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Gaibani P, Mazzariol A, Secci B, Diani E, Gibellini D. Genomic characterization of a high pathogenic Escherichia coli causing bacterial meningitis in a newborn in Italy, 2022: E. coli neonatal meningitis. Diagn Microbiol Infect Dis 2024; 110:116397. [PMID: 39126826 DOI: 10.1016/j.diagmicrobio.2024.116397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 08/12/2024]
Abstract
Here, we characterize the complete genome sequence of Escherichia coli isolated from a newborn affected by bacterial meningitis in Italy. Genome of E. coli strain 1455 harbored a circular chromosome and two plasmids of 167.740-bp and 4.073-bp in length, respectively. E. coli 1455 belonged to the ST3, serotype O17:H18 and carried different determinants including resistance to B-lactams, tetracyclines, and quinolones. In addition, genome of E. coli strain 1455 harbored 5 integrated pro-phage regions mainly located in the chromosome, while most of the virulence factors associated to the invasiveness and clinical severity and different antimicrobial resistance determinants (blaTEM-1, tet(A) and qnrS1) were located in the 167-Kb plasmid. Taken together, our findings suggest a possible widespread of a virulence factors-carrying plasmid worldwide and highlight the importance of genomic characterization in the diffusion of public health threats.
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Affiliation(s)
- Paolo Gaibani
- Department of Diagnostics and Public Health, Microbiology Section, Verona University, Verona, Italy.
| | - Annarita Mazzariol
- Department of Diagnostics and Public Health, Microbiology Section, Verona University, Verona, Italy
| | | | - Erica Diani
- Department of Diagnostics and Public Health, Microbiology Section, Verona University, Verona, Italy
| | - Davide Gibellini
- Department of Diagnostics and Public Health, Microbiology Section, Verona University, Verona, Italy
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Liu M, Wu J, Zhao J, Xi Y, Jin Y, Yang H, Chen S, Long J, Duan G. Global epidemiology and genetic diversity of mcr-positive Klebsiella pneumoniae: A systematic review and genomic analysis. ENVIRONMENTAL RESEARCH 2024; 259:119516. [PMID: 38950813 DOI: 10.1016/j.envres.2024.119516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 07/03/2024]
Abstract
The rapid increase of mcr-positive Klebsiella pneumoniae (K. pneumoniae) has received considerable attention and poses a major public health concern. Here, we systematically analyzed the global distribution of mcr-positive K. pneumoniae isolates based on published articles as well as publicly available genomes. Combining strain information from 78 articles and 673 K. pneumoniae genomes, a total of 1000 mcr-positive K. pneumoniae isolates were identified. We found that mcr-positive K. pneumoniae has disseminated widely worldwide, especially in Asia, with a higher diversity of sequence types (STs). These isolates were disseminated in 57 countries and were associated with 12 different hosts. Most of the isolates were found in China and were isolated from human sources. Moreover, MLST analysis showed that ST15 and ST11 accounted for the majority of mcr-positive K. pneumoniae, which deserve sustained attention in further surveillance programs. mcr-1 and mcr-9 were the dominant mcr variants in mcr-positive K. pneumoniae. Furthermore, a Genome-wide association study (GWAS) demonstrated that mcr-1- and mcr-9-producing genomes exhibited different antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), thereby indicating a distinct evolutionary path. Notably, the phylogenetic analysis suggested that certain mcr-positive K. pneumoniae genomes from various geographical areas and hosts harbored a high degree of genetic similarities (<20 SNPs), suggesting frequent cross-region and cross-host clonal transmission. Overall, our results emphasize the significance of monitoring and exploring the transmission and evolution of mcr-positive K. pneumoniae in the context of "One health".
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Affiliation(s)
- Mengyue Liu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Wu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaxue Zhao
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanyan Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jinzhao Long
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
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Khan AS, Afrin S, Ahmed F, Rahman SR. Shotgun metagenomic analysis reveals the emergence of plasmid-encoded mcr-5.1 gene in hospital wastewater in Bangladesh. J Glob Antimicrob Resist 2024:S2213-7165(24)00158-9. [PMID: 39197657 DOI: 10.1016/j.jgar.2024.08.007] [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: 03/30/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
Colistin is considered the last line therapy for treating multidrug-resistant (MDR) bacterial infections in humans. Therefore, the spread of colistin resistance poses a serious threat to human, and environmental health. Though Bangladesh is known as a hotspot of AMR, limited studies have been carried out regarding the status of colistin resistance. Information on the emerging bacterial resistance is inevitable for protecting public health. Nowadays, wastewater analysis has been prioritized for metagenomics-enabled AMR surveillance. Our study on the metagenomic analysis of untreated hospital effluents first detected the colistin resistance-conferring mcr-5.1 gene in the hospital environment of Bangladesh. Phylogenetic tree and in silico AMR analysis confirmed the detection of this mcr-5 variant, which is located in a plasmid contig. The plasmid was untypeable and belonged to the bacteria from the Enterobacteriaceae family. The mcr-5.1 operon was embedded in a Tn3 transposon, suggesting the mobility of the gene. Tnshfr1 transposon, chromate resistance protein ChrB, DNA invertase hin, and two MFS-type proteins were present in the genetic environment of mcr-5.1. Our findings provide evidence of the occurrence of mcr-5.1 in a hospital environment in Bangladesh, which calls for immediate attention and effective measures to contain the dissemination of colistin resistance in the environment.
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Affiliation(s)
- Abu Sayem Khan
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Sunjida Afrin
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Firoz Ahmed
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
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Torkan A, Askari Badouei M. Investigating the virulence-associated genes and antimicrobial resistance of Escherichia fergusonii Isolated from diseased ostrich chicks. Comp Immunol Microbiol Infect Dis 2024; 112:102226. [PMID: 39168034 DOI: 10.1016/j.cimid.2024.102226] [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: 06/21/2024] [Revised: 07/31/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024]
Abstract
This study investigates the presence of virulence-associated genes and antimicrobial resistance (AMR) in Escherichia fergusonii isolates obtained from ostrich chicks. A total of 287 isolates were recovered from 106 fecal samples from ostrich chicks suffering from diarrhea and subjected to molecular identification and biochemical characterization. E. fergusonii was detected in 10 samples (9.4 %) using two PCR-detection protocols. Notably, the isolates lacked various virulence genes commonly associated with pathogenic E. coli including elt, est, stx, eae, ehly, cdt, iss, iutA, iroN, hlyA, ompT, except for one isolate harboring the astA gene. Antimicrobial susceptibility testing revealed that all isolates were susceptible to ciprofloxacin, while high resistance was observed against amoxicillin clavulanate (AMC), trimethoprim-sulfamethoxazole (SXT), and doxycycline (D). Moreover, eight isolates displayed multidrug resistance (MDR) and four exhibited resistance to 9-11 antimicrobials. The most frequent resistance gene was sul2, which was present in all isolates; the other resistance genes detected consisted of int1 (4/10), int2 (3/10), blaCMY (2/10), and qnrS, blaTEM, blaCMY, blaCTX-M, and flo each were detected only in one E. fergusonii Isolate. Plasmid replicon typing identified the presence of I1 (7/10), N (5/10), and Y (1/10). This study provides valuable insights into the virulence and antimicrobial resistance of E. fergusonii isolates from ostrich chicks, highlighting the complexity of antimicrobial resistance mechanisms exhibited by these bacteria. Further research is essential to understand the transmission dynamics and clinical implications of these findings in veterinary and public health settings.
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Affiliation(s)
- Afagh Torkan
- Department of Pathobiology, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Mahdi Askari Badouei
- Department of Pathobiology, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran.
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Almanaa TN. Design of a novel multi-epitopes vaccine against Escherichia fergusonii: a pan-proteome based in- silico approach. Front Immunol 2023; 14:1332378. [PMID: 38143752 PMCID: PMC10739491 DOI: 10.3389/fimmu.2023.1332378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Escherichia fergusonii a gram-negative rod-shaped bacterium in the Enterobacteriaceae family, infect humans, causing serious illnesses such as urinary tract infection, cystitis, biliary tract infection, pneumonia, meningitis, hemolytic uremic syndrome, and death. Initially treatable with penicillin, antibiotic misuse led to evolving resistance, including resistance to colistin, a last-resort drug. With no licensed vaccine, the study aimed to design a multi-epitope vaccine against E. fergusonii. The study started with the retrieval of the complete proteome of all known strains and proceeded to filter the surface exposed virulent proteins. Seventeen virulent proteins (4 extracellular, 4 outer membranes, 9 periplasmic) with desirable physicochemical properties were identified from the complete proteome of known strains. Further, these proteins were processed for B-cell and T-cell epitope mapping. Obtained epitopes were evaluated for antigenicity, allergenicity, solubility, MHC-binding, and toxicity and the filtered epitopes were fused by specific linkers and an adjuvant into a vaccine construct. Structure of the vaccine candidate was predicted and refined resulting in 78.1% amino acids in allowed regions and VERIFY3D score of 81%. Vaccine construct was docked with TLR-4, MHC-I, and MHC-II, showing binding energies of -1040.8 kcal/mol, -871.4 kcal/mol, and -1154.6 kcal/mol and maximum interactions. Further, molecular dynamic simulation of the docked complexes was carried out resulting in a significant stable nature of the docked complexes (high B-factor and deformability values, lower Eigen and high variance values) in terms of intermolecular binding conformation and interactions. The vaccine was also reported to stimulate a variety of immunological pathways after administration. In short, the designed vaccine revealed promising predictions about its immune protective potential against E. fergusonii infections however experimental validation is needed to validate the results.
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Affiliation(s)
- Taghreed N. Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Feng J, Zhuang Y, Luo J, Xiao Q, Wu Y, Chen Y, Chen M, Zhang X. Prevalence of colistin-resistant mcr-1-positive Escherichia coli isolated from children patients with diarrhoea in Shanghai, 2016-2021. J Glob Antimicrob Resist 2023; 34:166-175. [PMID: 37355039 DOI: 10.1016/j.jgar.2023.06.006] [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: 04/25/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/26/2023] Open
Abstract
OBJECTIVES The emergence of the plasmid-mediated colistin resistance 1 (mcr-1) of Escherichia coli has become a global health concern. This study reports the prevalence of mcr-1 among E. coli isolates from patients with diarrheal disease in Shanghai and the genetic characterization of mcr-1-harbouring plasmids. METHODS A total of 1723 E. coli strains were collected from the faeces of patients with diarrheal disease in all sentinel hospitals in Shanghai from 2016 to 2021. Antimicrobial susceptibility testing was performed by broth microdilution and plasmid conjunction transfer assay was carried out using E. coli C600 as the recipient. The mcr-1-positive E. coli strains (MCRPEC) were subjected to molecular characterization and bioinformatic analysis of the mcr-1-bearing plasmids that they harboured. RESULTS Only 5 (0.28%) strains were found to harbour the mcr-1 gene using PCR screening. Plasmid conjugation assay and whole-genome sequencing indicated that EC16500, one MCRPEC strain that co-exhibited mcr-1, blaTEM-1, blaOXA-1, qnrS1, qnrS2, arr-3, and catB3, could be conjugated to EC C600 by horizontal transfer with an average efficiency of 3.2 × 10-5. The plasmid pEC16500 harboured similar backbones as p70_2_15, pECGD-8-33, pNCYU-29-19-1_MCR1, and pIBMC_mcr1, and was shown to be encoded within a type IV secretion system (T4SS)-containing 32.6 kbp IncX4, next to the pap2-like membrane-associated gene, to form a 2.4-kb cassette. Furthermore, sequencing and phylogenetic analyses revealed a similarity between other MCR-1-homolog proteins, indicating that the five E. coli isolates were colistin-resistant. CONCLUSION Our data represents a significant snapshot of colistin resistance mcr-1 genes and highlights the need to increase active surveillance, especially among children under five years of age, in Shanghai. Great effort needs to be taken to avoid further dissemination of plasmid-mediated colistin resistance among clinically relevant Gram-negative bacterial pathogens.
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Affiliation(s)
- Jun Feng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Yuan Zhuang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Jiayuan Luo
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Quan Xiao
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Yitong Wu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Yong Chen
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Min Chen
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China.
| | - Xi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China.
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Wang C, Tang B, Wu J, Jin X, Ke S, Yang H, Liu Y. Detection of mcr-1-harbouring Escherichia coli by quantum dot labelling of synthetic small peptides mimicking lipopolysaccharide receptors. Int J Antimicrob Agents 2023; 62:106898. [PMID: 37343806 DOI: 10.1016/j.ijantimicag.2023.106898] [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: 01/04/2023] [Revised: 06/05/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Overuse of antibiotics and the emergence of multidrug-resistant bacteria has made colistin the last line of defence against complex infections. In previous studies, MCR-1-mediated colistin resistance was mainly detected through PCR or antimicrobial susceptibility testing. However, intuitive detection methods for phenotype are rarely reported. In this study, two small peptide antibodies were constructed for immunofluorescence detection of mcr-1-harbouring Escherichia coli: one was a small peptide labelled with a quantum dot antibody; and the other was a small peptide labelled with a fluorescein isothiocyanate (FITC) antibody. Whether using FITC or quantum dots, colistin-resistant bacteria in the sample could be qualitatively detected. The assembled antibodies achieved the desired goals in terms of sensitivity, specificity, precision and repeatability. The non-specific problem of sandwich antigen recognition of lipid A binding to small peptides in modified lipopolysaccharide (LPS) was resolved, and this relatively developed immunofluorescence technique standardised the detection process. Together, in addition to PCR, both fluorescent antibodies can be used for immunofluorescent detection of mcr-1-harbouring E. coli.
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Affiliation(s)
- Chenghao Wang
- Zhejiang key Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, Hangzhou 310013, China; School of Clinical Medicine, Hangzhou Medical College, Hangzhou 310053, China; Engineering Research Center of Novel Vaccine of Zhejiang Province, Hangzhou Medical College, Hangzhou 310013, China
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition; Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Jiusheng Wu
- College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Xi Jin
- Zhejiang key Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, Hangzhou 310013, China; Engineering Research Center of Novel Vaccine of Zhejiang Province, Hangzhou Medical College, Hangzhou 310013, China
| | - Shuwen Ke
- Zhejiang key Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, Hangzhou 310013, China; School of Clinical Medicine, Hangzhou Medical College, Hangzhou 310053, China; Engineering Research Center of Novel Vaccine of Zhejiang Province, Hangzhou Medical College, Hangzhou 310013, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-product Safety and Nutrition; Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China.
| | - Yuehuan Liu
- Zhejiang key Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, Hangzhou 310013, China; Engineering Research Center of Novel Vaccine of Zhejiang Province, Hangzhou Medical College, Hangzhou 310013, China.
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Feng J, Wu H, Zhuang Y, Luo J, Chen Y, Wu Y, Fei J, Shen Q, Yuan Z, Chen M. Stability and genetic insights of the co-existence of blaCTX-M-65, blaOXA-1, and mcr-1.1 harboring conjugative IncI2 plasmid isolated from a clinical extensively-drug resistant Escherichia coli ST744 in Shanghai. Front Public Health 2023; 11:1216704. [PMID: 37680274 PMCID: PMC10481164 DOI: 10.3389/fpubh.2023.1216704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023] Open
Abstract
Background Co-existence of colistin, β-lactam and carbapenem in multidrug-resistant Enterobacteriaceae isolates poses a serious threat to public health. In this study, we investigated and characterized the co-occurrence of blaCTX-M-65, blaOXA-1, and mcr-1.1 strain isolated from a clinical extensively-drug-resistant Escherichia coli ST744 in Shanghai. Methods Antimicrobial susceptibility test was carried out by agar dilution methods. Whole genome sequencing was conducted, and resistance genes, and sequence types of colistin in E. coli isolates were analyzed. Plasmid stability and amino acid mutations were assessed in E. coli isolates. Results A colistin resistant E. coli ST744, named ECPX221, was identified out of 145 fecal samples collected. The strain carries a 60,168 IncI2 plasmid with the mcr-1.1 gene. The strain also has blaCTX-M-65, blaOXA-1, dfrA14, qnrS1, cmlA5, arr2, ampC, aph(4)-Ia, sul1, and aadA5 resistance genes. The plasmid pECPX221 was capable of conjugation with an efficiency of 2.6 × 10-2. Notably, 45% of the transconjugants were determined as mcr-1.1-harboring in the colistin-free environment after 60 generation of passage. No mutations occurred in pmrB, mgrB, and phoPQ gene in the mcr-1.1-harboring transconjugants. Bioinformatic analysis indicated pECPX221 shared highly similar backbone with the previously reported mcr-1.1-harboring pAH62-1, pMFDS1339.1, pSCZE4, and p2018-10-2CC. Furthermore, sequencing and phylogenetic analyses revealed a similarity between other MCR-1-homolog proteins, indicating that ECPX221 was colistin resistant. Conclusion The stable transferable mcr-1.1-harboring plasmid found in the E. coli ST744 strain indicated the high risk to disseminate the extensively-drug-resistance phenotype among Enterobacteriaceae.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhengan Yuan
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Min Chen
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
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Okuno M, Tsuru N, Yoshino S, Gotoh Y, Yamamoto T, Hayashi T, Ogura Y. Isolation and Genomic Characterization of a Heat-Labile Enterotoxin 1-Producing Escherichia fergusonii Strain from a Human. Microbiol Spectr 2023; 11:e0049123. [PMID: 37432125 PMCID: PMC10434266 DOI: 10.1128/spectrum.00491-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
Escherichia fergusonii strains have been isolated from patients with diarrhea, but their virulence determinant has not been well elucidated. Here, we report the first isolation of a heat-labile enterotoxin 1 (LT1)-producing E. fergusonii strain (strain 30038) from a patient in Japan. The complete genome sequence of strain 30038 was determined and subjected to comparative genomics and phylogenetic analyses with 195 publicly available genomes of E. fergusonii. In addition to strain 30038, the elt1 gene was also identified in an E. fergusonii strain that is phylogenetically distinct and which was isolated from poultry in the United Kingdom. Fine genomic comparison revealed that these two strains share comparable elt1-bearing plasmids. However, an intriguing distinction arises in strain 30038, wherein the plasmid has integrated into the chromosome via a recombination process mediated by an insertion sequence. The production of active LT1 toxin by strain 30038 was verified through an in vitro assay using cultured cells. A large plasmid carrying 11 antimicrobial resistance genes was also identified in strain 30038. Our results indicate that extensive surveillance of elt1-positive E. fergusonii strains as diarrheagenic pathogens is needed. IMPORTANCE Escherichia fergusonii, a species closely related to Escherichia coli, is known to cause sporadic conditions in humans, including diarrhea. However, the critical virulence factors in E. fergusonii clinical isolates remain to be identified. This study shows the first isolation of an E. fergusonii strain carrying the elt1 gene, which encodes heat-labile enterotoxin 1, from a patient with diarrhea. Our analysis of public databases also revealed the presence of elt1-positive E. fergusonii strains isolated from poultry in the United Kingdom. Interestingly, while the elt1 gene in the poultry isolate was present on a large plasmid, in the human isolate it was integrated into the chromosome, which may confer stability on the elt1-carrying genetic element. Our findings highlight the need for extensive surveillance of elt1-positive E. fergusonii strains in livestock animals.
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Affiliation(s)
- Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Nami Tsuru
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | - Shuji Yoshino
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Yamamoto
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
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Wang J, Huang Y, Guan C, Li J, Yang H, Zhao G, Liu C, Ma J, Tang B. Characterization of an Escherichia coli Isolate Coharboring the Virulence Gene astA and Tigecycline Resistance Gene tet(X4) from a Dead Piglet. Pathogens 2023; 12:903. [PMID: 37513750 PMCID: PMC10385434 DOI: 10.3390/pathogens12070903] [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: 04/14/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
tet(X4) is the critical resistance gene for tigecycline degradation that has been continually reported in recent years. In particular, pathogenic bacteria carrying tet(X4) are a severe threat to human health. However, information describing Escherichia coli coharboring tet(X4) with virulence genes is limited. Here, we isolated an E. coli strain coharboring tet(X4) and the heat-stable toxin gene astA from a dead piglet. The strain named 812A1-131 belongs to ST10. The genome was sequenced using the Nanopore and Illumina platforms. The virulence genes astA and tet(X4) are located on the chromosome and in the IncHI1-type plasmid p812A1-tetX4-193K, respectively. The plasmid could be conjugatively transferred to recipient E. coli J53 with high frequency. In vivo experiments showed that strain 812A1-131 is pathogenic to Galleria mellonella and could colonize the intestines of mice. In summary, pathogenic E. coli could receive a plasmid harboring the tet(X4) gene, which can increase the difficulty of treatment. The prevalence and transmission mechanisms of pathogenic bacteria coharboring the tet(X4) gene need more attention.
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Affiliation(s)
- Jianmei Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuting Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Chunjiu Guan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jie Li
- College of Life Science, Liaocheng University, Liaocheng 252000, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guoping Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Canying Liu
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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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: 5] [Impact Index Per Article: 5.0] [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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12
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Talat A, Miranda C, Poeta P, Khan AU. Farm to table: colistin resistance hitchhiking through food. Arch Microbiol 2023; 205:167. [PMID: 37014461 DOI: 10.1007/s00203-023-03476-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.
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Affiliation(s)
- Absar Talat
- Medical and Molecular Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Carla Miranda
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Department of Sciences, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal
- Toxicology Research Unit (TOXRUN), IUCS, CESPU, CRL, Gandra, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, Caparica, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-Os-Montes and Alto Douro (UTAD)UTAD, Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Asad U Khan
- Medical and Molecular Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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13
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Ma J, Wang J, Yang H, Su M, Li R, Bai L, Feng J, Huang Y, Yang Z, Tang B. IncHI1 plasmids mediated the tet(X4) gene spread in Enterobacteriaceae in porcine. Front Microbiol 2023; 14:1128905. [PMID: 37065147 PMCID: PMC10098456 DOI: 10.3389/fmicb.2023.1128905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/14/2023] [Indexed: 04/04/2023] Open
Abstract
The tigecycline resistance gene tet(X4) was widespread in various bacteria. However, limited information about the plasmid harboring the tet(X4) gene spread among the different species is available. Here, we investigated the transmission mechanisms of the tet(X4) gene spread among bacteria in a pig farm. The tet(X4) positive Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae and Enterobacter hormaeche were identified in the same farm. The whole genome sequencing (WGS) analysis showed that the K. pneumoniae belonged to ST727 (n = 11) and ST3830 (n = 1), E. cloacae and E. hormaeche belonged to ST524 (n = 1) and ST1862 (n = 1). All tet(X4) genes were located on the IncHI1 plasmids that could be conjugatively transferred into the recipient E. coli C600 at 30°C. Moreover, a fusion plasmid was identified that the IncHI1 plasmid recombined with the IncN plasmid mediated by ISCR2 during the conjugation from strains B12L to C600 (pB12L-EC-1). The fusion plasmid also has been discovered in a K. pneumoniae (K1L) that could provide more opportunities to spread antimicrobial resistance genes. The tet(X4) plasmids in these bacteria are derived from the same plasmid with a similar structure. Moreover, all the IncHI1 plasmids harboring the tet(X4) gene in GenBank belonged to the pST17, the newly defined pMLST. The antimicrobial susceptibility testing was performed by broth microdilution method showing the transconjugants acquired the most antimicrobial resistance from the donor strains. Taken together, this report provides evidence that IncHI1/pST17 is an important carrier for the tet(X4) spread in Enterobacteriaceae species, and these transmission mechanisms may perform in the environment.
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Martins JCL, Pintor-Cora A, Alegría Á, Santos JA, Herrera-Arias F. Characterization of ESBL-producing Escherichia spp. and report of an mcr-1 colistin-resistance Escherichia fergusonni strain from minced meat in Pamplona, Colombia. Int J Food Microbiol 2023; 394:110168. [PMID: 36931145 DOI: 10.1016/j.ijfoodmicro.2023.110168] [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: 10/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
Foods of animal origin are increasingly considered a source of extended spectrum β-lactamase (ESBL) producing bacteria which can disseminate throughout the food chain and become a health concern for humans. This work aimed to evaluate the occurrence of ESBL-producing Escherichia coli in 100 retail minced meat samples taken in markets in Pamplona, Colombia. A total of 19 ESBL-producing isolates were obtained, 18 identified as E. coli and one as E. fergusonii. Fifteen isolates (78.9 %) carried blaCTX-M and blaTEM genes, one (5.2 %) blaSHV and blaTEM genes, one isolate (5.2 %) carried blaCTX-M and one (5.2 %) blaSHV alone. The majority of CTX-M-positive E. coli isolates carried the blaCTX-M-15 gene (13 isolates), being the blaCTX-M-9, blaCTX-M-2, and blaCTX-M-8 (one isolate each) also detected. Two SHV-positive isolates presented the blaSHV-5 and blaSHV-12 allele. The isolate identified as E. fergusonii was positive for blaCTX-M-65 gene and mcr-1 gene. Sixteen isolates (84.2 %) belonged to phylogroups A and B1 and grouped together in the phylogenetic tree obtained by MLST; phylogroups E and F were also detected. Transfer of ESBL resistance was demonstrated for the E. fergusonii isolate. Whole genome sequencing of this isolate revealed the presence of plasmids carrying additional resistance genes. This investigation showed the high prevalence of ESBL-producing E. coli in retail samples of minced meat. Also, the isolation of a strain of E. fergusonii is an additional concern, as some resistance genes are located in mobile elements, which can be transmitted to other bacteria. These evidences support the increasing public health concern considering the spreading of resistance genes through the food chain.
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Affiliation(s)
- Joana C L Martins
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain
| | - Alberto Pintor-Cora
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain.
| | - Ángel Alegría
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain.
| | - Fanny Herrera-Arias
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain; Departamento de Microbiología, Facultad de Ciencias Básicas, Universidad de Pamplona, Pamplona, Colombia.
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15
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Rather RA, Ara S, Padder SA, Sharma S, Pathak SP, Baba TR. Seasonal fluctuation of water quality and ecogenomic phylogeny of novel potential microbial pollution indicators of Veshaw River Kashmir-Western Himalaya. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 320:121104. [PMID: 36682619 DOI: 10.1016/j.envpol.2023.121104] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Nearly a billion people, especially in underdeveloped nations, need safe drinking water. Indian studies suggest that most drinking water sources have high coliform levels, and quality assurance is required. This study was conducted in rural parts of South Kashmir in the Western Himalaya from February 2019 to January 2020. Standard river water sampling was done from upstream to downstream of the river. This study examined the detection, molecular identification, and chemical water quality of coliform-contaminated drinking water, which sums up river water pollution. Water quality varied significantly, indicating downstream contamination. Sangam (downstream) had the highest coliform count, showing 72.2600 cfu per litre in summer, while Kongwaton (upstream), near the Veshaw River, had no coliform count in winter. In summer, Sangam (downstream) had the highest water quality metrics (pH 6.847, Electrical conductivity (EC) 71.620 dS/m, Biological oxygen demand (BOD) 1.120 mg/L, and Chemical oxygen demand (COD) 24.637 mg/L) in all seasons. The lowest winter water quality metrics in Kongwaton were pH 8.947, EC 253.680 dS/m, BOD 4.963 mg/L, and COD 51.440 mg/L. Coliforms in water suggest faecal contamination. This study examines the water quality attributes of drinking water and associated factors to determine river pollution. Total DNA was collected and sequenced for 16 S rDNA and metagenomics. Universal primers were used to amplify the bacterial 16 S rRNA. Using BLAST, the amplified 16 S rRNA gene sequence was matched to the NCBI database. A metagenomic study revealed 27 species with different relative abundance. These species include Escherichia coli, E. fergusonii, E. albertii, Klebsiella grimontii, and Shigella dysenteriae. This study is thought to be the first to discriminate against E. fergusonii, E. albertii, K. grimontii, and S. dysenteriae from E. coli and to report on E. fergusonii and E. albertii, K. grimontii, and S. dysenteriae in the river Veshaw water sources in Kulgam, Western Himalaya.
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Affiliation(s)
- Rauoof Ahmad Rather
- Division of Environmental Sciences, FoH, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Kashmir, Jammu &Kashmir, 190025, India.
| | - Shoukat Ara
- Division of Environmental Sciences, FoH, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Kashmir, Jammu &Kashmir, 190025, India
| | - Shahid Ahmad Padder
- Division of Basic Sciences and Humanities, FoH, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Kashmir, Jammu &Kashmir, 190025, India
| | - Sanjeev Sharma
- Dr. Ambedkar International Centre, Ministry of Social Justice & Empowerment, Govt. of India, 15 Janpath, New Delhi, 110001, India
| | - Shiv Poojan Pathak
- Dr. Ambedkar International Centre, Ministry of Social Justice & Empowerment, Govt. of India, 15 Janpath, New Delhi, 110001, India
| | - Tawseef Rehman Baba
- Division of Fruit Sciences, FoH, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Kashmir, Jammu &Kashmir, 190025, India
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16
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Tang B, Guan C, Lin H, Liu C, Yang H, Zhao G, Yue M. Emergence of co-existence of mcr-1 and bla NDM-5 in Escherichia fergusonii. Int J Antimicrob Agents 2023; 61:106742. [PMID: 36736926 DOI: 10.1016/j.ijantimicag.2023.106742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/29/2022] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Chunjiu Guan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China; School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Canying Liu
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products and Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Min Yue
- Hainan Institute, Zhejiang University, Hangzhou, China; Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, National Medical Centre for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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17
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Srinivas K, Ghatak S, Pyngrope DA, Angappan M, Milton AAP, Das S, Lyngdoh V, Lamare JP, Prasad MCB, Sen A. Avian strains of emerging pathogen Escherichia fergusonii are phylogenetically diverse and harbor the greatest AMR dissemination potential among different sources: Comparative genomic evidence. Front Microbiol 2023; 13:1080677. [PMID: 36741902 PMCID: PMC9895846 DOI: 10.3389/fmicb.2022.1080677] [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: 10/26/2022] [Accepted: 12/30/2022] [Indexed: 01/21/2023] Open
Abstract
Introduction Escherichia fergusonii is regarded as an emerging pathogen with zoonotic potential. In the current study, we undertook source-wise comparative genomic analyses (resistome, virulome, mobilome and pangenome) to understand the antimicrobial resistance, virulence, mobile genetic elements and phylogenetic diversity of E. fergusonii. Methods Six E. fergusonii strains (5 multidrug resistant strains and 1 biofilm former) were isolated from poultry (duck faeces and retail chicken samples). Following confirmation by phenotypic and molecular methods, the isolates were further characterized and their genomes were sequenced. Comparative resisto-virulo-mobilome analyses and pangenomics were performed for E. fergusonii genomes, while including 125 other E. fergusonii genomes available from NCBI database. Results and discussion Avian and porcine strains of E. fergusonii were found to carry significantly higher number of antimicrobial resistance genes (p < 0.05) and mobile genetic elements (plasmids, transposons and integrons) (p < 0.05), while the pathogenic potential of bovine strains was significantly higher compared to other strains (p < 0.05). Pan-genome development trends indicated open pan-genome for all strains (0 < γ < 1). Genomic diversity of avian strains was found to be greater than that from other sources. Phylogenetic analysis revealed close clustering among isolates of similar isolation source and geographical location. Indian isolates of E. fergusonii clustered closely with those from Chinese and a singleton Australian isolate. Overall, being the first pangenomic study on E. fergusonii, our analysis provided important cues on genomic features of the emerging pathogen E. fergusonii while highlighting the potential role of avian strains in dissemination of AMR.
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Affiliation(s)
- Kandhan Srinivas
- Division of Veterinary Public Health, ICAR – Indian Veterinary Research Institute, Bareilly, India,Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | - Sandeep Ghatak
- Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India,*Correspondence: Sandeep Ghatak,
| | - Daniel Aibor Pyngrope
- Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | - Madesh Angappan
- Division of Veterinary Public Health, ICAR – Indian Veterinary Research Institute, Bareilly, India,Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | - Arockiasamy Arun Prince Milton
- Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India,Arockiasamy Arun Prince Milton,
| | - Samir Das
- Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | - Vanita Lyngdoh
- Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | - John Pynhun Lamare
- Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | - Mosuri Chendu Bharat Prasad
- Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | - Arnab Sen
- Division of Animal and Fisheries Sciences, ICAR Research Complex for North Eastern Hill Region, Umiam, India
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Ma J, Tang B, Lin J, Ed-Dra A, Lin H, Wu J, Dong Y, Yang H, Yue M. Genome Assessment of Carbapenem- and Colistin-Resistant Escherichia coli from Patients in a Sentinel Hospital in China. Cells 2022; 11:3480. [PMID: 36359876 PMCID: PMC9653657 DOI: 10.3390/cells11213480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial-resistant (AMR) pathogens are a significant threat to public health worldwide. However, the primary carrier of AMR genes, particularly against last-resort antibiotics, is still only partially studied in Chinese hospitals. In a sentinel hospital in China, we collected 157 E. coli strains from patients between January and July 2021. One blaNDM-1-, nine blaNDM-5-, and one mcr-1-positive E. coli recovered from inpatients were identified as resistant to meropenem and colistin. There are 37 virulence genes discovered in the 11 strains, including astA in strain EC21Z-147 (O128: H4), which belongs to the enteroaggregative E. coli (EAEC). The blaNDM gene is distributed into distinct ST types, including ST48, ST616, ST410, ST711, and ST2003, while the mcr-1 gene was identified in ST117. The conjugative plasmids IncX3, IncI1-I, and IncI2 mediated the blaNDM-5 and mcr-1 genes detected among inpatients. Notably, the youngest age at which mcr-1-positive E. coli has been reported was at one day old, in a child in which the strain is closely related to strains with animal origins. Hospitals are major environments for the spread and dissemination of critical virulence and AMR genes, which requires active monitoring systems at the genome level to surveil the spread of virulence and AMR.
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Affiliation(s)
- Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiahui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | | | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jing Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuzhi Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Min Yue
- Hainan Institute of Zhejiang University, Sanya 572025, China
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310058, China
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Zhou W, Lin R, Zhou Z, Ma J, Lin H, Zheng X, Wang J, Wu J, Dong Y, Jiang H, Yang H, Yang Z, Tang B, Yue M. Antimicrobial resistance and genomic characterization of Escherichia coli from pigs and chickens in Zhejiang, China. Front Microbiol 2022; 13:1018682. [PMID: 36353453 PMCID: PMC9638057 DOI: 10.3389/fmicb.2022.1018682] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli is considered an opportunistic pathogen and an indicator for antimicrobial resistance (AMR) monitoring. Despite many reports on its AMR monitoring, studies based on genome-based analysis of AMR genes are still insufficient. Here, 181 E. coli strains were isolated from anal swab samples collected from pigs and chickens of animal farms located in Eastern China and sequenced through the Illumina platform. The results showed that 87.85% (159/181) of the E. coli isolates were multidrug-resistant (MDR). Ampicillin (AMP)- spectinomycin (SPT)- tetracycline (TET)- florfenicol (FFC)- sulfisoxazole (SF)- trimethoprim/sulfamethoxazole (SXT) was the predominant AMR pattern. By whole-genome sequencing, we found that ST10 (10.49%, 19/181) and ST48 (7.18%, 13/181) were major sequence types. IncFIB and IncX1 were the most prevalent plasmid replicons. The AMR genes bla NDM-5 (1.10%, 2/181), mcr-1 (1.10%, 2/181), tet(X4) (1.10%, 2/181), and cfr (6.08%, 2/181) were also found in these isolates. In addition, among the 169 virulence genes detected, we identified astA (37.02%, 67/181), hlyA (1.66%, 3/181), hlyB (1.66%, 3/181) and hlyD (1.66%, 3/181), which were closely related to heat-stable enterotoxin 1 and α-hemolysin. In addition, there were 33 virulence genes associated with the iron uptake system, and 46 were adhesion-related genes. Our study highlighted the need for routine surveillance of AMR with advanced genomic approaches, providing up-to-date data on the prevalence of AMR for the development and execution of antimicrobial stewardship policy.
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Affiliation(s)
- Wei Zhou
- Zhejiang Provincial Center for Animal Disease Prevention and Control, Hangzhou, China
| | - Rumeng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,School of Food Science and Technology, Jiangnan University, Wuxi, China,Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, China
| | - Zhijin Zhou
- Zhejiang Provincial Center for Animal Disease Prevention and Control, Hangzhou, China
| | - Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,The Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xue Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jingge Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jing Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuzhi Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, China
| | - Han Jiang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhangnv Yang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China,*Correspondence: Zhangnv Yang,
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China,Biao Tang,
| | - Min Yue
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China,Min Yue,
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20
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Ma J, Zhou W, Wu J, Liu X, Lin J, Ji X, Lin H, Wang J, Jiang H, Zhou Q, Zhao G, Yang H, Tang B. Large-Scale Studies on Antimicrobial Resistance and Molecular Characterization of Escherichia coli from Food Animals in Developed Areas of Eastern China. Microbiol Spectr 2022; 10:e0201522. [PMID: 35950758 PMCID: PMC9430128 DOI: 10.1128/spectrum.02015-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/22/2022] [Indexed: 12/01/2022] Open
Abstract
Widely distributed multidrug-resistant (MDR) bacteria threaten animals and human health. Nevertheless, few antimicrobial resistance (AMR) surveys of large-scale animal-derived bacteria have been explored. Here, 1,468 (97.54%) Escherichia coli strains were isolated from 1,505 pig (1,060) and chicken (445) anal swab samples from 11 cities in Zhejiang Province, China, in 2020. These isolates had a high resistance to tetracycline (92.92%), sulfisoxazole (93.05%), florfenicol (83.11%), and ampicillin (78.27%). More than 88.68% of the strains were MDR bacteria. A low AMR ratio to the "last-resort" antimicrobials tigecycline (0.75%), colistin (1.36%), and meropenem (0.75%) were found. The AMR of E. coli from pigs was higher than that of chickens. Eighteen strains among 31 MDR strains that were resistant to "last-resort" antimicrobials could transfer the AMR genes (mcr-1, tet(X), and blaNDM) to the recipient strain J53, which confer colistin, tigecycline, and carbapenem resistance, respectively. The homology among mcr-1-carrying isolates was relatively high, and the sequence types were mainly ST5529, ST101, and ST354, while the homology of isolates harboring tet(X4) and blaNDM-5 genes were different. The mcr-1, blaNDM-5, and tet(X4) genes in strains LS45, JH51, and TZ118 were identified on the Incl2, IncHI2, and IncX1 plasmids, respectively. Moreover, tet(A), sul2, floR, and blaTEM-1B were the most common ARGs in 31 strains. Additionally, the heavy metals copper and zinc had a significant correlation with amoxicillin/clavulanate and tetracycline resistance. Controlling the movement of animals between cities and reducing the use of antimicrobials are effective methods to reduce the threat of AMR bacteria. IMPORTANCE Pigs and chickens are the most common food animals that are the important vectors for spreading antimicrobial-resistant pathogens among animals and humans. Limited systematic AMR monitoring of these food animal origin bacteria had been reported, especially in developed areas of China. Our study provides a comprehensive and systematic study of AMR in Escherichia coli from eastern China. The AMR of E. coli strains among the animals or cities has statistically significant differences. Moreover, the mcr-1, tet(X4), and blaNDM-5 genes, considered resistant to the last line of AMR, were identified in part of farms. The transferability and the prevalence of these AMR strains were intensively studied. Our monitoring is comparable to human clinical research and has an essential reference for public health safety. These findings will provide early warning for AMR strains and guide the clinical use of antibiotics to control the spread of antibiotic resistance.
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Affiliation(s)
- Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Wei Zhou
- Zhejiang Provincial Center for Animal Disease Prevention and Control, Hangzhou Zhejiang, China
| | - Jing Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiaofeng Liu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Jiahui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiaofeng Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jianmei Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Han Jiang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, Zhejiang, China
| | - Qianjin Zhou
- School of Marine Science, Ningbo University, Ningbo, Zhejiang, China
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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21
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Guan C, Tang B, Yang H, Ma J, Huang Y, Liu C. Emergence of plasmid-mediated tigecycline resistance gene, tet(X4), in Escherichia fergusonii from pigs. J Glob Antimicrob Resist 2022; 30:249-251. [DOI: 10.1016/j.jgar.2022.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022] Open
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