Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa

Mohamed E. El Zowalaty; Linda Falgenhauer; Stephen Forsythe; Yosra A. Helmy

doi:10.1016/j.jgar.2023.03.007

Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa

Mohamed E. El Zowalaty, Linda Falgenhauer, Stephen Forsythe, Yosra A. Helmy

Research output: Contribution to journal › Comment/debate

Abstract

Objectives: Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa. Methods: The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees. Results: Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (bla_ACT-9), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes. The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin. Conclusion: The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance.

Original language	English
Pages (from-to)	231-237
Number of pages	7
Journal	Journal of Global Antimicrobial Resistance
Volume	33
DOIs	https://doi.org/10.1016/j.jgar.2023.03.007
State	Published - Jun 2023

Bibliographical note

Funding Information:
The project was supported in part by funding from the United States National Institutes of Health/Food and Drug Administration (USA/NIH/FDA) under award 1U18FD006780-01, the Hessian Ministry of Higher Education, Research and Arts within the project HuKKH (Hessisches Universitaeres Kompetenzzentrum Krankenhaus Hygiene). The project was also supported by discretionary funds from Prof. Dr Mohamed Ezzat El Zowalaty and from Dr Yosra A. Helmy through start-up fund from the Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, USA.

Funding Information:
The project was supported in part by funding from the United States National Institutes of Health/Food and Drug Administration (USA/NIH/FDA) under award 1U18FD006780-01, the Hessian Ministry of Higher Education, Research and Arts within the project HuKKH (Hessisches Universitaeres Kompetenzzentrum Krankenhaus Hygiene). The project was also supported by discretionary funds from Prof. Dr Mohamed Ezzat El Zowalaty and from Dr Yosra A. Helmy through start-up fund from the Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, USA. None declared. This study was approved by the Animal Research Ethics Committee of the University of KwaZulu-Natal (Durban, South Africa) [reference numbers. AREC 071/017 and AREC 014/018; and South Africa Department of Agriculture, Forestry and Fishery Act No. 35 of 1984 Section 20 approval reference no. 12/11/1/5]. This whole-genome shotgun has been deposited at DDBJ/ENA/GenBank under BioProject numberPRJNA716986 (BioSample accession numbersSAMN23419542,SAMN23419545, andSAMN23419546 and GenBank accession numbersJAJNQS000000000,JAJNNI000000000, andJAJNNH000000000 for MEZLN61, MEZEK193, and MEZEK194 respectively). The versions described in this paper are the first versions, JAJNQS000000000.1, JAJNNI000000000.1 and JAJNNH000000000.1. The sequences have been submitted to the Sequence Read Archive (SRA) under accession numbersSRR17485926,SRR17485923, andSRR17485922 for MEZLN61, MEZEK193, and MEZEK194, respectively. We thank the staff from the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, and Genomic Center at the University of Minnesota, St. Paul, Minnesota, and the College of Veterinary Medicine, North Carolina State University, North Carolina, for their cooperation and help throughout the project. We also thank farm owners, students and staff for their assistance during sample collection. The authors thank the NCBI GenBank submission staff for help and cooperation with the genome upload and deposition process.

Publisher Copyright:
© 2023 The Authors

Keywords

Colistin
Enterobacter kobei
Genome sequence
Lelliottia nimipressuralis
Sequence type 54
Wastewater
mcr-9

ASJC Scopus subject areas

Microbiology
Immunology and Allergy
Immunology
Microbiology (medical)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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El Zowalaty, M. E., Falgenhauer, L., Forsythe, S., & Helmy, Y. A. (2023). Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa. Journal of Global Antimicrobial Resistance, 33, 231-237. https://doi.org/10.1016/j.jgar.2023.03.007

@article{bc1aa818190645f2963fe95c3f448d10,

title = "Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa",

abstract = "Objectives: Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa. Methods: The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees. Results: Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (blaACT-9), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes. The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin. Conclusion: The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance.",

keywords = "Colistin, Enterobacter kobei, Genome sequence, Lelliottia nimipressuralis, Sequence type 54, Wastewater, mcr-9",

author = "{El Zowalaty}, {Mohamed E.} and Linda Falgenhauer and Stephen Forsythe and Helmy, {Yosra A.}",

note = "Funding Information: The project was supported in part by funding from the United States National Institutes of Health/Food and Drug Administration (USA/NIH/FDA) under award 1U18FD006780-01, the Hessian Ministry of Higher Education, Research and Arts within the project HuKKH (Hessisches Universitaeres Kompetenzzentrum Krankenhaus Hygiene). The project was also supported by discretionary funds from Prof. Dr Mohamed Ezzat El Zowalaty and from Dr Yosra A. Helmy through start-up fund from the Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, USA. Funding Information: The project was supported in part by funding from the United States National Institutes of Health/Food and Drug Administration (USA/NIH/FDA) under award 1U18FD006780-01, the Hessian Ministry of Higher Education, Research and Arts within the project HuKKH (Hessisches Universitaeres Kompetenzzentrum Krankenhaus Hygiene). The project was also supported by discretionary funds from Prof. Dr Mohamed Ezzat El Zowalaty and from Dr Yosra A. Helmy through start-up fund from the Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, USA. None declared. This study was approved by the Animal Research Ethics Committee of the University of KwaZulu-Natal (Durban, South Africa) [reference numbers. AREC 071/017 and AREC 014/018; and South Africa Department of Agriculture, Forestry and Fishery Act No. 35 of 1984 Section 20 approval reference no. 12/11/1/5]. This whole-genome shotgun has been deposited at DDBJ/ENA/GenBank under BioProject numberPRJNA716986 (BioSample accession numbersSAMN23419542,SAMN23419545, andSAMN23419546 and GenBank accession numbersJAJNQS000000000,JAJNNI000000000, andJAJNNH000000000 for MEZLN61, MEZEK193, and MEZEK194 respectively). The versions described in this paper are the first versions, JAJNQS000000000.1, JAJNNI000000000.1 and JAJNNH000000000.1. The sequences have been submitted to the Sequence Read Archive (SRA) under accession numbersSRR17485926,SRR17485923, andSRR17485922 for MEZLN61, MEZEK193, and MEZEK194, respectively. We thank the staff from the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, and Genomic Center at the University of Minnesota, St. Paul, Minnesota, and the College of Veterinary Medicine, North Carolina State University, North Carolina, for their cooperation and help throughout the project. We also thank farm owners, students and staff for their assistance during sample collection. The authors thank the NCBI GenBank submission staff for help and cooperation with the genome upload and deposition process. Publisher Copyright: {\textcopyright} 2023 The Authors",

year = "2023",

month = jun,

doi = "10.1016/j.jgar.2023.03.007",

language = "English",

volume = "33",

pages = "231--237",

journal = "Journal of Global Antimicrobial Resistance",

issn = "2213-7165",

publisher = "Elsevier BV",

}

El Zowalaty, ME, Falgenhauer, L, Forsythe, S & Helmy, YA 2023, 'Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa', Journal of Global Antimicrobial Resistance, vol. 33, pp. 231-237. https://doi.org/10.1016/j.jgar.2023.03.007

Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa. / El Zowalaty, Mohamed E.; Falgenhauer, Linda; Forsythe, Stephen et al.
In: Journal of Global Antimicrobial Resistance, Vol. 33, 06.2023, p. 231-237.

Research output: Contribution to journal › Comment/debate

TY - JOUR

T1 - Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa

AU - El Zowalaty, Mohamed E.

AU - Falgenhauer, Linda

AU - Forsythe, Stephen

AU - Helmy, Yosra A.

N1 - Funding Information: The project was supported in part by funding from the United States National Institutes of Health/Food and Drug Administration (USA/NIH/FDA) under award 1U18FD006780-01, the Hessian Ministry of Higher Education, Research and Arts within the project HuKKH (Hessisches Universitaeres Kompetenzzentrum Krankenhaus Hygiene). The project was also supported by discretionary funds from Prof. Dr Mohamed Ezzat El Zowalaty and from Dr Yosra A. Helmy through start-up fund from the Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, USA. Funding Information: The project was supported in part by funding from the United States National Institutes of Health/Food and Drug Administration (USA/NIH/FDA) under award 1U18FD006780-01, the Hessian Ministry of Higher Education, Research and Arts within the project HuKKH (Hessisches Universitaeres Kompetenzzentrum Krankenhaus Hygiene). The project was also supported by discretionary funds from Prof. Dr Mohamed Ezzat El Zowalaty and from Dr Yosra A. Helmy through start-up fund from the Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, USA. None declared. This study was approved by the Animal Research Ethics Committee of the University of KwaZulu-Natal (Durban, South Africa) [reference numbers. AREC 071/017 and AREC 014/018; and South Africa Department of Agriculture, Forestry and Fishery Act No. 35 of 1984 Section 20 approval reference no. 12/11/1/5]. This whole-genome shotgun has been deposited at DDBJ/ENA/GenBank under BioProject numberPRJNA716986 (BioSample accession numbersSAMN23419542,SAMN23419545, andSAMN23419546 and GenBank accession numbersJAJNQS000000000,JAJNNI000000000, andJAJNNH000000000 for MEZLN61, MEZEK193, and MEZEK194 respectively). The versions described in this paper are the first versions, JAJNQS000000000.1, JAJNNI000000000.1 and JAJNNH000000000.1. The sequences have been submitted to the Sequence Read Archive (SRA) under accession numbersSRR17485926,SRR17485923, andSRR17485922 for MEZLN61, MEZEK193, and MEZEK194, respectively. We thank the staff from the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, and Genomic Center at the University of Minnesota, St. Paul, Minnesota, and the College of Veterinary Medicine, North Carolina State University, North Carolina, for their cooperation and help throughout the project. We also thank farm owners, students and staff for their assistance during sample collection. The authors thank the NCBI GenBank submission staff for help and cooperation with the genome upload and deposition process. Publisher Copyright: © 2023 The Authors

PY - 2023/6

Y1 - 2023/6

N2 - Objectives: Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa. Methods: The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees. Results: Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (blaACT-9), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes. The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin. Conclusion: The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance.

AB - Objectives: Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa. Methods: The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees. Results: Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (blaACT-9), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes. The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin. Conclusion: The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance.

KW - Colistin

KW - Enterobacter kobei

KW - Genome sequence

KW - Lelliottia nimipressuralis

KW - Sequence type 54

KW - Wastewater

KW - mcr-9

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DO - 10.1016/j.jgar.2023.03.007

M3 - Comment/debate

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AN - SCOPUS:85159043126

SN - 2213-7165

VL - 33

SP - 231

EP - 237

JO - Journal of Global Antimicrobial Resistance

JF - Journal of Global Antimicrobial Resistance

ER -

Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

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