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Genomic analysis and biological properties of the novel Serratia liquefaciens phage vB_SlqM_MQ-4. Arch Virol 2023; 168:38. [PMID: 36609610 DOI: 10.1007/s00705-022-05658-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/04/2022] [Indexed: 01/09/2023]
Abstract
A novel lytic Serratia liquefaciens phage, named vB_SlqM_MQ-4, was isolated from sewage. BLASTn analysis showed that the genome sequence of phage vB_SlqM_MQ-4 shared only 15% query coverage with that of Escherichia phage vB_EcoM-ep3, with 80.52% identity. Genomic analysis demonstrated that phage vB_SlqM_MQ-4 has a 43,534-bp dsDNA genome with 56% GC content and might be a member of a new genus in the order Caudoviricetes. Moreover, vB_SlqM_MQ-4 exhibited strong lytic performance with a short latent period (10 min) and a high burst size (267 PFU per cell) as well as a wide range of thermal (below 70 ℃) and pH tolerance (pH 4-12).
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Williams DJ, Grimont PAD, Cazares A, Grimont F, Ageron E, Pettigrew KA, Cazares D, Njamkepo E, Weill FX, Heinz E, Holden MTG, Thomson NR, Coulthurst SJ. The genus Serratia revisited by genomics. Nat Commun 2022; 13:5195. [PMID: 36057639 PMCID: PMC9440931 DOI: 10.1038/s41467-022-32929-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus. Phylogenomic analysis of the genus reveals a clearly-defined population structure which displays deep divisions and aligns with ecological niche, as well as striking congruence between historical biochemical phenotyping data and contemporary genomics data. We highlight the genomic, phenotypic and plasmid diversity of Serratia, and provide evidence of different patterns of gene flow across the genus. Our work provides a framework for understanding the emergence of clinical and other lineages of Serratia.
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Affiliation(s)
- David J Williams
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patrick A D Grimont
- Unité Biodiversité des Bactéries Pathogènes Emergentes, INSERM Unité 389, Institut Pasteur, Paris, France
| | - Adrián Cazares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Francine Grimont
- Unité Biodiversité des Bactéries Pathogènes Emergentes, INSERM Unité 389, Institut Pasteur, Paris, France
| | - Elisabeth Ageron
- Unité Biodiversité des Bactéries Pathogènes Emergentes, INSERM Unité 389, Institut Pasteur, Paris, France
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | | | - Daniel Cazares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elisabeth Njamkepo
- Institut Pasteur, Université de Paris, Unité des Bactéries Pathogènes Entériques, Paris, France
| | - François-Xavier Weill
- Institut Pasteur, Université de Paris, Unité des Bactéries Pathogènes Entériques, Paris, France
| | - Eva Heinz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Departments of Vector Biology and Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
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Arafa WAA, Fareed MF, Rabeh SA, Shaker RM. Ultrasound mediated green synthesis of rhodanine derivatives: Synthesis, chemical behavior, and antibacterial activity. PHOSPHORUS SULFUR 2016. [DOI: 10.1080/10426507.2016.1146276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Wael A. A. Arafa
- Chemistry Department, College of Science, Aljouf University, Sakaka, Aljouf, Kingdom of Saudi Arabia
- Chemistry Department, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Mervat F. Fareed
- Department of Home Economic, Faculty of Specific Education, Tanta University, Tanta, Egypt
| | - Saleh A. Rabeh
- Department of Biology, College of Science, Aljouf University, Sakaka, Aljouf, Kingdom of Saudi Arabia
- National Institute of Oceanography and Fisheries (NIOF), Inland Waters and Aquaculture Branch, Greater Cairo, Egypt
| | - Raafat M. Shaker
- Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
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Abstract
Serratia species, in particular Serratia marcescens, are significant human pathogens. S. marcescens has a long and interesting taxonomic, medical experimentation, military experimentation, and human clinical infection history. The organisms in this genus, particularly S. marcescens, were long thought to be nonpathogenic. Because S. marcescens was thought to be a nonpathogen and is usually red pigmented, the U.S. military conducted experiments that attempted to ascertain the spread of this organism released over large areas. In the process, members of both the public and the military were exposed to S. marcescens, and this was uncovered by the press in the 1970s, leading to U.S. congressional hearings. S. marcescens was found to be a certain human pathogen by the mid-1960s. S. marcescens and S. liquefaciens have been isolated as causative agents of numerous outbreaks and opportunistic infections, and the association of these organisms with point sources such as medical devices and various solutions given to hospitalized patients is striking. Serratia species appear to be common environmental organisms, and this helps to explain the large number of nosocomial infections due to these bacteria. Since many nosocomial infections are caused by multiply antibiotic-resistant strains of S. marcescens, this increases the danger to hospitalized patients, and hospital personnel should be vigilant in preventing nosocomial outbreaks due to this organism. S. marcescens, and probably other species in the genus, carries several antibiotic resistance determinants and is also capable of acquiring resistance genes. S. marcescens and S. liquefaciens are usually identified well in the clinical laboratory, but the other species are rare enough that laboratory technologists may not recognize them. 16S rRNA gene sequencing may enable better identification of some of the less common Serratia species.
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Samonis G, Vouloumanou EK, Christofaki M, Dimopoulou D, Maraki S, Triantafyllou E, Kofteridis DP, Falagas ME. Serratia infections in a general hospital: characteristics and outcomes. Eur J Clin Microbiol Infect Dis 2011; 30:653-60. [PMID: 21222011 DOI: 10.1007/s10096-010-1135-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 12/17/2010] [Indexed: 02/06/2023]
Abstract
We aimed to present our experience regarding infections caused by Serratia spp. in a region with relatively high antimicrobial resistance rates. We retrospectively reviewed the databases of the microbiological laboratory of the University Hospital of Heraklion, Crete (2/2004-12/2009). A total of 77 patients [67.5% men, mean age ± standard deviation (SD) = 56.9 ± 24.5 years) were identified; 37.7% were outpatients. Sixty-five (84.4%) of the 77 included patients had a Serratia marcescens isolate; the remaining 12 patients had a non-marcescens Serratia spp. The most frequently observed infections were respiratory tract infection (32.5%) and keratitis/endophthalmitis (20.8%). Seventy-three (94.9%) patients were cured. Four deaths were observed; three of them were considered as attributed to the Serratia infection. No difference was found regarding the characteristics and outcomes between patients with Serratia marcescens and non-marcescens infections. In addition, antipseudomonal penicillins and their combinations with beta-lactamase inhibitors, as well as carbapenemes, and fluoroquinolones exhibited high antimicrobial activity against both the tested Serratia marcescens and non-marcescens isolates. Our study adds useful information regarding the characteristics and outcomes of patients with Serratia infection, as well as the susceptibilities of the respective Serratia marcescens and non-marcescens isolates, in a region with relatively high levels of antimicrobial resistance.
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Affiliation(s)
- G Samonis
- Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
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Laupland KB, Parkins MD, Gregson DB, Church DL, Ross T, Pitout JDD. Population-based laboratory surveillance for Serratia species isolates in a large Canadian health region. Eur J Clin Microbiol Infect Dis 2007; 27:89-95. [PMID: 17960436 DOI: 10.1007/s10096-007-0400-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 09/22/2007] [Indexed: 12/29/2022]
Abstract
A population-based laboratory surveillance was conducted during a six-year period to define the incidence, demographic risk factors for acquisition, and anti-microbial susceptibilities of Serratia species isolates. A total of 715 incident Serratia species isolates were identified for an annual incidence of 10.8 per 100,000 residents; bacteremic disease occurred in 0.9 per 100,000 residents annually. The incidence increased with advancing age and males were at the highest risk. Ninety-two percent of the isolates were Serratia marcescens, and the majority (65%) of incident Serratia species isolates were of community onset. Ninety-five percent of isolates were susceptible to ciprofloxacin, 98% to gentamicin, 98% to trimethoprim/sulfamethoxazole, and >99% to imipenem. No yearly increase in resistance was observed. Serratia species isolation is most commonly of community onset and older patients and males are at increased risk. Despite reports of increasing resistance among Serratia species, the incidence in our region remains at a low stable rate.
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Affiliation(s)
- K B Laupland
- Department of Medicine, University of Calgary and Calgary Health Region, Calgary, AB, Canada.
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Abstract
Many bacteria use cell-cell communication to monitor their population density, synchronize their behaviour and socially interact. This communication results in a coordinated gene regulation and is generally called quorum sensing. In gram-negative bacteria, the most common quorum signal molecules are acylated homoserine lactones (AHLs), although other low-molecular-mass signalling molecules have been described such as Autoinducer-2 (AI-2). The phenotypes that are regulated in Serratia species by means of AHLs are remarkably diverse and of profound biological and ecological significance, and often interconnected with other global regulators. Furthermore, AHL- and AI-2-mediated systems (less profoundly studied) are continuously being discovered and explored in Serratia spp., many having interesting twists on the basic theme. Therefore, this review will highlight the current known quorum sensing systems in Serratia spp., including the important nosocomial pathogen Serratia marcescens.
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Affiliation(s)
- Rob Van Houdt
- Molecular and Cellular Biology, Institute for Health, Environment and Safety, Belgian Nuclear Research Centre SCK x CEN, Mol, Belgium.
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Paauw A, Verhoef J, Fluit AC, Blok HEM, Hopmans TEM, Troelstra A, Leverstein-van Hall MA. Failure to control an outbreak of qnrA1-positive multidrug-resistant Enterobacter cloacae infection despite adequate implementation of recommended infection control measures. J Clin Microbiol 2007; 45:1420-5. [PMID: 17314218 PMCID: PMC1865866 DOI: 10.1128/jcm.02242-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large outbreak with an aminoglycoside-resistant Enterobacter cloacae (AREC) clone occurred at the University Medical Center Utrecht beginning in 2001 and continued up through the time that this study was completed. This clone (genotype I) contains a conjugative R plasmid carrying the qnrA1, bla(CTX-M-9), and aadB genes, encoding resistance to quinolones, extended-spectrum beta-lactamases, and aminoglycosides, respectively. The aim of this study was to determine whether this clone was more transmissible than other AREC strains. Therefore, the dissemination of this genotype and of other E. cloacae strains was studied. In addition, infection control measures taken were evaluated. Pulsed-field gel electrophoresis analysis divided the 191 AREC strains into 42 different genotypes, of which 5 (12%) involved at least three patients. Aside from this outbreak (133 patients), only two other small outbreaks occurred, showing that the infection control measures were successful for all strains but one. Among 324 aminoglycoside-susceptible E. cloacae strains, 34/166 (20%) genotypes were identified from at least three patients, but only 4 involved small outbreaks. The outbreak strain was also detected in 11 of 15 other Dutch hospitals and caused outbreaks in at least 4. Evaluation of infection control measures showed that the outbreak strain disseminated throughout the hospital despite adequate implementation of internationally accepted guidelines on the control of multidrug-resistant Enterobacteriaceae (MRE). In conclusion, some MRE strains are better able to spread than others, and these strains may not be controlled by the current infection control guidelines. Strategies to identify such strains in an early phase and adapted guidelines for such "superbugs" are needed to prevent these clones from becoming endemic.
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Affiliation(s)
- Armand Paauw
- Eijkman-Winkler Center for Microbiology, Infectious Diseases and Inflammation, Department of Hospital Hygiene and Infection Prevention, University Medical Center Utrecht, Utrecht, The Netherlands.
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