. mirabilis PM1162 and the genetic context of its ARGs. This comprehensive genomic analysis of MDR P. mirabilis PM1162 provides a deeper understanding of its MDR mechanism and elucidates the horizontal spread of its ARGs, thus providing a basis for the containment and treatment of the bacteria.
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Affiliation(s)
- Jing Yang
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Ge Shan
- Department of Urology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Guangchao Yu
- Department of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jie Wei
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Qinghuan Zhang
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wen Su
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Qiuping Lin
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Zhixiong Zheng
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Guangliang Wu
- Department of Pharmacy, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Guangtian Li
- Department of Anesthesiology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Qing Chang
- Medical Department, Hengqin Branch of Zhuhai People's Hospital, Zhuhai, China
| | - Hong Yuan
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yanju He
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yanling Chen
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yi Zhang
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Haile Huang
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Wan Hu
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Rongqing Song
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China
| | - Yuqing Weng
- Department of Pulmonary and Critical Care Medicine, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai, China.
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China.
| | - Shengming Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, China.
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Delannoy S, Hoffer C, Youf R, Dauvergne E, Webb HE, Brauge T, Tran ML, Midelet G, Granier SA, Haenni M, Fach P, Brisabois A. High Throughput Screening of Antimicrobial Resistance Genes in Gram-Negative Seafood Bacteria. Microorganisms 2022; 10:microorganisms10061225. [PMID: 35744743 PMCID: PMC9230514 DOI: 10.3390/microorganisms10061225] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 01/24/2023] Open
Abstract
From a global view of antimicrobial resistance over different sectors, seafood and the marine environment are often considered as potential reservoirs of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs); however, there are few studies and sparse results on this sector. This study aims to provide new data and insights regarding the content of resistance markers in various seafood samples and sources, and therefore the potential exposure to humans in a global One Health approach. An innovative high throughput qPCR screening was developed and validated in order to simultaneously investigate the presence of 41 ARGs and 33 MGEs including plasmid replicons, integrons, and insertion sequences in Gram-negative bacteria. Analysis of 268 seafood isolates from the bacterial microflora of cod (n = 24), shellfish (n = 66), flat fishes (n = 53), shrimp (n = 10), and horse mackerel (n = 115) show the occurrence of sul-1, ant(3″)-Ia, aph(3')-Ia, strA, strB, dfrA1, qnrA, and blaCTX-M-9 genes in Pseudomonas spp., Providencia spp., Klebsiella spp., Proteus spp., and Shewanella spp. isolates and the presence of MGEs in all bacterial species investigated. We found that the occurrence of MGE may be associated with the seafood type and the environmental, farming, and harvest conditions. Moreover, even if MGE were detected in half of the seafood isolates investigated, association with ARG was only identified for twelve isolates. The results corroborate the hypothesis that the incidence of antimicrobial-resistant bacteria (ARB) and ARG decreases with increasing distance from potential sources of fecal contamination. This unique and original high throughput micro-array designed for the screening of ARG and MGE in Gram-negative bacteria could be easily implementable for monitoring antimicrobial resistance gene markers in diverse contexts.
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Affiliation(s)
- Sabine Delannoy
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
- Correspondence:
| | - Corine Hoffer
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Raphaëlle Youf
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Emilie Dauvergne
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Hattie E. Webb
- Department of Animal and Food Sciences, International Center for Food Safety Excellence, Texas Tech University, Lubbock, TX 79409, USA;
| | - Thomas Brauge
- Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Laboratory for Food Safety, ANSES, 62200 Boulogne-sur-Mer, France; (T.B.); (G.M.)
| | - Mai-Lan Tran
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Graziella Midelet
- Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Laboratory for Food Safety, ANSES, 62200 Boulogne-sur-Mer, France; (T.B.); (G.M.)
| | - Sophie A. Granier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, ANSES, 35306 Fougères, France;
| | - Marisa Haenni
- Antimicrobial Resistance and Bacterial Virulence Unit, Lyon Laboratory, Université de Lyon, ANSES, 69364 Lyon, France;
| | - Patrick Fach
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Anne Brisabois
- Strategy and Programs Department, ANSES, 94700 Maisons-Alfort, France;
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7
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Aeromonas: the multifaceted middleman in the One Health world. Curr Opin Microbiol 2021; 65:24-32. [PMID: 34717260 DOI: 10.1016/j.mib.2021.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 02/06/2023]
Abstract
Aeromonas is at the interface of all the One Health components and represents an amazingly sound test case in the One Health approach, from economic loss in aquaculture tochallenges related to antibiotic-resistant bacteria selected from the environment. In human health, infections following leech therapy is an outstanding example of such One Health challenges. Aeromonads are not only ubiquitous environmental bacteria, able to rapidly colonize and cause opportunistic infections in humans and animals, they are also capable of promoting interactions and gene exchanges between the One Health components. This makes this genus a key amplifier of genetic transfer, especially of antibiotic resistance genes.
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8
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Barraud O, Guichard E, Chainier D, Postil D, Chimot L, Mercier E, Frat JP, Desachy A, Lacherade JC, Mathonnet A, Bellec F, Giraudeau B, Ploy MC, François B. Integrons, a predictive biomarker for antibiotic resistance in acute sepsis: the IRIS study. J Antimicrob Chemother 2021; 77:213-217. [PMID: 34557914 DOI: 10.1093/jac/dkab348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/15/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Considering the increase in MDR Gram-negative bacteria (GNB), the choice of empirical antibiotic therapy is challenging. In parallel, use of broad-spectrum antibiotics should be avoided to decrease antibiotic selection pressure. Accordingly, clinicians need rapid diagnostic tools to narrow antibiotic therapy. Class 1-3 integrons, identified by intI1-3 genes, are genetic elements that play a major role in antibiotic resistance in GNB. OBJECTIVES The objective of the IRIS study was to evaluate the negative and positive predictive values (NPVs and PPVs, respectively) of intI1-3 as markers of antibiotic resistance. METHODS The IRIS study was an observational cross-sectional multicentre study that enrolled adult subjects with suspected urinary tract or intra-abdominal infections. intI1-3 were detected directly from routinely collected biological samples (blood, urine or intra-abdominal fluid) using real-time PCR. A patient was considered 'MDR positive' if at least one GNB, expressing acquired resistance to at least two antibiotic families among β-lactams, aminoglycosides, fluoroquinolones and/or co-trimoxazole, was isolated from at least one biological sample. RESULTS Over a 2 year period, 513 subjects were enrolled and 409 had GNB documentation, mostly Enterobacterales. intI1 and/or intI2 were detected in 31.8% of patients and 24.4% of patients were considered 'MDR positive'. The NPV of intI1 and/or intI2 as a marker of acquired antibiotic resistances was estimated at 92.8% (89.1%-95.5%). The NPVs for first-line antibiotics were all above 92%, notably >96% for resistance to third-generation cephalosporins. CONCLUSIONS The IRIS study strongly suggests that the absence of intI1 and intI2 in biological samples from patients with GNB-related infections is predictive of the absence of acquired resistances.
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Affiliation(s)
- Olivier Barraud
- Université Limoges, INSERM, CHU Limoges, UMR 1092, Limoges, France.,INSERM, CIC1435, CHU Limoges, Limoges, France
| | | | | | | | - Loïc Chimot
- CH Périgueux, Réanimation, Périgueux, France
| | | | - Jean-Pierre Frat
- CHU Poitiers, Réanimation médicale et médecine interne, Poitiers, France
| | - Arnaud Desachy
- CH Angoulême, Réanimation Polyvalente, Angoulême, France
| | | | | | - Frédéric Bellec
- CH Montauban, Réanimation-Surveillance continue, Montauban, France
| | | | | | - Bruno François
- Université Limoges, INSERM, CHU Limoges, UMR 1092, Limoges, France.,INSERM, CIC1435, CHU Limoges, Limoges, France.,CHU Limoges, Réanimation Polyvalente, Limoges, France
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9
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Pérez-Valdespino A, Pircher R, Pérez-Domínguez CY, Mendoza-Sanchez I. Impact of flooding on urban soils: Changes in antibiotic resistance and bacterial community after Hurricane Harvey. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:142643. [PMID: 33077230 DOI: 10.1016/j.scitotenv.2020.142643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Major perturbations in soil and water quality are factors that can negatively impact human health. In soil environments of urban areas, changes in antibiotic-resistance profiles may represent an increased risk of exposure to antibiotic-resistant bacteria via oral, dermal, or inhalation routes. We studied the perturbation of antibiotic-resistance profiles and microbial communities in soils following a major flooding event in Houston, Texas, caused by Hurricane Harvey. The main objective of this study was to examine the presence of targeted antibiotic-resistance genes and changes in the diversity of microbial communities in soils a short time (3-5 months) and a long time (18 months) after the catastrophic flooding event. Using polymerase chain reaction, we surveyed fourteen antibiotic-resistance elements: intI1, intI2, sul1, sul2, tet(A) to (E), tet(M), tet(O), tet(W), tet(X), and blaCMY-2. The number of antibiotic-resistance genes detected were higher in short-time samples compared to samples taken a long time after flooding. From all the genes surveyed, only tet(E), blaCMY-2, and intI1 were prevalent in short-time samples but not observed in long-time samples; thus, we propose these genes as indicators of exogenous antibiotic resistance in the soils. Sequencing of the V3-V4 region of the bacterial 16S rRNA gene was used to find that flooding may have affected bacterial community diversity, enhanced differences among bacterial lineages profiles, and affected the relative abundance of Actinobacteria, Verrucomicrobia, and Gemmatimonadetes. A major conclusion of this study is that antibiotic resistance profiles of soil bacteria are impacted by urban flooding events such that they may pose an enhanced risk of exposure for up to three to five months following the hurricane. The occurrence of targeted antibiotic-resistance elements decreased eighteen months after the hurricane indicating a reduction of the risk of exposure long time after Harvey.
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Affiliation(s)
- Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Ryan Pircher
- Department of Environmental and Occupational Health, School of Public Health, Texas A&M University, United States of America
| | - Citlali Y Pérez-Domínguez
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Itza Mendoza-Sanchez
- Department of Environmental and Occupational Health, School of Public Health, Texas A&M University, United States of America.
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10
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Identification of Tn 6835 and a Novel Genomic Island, MMGI-1, in a Pan-Resistant Morganella morganii Strain. Antimicrob Agents Chemother 2021; 65:AAC.02524-20. [PMID: 33468469 DOI: 10.1128/aac.02524-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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11
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Comparison of Class 2 Integron Integrase Activities. Curr Microbiol 2021; 78:967-978. [PMID: 33543359 DOI: 10.1007/s00284-021-02352-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 01/10/2021] [Indexed: 01/21/2023]
Abstract
Integrons play important roles in the dissemination of antimicrobial resistant genes among bacteria. Class 2 integrons usually has an internal stop codon, TAA, in integrase genes (intI2), leading to a truncated integrase, IntI2*. However, a few class 2 integrons with a natural full-length integrase have been reported. In this study, the sequences of natural full-length intI2 were extracted from INTEGRALL database and analyzed. A total of 236 sequences of intI2 were retrieved from INTEGRALL database, only seven of which were natural full-length intI2 genes and could be divided into five types according to their coding amino acid sequence. Quantitative real-time PCR was used to detect gene cassette sat2 integration and excision efficiency catalyzed by different natural full-length IntI2s. The results showed that all five IntI2s could catalyze attI2 × attCsat2 integration and attCdfrA1/sat2 × attCsat2/aadA1 excision in Escherichia coli. Integration and excision frequency catalyzed by IntI2A176 was highest and was about twofold as high as those catalyzed by IntI2S175_A176. The secondary structure of the IntI2 was predicted by online software. Polymorphisms of these five IntI2s were limited within residues 172, 174, 175, 176 and 256, and these residues were all far away from the predicted DNA binding regions or catalyzed sites. Influence of amino acid sequence polymorphisms of these natural full-length IntI2s on their catalyzed activities is limited.
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12
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Li D, Reid CJ, Kudinha T, Jarocki VM, Djordjevic SP. Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections. Microb Genom 2020; 6:mgen000475. [PMID: 33206038 PMCID: PMC8116683 DOI: 10.1099/mgen.0.000475] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Urinary tract infections (UTIs) are the most common bacterial infections requiring medical attention and a leading justification for antibiotic prescription. Trimethoprim is prescribed empirically for uncomplicated cases. UTIs are primarily caused by extraintestinal pathogenic Escherichia coli (ExPEC) and ExPEC strains play a central role in disseminating antimicrobial-resistance genes worldwide. Here, we describe the whole-genome sequences of trimethoprim-resistant ExPEC and/or ExPEC from recurrent UTIs (67 in total) from patients attending a regional Australian hospital from 2006 to 2008. Twenty-three sequence types (STs) were observed, with ST131 predominating (28 %), then ST69 and ST73 (both 7 %). Co-occurrence of trimethoprim-resistance genes with genes conferring resistance to extended-spectrum β-lactams, heavy metals and quaternary ammonium ions was a feature of the ExPEC described here. Seven trimethoprim-resistance genes were identified, most commonly dfrA17 (38 %) and dfrA12 (18 %). An uncommon dfrB4 variant was also observed. Two blaCTX-M variants were identified - blaCTX-M-15 (16 %) and blaCTX-M-14 (10 %). The former was always associated with dfrA12, the latter with dfrA17, and all blaCTX-M genes co-occurred with chromate-resistance gene chrA. Eighteen class 1 integron structures were characterized, and chrA featured in eight structures; dfrA genes featured in seventeen. ST131 H30Rx isolates possessed distinct antimicrobial gene profiles comprising aac(3)-IIa, aac(6)-Ib-cr, aph(3')-Ia, aadA2, blaCTX-M-15, blaOXA-1 and dfrA12. The most common virulence-associated genes (VAGs) were fimH, fyuA, irp2 and sitA (all 91 %). Virulence profile clustering showed ST131 H30 isolates carried similar VAGs to ST73, ST405, ST550 and ST1193 isolates. The sole ST131 H27 isolate carried molecular predictors of enteroaggregative E. coli/ExPEC hybrid strains (aatA, aggR, fyuA). Seven isolates (10 %) carried VAGs suggesting ColV plasmid carriage. Finally, SNP analysis of serial UTI patients experiencing worsening sequelae demonstrated a high proportion of point mutations in virulence factors.
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Affiliation(s)
- Dmitriy Li
- Ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Cameron J. Reid
- Ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Timothy Kudinha
- NSW Health Pathology, Microbiology, Orange Hospital, Orange, NSW 2800, Australia
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW 2800, Australia
| | - Veronica M. Jarocki
- Ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Otero-Olarra JE, Curiel-Quesada E, Baltazar-Cruz J, Aguilera-Arreola MG, Pérez-Valdespino A. Low Cassette Variability in Class 2 and Class 1 Integrons of Aeromonas spp. Isolated from Environmental Samples. Microb Drug Resist 2020; 26:794-801. [PMID: 31990611 DOI: 10.1089/mdr.2019.0250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Integrons are prokaryotic genetic elements known to carry and exchange antibiotic resistance gene cassettes through a site-specific recombinase called integrase. In this work, 107 Aeromonas isolates from environmental origin, including fish, water, and sediments, were investigated for the presence of integrons. Using specific primers for Class 1, 2 and 3 integrases, only Class 1 and Class 2 integrons were detected. Detection of Class 2 integrases and their associated variable regions required two rounds of polymerase chain reaction (PCR). Sequencing of the intI2 amplicons confirmed them as integrase-derived products. Class 1 integrons were detected in 26 out of 107 isolates. PCR amplification of the variable regions associated to these integrons revealed an outstanding homogeneity, 25 of them having variable regions with an identical dfrA12-orfF-aadA2 cassette array and one integron carrying only the dfrA16 cassette. To assess clone diversity, chromosomal DNA from isolates was subjected to enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR), which discarded clonality in all instances. Class 2 integrons were surprisingly more prevalent than Class1 integrons, being detected in 60 out of 107 isolates. Forty-six of them showed a unique ERIC profile, while the remaining 14 strains displayed profiles that could be grouped in five different patterns. Cassette arrangements of all Class 2 variable regions were those described as the most prevalent (dfrA1-sat2-aadA1). A rather startling result of this work is the sensitivity to trimethoprim, streptomycin, and streptothricin of most strains, despite the presence of the cognate resistance genes. To know the integron distribution in environmental Aeromonas species, a phylogenetic reconstruction was done using rpoD/gyrB or rpoD/gyrA gene sequences. Isolates bearing these elements corresponded to Aeromonas hydrophila, Aeromonas veronii, Aeromonas salmonicida, Aeromonas dhakensis, Aeromonas sanarellii, Aeromonas taiwanensis, Aeromonas media, Aeromonas caviae, Aeromonas jandaei, and Aeromonas sp. This work revealed an unusual high incidence of Class 2 integrons and a low variability of cassette arrangements in environmental Aeromonas species.
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Affiliation(s)
- Jorge Erick Otero-Olarra
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Everardo Curiel-Quesada
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jesús Baltazar-Cruz
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Ma Guadalupe Aguilera-Arreola
- Department of Microbiology, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico
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