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Lee J, Ju F, Beck K, Bürgmann H. Differential effects of wastewater treatment plant effluents on the antibiotic resistomes of diverse river habitats. THE ISME JOURNAL 2023; 17:1993-2002. [PMID: 37684524 PMCID: PMC10579368 DOI: 10.1038/s41396-023-01506-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/18/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
Wastewater treatment plants (WWTPs) are key sources of antimicrobial resistance genes (ARGs) that could influence the resistomes of microbial communities in various habitats of the receiving river ecosystem. However, it is currently unknown which habitats are most impacted and whether ARGs, like certain chemical contaminants, could be accumulated or enriched in the river ecosystem. We conducted a systematic metagenomic survey on the antibiotic resistomes of WWTP effluent, four riverine habitats (water, suspended particles, sediment, epilithic biofilm), and freshwater amphipod gut microbiomes. The impact of WWTP effluent on the downstream habitats was assessed in nine Swiss rivers. While there were significant differences in resistomes across habitats, the wastewater resistome was more similar to the resistome of receiving river water than to the resistomes of other habitats, and river water was the habitat most strongly impacted by the WWTPs effluent. The sulfonamide, beta-lactam, and aminoglycoside resistance genes were among the most abundant ARGs in the WWTP effluents, and especially aadA, sul1, and class A beta-lactamase genes showed significantly increased abundance in the river water of downstream compared to upstream locations (p < 0.05). However, this was not the case for the sediment, biofilm, and amphipod gut habitats. Accordingly, evidence for accumulation or enrichment of ARGs through the riverine food web was not identified. Our study suggests that monitoring riverine antimicrobial resistance determinants could be conducted using "co-occurrence" of aadA, sul1, and class A beta-lactamase genes as an indicator of wastewater-related pollution and should focus on the water as the most affected habitat.
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Affiliation(s)
- Jangwoo Lee
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland
- Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
- Departments of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, and Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China.
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.
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Islam OK, Islam I, Saha O, Rahaman MM, Sultana M, Bockmühl DP, Hossain MA. Genomic variability correlates with biofilm phenotypes in multidrug resistant clinical isolates of Pseudomonas aeruginosa. Sci Rep 2023; 13:7867. [PMID: 37188866 DOI: 10.1038/s41598-023-35056-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/11/2023] [Indexed: 05/17/2023] Open
Abstract
The multifactorial nature of Pseudomonas aeruginosa biofilm development and genomic variabilities implicates its resistance to conventional antimicrobials and virulence. Therefore, genetic determinants need to be extensively studied to block the early steps of biofilm or already formed biofilms. In this study, a total of 20 multidrug resistant (MDR) clinical P. aeruginosa isolates were evaluated for their biofilm forming abilities and related genes. Of the isolates tested, all of them showed surface attachment tendencies in nutrient limiting conditions, and classified as strong (SBF = 45%), moderate (MBF = 30%) and weak (WBF = 25%) biofilm formers. Complete genome sequencing of representative strong (DMC-27b), moderate (DMC-20c) and weak biofilm former (DMC-30b) isolates was performed. Analysis of biofilm related genes in the sequenced genomes revealed that, 80 of the 88 biofilm related genes possess 98-100% sequence identity to the reference PAO1 strain. Complete and partial sequence data of LecB proteins from tested isolates indicate that isolates containing PA14-like LecB sequences produced strong biofilms. All of the 7 pel operon protein coding genes in weak biofilm former isolate 30b showed significant nucleotide sequence variation with other tested isolates, and their corresponding proteins are 99% identical with the pel operon proteins of PA7. Bioinformatics analyses identified divergent sequence and structural features that separate PA7 like pel operon proteins from reference PAO1-like pel operon. Congo red and pellicle forming assays revealed that the sequence and structure variations may have interfered with the Pel production pathway and resulted in impaired Pel production in isolate 30b that has a PA7 like pel operon. Expression analysis also showed that both pelB and lecB genes were about 5 to 6 folds upregulated after 24 h in SBF 27b in comparison with WBF 30b. Our findings indicate significant genomic divergence in biofilm related genes of P. aeruginosa strains that affect their biofilm phenotypes.
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Affiliation(s)
- Ovinu Kibria Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Department of Microbiology, Jashore University of Science & Technology, Jashore, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Department of Microbiology, Noakhali University of Science & Technology, Noakhali, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Department of Microbiology, Noakhali University of Science & Technology, Noakhali, Bangladesh
| | | | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Dirk P Bockmühl
- Faculty of Life Science, Rhine-Waal University of Applied Science, Kleve, Germany
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.
- Department of Microbiology, Jashore University of Science & Technology, Jashore, Bangladesh.
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Li Q, Chen Q, Liang S, Wang W, Zhang B, Martín-Rodríguez AJ, Liang Q, Zhang F, Guo L, Xiong X, Hu R, Xiang L, Zhou Y. Coexistence of tmexCD3-toprJ1b tigecycline resistance genes with two novel bla VIM-2-carrying and bla OXA-10-carrying transposons in a Pseudomononas asiatica plasmid. Front Cell Infect Microbiol 2023; 13:1130333. [PMID: 36936768 PMCID: PMC10015498 DOI: 10.3389/fcimb.2023.1130333] [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: 12/23/2022] [Accepted: 02/06/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction Tigecycline and carbapenems are considered the last line of defense against microbial infections. The co-occurrence of resistance genes conferring resistance to both tigecycline and carbapenems in Pseudomononas asiatica was not investigated. Methods P. asiatica A28 was isolated from hospital sewage. Antibiotic susceptibility testing showed resistance to carbapenem and tigecycline. WGS was performed to analyze the antimicrobial resistance genes and genetic characteristics. Plasmid transfer by conjugation was investigated. Plasmid fitness costs were evaluated in Pseudomonas aeruginosa transconjugants including a Galleria mellonella infection model. Results Meropenem and tigecycline resistant P. asiatica A28 carries a 199, 972 bp long plasmid PLA28.4 which harbors seven resistance genes. Sequence analysis showed that the 7113 bp transposon Tn7389 is made up of a class I integron without a 5'CS terminal and a complete tni module flanked by a pair of 25bp insertion repeats. Additionally, the Tn7493 transposon, 20.24 kp long, with a complete 38-bp Tn1403 IR and an incomplete 30-bp Tn1403 IR, is made up of partial skeleton of Tn1403, a class I integron harboring bla OXA-10, and a Tn5563a transposon. Moreover, one tnfxB3-tmexC3.2-tmexD3b-toprJ1b cluster was found in the plasmid and another one in the the chromosome. Furthermore, plasmid PLA28.4 could be conjugated to P. aeruginosa PAO1, with high fitness cost. Discussion A multidrug-resistant plasmid carrying tmexCD3-toprJ1b and two novel transposons carrying bla VIM-2 and bla OXA-10 -resistant genes was found in hospital sewage, increasing the risk of transmission of antibiotic-resistant genes. These finding highlight the necessary of controlling the development and spread of medication resistance requires continuous monitoring and management of resistant microorganisms in hospital sewage.
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Affiliation(s)
- Qin Li
- Department of Pathogen Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Qiao Chen
- Department of Pathogen Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Shuang Liang
- Department of Oral prosthodontics, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Wei Wang
- Department of Pathogen Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Bingying Zhang
- Department of Pathogen Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | | | - Qinghua Liang
- Department of Pathogen Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Feiyang Zhang
- Department of Pathogen Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Ling Guo
- Department of Oral prosthodontics, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Xia Xiong
- Department of Dermatology, The First Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Renjing Hu
- Department of Laboratory Medicine, Jiangnan University Medical Center, Wuxi, China
- *Correspondence: Yingshun Zhou, ; Renjing Hu, ; Li Xiang,
| | - Li Xiang
- Department of Pathogen Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
- *Correspondence: Yingshun Zhou, ; Renjing Hu, ; Li Xiang,
| | - Yingshun Zhou
- Department of Pathogen Biology, School of Basic Medicine, Southwest Medical University, Luzhou, China
- Public Center of Experimental of Pathogen Biology Platform, Southwest Medical University, Luzhou, China
- *Correspondence: Yingshun Zhou, ; Renjing Hu, ; Li Xiang,
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Identification of a Stable Chromosomal Tandem Multicopy of blaVIM-63, a New blaVIM-2 Carbapenemase. J Bacteriol 2022; 204:e0008822. [PMID: 35758752 PMCID: PMC9295573 DOI: 10.1128/jb.00088-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
This study characterizes a new genetic structure containing a multicopy of a blaVIM-2 variant with an A676C substitution, blaVIM-63. This gene was detected on the chromosome of two carbapenem-resistant clinical strains of Citrobacter freundii ST22 recovered from two patients, separated by a 6-month period, and previously in Pseudomonas aeruginosa ST2242 from the same hospital unit. Short-read sequencing was used to characterize the new variant in both species, and long-read sequencing was used to characterize the genome of C. freundii. On the P. aeruginosa chromosome, the blaVIM-63 gene was inserted between ISPsy 42-type sequences, flanked by an intl1 sequence, nearby aph(3')-VI, and sul1. On the C. freundii chromosome, the blaVIM-63 gene was inserted into a Tn6230-like transposon as a stable five-tandem-repeat multimer, flanked by the same intl1 as in P. aeruginosa. This structure was stable across subcultures and did not change in the presence of carbapenems. The blaVIM-63 gene was cloned into the pCR-Blunt plasmid to study antimicrobial susceptibility patterns and into pET29a for kinetic activity analysis. VIM-63 showed higher Km values than VIM-2 for ceftazidime and cefepime and higher kcat values for cefotaxime, ceftazidime, imipenem, and ertapenem, without differences in MIC values. This is the first study to describe this new variant, VIM-63, in two different species with a chromosomal location integrated into different mobile elements and the first to describe a stable multimer of a metallo-β-lactamase. Despite the amino acid substitution, the susceptibility pattern of the new variant was similar to that of VIM-2. IMPORTANCE VIM group metallo-β-lactamases are usually captured by IntI1 integrases. This work describes the detection for the first time of a novel, previously unknown variant of VIM-2, VIM-63. This carbapenemase has been found on the chromosome of two different species, Citrobacter freundii and Pseudomonas aeruginosa, from the same hospital. The adjacent genetic environment of the blaVIM-63 gene would indicate that the capture of this gene by IntI1 has occurred in two different genetic events in each of the species, and in one there has been a stable integration of tandem copies of this gene.
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Lin H, Feng C, Zhu T, Li A, Liu S, Zhang L, Li Q, Zhang X, Lin L, Lu J, Lin X, Li K, Zhang H, Xu T, Li C, Bao Q. Molecular Mechanism of the β-Lactamase Mediated β-Lactam Antibiotic Resistance of Pseudomonas aeruginosa Isolated From a Chinese Teaching Hospital. Front Microbiol 2022; 13:855961. [PMID: 35572664 PMCID: PMC9096163 DOI: 10.3389/fmicb.2022.855961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/08/2022] [Indexed: 01/03/2023] Open
Abstract
Pseudomonas aeruginosa can cause infections in the blood, lungs (pneumonia), or other parts of the body after surgery. To investigate the molecular characteristics of β-lactam antibiotic resistance of P. aeruginosa isolated from a hospital population between 2015 and 2017, in this study, the antimicrobial susceptibility and the resistance gene profile of the bacteria were determined. The Pulsed-field gel electrophoresis (PFGE) was used to characterize the clonal relatedness and sequencing and comparative genomic analysis were performed to analyze the structure of the resistance gene-related sequences. As a result, of the 260 P. aeruginosa strains analyzed, the resistance rates for 6 β-lactam antibiotics ranged from 4.6 to 9.6%. A total of 7 genotypes of 44 β-lactamase genes were identified in 23 isolates (8.9%, 23/260). Four transconjugants from different donors carrying blaCARB-3 exhibited a phenotype of reduced susceptibility to piperacillin–tazobactam, ceftazidime, and cefepime, and 2 transconjugants harboring blaIMP-45 exhibited a phenotype of reduced susceptibility to carbapenems. blaCARB positive isolates (n = 12) presented six PFGE patterns, designated groups A to F. Two bla genes (blaIMP-45 and blaOXA-1) in PA1609 related to a class 1 integron (intI1-blaIMP-45-blaOXA-1-aac(6′)-Ib7-catB3-qacE∆1-sul1) were encoded on a plasmid (pPA1609-475), while the blaCARB-3 gene of PA1616 also related to a class 1 integron was located on the chromosome. The results suggest that β-lactam antibiotic resistance and clonal dissemination exist in this hospital population. It indicates the necessity for molecular surveillance in tracking β-lactamase-producing strains and emphasizes the need for epidemiological monitoring.
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Affiliation(s)
- Hailong Lin
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tingting Zhu
- Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Anqi Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shuang Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Li Lin
- Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Changchong Li
- Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
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Tenover FC. Using Molecular Diagnostics to Develop Therapeutic Strategies for Carbapenem-Resistant Gram-Negative Infections. Front Cell Infect Microbiol 2021; 11:715821. [PMID: 34650933 PMCID: PMC8505994 DOI: 10.3389/fcimb.2021.715821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/20/2021] [Indexed: 12/23/2022] Open
Abstract
Infections caused by multidrug-resistant Gram-negative organisms have become a global threat. Such infections can be very difficult to treat, especially when they are caused by carbapenemase-producing organisms (CPO). Since infections caused by CPO tend to have worse outcomes than non-CPO infections, it is important to identify the type of carbapenemase present in the isolate or at least the Ambler Class (i.e., A, B, or D), to optimize therapy. Many of the newer beta-lactam/beta-lactamase inhibitor combinations are not active against organisms carrying Class B metallo-enzymes, so differentiating organisms with Class A or D carbapenemases from those with Class B enzymes rapidly is critical. Using molecular tests to detect and differentiate carbapenem-resistance genes (CRG) in bacterial isolates provides fast and actionable results, but utilization of these tests globally appears to be low. Detecting CRG directly in positive blood culture bottles or in syndromic panels coupled with bacterial identification are helpful when results are positive, however, even negative results can provide guidance for anti-infective therapy for key organism-drug combinations when linked to local epidemiology. This perspective will focus on the reluctance of laboratories to use molecular tests as aids to developing therapeutic strategies for infections caused by carbapenem-resistant organisms and how to overcome that reluctance.
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Molecular Detection of Multidrug Resistant Salmonella Species Isolated from Broiler Farm in Bangladesh. Pathogens 2020; 9:pathogens9030201. [PMID: 32182918 PMCID: PMC7157442 DOI: 10.3390/pathogens9030201] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 01/06/2023] Open
Abstract
Multidrug resistant (MDR) Salmonella are a leading cause of foodborne diseases and serious human health concerns worldwide. In this study we detected MDR Salmonella in broiler chicken along with the resistance genes and class 1 integron gene intl1. A total of 100 samples were collected from broiler farms comprising 50 cloacal swabs, 35 litter and 15 feed samples. Overall prevalence of Salmonella was 35% with the highest detected in cloacal swabs. Among the Salmonella, 30 isolates were confirmed as S. enterica serovar Typhimurium using molecular methods of PCR. Disk diffusion susceptibility test revealed that all the Salmonella were classified as MDR with the highest resistance to tetracycline (97.14%), chloramphenicol (94.28%), ampicillin (82.85%) and streptomycin (77.14%). The most prevalent resistance genotypes were tetA (97.14%), floR (94.28%), blaTEM-1 (82.85%) and aadA1 (77.14%). In addition, among the MDR Salmonella, 20% were positive for class 1 integron gene (intl1). As far as we know, this is the first study describing the molecular basis of antibiotic resistance in MDR Salmonella from broiler farms in Bangladesh. In addition to tetA, floR, blaTEM-1, aadA1 and intl1 were also detected in the isolated MDR Salmonella. The detection of MDR Salmonella in broiler chicken carrying intl1 is of serious public health concern because of their zoonotic nature and possibilities to enter into the food chain.
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