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Luqman A, Saising J, Prasetya YA, Ammanath AV, Andini, Amala SN, Zulaika E, Kuswytasari ND, Goetz F, Wibowo AT. Detection of Vancomycin Resistant Genes in Intrinsically Antibiotic Resistant Bacteria from the Gut Microbiota of Indonesian Individuals. IRANIAN JOURNAL OF MEDICAL SCIENCES 2024; 49:302-312. [PMID: 38751872 PMCID: PMC11091268 DOI: 10.30476/ijms.2023.98767.3087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/27/2023] [Accepted: 07/14/2023] [Indexed: 05/18/2024]
Abstract
Background Antibiotic resistance is a global public health concern that has been exacerbated by the overuse and misuse of antibiotics, leading to the emergence of resistant bacteria. The gut microbiota, often influenced by antibiotic usage, plays a crucial role in overall health. Therefore, this study aimed to investigate the prevalence of antibiotic resistant genes in the gut microbiota of Indonesian coastal and highland populations, as well as to identify vancomycin-resistant bacteria and their resistant genes. Methods Stool samples were collected from 22 individuals residing in Pacet, Mojokerto, and Kenjeran, Surabaya Indonesia in 2022. The read count of antibiotic resistant genes was analyzed in the collected samples, and the bacterium concentration was counted by plating on the antibiotic-containing agar plate. Vancomycin-resistant strains were further isolated, and the presence of vancomycin-resistant genes was detected using a multiplex polymerase chain reaction (PCR). Results The antibiotic resistant genes for tetracycline, aminoglycosides, macrolides, beta-lactams, and vancomycin were found in high frequency in all stool samples (100%) of the gut microbiota. Meanwhile, those meant for chloramphenicol and sulfonamides were found in 86% and 16% of the samples, respectively. Notably, vancomycin-resistant genes were found in 16 intrinsically resistant Gram-negative bacterial strains. Among the detected vancomycin-resistant genes, vanG was the most prevalent (27.3%), while vanA was the least prevalent (4.5%). Conclusion The presence of multiple vancomycin resistance genes in intrinsically resistant Gram-negative bacterial strains demonstrated the importance of the gut microbiota as a reservoir and hub for the horizontal transfer of antibiotic resistant genes.
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Affiliation(s)
- Arif Luqman
- Department of Biology, Institute Teknologi Sepuluh Nopember, Surabaya, Indonesia
- Institute for Molecular Infection Biology (IMIB), Julius Maximilians University of Wuerzburg, Wuerzburg, Germany
| | - Jongkon Saising
- School of Health Science and Biomedical Technology Research Group for Vulnerable Populations, Mae Fah Luang University, Chiang Rai, Thailand
| | | | | | - Andini
- Department of Biology, Institute Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Siti Nur Amala
- Department of Biology, Institute Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Enny Zulaika
- Department of Biology, Institute Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | | | - Friedrich Goetz
- Microbial Genetics, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Anjar Tri Wibowo
- Department of Biology, Faculty of Science and Technology, Airlangga University, Surabaya, Indonesia
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Srifani A, Mirnawati M, Marlida Y, Rizal Y, Nurmiati N, Lee KW. Identification of novel probiotic lactic acid bacteria from soymilk waste using the 16s rRNA gene for potential use in poultry. Vet World 2024; 17:1001-1011. [PMID: 38911076 PMCID: PMC11188893 DOI: 10.14202/vetworld.2024.1001-1011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 06/25/2024] Open
Abstract
Background and Aim In-feed antibiotics have been used as antibiotic growth promoters (AGPs) to enhance the genetic potential of poultry. However, the long-term use of AGPs is known to lead to bacterial resistance and antibiotic residues in poultry meat and eggs. To address these concerns, alternatives to AGPs are needed, one of which is probiotics, which can promote the health of livestock without having any negative effects. In vitro probiotic screening was performed to determine the ability of lactic acid bacteria (LAB) isolated from soymilk waste to be used as a probiotic for livestock. Materials and Methods Four LAB isolates (designated F4, F6, F9, and F11) isolated from soymilk waste were used in this study. In vitro testing was performed on LAB isolates to determine their resistance to temperatures of 42°C, acidic pH, bile salts, hydrophobicity to the intestine, and ability to inhibit pathogenic bacteria. A promising isolate was identified using the 16S rRNA gene. Result All LAB isolates used in this study have the potential to be used as probiotics. On the basis of the results of in vitro testing, all isolates showed resistance to temperatures of 42°C and low pH (2.5) for 3 h (79.87%-94.44%) and 6 h (76.29%-83.39%), respectively. The survival rate at a bile salt concentration of 0.3% ranged from 73.24% to 90.39%, whereas the survival rate at a bile salt concentration of 0.5% ranged from 56.28% to 81.96%. All isolates showed the ability to attach and colonize the digestive tract with a hydrophobicity of 87.58%-91.88%. Inhibitory zones of LAB against pathogens ranged from 4.80-15.15 mm against Staphylococcus aureus, 8.85-14.50 mm against Salmonella enteritidis, and 6.75-22.25 mm against Escherichia coli. Although all isolates showed good ability as probiotics, isolate F4 showed the best probiotic ability. This isolate was identified as Lactobacillus casei strain T22 (JQ412731.1) using the 16S rRNA gene. Conclusion All isolates in this study have the potential to be used as probiotics. However, isolate F4 has the best probiotic properties and is considered to be the most promising novel probiotic for poultry.
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Affiliation(s)
- Anifah Srifani
- PMDSU Program, Graduate Program of Animal Feed and Nutrition Department, Faculty of Animal Science, Universitas Andalas, Padang, West Sumatera, Indonesia
| | - Mirnawati Mirnawati
- Department of Animal Feed and Nutrition, Faculty of Animal Science, Universitas Andalas, Padang, West Sumatera, Indonesia
| | - Yetti Marlida
- Department of Animal Feed and Nutrition, Faculty of Animal Science, Universitas Andalas, Padang, West Sumatera, Indonesia
| | - Yose Rizal
- Department of Animal Feed and Nutrition, Faculty of Animal Science, Universitas Andalas, Padang, West Sumatera, Indonesia
| | - Nurmiati Nurmiati
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Andalas, Padang, West Sumatera, Indonesia
| | - Kyung-Woo Lee
- Department of Animal Science and Technology, Sanghuh College of Life Sciences, Konkuk University, Seoul, South Korea
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Pereira A, Sidjabat HE, Davis S, Vong da Silva PG, Alves A, Dos Santos C, Jong JBDC, da Conceição F, Felipe NDJ, Ximenes A, Nunes J, Fária IDR, Lopes I, Barnes TS, McKenzie J, Oakley T, Francis JR, Yan J, Ting S. Prevalence of Antimicrobial Resistance in Escherichia coli and Salmonella Species Isolates from Chickens in Live Bird Markets and Boot Swabs from Layer Farms in Timor-Leste. Antibiotics (Basel) 2024; 13:120. [PMID: 38391506 PMCID: PMC10885974 DOI: 10.3390/antibiotics13020120] [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: 01/04/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
The rapid emergence of antimicrobial resistance is a global concern, and high levels of resistance have been detected in chicken populations worldwide. The purpose of this study was to determine the prevalence of antimicrobial resistance in Escherichia coli and Salmonella spp. isolated from healthy chickens in Timor-Leste. Through a cross-sectional study, cloacal swabs and boot swabs were collected from 25 live bird markets and two layer farms respectively. E. coli and Salmonella spp. from these samples were tested for susceptibility to six antimicrobials using a disk diffusion test, and a subset was tested for susceptibility to 27 antimicrobials using broth-based microdilution. E. coli and Salmonella spp. isolates showed the highest resistance towards either tetracycline or ampicillin on the disk diffusion test. E. coli from layer farms (odds ratio:5.2; 95%CI 2.0-13.1) and broilers (odds ratio:18.1; 95%CI 5.3-61.2) were more likely to be multi-drug resistant than those from local chickens. Based on the broth-based microdilution test, resistance to antimicrobials in the Timor-Leste Antimicrobial Guidelines for humans were low, except for resistance to ciprofloxacin in Salmonella spp. (47.1%). Colistin resistance in E. coli was 6.6%. Although this study shows that antimicrobial resistance in chickens was generally low in Timor-Leste, there should be ongoing monitoring in commercial chickens as industry growth might be accompanied with increased antimicrobial use.
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Affiliation(s)
- Abrao Pereira
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
| | - Hanna E Sidjabat
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
| | - Steven Davis
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
| | - Paulo Gabriel Vong da Silva
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
| | - Amalia Alves
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
| | - Cristibela Dos Santos
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
| | - Joanita Bendita da Costa Jong
- Ministry of Agriculture, Livestock, Fisheries and Forestry, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili, Timor-Leste
| | - Felisiano da Conceição
- Ministry of Agriculture, Livestock, Fisheries and Forestry, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili, Timor-Leste
| | - Natalino de Jesus Felipe
- Ministry of Agriculture, Livestock, Fisheries and Forestry, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili, Timor-Leste
| | - Augusta Ximenes
- Ministry of Agriculture, Livestock, Fisheries and Forestry, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili, Timor-Leste
| | - Junilia Nunes
- Ministry of Agriculture, Livestock, Fisheries and Forestry, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili, Timor-Leste
| | - Isménia do Rosário Fária
- Ministry of Agriculture, Livestock, Fisheries and Forestry, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili, Timor-Leste
| | - Isabel Lopes
- Ministry of Agriculture, Livestock, Fisheries and Forestry, Government of Timor-Leste, Av. Nicolao Lobato, Comoro, Dili, Timor-Leste
| | | | - Joanna McKenzie
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand
| | - Tessa Oakley
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
| | - Joshua R Francis
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
| | - Jennifer Yan
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
| | - Shawn Ting
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Dili, Timor-Leste
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Rizal S, Nurhapsari I, Fauziah I, Masrukhin M, Jatmiko YD. Prevalence of multidrug-resistant and extended-spectrum β-lactamase producing Escherichia coli from local and broiler chickens at Cibinong market, West Java, Indonesia. Vet World 2024; 17:179-184. [PMID: 38406353 PMCID: PMC10884567 DOI: 10.14202/vetworld.2024.179-184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/18/2023] [Indexed: 02/27/2024] Open
Abstract
Background and Aim Antimicrobial resistance (AMR) is becoming a public health concern. Foodborne pathogens are infectious agents that can be transmitted from animals to humans through food and can become resistant due to misuse and overuse of antibiotics, especially in poultry. This study aimed to detect the prevalence of multidrug-resistant and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from local and broiler chickens at the Cibinong market, West Java, Indonesia. Materials and Methods A total of 60 cloacal swab samples from 30 local and broiler chickens sold at the Cibinong market in West Java were obtained by random sampling. From these samples, 39 E. coli isolates were obtained after being cultured on eosin methylene blue agar and molecularly identified using polymerase chain reaction (PCR). Six antibiotic disks were used for the antibiotic sensitivity test against E. coli isolates cultured on Mueller-Hinton agar. PCR was performed to detect ESBL genes (blaTEM, blaSHV, and blaCTX-M). Results A total of 76.47% (39/51) cloacal swab samples were positive for E. coli. All E. coli isolates were sensitive to imipenem (100%), and 38 isolates were sensitive to cefoxitin (FOX) (97.4%). On average, the isolates were sensitive to amoxicillin-clavulanic acid (AMC) (69.2%) and ceftriaxone (CRO) (89.7%). E. coli isolates were occasionally resistant to enrofloxacin (25.64%), followed by gentamicin (20.51%), CRO (10.25%), AMC (7.69%), and FOX (2.56%). The prevalence of E. coli AMR was 10.25% (4/39). All four multidrug-resistant E. coli isolates (blaTEM and blaCTX-M) were confirmed to have the ESBL gene based on PCR. Conclusion The prevalence of multidrug-resistant and ESBL-producing E. coli is still found, proving that there is still inappropriate use of antibiotics and a need for strict supervision of their use, especially around Cibinong market, West Java.
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Affiliation(s)
- Syaiful Rizal
- Research Center for Applied Zoology, Research Organization for Life Science and Environment, National Research and Innovation Agency (BRIN), Indonesia, Soekarno Science and Techno Park, Jl. Raya Jakarta - Bogor KM. 46, Cibinong, Bogor 16911, West Java, Indonesia
| | - Intan Nurhapsari
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia
| | - Ima Fauziah
- Research Center for Applied Zoology, Research Organization for Life Science and Environment, National Research and Innovation Agency (BRIN), Indonesia, Soekarno Science and Techno Park, Jl. Raya Jakarta - Bogor KM. 46, Cibinong, Bogor 16911, West Java, Indonesia
| | - Masrukhin Masrukhin
- Research Center for Biosystematics and Evolution, Research Organization for Life Science and Environment, National Research and Innovation Agency (BRIN), Indonesia, Soekarno Science and Techno Park, Jl. Raya Jakarta - Bogor KM. 46, Cibinong, Bogor 16911, West Java, Indonesia
| | - Yoga Dwi Jatmiko
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia
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Luo S, Liao C, Peng J, Tao S, Zhang T, Dai Y, Ding Y, Ma Y. Resistance and virulence gene analysis and molecular typing of Escherichia coli from duck farms in Zhanjiang, China. Front Cell Infect Microbiol 2023; 13:1202013. [PMID: 37396302 PMCID: PMC10308044 DOI: 10.3389/fcimb.2023.1202013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The widespread use of antibiotics in animal agriculture has increased the resistance of Escherichia coli, and pathogenic E. coli often harbor complex virulence factors. Antimicrobial resistance in pathogenic bacteria can cause public health problems. Correlation analyses of the resistance, virulence, and serotype data from the pathogenic bacteria found on farms and in the surrounding environment can thus provide extremely valuable data to help improve public health management. Methods In this investigation, we have assessed the drug resistance and virulence genes as well as the molecular typing characteristics of 30 E. coli strains isolated from duck farms in the Zhanjiang area of China. Polymerase chain reaction was used to detect the drug resistance and virulence genes as well as serotypes, and whole-genome sequencing was used to analyze the multilocus sequence typing. Results The detection rates for the oqxA resistance gene and fimC virulence gene were highest (93.3%, respectively). There were no correlations between the drug resistance and virulence gene numbers in the same strain. The epidemic serotype was O81 (5/24), ST3856 was an epidemic sequence type, and strains I-9 and III-6 carried 11 virulence genes. The E. coli strains from the duck farms in the Zhanjiang area were thus found to have a broad drug resistance spectrum, various virulence genes, complex serotypes, and certain pathogenicity and genetic relationship. Discussion Monitoring the spread of pathogenic bacteria and the provision of guidance regarding the use of antibiotics in the livestock and poultry industries will be required in the future in the Zhanjiang area.
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Affiliation(s)
- Shuaishuai Luo
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Cuiyi Liao
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- College of Traditional Chinese Medicine, Zhanjiang University of Science and Technology, Zhanjiang, China
| | - Jinju Peng
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Songruo Tao
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Tengyue Zhang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yue Dai
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yuexia Ding
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yi Ma
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
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Prevalence and Antimicrobial Resistance of Escherichia coli, Salmonella and Vibrio Derived from Farm-Raised Red Hybrid Tilapia (Oreochromis spp.) and Asian Sea Bass (Lates calcarifer, Bloch 1970) on the West Coast of Peninsular Malaysia. Antibiotics (Basel) 2022; 11:antibiotics11020136. [PMID: 35203739 PMCID: PMC8868497 DOI: 10.3390/antibiotics11020136] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotics are widely used in intensive fish farming, which in turn increases the emergence of antimicrobial-resistant (AMR) bacteria in the aquatic environment. The current study investigates the prevalence and determines the antimicrobial susceptibility of E. coli, Salmonella, and Vibrio in farmed fishes on the west coast of Peninsular Malaysia. Over a period of 12 months, 32 aquaculture farms from the Malaysian states of Selangor, Negeri Sembilan, Melaka, and Perak were sampled. Both E. coli and Salmonella were highly resistant to erythromycin, ampicillin, tetracycline, and trimethoprim, while Vibrio was highly resistant to ampicillin and streptomycin. Resistance to the antibiotics listed as the highest priority and critically important for human therapy, such as colistin in E. coli (18.1%) and Salmonella (20%) in fish, is a growing public health concern. The multi-drug resistance (MDR) levels of E. coli and Salmonella in tilapia were 46.5% and 77.8%, respectively. Meanwhile, the MDR levels of E. coli, Salmonella, V. parahaemolyticus, V. vulnificus and V. cholerae in Asian seabass were 34%, 100%, 21.6%, 8.3% and 16.7%, respectively. Our findings provide much-needed information on AMR in aquaculture settings that can be used to tailor better strategies for the use of antibiotics in aquaculture production at the local and regional levels.
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