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El Zowalaty ME, Falgenhauer L, Forsythe S, Helmy YA. 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. J Glob Antimicrob Resist 2023; 33:231-237. [PMID: 36948496 DOI: 10.1016/j.jgar.2023.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/23/2023] [Accepted: 03/07/2023] [Indexed: 03/24/2023] Open
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.
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Affiliation(s)
- Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi 41012, UAE.
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany; German Center for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany; Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
| | | | - Yosra A Helmy
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, Kentucky, USA.
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Lin J, Huang K, Huang JY, Xiong YR, Wei MM, Xiao N, Gao J, Ding XK, Ma ZY, Sang JH, Kong LX, Hong ZY, Li O. Lelliottia steviae sp. nov. isolated from Stevia rebaudiana Bertoni. Arch Microbiol 2022; 204:475. [PMID: 35829834 DOI: 10.1007/s00203-022-03033-2] [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: 01/05/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022]
Abstract
A Gram-negative, aerobic, chemoheterotrophic, rod-shaped, and motile bacterium, designated as LST-1T, was isolated from wild Stevia rebaudiana Bertoni and subjected to a polyphasic taxonomic analysis. The LST-1 strain grew optimally at 37 °C and pH 6.0-7.0 in the presence of 0.5% (w/v) NaCl. Phylogenetic analysis based on the 16S rDNA sequence indicated that LST-1 is closely related to Lelliottia jeotgali PFL01T (99.85%), Lelliottia nimipressuralis LMG10245T (98.82%), and Lelliottia amnigena LMG2784T (98.54%). Multi-locus sequence typing of concatenated partial atpD, infB, gyrB, and rpoB genes was performed to improve the resolution, and clear distinctions between the closest related type strains were observed. The results of average nucleotide identify analyses and DNA-DNA hybridization with four species (16S rDNA similarity > 98.65%) were less than 90 and 40%, respectively, verifying the distinct characteristics from other species of Lelliottia. The cellular fatty acid profile of the strain consisted of C16:0, Summed Feature3, and Summed Feature8 (possibly 16:1 w6c/16:1 w7c and 18:1 w6c) as major components. The major polar lipids included phosphatidylethanolamine, phosphatidylglycerol, an aminophospholipid, three non-characteristic phospholipids, and a non-characteristic lipid. The genome of LST-1T was 4,611,055 bp in size, with a G + C content of 55.02%. The unique combination of several phenotypic, chemotaxonomic, and genomic characteristics proved that strain LST-1T belongs to a novel species, for which the name Lelliottia steviae sp. nov. is proposed. The type strain is LST-1T (= CGMCC 1.19175T = JCM 34938T).Repositories: The genbank accession numbers for the 16S rRNA gene and genome sequences of strain LST-1T are MZ497264 and CP063663, respectively.
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Affiliation(s)
- Jing Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Ke Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Jing-Yu Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Yuan-Ru Xiong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Meng-Meng Wei
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Na Xiao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Jia Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Xuan-Kai Ding
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Zi-Yang Ma
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Jun-Hao Sang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Ling-Xian Kong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Zhi-Yun Hong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Ou Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
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Choi H, Hwang M, Chatterjee P, Jinadatha C, Navarathna DH. Rare Lelliottia nimipressuralis from a wound infection case report using whole genome sequencing-based bacterial identification. Diagn Microbiol Infect Dis 2021; 101:115538. [PMID: 34619568 DOI: 10.1016/j.diagmicrobio.2021.115538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/18/2022]
Abstract
Identification of clinical bacterial isolates is an essential first step to provide guidelines for treatment of pathogenic bacterial infection. Infection occurred in a laceration along the medial aspect of left upper arm of a 71-year-old female. Conventional biochemical testing and MALDI-TOF MS identification failed to correctly identify a bacterial isolate. Using whole genome sequencing, the isolate was identified as Lelliottia nimipressuralis. WGS can overcome the limitations of conventional phenotypic and molecular identification methods and successfully identified a rare pathogen. This case is the first report of a human infection of L. nimipressuralis.
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Affiliation(s)
- Hosoon Choi
- Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA
| | - Munok Hwang
- Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA
| | - Piyali Chatterjee
- Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA
| | - Chetan Jinadatha
- Department of Medicine, Central Texas Veterans Health Care System, Temple, TX, USA; Department of Medicine, College of Medicine, Texas A&M Health Science Center, Bryan, TX, USA
| | - Dhammika H Navarathna
- Department of Pathology and Laboratory Medicine Services, Central Texas Veterans Health Care System, Temple, TX, USA.
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Davin-Regli A, Lavigne JP, Pagès JM. Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance. Clin Microbiol Rev 2019; 32:e00002-19. [PMID: 31315895 PMCID: PMC6750132 DOI: 10.1128/cmr.00002-19] [Citation(s) in RCA: 250] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. First described in 1960, this group member has proven to be more complex as a result of the exponential evolution of phenotypic and genotypic methods. Today, 22 species belong to the Enterobacter genus. These species are described in the environment and have been reported as opportunistic pathogens in plants, animals, and humans. The pathogenicity/virulence of this bacterium remains rather unclear due to the limited amount of work performed to date in this field. In contrast, its resistance against antibacterial agents has been extensively studied. In the face of antibiotic treatment, it is able to manage different mechanisms of resistance via various local and global regulator genes and the modulation of the expression of different proteins, including enzymes (β-lactamases, etc.) or membrane transporters, such as porins and efflux pumps. During various hospital outbreaks, the Enterobacter aerogenes and E. cloacae complex exhibited a multidrug-resistant phenotype, which has stimulated questions about the role of cascade regulation in the emergence of these well-adapted clones.
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Affiliation(s)
- Anne Davin-Regli
- INSERM, SSA, IRBA, MCT, Aix Marseille University, Marseille, France
| | - Jean-Philippe Lavigne
- Department of Microbiology, U1047, INSERM, University Montpellier and University Hospital Nîmes, Nîmes, France
| | - Jean-Marie Pagès
- INSERM, SSA, IRBA, MCT, Aix Marseille University, Marseille, France
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Kabanova AP, Shneider MM, Korzhenkov AA, Bugaeva EN, Miroshnikov KK, Zdorovenko EL, Kulikov EE, Toschakov SV, Ignatov AN, Knirel YA, Miroshnikov KA. Host Specificity of the Dickeya Bacteriophage PP35 Is Directed by a Tail Spike Interaction With Bacterial O-Antigen, Enabling the Infection of Alternative Non-pathogenic Bacterial Host. Front Microbiol 2019; 9:3288. [PMID: 30687274 PMCID: PMC6336734 DOI: 10.3389/fmicb.2018.03288] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/18/2018] [Indexed: 11/13/2022] Open
Abstract
Dickeya solani is a recently emerged virulent bacterial potato pathogen that poses a major threat to world agriculture. Because of increasing antibiotic resistance and growing limitations in antibiotic use, alternative antibacterials such as bacteriophages are being developed. Myoviridae bacteriophages recently re-ranked as a separate Ackermannviridae family, such as phage PP35 described in this work, are the attractive candidates for this bacterial biocontrol. PP35 has a very specific host range due to the presence of tail spike protein PP35 gp156, which can depolymerize the O-polysaccharide (OPS) of D. solani. The D. solani OPS structure, →2)-β-D-6-deoxy-D-altrose-(1→, is so far unique among soft-rot Pectobacteriaceae, though it may exist in non-virulent environmental Enterobacteriaceae. The phage tail spike depolymerase degrades the shielding polysaccharide, and launches the cell infection process. We hypothesize that non-pathogenic commensal bacteria may maintain the population of the phage in soil environment.
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Affiliation(s)
- Anastasia P Kabanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Research Center "PhytoEngineering" Ltd., Rogachevo, Russia
| | - Mikhail M Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Kirill K Miroshnikov
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Evelina L Zdorovenko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Eugene E Kulikov
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Stepan V Toschakov
- Immanuel Kant Baltic Federal University, Kaliningrad, Russia.,Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | | | - Yuriy A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Research Center "PhytoEngineering" Ltd., Rogachevo, Russia
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Lelliottia jeotgali sp. nov., isolated from a traditional Korean fermented clam. Int J Syst Evol Microbiol 2018; 68:1725-1731. [DOI: 10.1099/ijsem.0.002737] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
The genus Lelliottia was recently created from the group of environmental gammaproteobacteria previously included in the genus Enterobacter. Here, we report the complete genome sequence of phD2B, the first (according to our current knowledge) known phage that infects bacterium from the taxon.
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Mezzatesta ML, Gona F, Stefani S. Enterobacter cloacae complex: clinical impact and emerging antibiotic resistance. Future Microbiol 2014; 7:887-902. [PMID: 22827309 DOI: 10.2217/fmb.12.61] [Citation(s) in RCA: 316] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Species of the Enterobacter cloacae complex are widely encountered in nature, but they can act as pathogens. The biochemical and molecular studies on E. cloacae have shown genomic heterogeneity, comprising six species: Enterobacter cloacae, Enterobacter asburiae, Enterobacter hormaechei, Enterobacter kobei, Enterobacter ludwigii and Enterobacter nimipressuralis, E. cloacae and E. hormaechei are the most frequently isolated in human clinical specimens. Phenotypic identification of all species belonging to this taxon is usually difficult and not always reliable; therefore, molecular methods are often used. Although the E. cloacae complex strains are among the most common Enterobacter spp. causing nosocomial bloodstream infections in the last decade, little is known about their virulence-associated properties. By contrast, much has been published on the antibiotic-resistance features of these microorganisms. In fact, they are capable of overproducing AmpC β-lactamases by derepression of a chromosomal gene or by the acquisition of a transferable ampC gene on plasmids conferring the antibiotic resistance. Many other resistance determinants that are able to render ineffective almost all antibiotic families have been recently acquired. Most studies on antimicrobial susceptibility are focused on E. cloacae, E. hormaechei and E. asburiae; these studies reported small variations between the species, and the only significant differences had no discriminating features.
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Affiliation(s)
- Maria Lina Mezzatesta
- Department of Bio-Medical Sciences, Section of Microbiology, University of Catania, Via Androne 81, 95124 Catania, Italy.
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Woo KS, Choi JL, Kim BR, Kim JE, Kim KH, Kim JM, Han JY. Outbreak of pseudomonas oryzihabitans pseudobacteremia related to contaminated equipment in an emergency room of a tertiary hospital in Korea. Infect Chemother 2014; 46:42-4. [PMID: 24693469 PMCID: PMC3970301 DOI: 10.3947/ic.2014.46.1.42] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/29/2013] [Accepted: 10/30/2013] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas oryzihabitans is frequently found in various sites within hospital settings, including sink drains and respiratory therapy equipment. Although it rarely causes human infections, P. oryzihabitans has recently been considered a potential nosocomial pathogen, especially in immunocompromised hosts. We report our experience of an outbreak of P. oryzihabitans pseudobacteremia, presumably due to faulty aseptic preparation of a saline gauze canister.
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Affiliation(s)
- Kwang-Sook Woo
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Jae-Lim Choi
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Bo-Ram Kim
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Ji-Eun Kim
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Kyeong-Hee Kim
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Jeong-Man Kim
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
| | - Jin-Yeong Han
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
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