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Lencina FA, Bertona M, Stegmayer MA, Olivero CR, Frizzo LS, Zimmermann JA, Signorini ML, Soto LP, Zbrun MV. Prevalence of colistin-resistant Escherichia coli in foods and food-producing animals through the food chain: A worldwide systematic review and meta-analysis. Heliyon 2024; 10:e26579. [PMID: 38434325 PMCID: PMC10904249 DOI: 10.1016/j.heliyon.2024.e26579] [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: 01/05/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
The purpose of this systematic review and meta-analysis was to summarize the available scientific evidence on the prevalence of colistin-resistant Escherichia coli strains isolated from foods and food-producing animals, the mobile colistin-resistant genes involved, and the impact of the associated variables. A systematic review was carried out in databases according to selection criteria and search strategies established a priori. Random-effect meta-analysis models were fitted to estimate the prevalence of colistin-resistant Escherichia coli and to identify the factors associated with the outcome. In general, 4.79% (95% CI: 3.98%-5.76%) of the food and food-producing animal samples harbored colistin-resistant Escherichia coli (total number of colistin-resistant Escherichia coli/total number of samples), while 5.70% (95% confidence interval: 4.97%-6.52%) of the E. coli strains isolated from food and food-producing animal samples harbored colistin resistance (total number of colistin-resistant Escherichia coli/total number of Escherichia coli isolated samples). The prevalence of colistin-resistant Escherichia coli increased over time (P < 0.001). On the other hand, 65.30% (95% confidence interval: 57.77%-72.14%) of colistin resistance was mediated by the mobile colistin resistance-1 gene. The mobile colistin resistance-1 gene prevalence did not show increases over time (P = 0.640). According to the findings, other allelic variants (mobile colistin resistance 2-10 genes) seem to have less impact on prevalence. A higher prevalence of colistin resistance was estimated in developing countries (P < 0.001), especially in samples (feces and intestinal content, meat, and viscera) derived from poultry and pigs (P < 0.001). The mobile colistin resistance-1 gene showed a global distribution with a high prevalence in most of the regions analyzed (>50%). The prevalence of colistin-resistant Escherichia coli and the mobile colistin resistance-1 gene has a strong impact on the entire food chain. The high prevalence estimated in the retail market represents a potential risk for consumers' health. There is an urgent need to implement based-evidence risk management measures under the "One Health" approach to guarantee public health, food safety, and a sustainable future.
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Affiliation(s)
- Florencia Aylen Lencina
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
| | - Matías Bertona
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
| | - María Angeles Stegmayer
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
| | - Carolina Raquel Olivero
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
| | - Laureano Sebastián Frizzo
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
| | - Jorge Alberto Zimmermann
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
| | - Marcelo Lisandro Signorini
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - Lorena Paola Soto
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
| | - María Virginia Zbrun
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
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Bhattarai RK, Basnet HB, Dhakal IP, Devkota B. Antimicrobial resistance of avian pathogenic Escherichia coli isolated from broiler, layer, and breeder chickens. Vet World 2024; 17:480-499. [PMID: 38595648 PMCID: PMC11000482 DOI: 10.14202/vetworld.2024.480-499] [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: 10/18/2023] [Accepted: 01/24/2024] [Indexed: 04/11/2024] Open
Abstract
Background and Aim Antimicrobials are extensively used in poultry production for growth promotion as well as for the treatment and control of diseases, including avian pathogenic Escherichia coli (APEC). Poor selection, overuse, and misuse of antimicrobial agents may promote the emergence and dissemination of antimicrobial resistance (AMR) in APEC. This study aimed to assess antimicrobial susceptibility patterns and detect antibiotic resistance genes (ARGs) in APEC isolated from clinical cases of colibacillosis in commercial broiler, layer, and breeder chickens. Materials and Methods A total of 487 APEC were isolated from 539 across 300 poultry farms in various regions of Nepal. Antimicrobial susceptibility patterns was determined using the Kirby-Bauer disk diffusion and broth microdilution methods. The index of AMR, such as multiple antibiotic resistance (MAR) index, resistance score (R-score), and multidrug resistance (MDR) profile, were determined. Polymerase chain reaction was employed to detect multiple ARGs and correlations between phenotypic and genotypic resistance were analyzed. Results The prevalence of APEC was 91% (487/539). All of these isolates were found resistant to at least one antimicrobial agent, and 41.7% of the isolates were resistant against 8-9 different antimicrobials. The antibiogram of APEC isolates overall showed the highest resistance against ampicillin (99.4%), whereas the highest intermediate resistance was observed in enrofloxacin (92%). The MAR index and R-score showed significant differences between broiler and layers, as well as between broiler breeder and layers. The number of isolates that were resistant to at least one agent in three or more antimicrobial categories tested was 446 (91.6%) and were classified as MDR-positive isolates. The ARGs were identified in 439 (90.1%) APEC isolates, including the most detected mobilized colistin resistance (mcr1) which was detected in the highest (52.6%) isolates. Overall, resistance gene of beta-lactam (blaTEM), mcr1, resistance gene of sulphonamide (sul1) and resistance gene of tetracycline (tetB) (in broiler), were detected in significantly higher than other tested genes (p < 0.001). When examining the pair-wise correlations, a significant phenotype-phenotype correlation (p < 0.001) was observed between levofloxacin and ciprofloxacin, chloramphenicol and tetracycline with doxycycline. Similarly, a significant phenotype-genotype correlation (p < 0.001) was observed between chloramphenicol and the tetB, and colistin with blaTEM and resistance gene of quinolone (qnrA). Conclusion In this study, the current state of APEC AMR in commercial chickens is revealed for the first time in Nepal. We deciphered the complex nature of AMR in APEC populations. This information of molecular surveillance is useful to combat AMR in APEC and to contribute to manage APEC associated diseases and develop policies and guidelines to enhance the commercial chicken production.
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Affiliation(s)
- Rebanta K Bhattarai
- Department of Veterinary Microbiology and Parasitology, Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Nepal
| | - Hom B Basnet
- Department of Veterinary Microbiology and Parasitology, Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Nepal
| | - Ishwari P Dhakal
- Department of Medicine and Public Health, Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Nepal
| | - Bhuminand Devkota
- Department of Theriogenology, Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Nepal
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Karim MR, Zakaria Z, Hassan L, Faiz NM, Ahmad NI. The occurrence and molecular detection of mcr-1 and mcr-5 genes in Enterobacteriaceae isolated from poultry and poultry meats in Malaysia. Front Microbiol 2023; 14:1208314. [PMID: 37601372 PMCID: PMC10435970 DOI: 10.3389/fmicb.2023.1208314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
The advent of antimicrobials-resistant (AMR), including colistin-resistant bacteria, poses a significant challenge to animal and human health, food safety, socio-economic growth, and the global environment. This study aimed to ascertain the colistin resistance prevalence and molecular mechanisms of colistin resistance in Enterobacteriaceae. The colistin resistance was determined using broth microdilution assay, PCR; and Sanger sequencing of mcr genes responsible for colistin resistance in Enterobacteriaceae (n = 627), including Escherichia coli (436), Salmonella spp. (n = 140), and Klebsiella pneumoniae (n = 51), obtained from chicken and chicken meats. Out of 627 Enterobacteriaceae, 8.6% of isolates exhibited colistin resistance phenotypically. Among these colistin resistant isolates, 9.3% (n = 37) were isolated from chicken meat, 7.2% (n = 11) from the cloacal swab of chicken and 7.9% (n = 6) from the litter samples. Overall, 12.96% of colistin-resistant isolates were positive with mcr genes, in which mcr-1 and mcr-5 genes were determined in 11.11% and 1.85% of colistin-resistant isolates, respectively. The E. coli isolates obtained from chicken meats, cloacal swabs and litter samples were found positive for mcr-1, and Salmonella spp. originated from the chicken meat sample was observed with mcr-5, whereas no mcr genes were observed in K. pneumoniae strains isolated from any of the collected samples. The other colistin resistance genes, including mcr-2, mcr-3, mcr-4, mcr-6, mcr-7, mcr-8, mcr-9, and mcr-10 were not detected in the studied samples. The mcr-1 and mcr-5 genes were sequenced and found to be 100% identical to the mcr-1 and mcr-5 gene sequences available in the NCBI database. This is the first report of colistin resistance mcr-5 gene in Malaysia which could portend the emergence of mcr-5 harboring bacterial strains for infection. Further studies are needed to characterize the mr-5 harbouring bacteria for the determination of plasmid associated with mcr-5 gene.
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Affiliation(s)
- Md Rezaul Karim
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
- Bangladesh Livestock Research Institute, Dhaka, Bangladesh
| | - Zunita Zakaria
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
| | - Latiffah Hassan
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
| | - Nik Mohd Faiz
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
| | - Nur Indah Ahmad
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
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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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Karim MR, Zakaria Z, Hassan L, Mohd Faiz N, Ahmad NI. Antimicrobial Resistance Profiles and Co-Existence of Multiple Antimicrobial Resistance Genes in mcr-Harbouring Colistin-Resistant Enterobacteriaceae Isolates Recovered from Poultry and Poultry Meats in Malaysia. Antibiotics (Basel) 2023; 12:1060. [PMID: 37370378 DOI: 10.3390/antibiotics12061060] [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: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The co-existence of the colistin resistance (mcr) gene with multiple drug-resistance genes has raised concerns about the possibility of the development of pan-drug-resistant bacteria that will complicate treatment. This study aimed to investigate the antibiotic resistance profiles and co-existence of antibiotic resistance genes among the colistin-resistant Enterobacteriaceae isolates recovered from poultry and poultry meats. The antibiotic susceptibility to various classes of antibiotics was performed using the Kirby-Bauer disk diffusion method and selected antimicrobial resistance genes were detected using PCR in a total of 54 colistin-resistant Enterobacteriaceae isolates including Escherichia coli (E. coli) (n = 32), Salmonella spp. (n = 16) and Klebsiella pneumoniae (K. pneumoniae) (n = 6) isolates. Most of the isolates had multi-drug resistance (MDR), with antibiotic resistance against up to seven classes of antibiotics. All mcr-harbouring, colistin-resistant Enterobacteriaceae isolates showed this MDR (100%) phenotype. The mcr-1 harbouring E. coli isolates were co-harbouring multiple antibiotic resistance genes. The seven most commonly identified resistance genes (blaTEM, tetA, floR, aac-3-IV, aadA1, fosA, aac(6_)-lb) were detected in an mcr-1-harbouring E. coli isolate recovered from a cloacal swab. The mcr-5 harbouring Salmonella spp. isolate recovered from poultry meats was positive for blaTEM, tetA, floR, aac-3-IV, fosA and aac(6_)-lb genes. In conclusion, the colistin-resistant Enterobacteriaceae with mcr genes co-existing multiple clinically important antimicrobial resistance genes in poultry and poultry meats may cause potential future threats to infection treatment choices in humans and animals.
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Affiliation(s)
- Md Rezaul Karim
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh
| | - Zunita Zakaria
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Latiffah Hassan
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Nik Mohd Faiz
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Nur Indah Ahmad
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
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Bhusal B, Yadav B, Dawadi P, Rijal KR, Ghimire P, Banjara MR. Multi-drug Resistance, β-Lactamases Production, and Coexistence of bla NDM-1 and mcr-1 in Escherichia coli Clinical Isolates From a Referral Hospital in Kathmandu, Nepal. Microbiol Insights 2023; 16:11786361231152220. [PMID: 36741474 PMCID: PMC9893399 DOI: 10.1177/11786361231152220] [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: 12/07/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023] Open
Abstract
The ability of pathogenic Escherichia coli to produce carbapenemase enzymes is a characteristic that allows them to resist various antibiotics, including last-resort antibiotics like colistin and carbapenem. Our objectives were to identify rapidly developing antibiotic resistance (AR), assess β-lactamases production, and detect mcr-1 and bla NDM-1 genes in the isolates. A prospective cross-sectional study was carried out in a referral hospital located in Kathmandu from November 2019 to December 2020 using standard laboratory and molecular protocols. Among 77 total E. coli isolates, 64 (83.1%) of them were categorized as MDR. Phenotypically 13 (20.3%) colistin-resistant, 30 (46.9%) ESBL and 8 (12.5%) AmpC producers, and 5 (7.8%) ESBL/AmpC co-producers were distributed among MDR-E. coli. Minimum inhibitory concentrations (MIC) against the majority of MDR isolates were exhibited at 1 g/L. Of these 77 E. coli isolates, 24 (31.2%) were carbapenem-resistant. Among these carbapenem-resistant bacteria, 11 (45.9%) isolates were reported to be colistin-resistant, while 15 (62.5%) and 2 (8.3%) were MBL and KPC producers, respectively. Out of 15 MBL producers, 6 (40%) harbored bla NDM-1, and 8 (61.5%) out of 13 colistin-resistant pathogens possessed mcr-1. The resistance by colistin- and carbapenem were statistically associated (P < .001). However, only 2 (18.2%) of the co-resistant bacteria were found to have both genes. Our study revealed the highly prevalent MDR and the carbapenem-resistant E. coli and emphasized that the pathogens possess a wide range of capabilities to synthesize β-lactamases. These findings could assist to expand the understanding of AR in terms of enzyme production.
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Affiliation(s)
- Bhimarjun Bhusal
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal
| | - Bindeshwar Yadav
- Shahid Gangalal National Heart Center,
Kathmandu, Bagmati, Nepal
| | - Prabin Dawadi
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal
| | - Komal Raj Rijal
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal
| | - Prakash Ghimire
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal
| | - Megha Raj Banjara
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal,Megha Raj Banjara, Central Department of
Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Bagmati 44618, Nepal.
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Lemlem M, Aklilu E, Mohammed M, Kamaruzzaman F, Zakaria Z, Harun A, Devan SS. Molecular detection and antimicrobial resistance profiles of Extended-Spectrum Beta-Lactamase (ESBL) producing Escherichia coli in broiler chicken farms in Malaysia. PLoS One 2023; 18:e0285743. [PMID: 37205716 DOI: 10.1371/journal.pone.0285743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
Antimicrobial resistance is one of the major public health threats globally. This challenge has been aggravated with the overuse and misuse of antibiotics in food animals and humans. The present study aimed to investigate the prevalence of Extended-Spectrum β-lactamase (ESBL) genes in Escherichia coli (E. coli) isolated from broiler chickens in Kelantan, Malaysia. A total of 320 cloacal swabs were collected from farms in different districts of Kelantan and were analyzed using routine bacteriology, antimicrobial susceptibility test, and molecular techniques for further identification and characterization of ESBL encoding genes. Based on PCR detection for the E. coli species-specific Pho gene, 30.3% (97/320) of isolates were confirmed as E. coli, and 84.5% (82/97) of the isolates were positive for at least one ESBL gene. Majority of the isolates, 62.9% (61/97) were harboring blaCTX-M followed by 45.4% (44/97) of blaTEM genes, while 16.5% (16/97) of the isolates were positive for both mcr-1 and ESBL genes. Overall, 93.8% (90/97) of the E. coli were resistant to three or more antimicrobials; indicating that the isolates were multi-drug resistance. 90.7% of multiple antibiotic resistance (MAR) index value greater than 0.2, would also suggest the isolates were from high-risk sources of contamination. The MLST result shows that the isolates are widely diverse. Our findings provide insight into the alarmingly high distribution of antimicrobial resistant bacteria, mainly ESBL producing E. coli in apparently healthy chickens indicating the role of food animals in the emergence and spread of antimicrobial resistance, and the potential public health threats it may pose.
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Affiliation(s)
- Mulu Lemlem
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Baharu, Malaysia
- Department of Medical Microbiology and Immunology, College of Health Science, Mekelle University, Tigray, Ethiopia
| | - Erkihun Aklilu
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Baharu, Malaysia
| | - Maizan Mohammed
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Baharu, Malaysia
| | | | - Zunita Zakaria
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Azian Harun
- School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Susmita Seenu Devan
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Baharu, Malaysia
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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: 24] [Impact Index Per Article: 12.0] [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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Prevalence of polymyxin resistance through the food chain, the global crisis. J Antibiot (Tokyo) 2022; 75:185-198. [PMID: 35079146 DOI: 10.1038/s41429-022-00502-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 09/30/2021] [Accepted: 10/10/2021] [Indexed: 12/24/2022]
Abstract
Antimicrobial resistance is one of the vital challenges facing global health today. Multi-drug resistant (MDR) infections are often treated with the narrow-spectrum drugs, colistin (polymyxin E) or polymyxin B, which are last-resort antibiotics for human therapeutics that are effective against Gram-negative bacteria. Unfortunately, resistance to these polymyxins has occurred because of selective pressure caused by the inappropriate use of those antibiotics, especially in farming. The mechanisms of resistance to polymyxins are mediated through intrinsic, mutational, or genetic alteration in chromosomal genes. The mechanism includes the regulatory network controlling chemical modifications of lipid A moiety of lipopolysaccharide, reducing the negative charge of lipid A and its affinity for polymyxins. Additionally, the unique mobile colistin/polymyxin B resistance (mcr) gene reported in Enterobacteriales is responsible for the horizontal dissemination of resistance to polymyxins via the food chain. There is now an urgent need to increase surveillance for detecting resistance to polymyxins. Therefore, this review presents an overview of presently available scientific literature on the mechanism of resistance to polymyxins, with their associated gene variants, evaluation methods, resistance transmission through the food chain via food bacteria, and related risk factors. We further focus on the significant implications of polymyxins usage in India and future views for food safety to preserve polymyxin activity.
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Karade S, Sen S, Shergill SPS, Jani K, Shouche Y, Gupta RM. Whole genome sequence of colistin-resistant Escherichia coli from western India. Med J Armed Forces India 2020; 77:297-301. [PMID: 34305283 DOI: 10.1016/j.mjafi.2020.10.008] [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] [Received: 05/20/2020] [Accepted: 10/09/2020] [Indexed: 02/05/2023] Open
Abstract
Background With virtually dried out new antibiotic discovery pipeline, emergence and spread of antimicrobial resistance is a cause for global concern. Colistin, a cyclic polypeptide antibiotic, often regarded as last resort for multi drug resistance gram-negative bacteria, is also rendered ineffective by horizontal transfer of resistance genes. Surveillance of colistin resistance in GNB is essential to ascertain molecular epidemiology. Methods Whole genome sequencing (WGS) of an unusual colistin resistant urinary isolate of Escherichia coli was performed using Illumina MiSeq platform using 2x250bp V2 chemistry by following the manufactures protocol (Illumina Inc. USA). Multiple web-based bio-informatic tools were utilized to ascertain antibiotic resistant genes. Results An approximate 5.4 Mb of genome of the urinary isolate AFMC_UC19 was sequenced successfully. Mobile colistin resistance gene (mcr) on the plasmid responsible for horizontal spread was absent in the isolate. Conclusion Colistin resistance has been reported previously in Klebsiella pneumoniae and it is a rare occurrence in Escherichia coli in Indian setting. Although the isolate lack mcr mediated colistin resistance, emergence and spread of colistin resistant in gram-negative bacteria pose a threat.
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Affiliation(s)
- Santosh Karade
- Associate Professor, Department of Microbiology, Armed Forces Medical College, Pune 40, India
| | - Sourav Sen
- Professor & Head, Department of Microbiology, Armed Forces Medical College, Pune 40, India
| | - S P S Shergill
- Associate Professor, Department of Microbiology, Armed Forces Medical College, Pune 40, India
| | - Kunal Jani
- Research Associate, National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Yogesh Shouche
- Principal Investigator & Professor Emeritus, National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - R M Gupta
- Dean & Dy Commandant, Armed Forces Medical College, Pune 40, India
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Kumar H, Chen BH, Kuca K, Nepovimova E, Kaushal A, Nagraik R, Bhatia SK, Dhanjal DS, Kumar V, Kumar A, Upadhyay NK, Verma R, Kumar D. Understanding of Colistin Usage in Food Animals and Available Detection Techniques: A Review. Animals (Basel) 2020; 10:ani10101892. [PMID: 33081121 PMCID: PMC7602861 DOI: 10.3390/ani10101892] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Progress in the medical profession is determined by the achievements and effectiveness of new antibiotics in the treatment of microbial infections. However, the development of multiple-drug resistance in numerous bacteria, especially Gram-negative bacteria, has limited the treatment options. Due to this resistance, the resurgence of cyclic polypeptide drugs like colistin remains the only option. The drug, colistin, is a well-known growth inhibitor of Gram-negative bacteria like Acinetobacter baumanni, Enterobacter cloacae, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Technological advancements have uncovered the role of the mcr-1(mobilized colistin resistance) gene, which is responsible for the development of resistance in Gram-negative bacteria, which make them distinct from other bacteria without this gene. Additionally, food animals have been determined to be the reservoir for colistin resistance microbes, from which they spread to other hosts. Due to the adverse effects of colistin, many developed countries have prohibited its usage in animal foods, but developing countries are still using colistin in animal food production, thereby imposing a major risk to the public health. Therefore, there is a need for implementation of sustainable measures in livestock farms to prevent microbial infection. This review highlights the negative effects (increased resistance) of colistin consumption and emphasizes the different approaches used for detecting colistin in animal-based foods as well as the challenges associated with its detection.
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Affiliation(s)
- Harsh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India; (H.K.); (R.N.); (A.K.)
| | - Bing-Huei Chen
- Department of Food Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan;
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
- Biomedical Research Center, University Hospital Hradec Kralove, 50003 Hradec Kralove, Czech Republic
- Correspondence: (K.K.); (D.K.); Tel.: +420-603-289-166 (K.K.)
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Ankur Kaushal
- Centre of Nanotechnology, Amity University, Manesar, Gurugram-122413, Haryana, India;
| | - Rupak Nagraik
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India; (H.K.); (R.N.); (A.K.)
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Korea;
| | - Daljeet Singh Dhanjal
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield MK430AL, UK;
| | - Anil Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India; (H.K.); (R.N.); (A.K.)
| | - Navneet Kumar Upadhyay
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India;
| | - Rachna Verma
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India;
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, H.P., India; (H.K.); (R.N.); (A.K.)
- Correspondence: (K.K.); (D.K.); Tel.: +420-603-289-166 (K.K.)
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Mohammed Jajere S, Hassan L, Zakaria Z, Abu J, Abdul Aziz S. Antibiogram Profiles and Risk Factors for Multidrug Resistance of Salmonella enterica Recovered from Village Chickens ( Gallus gallus domesticus Linnaeus) and Other Environmental Sources in the Central and Southern Peninsular Malaysia. Antibiotics (Basel) 2020; 9:E701. [PMID: 33076451 PMCID: PMC7602575 DOI: 10.3390/antibiotics9100701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 12/18/2022] Open
Abstract
The emergence of multidrug resistance (MDR), including colistin resistance, among Enterobacteriaceae recovered from food animals poses a serious public health threat because of the potential transmission of these resistant variants to humans along the food chain. Village chickens or Ayam Kampung are free-range birds and are preferred by a growing number of consumers who consider these chickens to be organic and more wholesome. The current study investigates the antibiogram profiles of Salmonella isolates recovered from village chicken flocks in South-central Peninsular Malaysia. A total of 34 isolates belonging to eight serotypes isolated from village chickens were screened for resistance towards antimicrobials including colistin according to the WHO and OIE recommendations of critical antibiotics. S. Weltevreden accounted for 20.6% of total isolates, followed by serovars Typhimurium and Agona (17.6%). The majority of isolates (73.5%) demonstrated resistance to one or more antimicrobials. Eight isolates (23.5%) were resistant to ≥3 antimicrobial classes. Colistin resistance (minimum inhibitory concentrations: 4-16 mg/L) was detected among five isolates (14.7%), including S. Weltevreden, S. Albany, S. Typhimurium, and Salmonella spp. Univariable analysis of risk factors likely to influence the occurrence of MDR Salmonella revealed that the flock size, poultry production system, and use of antibiotics in the farm were not significantly (p > 0.05) associated with MDR Salmonella. The current study highlights that MDR Salmonella occur at a lower level in village chickens compared to that found in live commercial chickens. However, MDR remains a problem even among free-range chickens with minimal exposure to antibiotics.
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Affiliation(s)
| | - Latiffah Hassan
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor 43400 UPM, Malaysia; (S.M.J.); (Z.Z.); (J.A.); (S.A.A.)
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Joshi PR, Thummeepak R, Leungtongkam U, Pooarlai R, Paudel S, Acharya M, Dhital S, Sitthisak S. The emergence of colistin-resistant Escherichia coli in chicken meats in Nepal. FEMS Microbiol Lett 2020; 366:5637862. [PMID: 31755930 DOI: 10.1093/femsle/fnz237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/21/2019] [Indexed: 12/26/2022] Open
Abstract
The emergence and dissemination of colistin resistance among Gram-negative bacteria is a global problem. We initiated a surveillance of colistin-resistant and -susceptible Escherichia coli in raw meats from chicken in Nepal. A total of 180 meat samples were collected; from these, 60 E. coli strains were isolated (33.33%), of which 16 (26.66%) were colistin-resistant and harboured the mcr-1 gene. All isolates were characterised by antibiotic susceptibility testing, the presence of antibiotic resistance genes, phylogenetic analysis and plasmid replicon typing. Most of the colistin-resistant E. coli had the antibiotic resistant pattern CIP/CN/SXT/TE (43.75%). Coexistence of tet, qnr, sul and dfr genes was detected in both colistin-resistant and -susceptible E. coli. Most colistin-resistant E. coli strains belonged to phylogroup C, whereas 10% of isolates belonged to phylogroup D. Inc FIB was the dominant plasmid Inc type in the isolates. Dissemination of antibiotic-resistant E. coli in raw meats is a public health concern in Nepal and requires further investigation to ascertain the sources of contamination.
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Affiliation(s)
| | - Rapee Thummeepak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Udomluk Leungtongkam
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Renukar Pooarlai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Saroj Paudel
- Nepalese Farming Institute, Maitidevi, Kathmandu, Nepal
| | | | - Samita Dhital
- Nepalese Farming Institute, Maitidevi, Kathmandu, Nepal
| | - Sutthirat Sitthisak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
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Amin MB, Sraboni AS, Hossain MI, Roy S, Mozmader TAU, Unicomb L, Rousham EK, Islam MA. Occurrence and genetic characteristics of mcr-1-positive colistin-resistant E. coli from poultry environments in Bangladesh. J Glob Antimicrob Resist 2020; 22:546-552. [PMID: 32344122 DOI: 10.1016/j.jgar.2020.03.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES Colistin is one of the last-resort antibiotics for the treatment of multidrug-resistant (MDR) Gram-negative bacterial infections. We determined the occurrence and characteristics of mcr-1-producing Escherichia coli obtained from live bird markets (LBMs), rural poultry farms (RPFs) and rural household backyard poultry environments (HBPs) in Bangladesh. METHODS We tested 104 extended-spectrum β-lactamase (ESBL)-producing E. coli isolated during 2017-2018 from poultry sources for colistin resistance. We analysed the resistant isolates for the mcr genes and characterized mcr-positive isolates for antibiotic susceptibility, antibiotic resistance genes, transmissible plasmids and clonal diversity. RESULTS Of 104 isolates, 98 (94%) had MICcolistin ≥4 μg/mL and 14 (13.5%) were positive for mcr-1, of which 10 were from LBMs (n = 10), 3 were from RPFs and 1 was from an HBP. All 14 mcr-1 E. coli were resistant to third-generation cephalosporin and tetracycline, whereas 12 were resistant to fluoroquinolone and sulfamethoxazole, 10 were resistant to aminoglycosides and 3 were resistant to nitrofurantoin. Four isolates carried conjugative mcr-1 plasmid of 23-55 MDa in size. The 55 MDa plasmid found in two isolates carried additional resistant genes including blaCTX-M-group-1 and blaTEM-1 (ESBL), qnrB (fluoroquinolone), and rmtB (aminoglycoside). These plasmids belong to the IncF family with additional replicons: HI1 and N. Enterobacterial repetitive intergenic consensus-polymerase chain reaction revealed a heterogeneous banding pattern of mcr-1-positive isolates. CONCLUSION We report a 13.5% prevalence of mcr-1-positive MDR E. coli in poultry faecal samples predominantly from LBMs in Bangladesh accentuating the need for safe disposal of poultry faeces and hygiene practices among people exposed to poultry.
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Affiliation(s)
- Mohammed Badrul Amin
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.
| | - Ajrin Sultana Sraboni
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Muhammed Iqbal Hossain
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subarna Roy
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tim Amin Uddin Mozmader
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Leanne Unicomb
- Environmental Intervention Unit, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Emily K Rousham
- Centre for Global Health and Human Development, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Mohammad Aminul Islam
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.
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