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Davies AR, Chisnall T, Akter S, Afrad MMH, Sadekuzzaman M, Badhy SC, Hasan MZ, Rahman MT, Smith RP, Card RM, Brum E, Chowdhury MGA. Genomic characterisation of Escherichia coli isolated from poultry at retail through Sink Surveillance in Dhaka, Bangladesh reveals high levels of multi-drug resistance. Front Microbiol 2024; 15:1418476. [PMID: 38873136 PMCID: PMC11169737 DOI: 10.3389/fmicb.2024.1418476] [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: 04/16/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
The surveillance of antimicrobial resistance (AMR) in commensal Escherichia coli from livestock at slaughter is widely employed to assess the potential for risk to humans. There is currently a limited understanding of AMR in Bangladesh poultry at retail in live bird markets, with studies focussing solely on phenotypic characterisation of resistance. To address this evidence gap we performed antimicrobial susceptibility testing and whole genome sequencing on E. coli obtained from chickens from live bird markets in Dhaka in 2018 (n = 38) and 2020 (n = 45). E. coli were isolated from caeca samples following ISO guidelines and sequenced using short and long read methods. Multidrug resistance was extremely common (n = 77) and there was excellent concordance between AMR phenotype and the presence of corresponding AMR genes or mutations. There was considerable genomic diversity, with 43 different sequence types detected. Public health considerations included the high occurrence of resistance to ciprofloxacin (n = 75) associated with plasmid-residing qnrS or mutations in the gyrA and parC chromosomal genes; and the detection of a tigecycline resistant isolate harbouring tet(X4) on an IncHI1A/B-IncFIA mosaic plasmid. Thirty-nine isolates were resistant to azithromycin and harboured mphA, with a significant increase in the incidence of resistance between 2018 and 2020. Although azithromycin is banned for veterinary use in Bangladesh it remains an important treatment option for humans. Interestingly, mphA confers high-level resistance to azithromycin and erythromycin, and the latter is commonly used on poultry farms in Bangladesh. Seven isolates were colistin resistant and carried mcr1. For two isolates hybrid assemblies revealed that mcr1 resided on a highly conserved IncHI2 plasmid that had 93% nucleotide identity to a plasmid from the published genome of an E. coli isolate of Bangladeshi human origin. Six isolates had resistance to third generation cephalosporins, associated with plasmid-residing bla CTX-M-55, bla CTX-M-65, or bla DHA-1. By employing phenotypic and genomic approaches for AMR surveillance we have provided new insights into the potential for One Health AMR linkages in Bangladesh. Employing similar approaches in human and environmental sectors will help inform the One Health approach to addressing AMR, and generate evidence to support mitigation measures such as improved antimicrobial stewardship.
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Affiliation(s)
- Alistair R. Davies
- FAO Reference Centre for AMR, Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Thomas Chisnall
- FAO Reference Centre for AMR, Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Shamima Akter
- Central Disease Investigation Laboratory (CDIL), Dhaka, Bangladesh
| | - Md. Mohibul Hassan Afrad
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka, Bangladesh
| | | | | | - Md. Zakiul Hasan
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka, Bangladesh
| | - Md. Taifur Rahman
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka, Bangladesh
| | - Richard P. Smith
- WOAH Collaborating Centre for Risk Analysis & Modelling, Department of Epidemiological Sciences, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Roderick M. Card
- FAO Reference Centre for AMR, Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Eric Brum
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka, Bangladesh
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Ali MW, Karmakar S, Utsho KS, Kabir A, Arif M, Islam MS, Rahman MT, Hassan J. First detection and characterization of mcr-1 colistin resistant E. coli from wild rat in Bangladesh. PLoS One 2024; 19:e0296109. [PMID: 38743696 PMCID: PMC11093362 DOI: 10.1371/journal.pone.0296109] [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: 11/26/2023] [Accepted: 04/14/2024] [Indexed: 05/16/2024] Open
Abstract
Colistin resistance is a global concern warning for a one health approach to combat the challenge. Colistin resistant E. coli and their resistance determinants are widely distributed in the environment, and rats could be a potential source of these isolates and resistant determinants to a diverse environmental setting. This study was aimed to determine the presence of colistin resistant E. coli (CREC) in wild rats, their antimicrobial resistance (AMR) phenotypes, and genotypic analysis of mcr-1 CREC through whole genome sequencing (WGS). A total of 39 rats were examined and CREC was isolated from their fecal pellets onto MacConkey agar containing colistin sulfate (1 μg/ mL). AMR of the CREC was determined by disc diffusion and broth microdilution was employed to determine MIC to colistin sulfate. CREC were screened for mcr genes (mcr-1 to mcr-8) and phylogenetic grouping by PCR. Finally, WGS of one mcr-1 CREC was performed to explore its genetic characteristics especially resistomes and virulence determinants. 43.59% of the rats carried CREC with one (2.56%) of them carrying CREC with mcr-1 gene among the mcr genes examined. Examination of seventeen (17) isolates from the CREC positive rats (n = 17) revealed that majority of them belonging to the pathogenic phylogroup D (52.94%) and B2 (11.76%). 58.82% of the CREC were MDR on disc diffusion test. Shockingly, the mcr-1 CREC showed phenotypic resistance to 16 antimicrobials of 8 different classes and carried the ARGs in its genome. The mcr-1 gene was located on a 60 kb IncI2 plasmid. On the other hand, ARGs related to aminoglycosides, phenicols, sulfonamides, tetracyclines and trimethoprims were located on a 288 kb mega-plasmid separately. The mcr-1 CREC carried 58 virulence genes including genes related to adhesion, colonization, biofilm formation, hemolysis and immune-evasion. The isolate belonged to ST224 and closely related to E. coli from different sources including UPEC clinical isolates from human based on cgMLST analysis. The current research indicates that rats might be a possible source of CREC, and the presence of mcr-1 and other ARGs on plasmid increases the risk of ARGs spreading and endangering human health and other environmental components through this infamous pest.
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Affiliation(s)
- Md. Wohab Ali
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Susmita Karmakar
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Kishor Sosmith Utsho
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Ajran Kabir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Arif
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Shafiqul Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Jayedul Hassan
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Che M, Fresno AH, Calvo-Fernandez C, Hasman H, Kurittu PE, Heikinheimo A, Hansen LT. Comparison of IncK- blaCMY-2 Plasmids in Extended-Spectrum Cephalosporin-Resistant Escherichia coli Isolated from Poultry and Humans in Denmark, Finland, and Germany. Antibiotics (Basel) 2024; 13:349. [PMID: 38667025 PMCID: PMC11047599 DOI: 10.3390/antibiotics13040349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/29/2024] Open
Abstract
Escherichia coli carrying IncK-blaCMY-2 plasmids mediating resistance to extended-spectrum cephalosporins (ESC) has been frequently described in food-producing animals and in humans. This study aimed to characterize IncK-blaCMY-2-positive ESC-resistant E. coli isolates from poultry production systems in Denmark, Finland, and Germany, as well as from Danish human blood infections, and further compare their plasmids. Whole-genome sequencing (Illumina) of all isolates (n = 46) confirmed the presence of the blaCMY-2 gene. Minimum inhibitory concentration (MIC) testing revealed a resistant phenotype to cefotaxime as well as resistance to ≥3 antibiotic classes. Conjugative transfer of the blaCMY-2 gene confirmed the resistance being on mobile plasmids. Pangenome analysis showed only one-third of the genes being in the core with the remainder being in the large accessory gene pool. Single nucleotide polymorphism (SNP) analysis on sequence type (ST) 429 and 1286 isolates showed between 0-60 and 13-90 SNP differences, respectively, indicating vertical transmission of closely related clones in the poultry production, including among Danish, Finnish, and German ST429 isolates. A comparison of 22 ST429 isolates from this study with 80 ST429 isolates in Enterobase revealed the widespread geographical occurrence of related isolates associated with poultry production. Long-read sequencing of a representative subset of isolates (n = 28) allowed further characterization and comparison of the IncK-blaCMY-2 plasmids with publicly available plasmid sequences. This analysis revealed the presence of highly similar plasmids in ESC-resistant E. coli from Denmark, Finland, and Germany pointing to the existence of common sources. Moreover, the analysis presented evidence of global plasmid transmission and evolution. Lastly, our results indicate that IncK-blaCMY-2 plasmids and their carriers had been circulating in the Danish production chain with an associated risk of spreading to humans, as exemplified by the similarity of the clinical ST429 isolate to poultry isolates. Its persistence may be driven by co-selection since most IncK-blaCMY-2 plasmids harbor resistance factors to drugs used in veterinary medicine.
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Affiliation(s)
- Meiyao Che
- National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (M.C.); (C.C.-F.)
| | - Ana Herrero Fresno
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Campus Terra, Universidade da Santiago de Compostela (USC), 27002 Lugo, Spain;
| | - Cristina Calvo-Fernandez
- National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (M.C.); (C.C.-F.)
| | - Henrik Hasman
- Reference Laboratory for Antibiotic Resistance, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark;
| | - Paula E. Kurittu
- Department of Food Health and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland; (P.E.K.); (A.H.)
| | - Annamari Heikinheimo
- Department of Food Health and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland; (P.E.K.); (A.H.)
- Microbiology Unit, Finnish Food Authority, Mustialankatu 3, 00790 Helsinki, Finland
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Kalalah AA, Koenig SSK, Bono JL, Bosilevac JM, Eppinger M. Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli. Front Microbiol 2024; 15:1364026. [PMID: 38562479 PMCID: PMC10982417 DOI: 10.3389/fmicb.2024.1364026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) of non-O157:H7 serotypes are responsible for global and widespread human food-borne disease. Among these serogroups, O26, O45, O103, O111, O121, and O145 account for the majority of clinical infections and are colloquially referred to as the "Big Six." The "Big Six" strain panel we sequenced and analyzed in this study are reference type cultures comprised of six strains representing each of the non-O157 STEC serogroups curated and distributed by the American Type Culture Collection (ATCC) as a resource to the research community under panel number ATCC MP-9. The application of long- and short-read hybrid sequencing yielded closed chromosomes and a total of 14 plasmids of diverse functions. Through high-resolution comparative phylogenomics, we cataloged the shared and strain-specific virulence and resistance gene content and established the close relationship of serogroup O26 and O103 strains featuring flagellar H-type 11. Virulence phenotyping revealed statistically significant differences in the Stx-production capabilities that we found to be correlated to the strain's individual stx-status. Among the carried Stx1a, Stx2a, and Stx2d phages, the Stx2a phage is by far the most responsive upon RecA-mediated phage mobilization, and in consequence, stx2a + isolates produced the highest-level of toxin in this panel. The availability of high-quality closed genomes for this "Big Six" reference set, including carried plasmids, along with the recorded genomic virulence profiles and Stx-production phenotypes will provide a valuable foundation to further explore the plasticity in evolutionary trajectories in these emerging non-O157 STEC lineages, which are major culprits of human food-borne disease.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
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Lemlem M, Aklilu E, Mohamed M, Kamaruzzaman NF, Zakaria Z, Harun A, Devan SS, Kamaruzaman INA, Reduan MFH, Saravanan M. Phenotypic and genotypic characterization of colistin-resistant Escherichia Coli with mcr-4, mcr-5, mcr-6, and mcr-9 genes from broiler chicken and farm environment. BMC Microbiol 2023; 23:392. [PMID: 38062398 PMCID: PMC10704802 DOI: 10.1186/s12866-023-03118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Colistin is an antibiotic used as a last-resort to treat multidrug-resistant Gram-negative bacterial infections. Colistin had been used for a long time in veterinary medicine for disease control and as a growth promoter in food-producing animals. This excessive use of colistin in food animals causes an increase in colistin resistance. This study aimed to determine molecular characteristics of colistin-resistant Escherichia coli in broiler chicken and chicken farm environments. RESULTS Four hundred fifty-three cloacal and farm environment samples were collected from six different commercial chicken farms in Kelantan, Malaysia. E. coli was isolated using standard bacteriological methods, and the isolates were tested for antimicrobial susceptibility using disc diffusion and colistin minimum inhibitory concentration (MIC) by broth microdilution. Multiplex PCR was used to detect mcr genes, and DNA sequencing was used to confirm the resistance genes. Virulence gene detection, phylogroup, and multilocus sequence typing (MLST) were done to further characterize the E. coli isolates. Out of the 425 (94%; 425/453) E. coli isolated from the chicken and farm environment samples, 10.8% (48/425) isolates were carrying one or more colistin-resistance encoding genes. Of the 48 colistin-resistant isolates, 54.2% (26/48) of the mcr positive isolates were genotypically and phenotypically resistant to colistin with MIC of colistin ≥ 4 μg/ml. The most prominent mcr gene detected was mcr-1 (47.9%; 23/48), followed by mcr-8 (18.8%; 9/48), mcr-7 (14.5%; 7/48), mcr-6 (12.5%; 6/48), mcr-4 (2.1%; 1/48), mcr-5 (2.1%; 1/48), and mcr-9 (2.1%; 1/48) genes. One E. coli isolate originating from the fecal sample was found to harbor both mcr-4 and mcr-6 genes and another isolate from the drinking water sample was carrying mcr-1 and mcr-8 genes. The majority of the mcr positive isolates were categorized under phylogroup A followed by phylogroup B1. The most prevalent sequence typing (ST) was ST1771 (n = 4) followed by ST206 (n = 3). 100% of the mcr positive E. coli isolates were multidrug resistant. The most frequently detected virulence genes among mcr positive E. coli isolates were ast (38%; 18/48) followed by iss (23%; 11/48). This is the first research to report the prevalence of mcr-4, mcr-5, mcr-6, mcr-7, and mcr-8 genes in E. coli from broiler chickens and farm environments in Malaysia. CONCLUSION Our findings suggest that broiler chickens and broiler farm environments could be reservoirs of colistin-resistant E. coli, posing a risk to public health and food safety.
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Affiliation(s)
- Mulu Lemlem
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia.
- Department of Medical Microbiology and Immunology, College of Health Science, Mekelle University, 231, Mekelle, Tigray, Ethiopia.
| | - Erkihun Aklilu
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia.
| | - Maizan Mohamed
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia
| | | | - Zunita Zakaria
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, 43400, Malaysia
| | - Azian Harun
- School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Kelantan, 15200, Malaysia
| | - Susmita Seenu Devan
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia
| | | | - Mohd Farhan Hanif Reduan
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, 16100, Malaysia
| | - Muthupandian Saravanan
- AMR and Nanotherapeutics Lab, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, 600077, India
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Malik H, Singh R, Kaur S, Dhaka P, Bedi JS, Gill JPS, Gongal G. Review of antibiotic use and resistance in food animal production in WHO South-East Asia Region. J Infect Public Health 2023; 16 Suppl 1:172-182. [PMID: 37977981 DOI: 10.1016/j.jiph.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance is an emerging global threat to public health. The resistant bacteria in food animals can be transferred to humans through the food chain. Limited information on antimicrobial usage and resistance in food animals is available in Southeast Asia due to inadequate monitoring or surveillance systems. A literature review was conducted on antimicrobial use and resistance in food animal production in Southeast Asia for the period 2011-2020, to assess the scope and extent of antibiotic use and resistance. The countries included in the study were Bangladesh, Bhutan, Democratic People's Republic of Korea, India, Indonesia, Maldives, Myanmar, Nepal, Sri Lanka, Thailand and Timor-Leste. The information was categorised by country, production type and findings regarding antibiotic use and resistance. A total of 108 publications were included in the review. Results showed widespread use of critically and highly important antibiotics in livestock, poultry and aquacultured fish and their products. To curb the growing threat of antibiotic resistance, Southeast Asian countries need to strengthen surveillance and regulatory controls of antimicrobial use in food animal production through "One Health" approach.
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Affiliation(s)
- Hina Malik
- Centre for One Health, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
| | - Randhir Singh
- Centre for One Health, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
| | - Simranpreet Kaur
- Centre for One Health, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
| | - Pankaj Dhaka
- Centre for One Health, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
| | - Jasbir Singh Bedi
- Centre for One Health, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
| | - J P S Gill
- Directorate of Research, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
| | - Gyanendra Gongal
- World Health Organization, Regional Office for South-East Asia, New Delhi 110002, India.
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Biswas U, Das S, Barik M, Mallick A. Situation Report on mcr-Carrying Colistin-Resistant Clones of Enterobacterales: A Global Update Through Human-Animal-Environment Interfaces. Curr Microbiol 2023; 81:12. [PMID: 37989899 DOI: 10.1007/s00284-023-03521-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 11/23/2023]
Abstract
In the twenty-first century, antibiotic resistance (ABR) is one of the acute medical emergencies around the globe, overwhelming human-animal-environmental interfaces. Hit-or-mis use of antibiotics exacerbates the crisis of ABR, dispersing transferable resistance traits and challenging treatment regimens based on life-saving drugs such as colistin. Colistin is the highest priority critically important antimicrobials for human medicine, but its long use as a growth promoter in animal husbandry reduces clinical efficacy. Since 2015, the emergence and spread of mobile colistin resistance (mcr)-carrying colistin-resistant clones of Enterobacterales have been markedly sustained in both humans and animals, especially in developing countries. Hospital and community transmissions of mcr clones pose a high risk for infection prevention and outbreaks at the national and international levels. Several public health and limited one health studies have highlighted the genomic insights of mcr clones, clarifying the chromosomal sequence types (STs) and plasmid incompatibility (Inc) types. But this information is segregated into humans and animals, and rarely are environmental sectors complicating the understanding of possibly intercontinental and sectoral transmission of these clones. India is the hotspot for superbugs, including mcr-carrying colistin-resistant isolates that threaten cross-border transmission. The current review provided an up-to-date worldwide scenario of mcr-carrying STs and plasmid Inc types among the Gram-negative bacilli of Enterobacterales across human-animal-environmental interfaces and correlated with the available information from India.
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Affiliation(s)
- Urmy Biswas
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Surojit Das
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Mili Barik
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Abhi Mallick
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
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Das T, Nath C, Das P, Ghosh K, Logno TA, Debnath P, Dash S, Devnath HS, Das S, Islam MZ. High prevalence of ciprofloxacin resistance in Escherichia coli isolated from chickens, humans and the environment: An emerging one health issue. PLoS One 2023; 18:e0294043. [PMID: 37983240 PMCID: PMC10659180 DOI: 10.1371/journal.pone.0294043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 09/29/2023] [Indexed: 11/22/2023] Open
Abstract
The emergence of antimicrobial resistance in commensal bacteria poses a serious public health burden worldwide. Commensals can disseminate the resistance genes to pathogenic bacteria causing life-threatening infections. This cross-sectional study was designed to investigate the antimicrobial resistance pattern and molecular mechanism(s) of ciprofloxacin resistance in commensal E. coli from three major one health components (humans, animals and the environment) in Bangladesh. Samples were randomly collected from broiler chickens, broiler farm environments and hospitalized human patients from the same geographical area. Isolation and identification of E. coli were performed following standard bacteriological techniques. Antimicrobial susceptibility testing (AST) was performed by disk diffusion and broth microdilution methods. Mutation at the quinolone-resistance determining region (QRDR) was analyzed by sequencing. Of 450 samples, a total of 287 (63.8%; 95% CI 59.2-68.1%) E. coli strains was isolated, where 240 (83.6%; 95% CI 78.9-87.5%) strains were phenotypically resistant to ciprofloxacin. The prevalence of ciprofloxacin-resistant E. coli in broiler chicken, broiler farm environments and hospitalized human patients are 77.6%, 88.8% and 89% respectively. In AST against nine antimicrobials, all the isolates were found to be multidrug-resistant (MDR). The minimum inhibitory concentration (MIC) of ciprofloxacin was ranged from 4 to >128mg/L. Point mutations were detected in several sites of QRDR, specifically at 83 and 87 amino acid positions in gyrA gene, and 56, 57, 78, 80 and 84 amino acid positions in parC gene. Mutations resulted in amino acid substitutions. Phylogenetic analysis of gyrA and parC gene sequences showed a close relationship between the strains isolated from different sources. This study demonstrates a high prevalence of ciprofloxacin resistance in commensal E. coli in humans, animals and environment interface and their genealogically similarity poses an alarming public health consequence.
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Affiliation(s)
- Tridip Das
- Poultry Research and Training Centre, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Chandan Nath
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Pallabi Das
- Chattogram Maa-O-Shishu Hospital, Chattogram, Bangladesh
| | - Keya Ghosh
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Tahia Ahmed Logno
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Pankqj Debnath
- Department of Molecular Life Science, Faculty of Biology, Friedrich Schiller University Jena, Jena, Germany
| | - Shuvo Dash
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, Bangladesh
| | | | - Shubhagata Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Sciences and Health, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Md Zohorul Islam
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Nath C, Das T, Islam MS, Hasib FMY, Singha S, Dutta A, Barua H, Islam MZ. Colistin Resistance in Multidrug-Resistant Escherichia coli Isolated from Retail Broiler Meat in Bangladesh. Microb Drug Resist 2023; 29:523-532. [PMID: 37699212 DOI: 10.1089/mdr.2023.0026] [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] [Indexed: 09/14/2023] Open
Abstract
The emergence of colistin resistance in Escherichia coli is a global public health concern. Contaminated food can accelerate the spread of colistin-resistant E. coli to humans. This study aimed to detect and characterize colistin-resistant E. coli from broiler meat in Bangladesh. We analyzed 136 pooled broiler meat samples from 240 carcasses collected from 40 live bird markets in urban and rural areas and 8 metropolitan supermarkets. The mean count of E. coli in broiler meat samples collected from rural retail shops, metropolitan supermarkets, and urban retail shops was 5.3 ± 1.1, 4.1 ± 1.4, and 3.9 ± 0.8 log10 colony-forming unit per gram, respectively. Colistin-resistant E. coli (minimum inhibitory concentration >2 mg/L) was found in 78% (95% confidence interval 70.2-84.1%) of the samples. All colistin-resistant isolates harbored the mcr-1 gene, while the rest of the mcr genes (mcr-2 to mcr-9) were not detected. Most colistin-resistant E. coli isolates (98%) showed coresistance to tetracycline, sulfamethoxazole/trimethoprim followed by ciprofloxacin (95%). Alarmingly, all of the colistin-resistant isolates were found to be multidrug resistant. Phylogenetic analysis showed close similarities of the mcr-1 gene sequences of this study with many strains of Enterobacterales isolated from humans, animals, and the environment. This study detected colistin-resistant E. coli contamination in broiler meat, which can pose a serious public health threat.
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Affiliation(s)
- Chandan Nath
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Tridip Das
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Sciences and Health, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Md Sirazul Islam
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - F M Yasir Hasib
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Hong Kong SAR, China
| | - Shuvo Singha
- Department of Veterinary and Animal Sciences, Università degli Studi di Milano, Lodi, Italy
| | - Avijit Dutta
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Himel Barua
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Md Zohorul Islam
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
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10
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Browne K, Kuppusamy R, Walsh WR, Black DS, Willcox MDP, Kumar N, Chen R. Antimicrobial Peptidomimetics Prevent the Development of Resistance against Gentamicin and Ciprofloxacin in Staphylococcus and Pseudomonas Bacteria. Int J Mol Sci 2023; 24:14966. [PMID: 37834415 PMCID: PMC10573972 DOI: 10.3390/ijms241914966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Bacteria readily acquire resistance to traditional antibiotics, resulting in pan-resistant strains with no available treatment. Antimicrobial resistance is a global challenge and without the development of effective antimicrobials, the foundation of modern medicine is at risk. Combination therapies such as antibiotic-antibiotic and antibiotic-adjuvant combinations are strategies used to combat antibiotic resistance. Current research focuses on antimicrobial peptidomimetics as adjuvant compounds, due to their promising activity against antibiotic-resistant bacteria. Here, for the first time we demonstrate that antibiotic-peptidomimetic combinations mitigate the development of antibiotic resistance in Staphylococcus aureus and Pseudomonas aeruginosa. When ciprofloxacin and gentamicin were passaged individually at sub-inhibitory concentrations for 10 days, the minimum inhibitory concentrations (MICs) increased up to 32-fold and 128-fold for S. aureus and P. aeruginosa, respectively. In contrast, when antibiotics were passaged in combination with peptidomimetics (Melimine, Mel4, RK758), the MICs of both antibiotics and peptidomimetics remained constant, indicating these combinations were able to mitigate the development of antibiotic-resistance. Furthermore, antibiotic-peptidomimetic combinations demonstrated synergistic activity against both Gram-positive and Gram-negative bacteria, reducing the concentration needed for bactericidal activity. This has significant potential clinical applications-including preventing the spread of antibiotic-resistant strains in hospitals and communities, reviving ineffective antibiotics, and lowering the toxicity of antimicrobial chemotherapy.
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Affiliation(s)
- Katrina Browne
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
- Surgical and Orthopaedic Research Laboratories (SORL), Prince of Wales Clinical School, Prince of Wales Hospital, University of New South Wales (UNSW), Randwick 2031, Australia
| | - Rajesh Kuppusamy
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
- School of Optometry and Vision Science, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
| | - William R. Walsh
- Surgical and Orthopaedic Research Laboratories (SORL), Prince of Wales Clinical School, Prince of Wales Hospital, University of New South Wales (UNSW), Randwick 2031, Australia
| | - David StC Black
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
| | - Naresh Kumar
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
| | - Renxun Chen
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia
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11
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Materon IC, Palzkill T. Structural biology of MCR-1-mediated resistance to polymyxin antibiotics. Curr Opin Struct Biol 2023; 82:102647. [PMID: 37399693 PMCID: PMC10527939 DOI: 10.1016/j.sbi.2023.102647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 07/05/2023]
Abstract
Polymyxins, a last resort antibiotic, target the outer membrane of pathogens and are used to address the increasing prevalence of multidrug-resistant Gram-negative bacteria. The plasmid-encoded enzyme MCR-1 confers polymyxin resistance to bacteria by modifying the outer membrane. Transferable resistance to polymyxins is a major concern; therefore, MCR-1 is an important drug target. In this review, we discuss recent structural and mechanistic aspects of MCR-1 function, its variants and homologs, and how they are relevant to polymyxin resistance. Specifically, we discuss work on polymyxin-mediated disruption of the outer and inner membranes, computational studies on the catalytic mechanism of MCR-1, mutagenesis and structural analysis concerning residues important for substrate binding in MCR-1, and finally, advancements in inhibitors targeting MCR-1.
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Affiliation(s)
- Isabel Cristina Materon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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12
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Qin C, Tang N, Gan Y, Zhao H, Li Y, Tian GB, Yang YY, Yuan P, Ding X. Liposomes Co-Delivering Curcumin and Colistin to Overcome Colistin Resistance in Bacterial Infections. Adv Healthc Mater 2023; 12:e2202903. [PMID: 37523195 DOI: 10.1002/adhm.202202903] [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: 11/10/2022] [Revised: 07/21/2023] [Indexed: 08/01/2023]
Abstract
Antibiotic colistin is the last line of defense against multidrug-resistant (MDR) Gram-negative bacterial infections. Emergence of colistin resistance in microbes is a critical challenge. Herein, curcumin is discovered, for the first time, to reverse the resistance phenotype of colistin-resistant bacteria via a checkerboard assay. For the co-delivery of curcumin and colistin, negatively charged poly(ethylene glycol)-functionalized liposomes encapsulating both drugs (Lipo-cc) are prepared. Killing kinetics and live/dead assays confirm the antibacterial activity of Lipo-cc against colistin-resistant bacteria, which is more potent than that of the free curcumin and colistin combination. Mechanistical studies reveal that Lipo-cc restores the affinity of colistin for the bacterial membrane and improves the uptake of curcumin, which leads to reduced efflux pump activity, achieving a synergistic effect of colistin and curcumin. At the effective antibacterial dose, Lipo-cc does not exhibit any toxicity. The therapeutic efficacy of Lipo-cc is further demonstrated in an intestinal bacterial infection model induced with colistin-resistant Escherichia coli. Lipo-cc reduces the bacterial burden with over 6-log reduction and alleviated inflammation caused by infection. Importantly, unlike colistin, Lipo-cc does not affect the homeostasis of the intestinal flora. Taken together, Lipo-cc successfully overcame colistin resistance, indicating its potential for the treatment of colistin-resistant bacterial infections.
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Affiliation(s)
- Chengyuan Qin
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, 518107, Shenzhen, P. R. China
| | - Ning Tang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, 518107, Shenzhen, P. R. China
| | - Yingying Gan
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, 518107, Shenzhen, P. R. China
| | - Huimin Zhao
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, 518107, Shenzhen, P. R. China
| | - Yuzhen Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, 518107, Shenzhen, P. R. China
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, P. R. China
| | - Yi Yan Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Singapore, 138668, Singapore
| | - Peiyan Yuan
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, 518107, Shenzhen, P. R. China
| | - Xin Ding
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, 518107, Shenzhen, P. R. China
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13
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Ibrahim N, Boyen F, Mohsin MAS, Ringenier M, Berge AC, Chantziaras I, Fournié G, Pfeiffer D, Dewulf J. Antimicrobial Resistance in Escherichia coli and Its Correlation with Antimicrobial Use on Commercial Poultry Farms in Bangladesh. Antibiotics (Basel) 2023; 12:1361. [PMID: 37760658 PMCID: PMC10525429 DOI: 10.3390/antibiotics12091361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial resistance is a global concern, posing risks to human and animal health. This research quantified antimicrobial resistance (AMR) in E. coli isolates from poultry fecal and environmental samples in Bangladesh and explored their association with antimicrobial use (AMU). We screened 725 fecal and 250 environmental samples from 94 conventional broilers and 51 Sonali farms for E. coli presence using MALDI-TOF mass spectrometry. AMU data were collected at flock levels, expressed as treatment incidence (TI), while minimum inhibitory concentrations (MIC) for 14 antibiotics were determined on five fecal E. coli isolates per farm and on all environmental isolates. MIC results were interpreted using human clinical breakpoints and EUCAST epidemiological cut-off values (ECOFFs). Acquired resistance against commonly used antimicrobial agents such as ciprofloxacin, tetracycline and ampicillin, was extremely high and predominantly clinically relevant. There was a moderate correlation between fecal and environmental antibiotic resistance index (ARI), but there was no significant correlation between AMU and AMR, suggesting that the observed AMR prevalence is unrelated to current AMU in poultry, but may be due to high historical AMU. A high level of multidrug resistance, including against critically important antimicrobials, was found in both farm types. Therefore, an AMR/AMU surveillance program is urgently needed in the poultry production sector of Bangladesh.
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Affiliation(s)
- Nelima Ibrahim
- Faculty of Veterinary Medicine, Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
- Department of Livestock Services, Dhaka 1215, Bangladesh
| | - Filip Boyen
- Faculty of Veterinary Medicine, Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Md. Abu Shoieb Mohsin
- Department of Medicine and Surgery, Chattogram Veterinary and Animal Sciences University, Chattogram 4202, Bangladesh;
| | - Moniek Ringenier
- Faculty of Veterinary Medicine, Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Anna Catharina Berge
- Faculty of Veterinary Medicine, Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Ilias Chantziaras
- Faculty of Veterinary Medicine, Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Guillaume Fournié
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280 Marcy l’Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122 Saint Genes Champanelle, France
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Royal College Street, London NW1 0TU, UK
| | - Dirk Pfeiffer
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Royal College Street, London NW1 0TU, UK
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Jeroen Dewulf
- Faculty of Veterinary Medicine, Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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Anyanwu MU, Jaja IF, Okpala COR, Njoga EO, Okafor NA, Oguttu JW. Mobile Colistin Resistance ( mcr) Gene-Containing Organisms in Poultry Sector in Low- and Middle-Income Countries: Epidemiology, Characteristics, and One Health Control Strategies. Antibiotics (Basel) 2023; 12:1117. [PMID: 37508213 PMCID: PMC10376608 DOI: 10.3390/antibiotics12071117] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023] Open
Abstract
Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority critically important antibiotics (HP-CIAs) used to treat infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs), and this has led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. Through horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) (especially ISApl1), transposons (predominantly Tn6330), and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9, and mcr-10 in the poultry sector in LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Citrobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas, and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3, and mcr-10 genes have also been integrated into the chromosomes of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often coexpress mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone, and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Health triad include contact with poultry birds, feed/drinking water, manure, poultry farmers and their farm workwear, farming equipment, the consumption and sale of contaminated poultry meat/egg and associated products, etc. The use of pre/probiotics and other non-antimicrobial alternatives in the raising of birds, the judicious use of non-critically important antibiotics for therapy, the banning of nontherapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, the development of rapid diagnostic test kits, and the intensified surveillance of mcr genes, among others, could effectively control the spread of MGCB from the poultry sector in LMICs.
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Affiliation(s)
| | - Ishmael Festus Jaja
- Department of Livestock and Pasture Science, University of Fort Hare, Alice 5700, South Africa
| | - Charles Odilichukwu R Okpala
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
- UGA Cooperative Extension, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA
| | - Emmanuel Okechukwu Njoga
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka 400001, Nigeria
| | | | - James Wabwire Oguttu
- Department of Agriculture and Animal Health, Florida Campus, University of South Africa, Johannesburg 1709, South Africa
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15
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Umair M, Hassan B, Farzana R, Ali Q, Sands K, Mathias J, Afegbua S, Haque MN, Walsh TR, Mohsin M. International manufacturing and trade in colistin, its implications in colistin resistance and One Health global policies: a microbiological, economic, and anthropological study. THE LANCET. MICROBE 2023; 4:e264-e276. [PMID: 36931291 DOI: 10.1016/s2666-5247(22)00387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 03/16/2023]
Abstract
BACKGROUND The emergence of colistin-resistant Enterobacterales is a global public health concern, yet colistin is still widely used in animals that are used for food as treatment, metaphylaxis, prophylaxis, and growth promotion. Herein, we investigate the effect of colistin-resistant Enterobacterales in Pakistan, global trade of colistin, colistin use at the farm level, and relevant socioeconomic factors. METHODS We conducted a microbiological, economic, and anthropological study of colistin-resistant Escherichia coli in humans, animals, and the environment and international trade and knowledge of colistin in Pakistan, Bangladesh, Nigeria, China, India, and Viet Nam. We collected backyard poultry cloacal swabs, commercial broiler cloacal swabs, cattle and buffalo rectal swabs, human rectal swabs, wild bird droppings, cattle and buffalo meat, sewage water, poultry flies, chicken meat, and canal water from 131 sites across Faisalabad, Pakistan, to be tested for mcr-1-positive and mcr-3-positive Escherichia coli. We recruited new patients admitted to Allied Hospital, Faisalabad, Pakistan, with abdominal pain and diarrhoea for rectal swabs. Patients with dysentery and those who were already on antibiotic treatment were excluded. Data for colistin trade between 2017 and 2020, including importation, manufacturing, and usage, were accessed from online databases and government sources in Pakistan, Bangladesh, and Nigeria. We recruited participants from poultry farms and veterinary drug stores in Pakistan and Nigeria to be interviewed using a structured questionnaire. International manufacturing, import, and export data; value analysis; and trade routes of colistin pharmaceutical raw material (PRM), feed additive, and finished pharmaceutical products (FPPs) were accessed from 2017-21 export data sets. FINDINGS We collected 1131 samples between May 12, 2018, and July 1, 2019: backyard poultry cloacal swabs (n=100), commercial broiler cloacal swabs (n=102), cattle and buffalo rectal swabs (n=188), human rectal swabs (n=200), wild bird droppings (n=100), cattle and buffalo meat (n=100), sewage water (n=90), poultry flies (n=100), chicken meat (n=100), and canal water (n=51). We recruited 200 inpatients at Allied Hospital, Faisalabad, Pakistan, between Nov 15, 2018, and Dec 14, 2018, for rectal swabs. We recruited 21 participants between Jan 1, 2020, and Dec 31, 2020, from poultry farms and drug stores in Pakistan and Nigeria to be interviewed. 75 (7%) of 1131 samples contained mcr-1-positive E coli, including wild bird droppings (25 [25%] of 100), commercial broiler cloacal swabs (17 [17%] of 100), backyard poultry cloacal swabs (one [1%] of 100), chicken meat (13 [13%] of 100), cattle and buffalo meat (two [2%] of 100), poultry flies (eight [8%] of 100), sewage water (six [7%] of 90), and human rectal swabs (three [2%] of 200). During 2017-20, Pakistan imported 275·5 tonnes (68·9 tonnes per year, 95% CI 41·2-96·6) of colistin as PRM, all sourced from China, 701·9 tonnes (175·5 tonnes per year, 140·9-210·1) of colistin as feed additives from China and Viet Nam, and 63·0 tonnes (15·8 tonnes per year, 10·4-21·1) of colistin as FPPs from various countries in Asia and Europe. For Bangladesh and Nigeria, colistin PRM and FPPs were imported from China and Europe. Colistin knowledge and usage practices in Pakistan and Nigeria were unsatisfactory in terms of understanding of the effects on human medicine and usage other than for treatment purposes. China is the major manufacturer of PRM and feed additive colistin and exported a total of 2664·8 tonnes (666·2 tonnes per year, 95% CI 262·1 to 1070·2) of PRM and 2570·2 tonnes (642·6 tonnes per year, -89·4 to 1374·5) of feed additive in 1330 shipments during 2018-21 to 21 countries. INTERPRETATION Regardless of 193 countries signing the UN agreement to tackle antimicrobial resistance, trading of colistin as PRM, FPPs, and feed additive or growth promoter in low-income and middle-income countries continues unabated. Robust national and international laws are urgently required to mitigate the international trade of this antimicrobial listed on WHO Critically Important Antimicrobials for Human Medicine. FUNDING Pakistan Agricultural Research Council and INEOS Oxford Institute for Antimicrobial Research TRANSLATION: For the Urdu translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Muhammad Umair
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan; INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Brekhna Hassan
- School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Refath Farzana
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Qasim Ali
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan; Department of Virology, National Institutes of Health, Islamabad, Pakistan
| | - Kirsty Sands
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK; School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Jordan Mathias
- School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Seniyat Afegbua
- Department of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | | | - Timothy R Walsh
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan.
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Ali MW, Utsho KS, Karmakar S, Hoque MN, Rahman MT, Hassan J. First report on the molecular characteristics of mcr-1 colistin resistant E. coli isolated from retail broiler meat in Bangladesh. Int J Food Microbiol 2023; 388:110065. [PMID: 36610233 DOI: 10.1016/j.ijfoodmicro.2022.110065] [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: 10/21/2022] [Revised: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022]
Abstract
Poultry meat is considered as a potential source of colistin resistant Escherichia coli (CREC). This study aimed to determine the prevalence and characteristics of CREC in broiler meat and ascertain their possible zoonotic potential(s). Broiler meat (n = 104) comprising 26 of each of the thigh, breast, liver, and proventriculus-gizzard was purchased from the retail outlets, Bangladesh. CREC was isolated from the meat samples on MacConkey agar plates containing colistin sulfate followed by PCR confirmation, mcr subtyping (mcr-1 to mcr-5), phylogenetic grouping and detailed molecular characterization through whole genome sequencing (WGS). Antimicrobial resistance of the CREC isolates were evaluated by disc diffusion method and MIC (minimum inhibitory concentration) of colistin sulfate was determined by broth microdilution. The investigation revealed 58 (55.77 %) of 104 samples as positive for CREC, and 53 (91.38 %) of CREC isolates carried mcr-1 gene with no other mcr subtypes evident. Most of the CREC belonged to commensal E. coli (66.04 %) with some pathogenic phylotypes (33.96 %) based on dichotomous decision tree. All the mcr-1 CREC isolates were multidrug-resistant (MDR) and had MICs of 4-8 μg/mL colistin sulfate. WGS of a commensal MDR mcr-1 CREC strain 1ChBEc2mcr revealed as a potential human pathogen belonging to ST162 that harbored 60 virulence factors associated genes (VFGs). The mcr-1 gene in 1ChBEc2mcr genome was located on a plasmid (p1ChBEc2mcr) and showed nucleotide similarities (>95 %) to another plasmid reported from human E. coli in Bangladesh. Beyond mcr-1 gene, this plasmid (p1ChBEc2mcr) also harbored genes related to aminoglycoside, beta-lactams, macrolides, and tetracycline resistance. Presence of similar mcr-1 carrying plasmids in broiler and human CREC denotes a threat of possibly human to avian (broiler) or vice-versa transfer of mcr-1 CREC through close contact as prevailing in the retail outlets of Bangladesh.
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Affiliation(s)
- Md Wohab Ali
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Kishor Sosmith Utsho
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Susmita Karmakar
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Nazmul Hoque
- Department of Gynecology, Obstetrics & Reproductive Health, Faculty of Veterinary Medicine & Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jayedul Hassan
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
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17
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Mmatli M, Mbelle NM, Osei Sekyere J. Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update. Front Cell Infect Microbiol 2022; 12:941358. [PMID: 36093193 PMCID: PMC9462459 DOI: 10.3389/fcimb.2022.941358] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/01/2022] [Indexed: 12/28/2022] Open
Abstract
Background Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane. Results and discussion Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI2 conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins. Conclusion The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, United States
- Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
- *Correspondence: John Osei Sekyere, ;
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Worldwide Prevalence of mcr-mediated Colistin-Resistance Escherichia coli in Isolates of Clinical Samples, Healthy Humans, and Livestock-A Systematic Review and Meta-Analysis. Pathogens 2022; 11:pathogens11060659. [PMID: 35745513 PMCID: PMC9230117 DOI: 10.3390/pathogens11060659] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Antimicrobial resistance is a serious public-health problem throughout the world. Escherichia coli, the most common Gram-negative microorganism, has developed different resistance mechanisms, making treating infections difficult. Colistin is considered a last-resort drug in the treatment of infections caused by E. coli. Plasmid-mediated mobile-colistin-resistant (mcr) genes in E. coli, now disseminated globally, are considered a major public-health threat. Humans, chickens, and pigs are the main reservoirs for E. coli and the sources of antibiotic resistance. Hence, an up-to-date and precise estimate of the global prevalence of mcr resistance genes in these reservoirs is necessary to understand more precisely the worldwide spread and to more effectively implement control and prevention strategies. Methodology: Publications were identified in the PubMed database on the basis of the PRISMA guidelines. English full-text articles were selected from December 2014 to March 2021. Descriptive statistics and a meta-analysis were performed in Excel and R software, respectively. Colistin resistance was defined as the molecular-genetic detection of the mcr genes. The crude and estimated prevalence were calculated for each host and continent. The studies were divided into two groups; community-based when they involved isolates from healthy humans, chickens, or pigs, and clinical studies when they involved only hospital, outpatient, or laboratory isolates. Results: A total of 1278 studies were identified and 218 were included in this systematic review and meta-analysis, divided into community studies (159 studies) and clinical studies (59 studies). The general prevalence of mcr-mediated colistin-resistant E. coli (mcrMCRE) was 6.51% (n = 11,583/177,720), reported in 54 countries and on five continents; Asia with 119 studies followed by Europe with 61 studies registered the most articles. Asia reported the major diversity of mcr-variants (eight of nine, except mcr-2). Worldwide, chickens and pigs proved to be the principal reservoir of mcr with an estimated prevalence of 15.8% and 14.9%, respectively. Healthy humans and clinical isolates showed a lower prevalence with 7.4% and 4.2% respectively. Conclusions: In this systematic review and meta-analysis, the worldwide prevalence of mcr in E. coli isolated from healthy humans, chickens, and pigs was investigated. A wide prevalence and distribution of mcr genes was demonstrated on all continents in E. coli isolates from the selected reservoirs. Understanding the epidemiology and occurrence in the reservoirs of mcr in E. coli on different continents of the world facilitates tracing how mcr genes are transmitted and determining the infection risks for humans. This knowledge can be used to reduce the incidence of zoonotic transmission by implementing the appropriate control programs.
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Menck-Costa MF, Baptista AAS, Gazal LEDS, Justino L, Sanches MS, de Souza M, Nishio EK, Queiroz Dos Santos B, Cruz VD, Berbert JVM, Gonçalves BC, Andrade G, Vespero EC, Nakazato G, Kobayashi RKT. High-Frequency Detection of fosA3 and bla CTX-M-55 Genes in Escherichia coli From Longitudinal Monitoring in Broiler Chicken Farms. Front Microbiol 2022; 13:846116. [PMID: 35663865 PMCID: PMC9158547 DOI: 10.3389/fmicb.2022.846116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Considering the worrying emergence of multidrug resistance, including in animal husbandry and especially in food-producing animals, the need to detect antimicrobial resistance strains in poultry environments is relevant, mainly considering a One Health approach. Thus, this study aimed to conduct longitudinal monitoring of antimicrobial resistance in broiler chicken farms, with an emphasis on evaluating the frequency of resistance to fosfomycin and β-lactams. Escherichia coli was isolated from broiler chicken farms (cloacal swabs, meconium, poultry feed, water, poultry litter, and Alphitobius diaperinus) in northern Paraná from 2019 to 2020 during three periods: the first period (1st days of life), the second period (20th to 25th days of life), and third period (40th to 42nd days of life). Antibiogram tests and the detection of phenotypic extended-spectrum β-lactamase (ESBL) were performed, and they were confirmed by seaching for genes from the blaCTX–M group. The other resistance genes searched were mcr-1 and fosA3. Some ESBL blaCTX–M–1 group strains were selected for ESBL identification by sequencing and enterobacterial repetitive intergenic consensus-polymerase chain reaction analysis. To determine the transferability of the blaCTX–M–1– and fosA3-carrying plasmids, strains were subjected to conjugation experiments. A total of 507 E. coli were analyzed: 360 from cloacal swabs, 24 from meconium samples, 3 from poultry feed samples, 18 from water samples, 69 from poultry litter samples, and 33 from A. diaperinus samples. Among the strain isolate, 80% (406/507) were multidrug-resistant (MDR), and 51% (260/507) were ESBL-positive, with the blaCTX–M–1 group being the most frequent. For the fosA3 gene, 68% (344/507) of the strains isolated were positive, deserves to be highlighted E. coli isolated from day-old chickens (OR 6.34, CI 2.34–17.17), when compared with strains isolated from other origins (poultry litter, A. diaperinus, water, and poultry feed). This work alerts us to the high frequency of the fosA3 gene correlated with the CTX-M-1 group (OR 3.57, CI 95% 2.7–4.72, p < 0.05), especially the blaCTX–M–55 gene, in broiler chickens. This profile was observed mainly in day-old chicken, with a high percentage of E. coli that were MDR. The findings emphasize the importance of conducting longitudinal monitoring to detect the primary risk points during poultry production.
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Affiliation(s)
- Maísa Fabiana Menck-Costa
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Ana Angelita Sampaio Baptista
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | | | - Larissa Justino
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | - Matheus Silva Sanches
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Marielen de Souza
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | - Erick Kenji Nishio
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Beatriz Queiroz Dos Santos
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | - Victor Dellevedove Cruz
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - João Vitor Monteiro Berbert
- Department of Preventive Veterinary Medicine, Avian Medicine Laboratory, State University of Londrina, Londrina, Brazil
| | - Bruna Carolina Gonçalves
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Galdino Andrade
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
| | - Eliana Carolina Vespero
- Department of Pathology, Clinical Analysis and Toxicology, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Gerson Nakazato
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Londrina, Brazil
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Epidemiological Prevalence of Phenotypical Resistances and Mobilised Colistin Resistance in Avian Commensal and Pathogenic E. coli from Denmark, France, The Netherlands, and the UK. Antibiotics (Basel) 2022; 11:antibiotics11050631. [PMID: 35625275 PMCID: PMC9137498 DOI: 10.3390/antibiotics11050631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 01/10/2023] Open
Abstract
Colistin has been used for the treatment of non-invasive gastrointestinal infections caused by avian pathogenic E. coli (APEC). The discovery of mobilised colistin resistance (mcr) in E. coli has instigated a One Health approach to minimise colistin use and the spread of resistance. The aim of this study was to compare colistin susceptibility of APECs (collected from Denmark n = 25 and France n = 39) versus commensal E. coli (collected from the Netherlands n = 51 and the UK n = 60), alongside genetic (mcr-1−5) and phenotypic resistance against six other antimicrobial classes (aminoglycosides, cephalosporins, fluoroquinolones, penicillins, sulphonamides/trimethoprim, tetracyclines). Minimum inhibitory concentration (MIC) values were determined using a broth microdilution method (EUCAST guidelines), and phenotypic resistance was determined using disk diffusion. Colistin MIC values of APEC were significantly lower than those for commensals by 1 dilution (p < 0.0001, Anderson-Darling test), and differences in distributions were observed between countries. No isolate carried mcr-1−5. Three phenotypically resistant isolates were identified in 2/62 APEC and 1/111 commensal isolates. Gentamicin or gentamicin−ceftriaxone co-resistance was observed in two of these isolates. This study showed a low prevalence of phenotypic colistin resistance, with no apparent difference in colistin resistance between commensal E. coli strains and APEC strains.
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Nadimpalli ML, Lanza VF, Montealegre MC, Sultana S, Fuhrmeister ER, Worby CJ, Teichmann L, Caduff L, Swarthout JM, Crider YS, Earl AM, Brown J, Luby SP, Islam MA, Julian TR, Pickering AJ. Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children. Nat Microbiol 2022; 7:620-629. [PMID: 35422497 PMCID: PMC9249080 DOI: 10.1038/s41564-022-01101-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/24/2022] [Indexed: 02/07/2023]
Abstract
Healthy development of the gut microbiome provides long-term health benefits. Children raised in countries with high infectious disease burdens are frequently exposed to diarrhoeal pathogens and antibiotics, which perturb gut microbiome assembly. A recent cluster-randomized trial leveraging >4,000 child observations in Dhaka, Bangladesh, found that automated water chlorination of shared taps effectively reduced child diarrhoea and antibiotic use. In this substudy, we leveraged stool samples collected from 130 children 1 year after chlorine doser installation to examine differences between treatment and control children's gut microbiota. Water chlorination was associated with increased abundance of several bacterial genera previously linked to improved gut health; however, we observed no effects on the overall richness or diversity of taxa. Several clinically relevant antibiotic resistance genes were relatively more abundant in the gut microbiome of treatment children, possibly due to increases in Enterobacteriaceae. While further studies on the long-term health impacts of drinking chlorinated water would be valuable, we conclude that access to chlorinated water did not substantially impact child gut microbiome development in this setting, supporting the use of chlorination to increase global access to safe drinking water.
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Affiliation(s)
- Maya L. Nadimpalli
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA,Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
| | - Val F. Lanza
- Bioinformatics Unit, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain,Network Research Center for Infectious Diseases (CIBERINFEC), Spain
| | | | - Sonia Sultana
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Erica R. Fuhrmeister
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Colin J. Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA
| | - Lisa Teichmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jenna M. Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Yoshika S. Crider
- Energy and Resources Group, University of California Berkeley, Berkeley, CA, USA,King Center on Global Development, Stanford University, Stanford, CA, USA
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen P. Luby
- Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Mohammad Aminul Islam
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland,Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Timothy R. Julian
- Network Research Center for Infectious Diseases (CIBERINFEC), Spain,Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Amy J. Pickering
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA,Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA,Blum Center for Developing Economies, University of California, Berkeley, CA, USA,Correspondence and requests for materials should be addressed to Dr. Amy Pickering () and Dr. Tim Julian ()
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22
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Musa L, Proietti PC, Marenzoni ML, Stefanetti V, Kika TS, Blasi F, Magistrali CF, Toppi V, Ranucci D, Branciari R, Franciosini MP. Susceptibility of Commensal E. coli Isolated from Conventional, Antibiotic-Free, and Organic Meat Chickens on Farms and at Slaughter toward Antimicrobials with Public Health Relevance. Antibiotics (Basel) 2021; 10:1321. [PMID: 34827259 PMCID: PMC8614865 DOI: 10.3390/antibiotics10111321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 11/20/2022] Open
Abstract
The spread of resistant bacteria from livestock to the food industry promoted an increase of alternative poultry production systems, such as organic and antibiotic-free ones, based on the lack of antimicrobial use, except in cases in which welfare is compromised. We aimed to investigate the antibiotic susceptibility of commensal Escherichia coli isolated from organic, antibiotic-free, and conventional broiler farms and slaughterhouses toward several antimicrobials critically important for human health. To assess antimicrobial susceptibility, all E. coli isolates and extended spectrum beta-lactamase (ESBL) E. coli were analysed by the microdilution method. The prevalence of tigecycline, azithromycin and gentamicin E. coli-resistant strains was highest in organic samplings. Conversely, the lowest prevalence of resistant E. coli strains was observed for cefotaxime, ceftazidime and ciprofloxacin in organic systems, representing a significant protective factor compared to conventional systems. All E. coli strains were colistin-susceptible. Contamination of the external environment by drug-resistant bacteria could play a role in the presence of resistant strains detected in organic systems. Of interest is the highest prevalence of cephalosporin resistance of E. coli in conventional samplings, since they are not permitted in poultry. Our results suggest that monitoring of antibiotic resistance of the production chain may be helpful to detect "risks" inherent to different rearing systems.
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Affiliation(s)
- Laura Musa
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (L.M.); (M.L.M.); (V.S.); (V.T.); (D.R.); (R.B.); (M.P.F.)
| | - Patrizia Casagrande Proietti
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (L.M.); (M.L.M.); (V.S.); (V.T.); (D.R.); (R.B.); (M.P.F.)
| | - Maria Luisa Marenzoni
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (L.M.); (M.L.M.); (V.S.); (V.T.); (D.R.); (R.B.); (M.P.F.)
| | - Valentina Stefanetti
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (L.M.); (M.L.M.); (V.S.); (V.T.); (D.R.); (R.B.); (M.P.F.)
| | - Tana Shtylla Kika
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Agricultural University of Tirana, Koder Kamez, 1029 Tirana, Albania;
| | - Francesca Blasi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06124 Perugia, Italy; (F.B.); (C.F.M.)
| | - Chiara Francesca Magistrali
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06124 Perugia, Italy; (F.B.); (C.F.M.)
| | - Valeria Toppi
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (L.M.); (M.L.M.); (V.S.); (V.T.); (D.R.); (R.B.); (M.P.F.)
| | - David Ranucci
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (L.M.); (M.L.M.); (V.S.); (V.T.); (D.R.); (R.B.); (M.P.F.)
| | - Raffaella Branciari
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (L.M.); (M.L.M.); (V.S.); (V.T.); (D.R.); (R.B.); (M.P.F.)
| | - Maria Pia Franciosini
- Department of Veterinary Medicine, Via S. Costanzo 4, 06126 Perugia, Italy; (L.M.); (M.L.M.); (V.S.); (V.T.); (D.R.); (R.B.); (M.P.F.)
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Smelikova E, Tkadlec J, Krutova M. How to: screening for mcr-mediated resistance to colistin. Clin Microbiol Infect 2021; 28:43-50. [PMID: 34537365 DOI: 10.1016/j.cmi.2021.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Colistin belongs to the last-resort antibiotics. The discovery of plasmid-bound colistin resistance mediated by the mcr-gene(s) is of great concern because, given its biological potential, there is a risk of its rapid spread. OBJECTIVES To discuss the current literature on the methods for the screening for mcr-mediated resistance to colistin. SOURCES Literature was drawn from a search of PubMed from 1 January 2016 to 26 April 2021. CONTENT The selective culture-based or culture-independent approach can be used for the screening of mcr-mediated resistance to colistin in clinical samples. Rapid Polymyxin NP, Colistin Drop or Colistin Agar Spot tests are applicable for the selection of isolates with a suspected resistance to colistin that has to be confirmed by broth microdilution. The mcr-mediated resistance to colistin can be confirmed by the detection of the causal gene(s) or by phenotype using EDTA-colistin broth disc elution; production of the MCR-1 enzyme can be confirmed with lateral flow immunoassay, using matrix-assisted laser desorption/ionization time-of flight or liquid chromatography-based mass spectrometry. Whole-genome sequencing (WGS) is the ultimate typing method. When a WGS platform is not available at a healthcare facility, a WGS-outsourced service, in combination with freely available bioinformatics tools, allows for the characterization of the mcr-gene(s) carrying isolates. IMPLICATIONS mcr-mediated colistin resistance should be monitored through active targeted screening. The broth microdilution method is required for colistin susceptibility testing but as only a selected number of clinical isolates are tested, colistin resistance, including mcr-mediated, may remain undetected. In mcr-1-positive Escherichia coli isolates, the MIC to colistin can range from 2 to 8 mg/L, so it is proposed that Enterobacterales with a colistin MIC of 2 mg/L should also be included in the mcr-mediated colistin resistance screening and those with a confirmed mcr-genotype and/or MCR-phenotype should be considered to be colistin-resistant.
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Affiliation(s)
- Eva Smelikova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Czech Republic
| | - Jan Tkadlec
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Czech Republic
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Czech Republic.
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Chowdhury S, Ghosh S, Aleem MA, Parveen S, Islam MA, Rashid MM, Akhtar Z, Chowdhury F. Antibiotic Usage and Resistance in Food Animal Production: What Have We Learned from Bangladesh? Antibiotics (Basel) 2021; 10:1032. [PMID: 34572614 PMCID: PMC8467341 DOI: 10.3390/antibiotics10091032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023] Open
Abstract
Irrational and inappropriate use of antibiotics in commercial chicken and aquaculture industries can accelerate the antibiotic resistance process in humans and animals. In Bangladesh, the growing commercial chicken and aquaculture industries are playing significantly important roles in the food value chain. It is necessary to know the antibiotic usage practices and antibiotic resistance in food animal production to design rational policies, guidelines, and interventions. We conducted a narrative review to understand the level of antibiotic usage and resistance in food animal production in Bangladesh. Information about antibiotic usage in different food animal production systems, including commercial chickens and aquaculture in Bangladesh is inadequate. Only a few small-scale studies reported that the majority (up to 100%) of the broiler and layer chicken farms used antibiotics for treating and preventing diseases. However, numerous studies reported antibiotic-resistant bacteria of public health importance in commercial chicken, fish, livestock, and animal origin food. The isolates from different pathogenic bacteria were found resistant against multiple antibiotics, including quinolones, the third or fourth generation of cephalosporins, and polymyxins. Veterinary practitioners empirically treat animals with antibiotics based on presumptive diagnosis due to inadequate microbial diagnostic facilities in Bangladesh. Intensive training is helpful to raise awareness among farmers, feed dealers, and drug sellers on good farming practices, standard biosecurity practices, personal hygiene, and the prudent use of antibiotics. Urgently, the Government of Bangladesh should develop and implement necessary guidelines to mitigate irrational use of antibiotics in food animals using a multi-sectoral One Health approach.
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Affiliation(s)
- Sukanta Chowdhury
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (S.G.); (M.A.A.); (S.P.); (M.A.I.); (M.M.R.); (Z.A.); (F.C.)
| | - Sumon Ghosh
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (S.G.); (M.A.A.); (S.P.); (M.A.I.); (M.M.R.); (Z.A.); (F.C.)
| | - Mohammad Abdul Aleem
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (S.G.); (M.A.A.); (S.P.); (M.A.I.); (M.M.R.); (Z.A.); (F.C.)
- School of Population Health, University of New South Wales (UNSW), Sydney, NSW 1466, Australia
| | - Shahana Parveen
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (S.G.); (M.A.A.); (S.P.); (M.A.I.); (M.M.R.); (Z.A.); (F.C.)
| | - Md. Ariful Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (S.G.); (M.A.A.); (S.P.); (M.A.I.); (M.M.R.); (Z.A.); (F.C.)
| | - Md. Mahbubur Rashid
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (S.G.); (M.A.A.); (S.P.); (M.A.I.); (M.M.R.); (Z.A.); (F.C.)
| | - Zubair Akhtar
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (S.G.); (M.A.A.); (S.P.); (M.A.I.); (M.M.R.); (Z.A.); (F.C.)
| | - Fahmida Chowdhury
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (S.G.); (M.A.A.); (S.P.); (M.A.I.); (M.M.R.); (Z.A.); (F.C.)
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Knowledge, Attitude, and Practices on Antimicrobial Use and Antimicrobial Resistance among Commercial Poultry Farmers in Bangladesh. Antibiotics (Basel) 2021; 10:antibiotics10070784. [PMID: 34203195 PMCID: PMC8300693 DOI: 10.3390/antibiotics10070784] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/22/2023] Open
Abstract
Antimicrobial resistance (AMR) has become an emerging health issue globally, posing a threat to zoonotic pathogens and foodborne diseases. In Bangladesh, the poultry sector supplies the majority of the demand for animal-source protein. The irrational and excessive use of antimicrobials (AMU) has been observed in the poultry sector. The development of AMR is associated with many factors, including the knowledge and attitudes of poultry farmers. Therefore, AMR reduction requires intervention from all the stockholders, including the farmers who are considered as end users of antimicrobials. This current research conducted a cross-sectional study to assess the knowledge, attitudes, and practices (KAP) of poultry farmers on AMU and AMR in Bangladesh. We determined the KAP of poultry farmers (broiler and layer farmers) of some selected districts of the country using a tested and paper-based questionnaire. The results demonstrated that most of the respondents have insufficient KAP regarding AMU and AMR. The respondents used a variety of antimicrobials primarily in the treatment of various diseases in poultry. One-third of the farmers did not seek antimicrobials from registered vets. Instead, they depended on others or themselves. The factor score analysis further revealed that the farmers’ demographic and socioeconomic variables were significant factors influencing the KAP. An adjusted logistic regression analysis showed that older farmers with 9–12 years of farming experience and graduate-level education, engaging in medium-sized layer farming, were more likely to have correct KAP on AMU and AMR. Further, farmers from the Cox’s Bazar region showed correct knowledge, whereas farmers of the Chattogram region showed a correct attitude towards AMU and AMR. A Spearman’s rank-order correlation revealed a positive association between knowledge–attitudes and knowledge–practices. The findings of the current investigation provide baseline evidence about the KAP of poultry farmers from low-income resources and offer insights into designing interventions and policies for the use of AMU and AMR in Bangladesh.
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Prevalence of Colistin-Resistant Bacteria among Retail Meats in Japan. Food Saf (Tokyo) 2021; 9:48-56. [PMID: 34249589 PMCID: PMC8254848 DOI: 10.14252/foodsafetyfscj.d-21-00002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
Colistin (CST) is considered the last resort for the treatment of infectious diseases due to multidrug-resistant bacteria. Since the mcr-1 gene has been reported in Enterobacteriaceae isolated from food, animals, and humans in China, the prevalence of CST-resistant bacteria has been of great concern. Here, we investigated the prevalence of CST resistance and plasmid-mediated colistin-resistance genes (mcr) in gram-negative bacteria isolated among retail meats in Japan. CST-resistant bacteria were isolated from 310 domestic retail meats (103 chicken meat, 103 pork, and 104 beef) purchased between May 2017 and July 2018 from retail shops in Japan using CST-containing media and antimicrobial susceptibility testing. The mcr gene was investigated in isolates with a CST minimum inhibitory concentration of ≥1 μg/mL. Excluding the intrinsically CST-resistant isolates, CST-resistant bacteria were isolated from 39 of the total chicken meats (37.9%), 19 of the pork samples (18.4%), and 18 of the beef samples (17.3%). A total of 459 isolates were identified, out of which 99 were CST-resistant. CST resistance (resistance breakpoints: Aeromonas, >4 μg/mL; others, >2 μg/mL) was found in Aeromonas spp. (48/206, 23.3%), Yersinia spp. (5/112, 4.5%), Escherichia coli (23/39, 59%), Citrobacter spp. (4/26, 15.4%), Klebsiella spp. (2/23, 8.7%), Raoultella spp. (2/16, 12.5%), Enterobacter spp. (7/14, 50%), Pseudomonas spp. (1/8, 12.5%), Pantoea spp. (5/7, 71.4%), Ewingella spp. (1/4, 25%), and Kluyvera spp. (1/2, 50%). The mcr gene was detected in 16 isolates: mcr-1 in 14 isolates of E. coli from 10 chicken samples (9.7%), and mcr-3 in two isolates of Aeromonas sobria from pork and chicken samples (each 1.0%). The findings of this study highlight the necessity of surveillance of CST resistance and resistance genes in bacteria that contaminate retail meats.
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Das T, Islam MZ, Rana EA, Dutta A, Ahmed S, Barua H, Biswas PK. Abundance of Mobilized Colistin Resistance Gene ( mcr-1) in Commensal Escherichia coli from Diverse Sources. Microb Drug Resist 2021; 27:1585-1593. [PMID: 33909471 DOI: 10.1089/mdr.2020.0433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aims: Antimicrobial resistance (AMR) spreads not only by pathogenic but also by commensal bacteria, and the latter can become a reservoir for resistance genes. This study was aimed to investigate the AMR patterns along with the presence of mobilized colistin resistance (mcr) genes in commensal Escherichia coli circulating in chickens, farm environments, street foods, and human patients. Materials and Methods: By a cross-sectional survey, isolates obtained from 530 samples were tested for their AMR profiles against 9 antimicrobials. Minimum inhibitory concentration (MIC) of the phenotypically colistin-resistant isolates was determined and screened for a set of mcr genes followed by sequencing of mcr-1 gene in the multidrug-resistant (MDR) isolates. Results: A total of 313 E. coli strains were isolated and confirmed by polymerase chain reaction. Antimicrobial susceptibility testing revealed that about 98% (confidence interval [95% CI] 95-99) of the isolates were MDR, and 58% (95% CI 52-63) isolates exhibited resistance to colistin. MIC values of colistin against the isolates ranged from 4 to 64 mg/L. Except for human patients, 20.4% colistin-resistant isolates from other sources of isolation had mcr-1 gene. Conclusions: There is abundance of commensal MDR E. coli strains with the acquisition of mcr-1 gene circulating in chickens and farm environments in Bangladesh.
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Affiliation(s)
- Tridip Das
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh.,Poultry Research and Training Centre, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Md Zohorul Islam
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Eaftekhar Ahmed Rana
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Avijit Dutta
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Shahana Ahmed
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Himel Barua
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Paritosh Kumar Biswas
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh.,Poultry Research and Training Centre, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
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Nikkhahi F, Robatjazi S, Niazadeh M, Javadi A, Shahbazi G, Aris P, Marashi S, Emam N. First detection of mobilized colistin resistance mcr-1 gene in Escherichia coli isolated from livestock and sewage in Iran. New Microbes New Infect 2021; 41:100862. [PMID: 33996103 PMCID: PMC8086131 DOI: 10.1016/j.nmni.2021.100862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/17/2021] [Accepted: 03/04/2021] [Indexed: 11/23/2022] Open
Abstract
Currently, few studies have investigated the mechanisms of resistance to colistin in Iran. The aim of this study was to investigate mcr-harbouring Escherichia coli dissemination in livestock and sewage in Iran. A total of 115 samples from cows (n = 38), chickens (n = 47) and urban sewage samples (n = 30) were collected. The presence of genes including mcr1–6 and ampC β-lactamase (blaMOX, blaCIT, blaDHA, blaACC, blaEBC, blaFOX) for colistin-resistant isolates was investigated by multiplex PCR method. Genetic association of colistin-resistant strains was also evaluated by ERIC PCR. Sixty-five isolates were identified as E. coli. Meaningless were resistant to colistin. The highest (26.1%) and lowest (3.07%) resistance were shown to ampicillin and meropenem respectively. Among the three colistin-resistant isolates, 2 (66%) were multidrug resistant, with one of them being mcr-1 positive and the other one positive for DHA ampC β-lactamase gene. No mcr2–6 genes were found. Minimum inhibitory concentration of mcr-producing isolate was 4 mg/L by microbroth dilution. This study reports, first the detection of mcr-1 in E. coli from farm animals in Iran, a finding that is indicative of a global distribution of this plasmidic element and threatning the use of colistin as a last resort antibiotic. No clonal relationship was observed between the colistin-resistant E. coli isolates by ERIC-PCR. Monitoring the presence of these strains in animal sources help as to controlling the spread of resistance genes from animal to human is vital.
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Affiliation(s)
- F. Nikkhahi
- Medical Microbiology Research Center, Iran
- Corresponding author: F. Nikkhahi, Medical Microbiology Research Center, Qazvin University of Medical Sciences, PO Box 34199, 15315, Qazvin, Iran.
| | | | | | - A. Javadi
- Department of Biostatics, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - P. Aris
- Medical Microbiology Research Center, Iran
| | | | - N. Emam
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Uddin MB, Hossain SB, Hasan M, Alam MN, Debnath M, Begum R, Roy S, Harun-Al-Rashid A, Chowdhury MSR, Rahman MM, Hossain MM, Elahi F, Chowdhury MYE, Järhult JD, El Zowalaty ME, Ahmed SSU. Multidrug Antimicrobial Resistance and Molecular Detection of mcr-1 Gene in Salmonella Species Isolated from Chicken. Animals (Basel) 2021; 11:206. [PMID: 33467777 PMCID: PMC7829884 DOI: 10.3390/ani11010206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/02/2021] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Colistin (polymyxin E) is widely used in animal and human medicine and is increasingly used as one of the last-resort antibiotics against Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant Gram-negative bacteria, resistance to this antibiotic ought to be monitored. The study was undertaken to elucidate the molecular mechanisms, genetic relationships and phenotype correlations of colistin-resistant isolates. Here, we report the detection of the mcr-1 gene in chicken-associated Salmonella isolates in Bangladesh and its in-silico functional analysis. Out of 100 samples, 82 Salmonella spp. were isolated from chicken specimens (liver, intestine). Phenotypic disc diffusion and minimum inhibitory concentration (MIC) assay using different antimicrobial agents were performed. Salmonella isolates were characterized using PCR methods targeting genus-specific invA and mcr-1 genes with validation for the functional analysis. The majority of the tested Salmonella isolates were found resistant to colistin (92.68%), ciprofloxacin (73.17%), tigecycline (62.20%) and trimethoprim/sulfamethoxazole (60.98%). When screened using PCR, five out of ten Salmonella isolates were found to carry the mcr-1 gene. One isolate was confirmed for Salmonella enterica subsp. enterica serovar Enteritidis, and other four isolates were confirmed for Salmonella enterica subsp. enterica serovar Typhimurium. Sequencing and phylogenetic analysis revealed a divergent evolutionary relationship between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, rendering them resistant to colistin. Three-dimensional homology structural analysis of MCR-1 proteins and molecular docking interactions suggested that MCR-1 and LptA share a similar substrate binding cavity, which could be validated for the functional analysis. The comprehensive molecular and in-silico analyses of the colistin resistance mcr-1 gene of Salmonella spp. of chicken origin in the present study highlight the importance of continued monitoring and surveillance for antimicrobial resistance among pathogens in food chain animals.
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Affiliation(s)
- Md Bashir Uddin
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (S.M.B.H.); (M.N.A.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - S.M. Bayejed Hossain
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (S.M.B.H.); (M.N.A.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh;
| | - Mohammad Nurul Alam
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (S.M.B.H.); (M.N.A.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mita Debnath
- Kazi Farms Poultry Laboratory, Gazipur 1700, Bangladesh;
| | - Ruhena Begum
- Bangladesh Livestock Research Institute, Dhaka 1341, Bangladesh;
| | - Sawrab Roy
- Department of Microbiology and Immunology, Sylhet Agricultural University, Sylhet 3100, Bangladesh;
| | - Ahmed Harun-Al-Rashid
- Department of Aquatic Resource Management, Sylhet Agricultural University, Sylhet 3100, Bangladesh;
| | - Md. Shahidur Rahman Chowdhury
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (S.M.B.H.); (M.N.A.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Md. Mahfujur Rahman
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (S.M.B.H.); (M.N.A.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Md. Mukter Hossain
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (S.M.B.H.); (M.N.A.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Fazle Elahi
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea;
| | | | - Josef D. Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, SE 751 85 Uppsala, Sweden;
| | - Mohamed E. El Zowalaty
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, UAE
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, SE 75 123 Uppsala, Sweden
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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