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Aracil-Gisbert S, Fernández-De-Bobadilla MD, Guerra-Pinto N, Serrano-Calleja S, Pérez-Cobas AE, Soriano C, de Pablo R, Lanza VF, Pérez-Viso B, Reuters S, Hasman H, Cantón R, Baquero F, Coque TM. The ICU environment contributes to the endemicity of the " Serratia marcescens complex" in the hospital setting. mBio 2024; 15:e0305423. [PMID: 38564701 PMCID: PMC11077947 DOI: 10.1128/mbio.03054-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Serratia marcescens is an opportunistic pathogen historically associated with sudden outbreaks in intensive care units (ICUs) and the spread of carbapenem-resistant genes. However, the ecology of S. marcescens populations in the hospital ecosystem remains largely unknown. We combined epidemiological information of 1,432 Serratia spp. isolates collected from sinks of a large ICU that underwent demographic and operational changes (2019-2021) and 99 non-redundant outbreak/non-outbreak isolates from the same hospital (2003-2019) with 165 genomic data. These genomes were grouped into clades (1-4) and subclades (A and B) associated with distinct species: Serratia nematodiphila (1A), S. marcescens (1B), Serratia bockelmannii (2A), Serratia ureilytica (2B), S. marcescens/Serratia nevei (3), and S. nevei (4A and 4B). They may be classified into an S. marcescens complex (SMC) due to the similarity between/within subclades (average nucleotide identity >95%-98%), with clades 3 and 4 predominating in our study and publicly available databases. Chromosomal AmpC β-lactamase with unusual basal-like expression and prodigiosin-lacking species contrasted classical features of Serratia. We found persistent and coexisting clones in sinks of subclades 4A (ST92 and ST490) and 4B (ST424), clonally related to outbreak isolates carrying blaVIM-1 or blaOXA-48 on prevalent IncL/pB77-CPsm plasmids from our hospital since 2017. The distribution of SMC populations in ICU sinks and patients reflects how Serratia species acquire, maintain, and enable plasmid evolution in both "source" (permanent, sinks) and "sink" (transient, patients) hospital patches. The results contribute to understanding how water sinks serve as reservoirs of Enterobacterales clones and plasmids that enable the persistence of carbapenemase genes in healthcare settings, potentially leading to outbreaks and/or hospital-acquired infections.IMPORTANCEThe "hospital environment," including sinks and surfaces, is increasingly recognized as a reservoir for bacterial species, clones, and plasmids of high epidemiological concern. Available studies on Serratia epidemiology have focused mainly on outbreaks of multidrug-resistant species, overlooking local longitudinal analyses necessary for understanding the dynamics of opportunistic pathogens and antibiotic-resistant genes within the hospital setting. This long-term genomic comparative analysis of Serratia isolated from the ICU environment with isolates causing nosocomial infections and/or outbreaks within the same hospital revealed the coexistence and persistence of Serratia populations in water reservoirs. Moreover, predominant sink strains may acquire highly conserved and widely distributed plasmids carrying carbapenemase genes, such as the prevalent IncL-pB77-CPsm (pOXA48), persisting in ICU sinks for years. The work highlights the relevance of ICU environmental reservoirs in the endemicity of certain opportunistic pathogens and resistance mechanisms mainly confined to hospitals.
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Affiliation(s)
- Sonia Aracil-Gisbert
- Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Member of the ESCMID Study Group for Epidemiological Markers (ESGEM), Basel, Switzerland
- Member of the ESCMID Food- and Water-borne Infections Study Group (EFWISG), Basel, Switzerland
| | - Miguel D. Fernández-De-Bobadilla
- Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Member of the ESCMID Study Group for Epidemiological Markers (ESGEM), Basel, Switzerland
- Member of the ESCMID Food- and Water-borne Infections Study Group (EFWISG), Basel, Switzerland
| | - Natalia Guerra-Pinto
- Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Member of the ESCMID Study Group for Epidemiological Markers (ESGEM), Basel, Switzerland
- Member of the ESCMID Food- and Water-borne Infections Study Group (EFWISG), Basel, Switzerland
| | - Silvia Serrano-Calleja
- Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Ana Elena Pérez-Cobas
- Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Member of the ESCMID Study Group for Epidemiological Markers (ESGEM), Basel, Switzerland
- Member of the ESCMID Food- and Water-borne Infections Study Group (EFWISG), Basel, Switzerland
- Biomedical Research Center Network of Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Cruz Soriano
- Intensive Medicine, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- University of Alcalá (UAH), Madrid, Spain
| | - Raúl de Pablo
- Intensive Medicine, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- University of Alcalá (UAH), Madrid, Spain
| | - Val F. Lanza
- Biomedical Research Center Network of Infectious Diseases (CIBERINFEC), Madrid, Spain
- Bioinformatics Unit, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Blanca Pérez-Viso
- Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Sandra Reuters
- Member of the ESCMID Study Group for Epidemiological Markers (ESGEM), Basel, Switzerland
- Institute for Infection Prevention and Control, Medical Center–University of Freiburg, Freiburg, Germany
| | - Henrik Hasman
- Member of the ESCMID Study Group for Epidemiological Markers (ESGEM), Basel, Switzerland
- Member of the ESCMID Food- and Water-borne Infections Study Group (EFWISG), Basel, Switzerland
- Statens Serum Institut, Copenhagen, Denmark
| | - Rafael Cantón
- Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Biomedical Research Center Network of Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Fernando Baquero
- Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Biomedical Research Center Network of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Teresa M. Coque
- Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Member of the ESCMID Study Group for Epidemiological Markers (ESGEM), Basel, Switzerland
- Member of the ESCMID Food- and Water-borne Infections Study Group (EFWISG), Basel, Switzerland
- Biomedical Research Center Network of Infectious Diseases (CIBERINFEC), Madrid, Spain
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Sterzi L, Nodari R, Di Marco F, Ferrando ML, Saluzzo F, Spitaleri A, Allahverdi H, Papaleo S, Panelli S, Rimoldi SG, Batisti Biffignandi G, Corbella M, Cavallero A, Prati P, Farina C, Cirillo DM, Zuccotti G, Bandi C, Comandatore F. Genetic barriers more than environmental associations explain Serratia marcescens population structure. Commun Biol 2024; 7:468. [PMID: 38632370 PMCID: PMC11023947 DOI: 10.1038/s42003-024-06069-w] [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: 11/02/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.
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Affiliation(s)
- Lodovico Sterzi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Riccardo Nodari
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Federico Di Marco
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Laura Ferrando
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Saluzzo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Hamed Allahverdi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Stella Papaleo
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Sara Giordana Rimoldi
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, Milan, Italy
| | | | - Marta Corbella
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
| | | | - Paola Prati
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Pavia, Italy
| | - Claudio Farina
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, Bergamo, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
- Department of Paediatrics, Children's Hospital "V. Buzzi", Milano, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo Ed Enrica Invernizzi", University of Milan, 20133, Milan, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy.
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Dixit OVA, Behruznia M, Preuss AL, O’Brien CL. Diversity of antimicrobial-resistant bacteria isolated from Australian chicken and pork meat. Front Microbiol 2024; 15:1347597. [PMID: 38440146 PMCID: PMC10910072 DOI: 10.3389/fmicb.2024.1347597] [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: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 03/06/2024] Open
Abstract
Antimicrobial-resistant bacteria are frequently isolated from retail meat and may infect humans. To determine the diversity of antimicrobial-resistant bacteria in Australian retail meat, bacteria were cultured on selective media from raw chicken (n = 244) and pork (n = 160) meat samples obtained from all four major supermarket chains in the ACT/NSW, Australia, between March and June 2021. Antimicrobial susceptibility testing (AST) was performed for 13 critically and 4 highly important antibiotics as categorised by the World Health Organization (WHO) for a wide range of species detected in the meat samples. A total of 288 isolates underwent whole-genome sequencing (WGS) to identify the presence of antimicrobial resistance (AMR) genes, virulence genes, and plasmids. AST testing revealed that 35/288 (12%) of the isolates were found to be multidrug-resistant (MDR). Using WGS data, 232/288 (81%) of the isolates were found to harbour resistance genes for critically or highly important antibiotics. This study reveals a greater diversity of AMR genes in bacteria isolated from retail meat in Australia than previous studies have shown, emphasising the importance of monitoring AMR in not only foodborne pathogenic bacteria, but other species that are capable of transferring AMR genes to pathogenic bacteria.
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Affiliation(s)
- Ojas V. A. Dixit
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
- School of Medicine, Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Mahboobeh Behruznia
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Aidan L. Preuss
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Claire L. O’Brien
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
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Nagano DS, Taniguchi I, Ono T, Nakamura K, Gotoh Y, Hayashi T. Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes. Microb Genom 2023; 9. [PMID: 37966169 DOI: 10.1099/mgen.0.001135] [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] [Indexed: 11/16/2023] Open
Abstract
Plasmids play important roles in bacterial genome diversification. In the Serratia marcescens complex (SMC), a notable contribution of plasmids to genome diversification was also suggested by our recent analysis of >600 draft genomes. As accurate analyses of plasmids in draft genomes are difficult, in this study we analysed 142 closed genomes covering the entire complex, 67 of which were obtained in this study, and identified 132 plasmids (1.9-244.4 kb in length) in 77 strains. While the average numbers of plasmids in clinical and non-clinical strains showed no significant difference, strains belonging to clade 2 (one of the two hospital-adapted lineages) contained more plasmids than the others. Pangenome analysis revealed that of the 28 954 genes identified, 12.8 % were plasmid-specific, and 1.4 % were present in plasmids or chromosomes depending on the strain. In the latter group, while transposon-related genes were most prevalent (31.4 % of the function-predicted genes), genes related to antimicrobial resistance and heavy metal resistance accounted for a notable proportion (22.7 %). Mash distance-based clustering separated the 132 plasmids into 23 clusters and 50 singletons. Most clusters/singletons showed notably different GC contents compared to those of host chromosomes, suggesting their recent or relatively recent appearance in the SMC. Among the 23 clusters, 17 were found in only clinical or only non-clinical strains, suggesting the possible preference of their distribution on the environmental niches of host strains. Regarding the host strain phylogeny, 16 clusters were distributed in two or more clades, suggesting their interclade transmission. Moreover, for many plasmids, highly homologous plasmids were found in other species, indicating the broadness of their potential host ranges, beyond the genus, family, order, class or even phylum level. Importantly, highly homologous plasmids were most frequently found in Klebsiella pneumoniae and other species in the family Enterobacteriaceae, suggesting that this family, particularly K. pneumoniae, is the main source for plasmid exchanges with the SMC. These results highlight the power of closed genome-based analysis in the investigation of plasmids and provide important insights into the nature of plasmids distributed in the SMC.
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Affiliation(s)
- Debora Satie Nagano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tomoyuki Ono
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
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Shikov AE, Merkushova AV, Savina IA, Nizhnikov AA, Antonets KS. The man, the plant, and the insect: shooting host specificity determinants in Serratia marcescens pangenome. Front Microbiol 2023; 14:1211999. [PMID: 38029097 PMCID: PMC10656689 DOI: 10.3389/fmicb.2023.1211999] [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: 04/25/2023] [Accepted: 08/21/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Serratia marcescens is most commonly known as an opportunistic pathogen causing nosocomial infections. It, however, was shown to infect a wide range of hosts apart from vertebrates such as insects or plants as well, being either pathogenic or growth-promoting for the latter. Despite being extensively studied in terms of virulence mechanisms during human infections, there has been little evidence of which factors determine S. marcescens host specificity. On that account, we analyzed S. marcescens pangenome to reveal possible specificity factors. Methods We selected 73 high-quality genome assemblies of complete level and reconstructed the respective pangenome and reference phylogeny based on core genes alignment. To find an optimal pipeline, we tested current pangenomic tools and obtained several phylogenetic inferences. The pangenome was rich in its accessory component and was considered open according to the Heaps' law. We then applied the pangenome-wide associating method (pan-GWAS) and predicted positively associated gene clusters attributed to three host groups, namely, humans, insects, and plants. Results According to the results, significant factors relating to human infections included transcriptional regulators, lipoproteins, ABC transporters, and membrane proteins. Host preference toward insects, in its turn, was associated with diverse enzymes, such as hydrolases, isochorismatase, and N-acetyltransferase with the latter possibly exerting a neurotoxic effect. Finally, plant infection may be conducted through type VI secretion systems and modulation of plant cell wall synthesis. Interestingly, factors associated with plants also included putative growth-promoting proteins like enzymes performing xenobiotic degradation and releasing ammonium irons. We also identified overrepresented functional annotations within the sets of specificity factors and found that their functional characteristics fell into separate clusters, thus, implying that host adaptation is represented by diverse functional pathways. Finally, we found that mobile genetic elements bore specificity determinants. In particular, prophages were mainly associated with factors related to humans, while genetic islands-with insects and plants, respectively. Discussion In summary, functional enrichments coupled with pangenomic inferences allowed us to hypothesize that the respective host preference is carried out through distinct molecular mechanisms of virulence. To the best of our knowledge, the presented research is the first to identify specific genomic features of S. marcescens assemblies isolated from different hosts at the pangenomic level.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Anastasiya V. Merkushova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
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Hamzah AS. Molecular Typing of fumC, icd, and mdh Genes in Serratia Marcescens. JOURNAL OF PHARMACY AND BIOALLIED SCIENCES 2023; 15:S871-S874. [PMID: 37694086 PMCID: PMC10485449 DOI: 10.4103/jpbs.jpbs_93_23] [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: 02/01/2023] [Revised: 02/16/2023] [Accepted: 02/28/2023] [Indexed: 09/12/2023] Open
Abstract
Aim Serratia marcescens genes fumC, icd, and mdh were molecularly typed in various groups of 200 clinical samples. Results According to the findings, 38 (19%) of the isolates are Serratia marcescens. All these bacterial isolates had their DNA extracted. Then, using particular primers, the genes fumC, icd, and mdh are detected and amplified. These genes were sequenced, and the results were aligned with NCBI sequences. Using the Geneious version 9 software, gene sequences were analyzed. Sequencing of these genes revealed variant regions when compared to global isolates in NCBI. Energy levels in bacterial cells may be impacted by TCA cycle enzyme variant sequence genes. Conclusion The bacterial sequences from Iraq that were listed in NCBI with an accession number were LC735551 is a gene bank. (Gene Bank: LC735550, 1 Iraqi 40 fumC gene. One Iraq 41 icd gene; gene accession number: LC735549.42 mdh gene in Iraq.).
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Affiliation(s)
- Alaa S. Hamzah
- Department of Anesthesia Techniques, Institute of Medical Technology, Middle Technical University, Baghdad, Iraq
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7
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Bizubac M, Balaci-Miroiu F, Filip C, Vasile CM, Herișeanu C, Marcu V, Stoica S, Cîrstoveanu C. Neonatal Brain Abscess with Serratia marcescens after Intrauterine Infection: A Case Report. Antibiotics (Basel) 2023; 12:antibiotics12040722. [PMID: 37107084 PMCID: PMC10135221 DOI: 10.3390/antibiotics12040722] [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: 03/02/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Brain abscesses are a possible complication of bacterial sepsis or central nervous system infection but are uncommon in the neonatal period. Gram-negative organisms often cause them, but Serratia marcescens is an unusual cause of sepsis and meningitis in this age group. This pathogen is opportunistic and frequently responsible for nosocomial infections. Despite the existing antibiotics and modern radiological tools, mortality and morbidity remain significant in this group of patients. We report an unusual unilocular brain abscess in a preterm neonate caused by Serratia marcescens. The infection had an intrauterine onset. The pregnancy was achieved through assisted human reproduction techniques. It was a high-risk pregnancy, with pregnancy-induced hypertension, imminent abortion, and required prolonged hospitalization of the pregnant woman with multiple vaginal examinations. The infant was treated with multiple antibiotic cures and percutaneous drainage of the brain abscess associated with local antibiotic treatment. Despite treatment, evolution was unfavorable, complicated by fungal sepsis (Candida parapsilosis) and multiple organ dysfunction syndrome.
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Affiliation(s)
- Mihaela Bizubac
- Department of Neonatal Intensive Care, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Neonatal Intensive Care Unit, "M.S. Curie" Children's Clinical Hospital, 041451 Bucharest, Romania
| | - Francisca Balaci-Miroiu
- Neonatal Intensive Care Unit, "M.S. Curie" Children's Clinical Hospital, 041451 Bucharest, Romania
| | - Cristina Filip
- Department of Pediatrics, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Department of Pediatric Cardiology, "M.S. Curie" Children's Clinical Hospital, 041451 Bucharest, Romania
| | - Corina Maria Vasile
- Department of Pediatric Cardiology, "M.S. Curie" Children's Clinical Hospital, 041451 Bucharest, Romania
- Department of Pediatric and Adult Congenital Cardiology, University Hospital of Bordeaux, 33600 Bordeaux, France
| | - Carmen Herișeanu
- Neonatal Intensive Care Unit, "M.S. Curie" Children's Clinical Hospital, 041451 Bucharest, Romania
- Ph.D. School Department, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Veronica Marcu
- Department of Radiology, "M.S. Curie" Children's Clinical Hospital, 041451 Bucharest, Romania
| | - Sergiu Stoica
- Department of Neurosurgery, Monza Hospital, 021967 Bucharest, Romania
| | - Catalin Cîrstoveanu
- Department of Neonatal Intensive Care, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Neonatal Intensive Care Unit, "M.S. Curie" Children's Clinical Hospital, 041451 Bucharest, Romania
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Shana SS, Sreenath KR, Sumithra TG, Krishnaveny SMS, Joshi KK, Nameer PO, Gopalakrishnan A. A Global-Scale Ecological Niche Modeling of the Emerging Pathogen Serratia marcescens to Aid in its Spatial Ecology. Curr Microbiol 2023; 80:59. [PMID: 36588127 DOI: 10.1007/s00284-022-03159-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/17/2022] [Indexed: 01/03/2023]
Abstract
Serratia marcescens is a big emerging concern for human health and coral biodiversity. Spatial ecology and the influencing factors on pathogen ecology, however, remain unknown. The study forms the first global risk assessment of S. marcescens. MaxEnt niche modeling was applied using two biotic and sixteen abiotic variables. The world was classified into five risk-level categories based on the pathogen ecology, and the world population exposed to S. marcescens infection was then quantified. The prepared model showed an area under the curve value of 0.918 ± 0.028, implying excellent prediction ability. The highly and moderately suitable areas occupied around 0.52% and 17.9% of the total global land area. The order of probability of having S. marcescens-related infections was Asia > North America > South America > Europe > Africa > Australia. Human population density and temperature were the most influential factors in the distribution. The moderate to high transmission risk zones contained 0.20% (1.61 billion people) of the human population. In brief, these results give novel insights into its spatial ecology and provide the risk maps that can be utilized to plan targeted strategic control measures against future invasions of this emerging pathogen.
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Affiliation(s)
- S S Shana
- Marine Biodiversity and Environment Management Division, Central Marine Fisheries Research Institute, Kochi, 682018, Kerala, India.,College of Climate Change and Environmental Science, Kerala Agricultural University, Thrissur, 680656, Kerala, India
| | - K R Sreenath
- Marine Biodiversity and Environment Management Division, Central Marine Fisheries Research Institute, Kochi, 682018, Kerala, India.
| | - T G Sumithra
- Marine Biotechnology, Fish Nutrition and Health Division, Central Marine Fisheries Research Institute, Kochi, 682018, Kerala, India
| | - S M S Krishnaveny
- Marine Biodiversity and Environment Management Division, Central Marine Fisheries Research Institute, Kochi, 682018, Kerala, India.,Cochin University of Science and Technology, Kalamassery, Kochi, 682022, Kerala, India
| | - K K Joshi
- Marine Biodiversity and Environment Management Division, Central Marine Fisheries Research Institute, Kochi, 682018, Kerala, India
| | - P O Nameer
- College of Climate Change and Environmental Science, Kerala Agricultural University, Thrissur, 680656, Kerala, India
| | - A Gopalakrishnan
- Marine Biotechnology, Fish Nutrition and Health Division, Central Marine Fisheries Research Institute, Kochi, 682018, Kerala, India
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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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10
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Kanj SS, Bassetti M, Kiratisin P, Rodrigues C, Villegas MV, Yu Y, van Duin D. Clinical data from studies involving novel antibiotics to treat multidrug-resistant Gram-negative bacterial infections. Int J Antimicrob Agents 2022; 60:106633. [PMID: 35787918 DOI: 10.1016/j.ijantimicag.2022.106633] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 06/15/2022] [Accepted: 06/26/2022] [Indexed: 11/05/2022]
Abstract
Multidrug-resistant (MDR) Gram-negative bacteria (GNB) are a critical threat to healthcare worldwide, worsening outcomes and increasing mortality among infected patients. Carbapenemase- and extended-spectrum β-lactamase-producing Enterobacterales, as well as carbapenemase-producing Pseudomonas and Acinetobacter spp., are common MDR pathogens. To address this threat, new antibiotics and combinations have been developed. Clinical trial findings support several combinations, notably ceftazidime-avibactam (CZA, a cephalosporin-β-lactamase inhibitor combination) which is effective in treating complicated urinary tract infections (cUTI), complicated intra-abdominal infections and hospital-acquired and ventilator-associated pneumonia caused by GNBs. Other clinically effective combinations include meropenem-vaborbactam (MVB), ceftolozane-tazobactam (C/T) and imipenem- relebactam (I-R). Cefiderocol is a recent siderophore β-lactam antibiotic that is useful against cUTIs caused by carbapenem-resistant Enterobacterales (CRE) and is stable against many β-lactamases. CRE are a genetically heterogeneous group that vary in different world regions and are a substantial cause of infections, among which Klebsiella pneumoniae are the most common. Susceptible CRE infections can be treated with fluoroquinolones, aminoglycosides or fosfomycin, but alternatives include CZA, MVB, I-R, cefiderocol, tigecycline and eravacycline. MDR Acinetobacter baumannii and Pseudomonas aeruginosa are increasingly common pathogens producing a range of different carbapenemases, and infections are challenging to treat, often requiring novel antibiotics or combinations. Currently, no single agent can treat all MDR-GNB infections, but new β-lactam-β-lactamase inhibitor combinations are often effective for different infection sites, and, when used appropriately, have the potential to improve outcomes. This article reviews clinical studies investigating novel β-lactam approaches for treatment of MDR-GNB infections.
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Key Words
- Antibiotic resistance
- BAT, best available treatment
- BL, β-lactamase
- BL–BLI, β-lactam-β-lactamase inhibitor
- BSI, bloodstream infection
- C/T, ceftolozane–tazobactam
- CAZ, ceftazidime
- CDC, Centers for Disease Control and Prevention
- CRAB, carbapenem-resistant Acinetobacter baumannii
- CRE, carbapenem-resistant Enterobacterales
- CRKP, carbapenem-resistant K. pneumoniae
- CRPA, carbapenem-resistant Pseudomonas aeruginosa
- CZA, ceftazidime–avibactam
- Clinical trial
- DBO, diazabicyclooctane
- ESBL, extended-spectrum β-lactamase
- FDA, US Food and Drug Administration
- GNB, Gram-negative bacteria
- Gram-negative bacteria Abbreviations: AVI, avibactam
- HAP, hospital-acquired pneumonia
- IAI, intra-abdominal infection
- ICU, intensive care unit
- IDSA, Infectious Diseases Society of America
- IPM, imipenem
- I–R, imipenem–relebactam
- KPC, Klebsiella pneumoniae carbapenemase
- MBL, metallo-β-lactamase
- MDR, multidrug-resistant
- MEM, meropenem
- MIC, minimum inhibitory concentration
- MVB, meropenem–vaborbactam
- NDM, New Delhi metallo-β-lactamase
- OXA, oxacillinase
- REL, relebactam
- US, United States
- UTI, urinary tract infection
- VAB, vaborbactam
- VAP, ventilator-associated pneumonia
- VIM, Verona integron-encoded metallo-β-lactamase
- XDR, extensively drug-resistant
- cIAI, complicated intra-abdominal infection
- cUTI, complicated urinary tract infection
- β-lactam-β-lactamase inhibitor
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Affiliation(s)
- Souha S Kanj
- Division of Infectious Diseases, American University of Beirut Medical Center, Beirut, Lebanon
| | - Matteo Bassetti
- Department of Health Science, University of Genoa, Italy; Infectious Diseases Clinic, Ospedale Policlinico San Martino Hospital - IRCCS, Genoa, Italy
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Camilla Rodrigues
- Department of Microbiology, P. D. Hinduja Hospital and Medical Research Centre, Mumbai, Maharashtra, India
| | - María Virginia Villegas
- Grupo de Investigaciones en Resistencia Antimicrobiana y Epidemiología Hospitalaria (RAEH), Universidad El Bosque, Bogotá D.C., Colombia
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
| | - David van Duin
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
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Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance. mSystems 2022; 7:e0138421. [PMID: 35695507 PMCID: PMC9238379 DOI: 10.1128/msystems.01384-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients. Here, we describe the diversity of bacteria sampled from hospitalized patients at a single center, as revealed through systematic analysis of bacterial isolate genomes. We sequenced the genomes of 3,004 bacterial isolates from hospitalized patients collected over a 25-month period. We identified bacteria belonging to 97 distinct species, which were distributed among 14 groups of related species. Within these groups, isolates could be distinguished from one another by both average nucleotide identity (ANI) and principal-component analysis of accessory genes (PCA-A). Core genome genetic distances and rates of evolution varied among species, which has practical implications for defining shared ancestry during outbreaks and for our broader understanding of the origins of bacterial strains and species. Finally, antimicrobial resistance genes and putative mobile genetic elements were frequently observed, and our systematic analysis revealed patterns of occurrence across the different species sampled from our hospital. Overall, this study shows how understanding the population structure of diverse pathogens circulating in a single health care setting can improve the discriminatory power of genomic epidemiology studies and can help define the processes leading to strain and species differentiation. IMPORTANCE Hospitalized patients are at increased risk of becoming infected with antibiotic-resistant organisms. We used whole-genome sequencing to survey and compare over 3,000 clinical bacterial isolates collected from hospitalized patients at a large medical center over a 2-year period. We identified nearly 100 different bacterial species, which we divided into 14 different groups of related species. When we examined how genetic relatedness differed between species, we found that different species were likely evolving at different rates within our hospital. This is significant because the identification of bacterial outbreaks in the hospital currently relies on genetic similarity cutoffs, which are often applied uniformly across organisms. Finally, we found that antibiotic resistance genes and mobile genetic elements were abundant and were shared among the bacterial isolates we sampled. Overall, this study provides an in-depth view of the genomic diversity and evolutionary processes of bacteria sampled from hospitalized patients, as well as genetic similarity estimates that can inform hospital outbreak detection and prevention efforts.
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Gilbert R, Tanenbaum N, Bhattacharya S. Asparagine biosynthesis as a mechanism of increased host lethality induced by Serratia marcescens in simulated microgravity environments. Heliyon 2022; 8:e09379. [PMID: 35592661 PMCID: PMC9111996 DOI: 10.1016/j.heliyon.2022.e09379] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/15/2022] [Accepted: 04/28/2022] [Indexed: 11/15/2022] Open
Abstract
While studies have shown an increase in pathogenicity in several microbes during spaceflight and after exposure to simulated microgravity, the mechanisms underlying these changes in phenotype are not understood across different pathogens, particularly in opportunistic pathogens. This study evaluates the mechanism for increased virulence of the opportunistic gram-negative bacterium, Serratia marcescens, in simulated microgravity. Low-shear modeled microgravity (LSMMG) is used in ground-based studies to simulate the effects of microgravity as experienced in spaceflight. Our previous findings showed that there was a significant increase in mortality rates of the Drosophila melanogaster host when infected with either spaceflight or LSMMG treated S. marcescens. Here, we report that LSMMG increases asparagine uptake and synthesis in S. marcescens and that the increased host lethality induced by LSMMG bacteria grown in rich media can be recapitulated in minimal media by adding only aspartate and glutamine, the substrates of asparagine biosynthesis. Interestingly, increased bacterial growth rate alone is not sufficient to contribute to maximal host lethality, since the addition of aspartate to minimal media caused an LSMMG-specific increase in bacterial growth rate that is comparable to that induced by the combination of aspartate and glutamine, but this increase in growth does not cause an equivalent rate of host mortality. However, the addition of both aspartate and glutamine cause both an increase in host mortality and an overexpression of asparagine pathway genes in a LSMMG-dependent manner. We also report that L-asparaginase-mediated breakdown of asparagine is an effective countermeasure for the increased host mortality caused by LSMMG-treated bacteria. This investigation underscores the importance of the asparagine utilization pathway by helping uncover molecular mechanisms that underlie increased mortality rates of a model host infected with microgravity-treated S. marcescens and provides a potential mitigation strategy.
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Genomic characterisation of an entomopathogenic strain of Serratia ureilytica in the critically endangered phasmid Dryococelus australis. PLoS One 2022; 17:e0265967. [PMID: 35442959 PMCID: PMC9020675 DOI: 10.1371/journal.pone.0265967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/10/2022] [Indexed: 11/19/2022] Open
Abstract
Between 2014 and 2019, unexpected mortalities were observed in a colony of Dryococelus australis, an endangered stick-insect kept at the Melbourne Zoo for a breeding and conservation program. Pure cultures of Serratia spp. were obtained from the haemolymph of moribund and recently deceased individuals. The combined bacteriological and histopathological observations suggested an infectious cause of these mortalities. Genotyping of Serratia sp. isolated from the insects and their environment revealed a predominant strain profile. A representative isolate, AM923, was entirely sequenced and compared to 616 publicly available Serratia spp. genomes, including 37 associated with insects. The genomes were distributed into 3 distinct groups, with 63% of the insect-associated isolates within a single clade (clade A) containing AM923, separated from most environmental/plant-associated strains (clade B) and human isolates (clade C). Average nucleotide identity and phylogenetic analyses identified AM923 as S. ureilytica and revealed similarities with putatively entomopathogenic strains. An experimental infection model in honey bees (Apis mellifera) confirmed the pathogenic potential of AM923. A urease operon was found in most insect isolates and a PCR assay, based on the ureB gene sequence, was used to confirm the presence of AM923 in experimentally infected bees. This species-specific PCR could be applied to detect entomopathogenic Serratia spp. in infected insects or their environment.
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Identification of distinct capsule types associated with Serratia marcescens infection isolates. PLoS Pathog 2022; 18:e1010423. [PMID: 35353877 PMCID: PMC9000132 DOI: 10.1371/journal.ppat.1010423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/11/2022] [Accepted: 03/07/2022] [Indexed: 01/13/2023] Open
Abstract
Serratia marcescens is a versatile opportunistic pathogen that can cause a variety of infections, including bacteremia. Our previous work established that the capsule polysaccharide (CPS) biosynthesis and translocation locus contributes to the survival of S. marcescens in a murine model of bacteremia and in human serum. In this study, we determined the degree of capsule genetic diversity among S. marcescens isolates. Capsule loci (KL) were extracted from >300 S. marcescens genome sequences and compared. A phylogenetic comparison of KL sequences demonstrated a substantial level of KL diversity within S. marcescens as a species and a strong delineation between KL sequences originating from infection isolates versus environmental isolates. Strains from five of the identified KL types were selected for further study and electrophoretic analysis of purified CPS indicated the production of distinct glycans. Polysaccharide composition analysis confirmed this observation and identified the constituent monosaccharides for each strain. Two predominant infection-associated clades, designated KL1 and KL2, emerged from the capsule phylogeny. Bacteremia strains from KL1 and KL2 were determined to produce ketodeoxynonulonic acid and N-acetylneuraminic acid, two sialic acids that were not found in strains from other clades. Further investigation of KL1 and KL2 sequences identified two genes, designated neuA and neuB, that were hypothesized to encode sialic acid biosynthesis functions. Disruption of neuB in a KL1 isolate resulted in the loss of sialic acid and CPS production. The absence of sialic acid and CPS production also led to increased susceptibility to internalization by a human monocytic cell line, demonstrating that S. marcescens phagocytosis resistance requires CPS. Together, these results establish the capsule genetic repertoire of S. marcescens and identify infection-associated clades with sialic acid CPS components.
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15
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Jepsen K, Falk W, Brune F, Cosgarea R, Fimmers R, Bekeredjian-Ding I, Jepsen S. Prevalence and Antibiotic Susceptibility Trends of Selected Enterobacteriaceae, Enterococci, and Candida albicans in the Subgingival Microbiota of German Periodontitis Patients: A Retrospective Surveillance Study. Antibiotics (Basel) 2022; 11:antibiotics11030385. [PMID: 35326848 PMCID: PMC8944811 DOI: 10.3390/antibiotics11030385] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
The periodontal microbiota is ecologically diverse and may facilitate colonization by bacteria of enteric origin (Enterobacteriaceae, Enterococci) and co-infections with Candida albicans, possibly producing subgingival biofilms with high antimicrobial tolerance. This retrospective surveillance study followed periodontitis-associated superinfection profiles in a large patient sample. From 2008 to 2015, biofilm samples from deep periodontal pockets were collected from a total of 16,612 German adults diagnosed with periodontitis. The presence of selected Enterobacteriaceae, Enterococci, and Candida albicans was confirmed in overnight cultures. Antimicrobial susceptibility of these clinical isolates was tested by disk diffusion with antibiotics routinely used for treatment of oral infections, e.g., amoxicillin (AML), amoxicillin/clavulanic acid (AMC), doxycycline (DO), and ciprofloxacin (CIP). The mean annual prevalence of patients harboring Enterobacteriaceae in periodontal plaques was 11.5% in total and ranged from 2.5% for Enterobacter cloacae to 3.6% for Klebsiella oxytoca, 1.1% for Klebsiella pneumoniae, 2.8% for Serratia marcescens, and 1.5% for Serratia liquefaciens. In comparison, the mean detection rates for microbiota typically found in the oral cavity were higher, e.g., 5.6% for Enterococcus spp. and 21.8% for Candida albicans. Among the Enterobacteriaceae, species harboring intrinsic resistance to AML (Enterobacter spp., Klebsiella spp., Serratia spp.) were predominant. Non-susceptibility to AMC was observed for Serratia spp. and Enterobacter cloacae. By contrast, Enterococcus spp. only showed non-susceptibility to DO and CIP. Trends for increasing resistance were found to AML in Serratia liquefaciens and to DO in Enterococcus spp. Trend analysis showed decreasing resistance to AMC in Serratia liquefaciens and Klebsiella oxytoca; and to DO in Serratia marcescens, liquefaciens, and Enterobacter cloacae. This study confirms the low but consistent presence of Enterobacteriaceae and Enterococci among the subgingival microbiota recovered from periodontitis specimen. Although their pathogenetic role in periodontal lesions remains unclear, their presence in the oral cavity should be recognized as a potential reservoir for development and spread of antibiotic resistance in light of antibiotic usage in oral infections.
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Affiliation(s)
- Karin Jepsen
- Department of Periodontology, Operative and Preventive Dentistry, University Hospital Bonn, Welschnonnenstrasse 17, 53111 Bonn, Germany; (F.B.); (R.C.); (S.J.)
- Correspondence: ; Tel.: +49-228-287-22480
| | - Wolfgang Falk
- Service Laboratory, Center for Oral & Dental Microbiology, 24103 Kiel, Germany;
| | - Friederike Brune
- Department of Periodontology, Operative and Preventive Dentistry, University Hospital Bonn, Welschnonnenstrasse 17, 53111 Bonn, Germany; (F.B.); (R.C.); (S.J.)
| | - Raluca Cosgarea
- Department of Periodontology, Operative and Preventive Dentistry, University Hospital Bonn, Welschnonnenstrasse 17, 53111 Bonn, Germany; (F.B.); (R.C.); (S.J.)
- Clinic for Periodontology and Peri-Implant Diseases, Philipps University Marburg, 35039 Marburg, Germany
- Clinic of Prosthodontics, Iuliu Hatieganu University Cluj-Napoca, 40006 Cluj-Napoca, Romania
| | - Rolf Fimmers
- Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, 53127 Bonn, Germany;
| | - Isabelle Bekeredjian-Ding
- Division of Microbiology, Paul-Ehrlich-Institut, 63225 Langen, Germany;
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, 53127 Bonn, Germany
| | - Søren Jepsen
- Department of Periodontology, Operative and Preventive Dentistry, University Hospital Bonn, Welschnonnenstrasse 17, 53111 Bonn, Germany; (F.B.); (R.C.); (S.J.)
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Ono T, Taniguchi I, Nakamura K, Nagano DS, Nishida R, Gotoh Y, Ogura Y, Sato MP, Iguchi A, Murase K, Yoshimura D, Itoh T, Shima A, Dubois D, Oswald E, Shiose A, Gotoh N, Hayashi T. Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex. Microb Genom 2022; 8:000793. [PMID: 35315751 PMCID: PMC9176281 DOI: 10.1099/mgen.0.000793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the 'S. marcescens complex'), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila, S. marcescens sensu stricto, S. ureilytica and S. surfactantfaciens, respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum β-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.
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Affiliation(s)
- Tomoyuki Ono
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Debora Satie Nagano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ruriko Nishida
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Mitsuhiko P. Sato
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Present address: Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Atsushi Iguchi
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, 889-8192, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Sakyou-ku, Kyoto, 6060-8501, Japan
| | - Dai Yoshimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Ayaka Shima
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- Present address: Anicon Insurance, Inc., 8-17-1 Nishi-shinjuku, Shinjuku, Tokyo, 160-0023, Japan
| | - Damien Dubois
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Eric Oswald
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Akira Shiose
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Naomasa Gotoh
- Kyoto Pharmaceutical University, Yamashiro, Kyoto, 607-8414, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- *Correspondence: Tetsuya Hayashi,
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Kate A, Bagga B, Ponnapati LP, Singh S, Shah S, Mohamed A, Joseph J. Clinico-microbiological Features and Treatment Outcomes of Serratia Keratitis and Comparison with Pseudomonas aeruginosa Keratitis. Ocul Immunol Inflamm 2022; 31:515-519. [PMID: 35212599 DOI: 10.1080/09273948.2022.2037660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
PURPOSE To describe clinico-microbiological features and outcomes of Serratia keratitis and to compare them with Pseudomonas aeruginosa keratitis. METHODS Cases of microbiologically proven Serratia keratitis and P. aeruginosa keratitis were reviewed. Data regarding demographic and clinical characteristics, and outcomes were recorded. RESULTS 39 patients with pure Serratia keratitis were included. Median presenting vision was 1.8 logMAR (IQR, 0.8-2.4) and median infiltrate size was 5 mm (IQR 3-7.8 mm). An ocular risk factor was present in 35 (89.7%) cases. S. marcescens was the most common species (31/39, 79.5%). Medical resolution was observed in 36/39 (92.3%) cases, while three (7.7%) eyes needed penetrating keratoplasty. On comparing with P. aeruginosa keratitis (58 eyes), no difference in outcomes (p = .14) was noted. CONCLUSION Serratia keratitis usually occurs in eyes with a compromised surface and has good resolution with medical therapy. Both Serratia and P. aeruginosa keratitis have similar outcomes.
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Affiliation(s)
- Anahita Kate
- The Cornea Institute, L V Prasad Eye Institute, Vijayawada, India
| | - Bhupesh Bagga
- The Cornea Institute, L V Prasad Eye Institute, Hyderabad, India
| | | | - Shalini Singh
- The Cornea Institute, L V Prasad Eye Institute, Hyderabad, India
| | - Sahil Shah
- The Cornea Institute, L V Prasad Eye Institute, Hyderabad, India
| | - Ashik Mohamed
- Ophthalmic Biophysics, L V Prasad Eye Institute, Hyderabad, India
| | - Joveeta Joseph
- Jhaveri Microbiology Centre, L V Prasad Eye Institute, Hyderabad, India
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Hou J, Mao D, Zhang Y, Huang R, Li L, Wang X, Luo Y. Long-term spatiotemporal variation of antimicrobial resistance genes within the Serratia marcescens population and transmission of S. marcescens revealed by public whole-genome datasets. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127220. [PMID: 34844350 DOI: 10.1016/j.jhazmat.2021.127220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
The development of antimicrobial resistance (AMR) is accelerated by the selective pressure exerted by the widespread use of antimicrobial drugs, posing an increasing danger to public health. However, long-term spatiotemporal variation in AMR genes in microorganisms, particularly in bacterial pathogens in response to antibiotic consumption, is not fully understood. Here, we used the NCBI RefSeq database to collect 478 whole-genome sequences for Serratia marcescens ranging from 1961 up to 2019, to document global long-term AMR trends in S. marcescens populations. In total, 100 AMR gene subtypes (16 AMR gene types) were detected in the genomes of S. marcescens populations. We identified 3 core resistance genes in S. marcescens genomes, and a high diversity of AMR genes was observed in S. marcescens genomes after corresponding antibiotics were discovered and introduced into clinical practice, suggesting the adaptation of S. marcescens populations to challenges with therapeutic antibiotics. Our findings indicate spatiotemporal variation of AMR genes in S. marcescens populations in relation to antibiotic consumption and suggest the potential transmission of S. marcescens isolates harboring AMR genes among countries and between the environment and the clinic, representing a public health threat that necessitates international solidarity to overcome.
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Affiliation(s)
- Jie Hou
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yulin Zhang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Ruiyang Huang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Linyun Li
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China.
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Nakanishi N, Komatsu S, Iwamoto T, Nomoto R. Characterization of a Novel Plasmid in Serratia marcescens Harbouring bla GES-5 Isolated from a Nosocomial Outbreak in Japan. J Hosp Infect 2021; 121:128-131. [PMID: 34906601 DOI: 10.1016/j.jhin.2021.11.022] [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: 10/13/2021] [Revised: 11/17/2021] [Accepted: 11/27/2021] [Indexed: 11/26/2022]
Abstract
Serratia marcescens is a nosocomial pathogen with carbapenem resistance, which limits the availability of effective treatment options. In this study, we performed molecular characterization of GES-5 carbapenemase-producing S. marcescens isolated from an outbreak in Japan. Comparative genetic analysis revealed that the blaGES-5-encoding plasmid p2020-O-9 is a unique plasmid contributing to carbapenem resistance. Furthermore, this study highlights the necessity of surveillance programs for monitoring novel, along with commonly occurring carbapenemases in clinical settings.
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Affiliation(s)
- Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-nakamachi, Chuo-ku, Kobe, Hyogo, 650-0046, Japan
| | - Shoko Komatsu
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-nakamachi, Chuo-ku, Kobe, Hyogo, 650-0046, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-nakamachi, Chuo-ku, Kobe, Hyogo, 650-0046, Japan
| | - Ryohei Nomoto
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-nakamachi, Chuo-ku, Kobe, Hyogo, 650-0046, Japan.
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20
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Third-Generation Cephalosporin Resistance in Intrinsic Colistin-Resistant Enterobacterales Isolated from Retail Meat. Antibiotics (Basel) 2021; 10:antibiotics10121437. [PMID: 34943649 PMCID: PMC8698362 DOI: 10.3390/antibiotics10121437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/12/2021] [Accepted: 11/20/2021] [Indexed: 12/28/2022] Open
Abstract
Consumption of retail meat contaminated with antimicrobial-resistant (AMR) bacteria is a common route for transmitting clinically relevant resistant bacteria to humans. Here, we investigated the genotypic and phenotypic resistance profiles of intrinsic colistin-resistant (ICR) Enterobacterales isolated from retail meats. ICR Enterobacterales were isolated from 103 samples of chicken, 103 samples of pork, and 104 samples of beef purchased from retail shops in Japan, using colistin-containing media, and their antimicrobial susceptibility was examined. Serratia spp. (440 isolates) showed resistance to cefotaxime (19 isolates, 4.3%), tetracycline (15 isolates, 3.4%), and other antimicrobials (<1%). Hafnia spp. (136) showed resistance to cefotaxime (12 isolates, 8.6%), ceftazidime (four isolates, 2.9%), and tetracycline (two isolates, 1.4%). Proteus spp. (39) showed resistance to chloramphenicol (four isolates, 10.3%), sulfamethoxazole-trimethoprim (four isolates, 10.3%), cefotaxime (two isolates, 5.1%), kanamycin (two isolates, 5.1%), and gentamicin (one isolate, 2.6%). Cedecea spp. (22) were resistant to tetracycline (two isolates, 9.1%) whereas Morganella spp. (11) were resistant to tetracycline (four isolates, 36.4%) and chloramphenicol (one isolate, 9.2%). The resistance genes blafonA, blaACC, and blaDHA were detected in cefotaxime-resistant Serratia spp., Hafnia spp., and Morganella spp. isolates, respectively. This emergence of antimicrobial resistance in ICR Enterobacterales may pose a public health risk.
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21
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A Genome-Scale Antibiotic Screen in Serratia marcescens Identifies YdgH as a Conserved Modifier of Cephalosporin and Detergent Susceptibility. Antimicrob Agents Chemother 2021; 65:e0078621. [PMID: 34491801 DOI: 10.1128/aac.00786-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serratia marcescens, a member of the order Enterobacterales, is adept at colonizing health care environments and is an important cause of invasive infections. Antibiotic resistance is a daunting problem in S. marcescens because, in addition to plasmid-mediated mechanisms, most isolates have considerable intrinsic resistance to multiple antibiotic classes. To discover endogenous modifiers of antibiotic susceptibility in S. marcescens, a high-density transposon insertion library was subjected to sub-MICs of two cephalosporins, cefoxitin, and cefepime, as well as the fluoroquinolone ciprofloxacin. Comparisons of transposon insertion abundance before and after antibiotic exposure identified hundreds of potential modifiers of susceptibility to these agents. Using single-gene deletions, we validated several candidate modifiers of cefoxitin susceptibility and chose ydgH, a gene of unknown function, for further characterization. In addition to cefoxitin, deletion of ydgH in S. marcescens resulted in decreased susceptibility to multiple third-generation cephalosporins and, in contrast, to increased susceptibility to both cationic and anionic detergents. YdgH is highly conserved throughout the Enterobacterales, and we observed similar phenotypes in Escherichia coli O157:H7 and Enterobacter cloacae mutants. YdgH is predicted to localize to the periplasm, and we speculate that it may be involved there in cell envelope homeostasis. Collectively, our findings provide insight into chromosomal mediators of antibiotic resistance in S. marcescens and will serve as a resource for further investigations of this important pathogen.
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Boas do Prado GV, Mendes ET, Martins RCR, Perdigão-Neto LV, Freire MP, Marchi AP, Côrtes MF, Lima VACDC, Rossi F, Guimarães T, Levin AS, Costa SF. Phenotypic and genotypic characteristics of a Carbapenem-resistant Serratia marcescens cohort and outbreak: describing an opportunistic pathogen. Int J Antimicrob Agents 2021; 59:106463. [PMID: 34715332 DOI: 10.1016/j.ijantimicag.2021.106463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/29/2021] [Accepted: 10/16/2021] [Indexed: 11/05/2022]
Abstract
Serratia marcescens is an emerging opportunistic pathogen with high genetic diversity. We described microbiological characteristics of isolates and also risk factors for infections caused by carbapenem-resistant S. marcescens(CrSm). A retrospective study of patients colonized(N=43) and infected(N=20) by CrSm over a three-year period was conducted. Polymerase chain reaction(PCR) for carbapenemases genes and molecular typing of all available strains was performed; Forty-two isolates were analyzed, including three environmental samples identified during an outbreak. Thirty-five CrSm carried blaKPC-2; one isolate was blaNDM-positive and four isolates carried blaOXA-101. The genomes were grouped into three clusters with 100% bootstrap; three patterns of mutations on ompC and ompF were found. The strains carried virulence genes related to invasion and hemolysis and the environmental strains presented less mutations on the virulence genes than clinical strains. The multivariate analysis showed that previous use of polymyxin(p=0.008) was an independent risk factor for infection by CrSm. Our study highlighted that blaKPC-2 in association with ompC, ompF mutation was the most frequent mechanism of resistance in our hospital, and that previous use of polymyxin was an independent risk factor for CrSm. There is a predominant clone, including the environmental isolates, suggesting that cross-transmission was involved in the dissemination of this pathogen.
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Affiliation(s)
- Gladys Villas Boas do Prado
- Medical Research Laboratory, Bacteriology -LIM-49, USP Medical School, Universidade de São Paulo, São Paulo, Brazil
| | - Elisa Teixeira Mendes
- Pontifical Catholic University of Campinas (Puc-Campinas) Center of Life Science, Postgraduate program in Health Science, Infectious Diseases.
| | | | - Lauro Vieira Perdigão-Neto
- Medical Research Laboratory, Bacteriology -LIM-49, USP Medical School, Universidade de São Paulo, São Paulo, Brazil
| | - Maristela Pinheiro Freire
- Infection Control Committee of Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula Marchi
- Medical Research Laboratory, Bacteriology -LIM-49, USP Medical School, Universidade de São Paulo, São Paulo, Brazil
| | - Marina Farrel Côrtes
- Medical Research Laboratory, Bacteriology -LIM-49, USP Medical School, Universidade de São Paulo, São Paulo, Brazil
| | | | - Flavia Rossi
- Department of Pathology, Division of Microbiology of the Central Laboratory (LIM 03), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Thais Guimarães
- Infection Control Committee of Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Anna Sara Levin
- Medical Research Laboratory, Bacteriology -LIM-49, USP Medical School, Universidade de São Paulo, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Silvia Figueiredo Costa
- Medical Research Laboratory, Bacteriology -LIM-49, USP Medical School, Universidade de São Paulo, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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da Silva KE, Rossato L, Jorge S, de Oliveira NR, Kremer FS, Campos VF, da Silva Pinto L, Dellagostin OA, Simionatto S. Three challenging cases of infections by multidrug-resistant Serratia marcescens in patients admitted to intensive care units. Braz J Microbiol 2021; 52:1341-1345. [PMID: 33829377 PMCID: PMC8324748 DOI: 10.1007/s42770-021-00477-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/26/2021] [Indexed: 11/28/2022] Open
Abstract
The occurrence of multidrug-resistant Serratia marcescens strains represents a serious public health threat. The purpose here is to report three cases of carbapenem-resistant S. marcescens infections with unfavorable clinical outcomes and provide a molecular description of the antibiotic resistance determinants at a genomic level. We performed bacterial identification by VITEK 2 and MALDI-TOF. The minimal inhibitory concentrations of antimicrobials were determined according to the Clinical and Laboratory Standards Institute guidelines, except for tigecycline, for which they were determined using Etest strips. Preliminary screening for the presence of carbapenemases was performed by ertapenem hydrolysis using MALDI-TOF MS. Whole-genome sequencing was provided to identify genes responsible for virulence and antimicrobial resistance. Here we report three challenging cases of S. marcescens that were resistant to the most commonly used antibiotics. Otherwise, we performed a genome description, which includes several genes involved in the resistance and virulence. These cases illustrate serious infection due to multidrug-resistant organisms and the complexity of treatment. Our results highlight the need to evaluate isolates regularly during long-term hospital stay to achieve optimal quality of clinical care and thus improve patient outcomes.
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Affiliation(s)
- Kesia Esther da Silva
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados - UFGD, Dourados, Mato Grosso do Sul, Brazil
| | - Luana Rossato
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados - UFGD, Dourados, Mato Grosso do Sul, Brazil
| | - Sérgio Jorge
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Natasha Rodrigues de Oliveira
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Frederico Schmitt Kremer
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Vinícius Farias Campos
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Luciano da Silva Pinto
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Odir Antonio Dellagostin
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Simone Simionatto
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados - UFGD, Dourados, Mato Grosso do Sul, Brazil.
- Cidade Universitária, Rodovia Dourados - Itahum km 12, Dourados, Mato Grosso do Sul, CEP: 79804970, Brazil.
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Matteoli FP, Pedrosa-Silva F, Dutra-Silva L, Giachini AJ. The global population structure and beta-lactamase repertoire of the opportunistic pathogen Serratia marcescens. Genomics 2021; 113:3523-3532. [PMID: 34400240 DOI: 10.1016/j.ygeno.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/15/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022]
Abstract
Serratia marcescens is a global spread nosocomial pathogen. This rod-shaped bacterium displays a broad host range and worldwide geographical distribution. Here we analyze an international collection of this multidrug-resistant, opportunistic pathogen from 35 countries to infer its population structure. We show that S. marcescens comprises 12 lineages; Sm1, Sm4, and Sm10 harbor 78.3% of the known environmental strains. Sm5, Sm6, and Sm7 comprise only human-associated strains which harbor smallest pangenomes, genomic fluidity and lowest levels of core recombination, indicating niche specialization. Sm7 and Sm9 lineages exhibit the most concerning resistome; blaKPC-2 plasmid is widespread in Sm7, whereas Sm9, also an anthropogenic-exclusive lineage, presents highest plasmid/lineage size ratio and plasmid-diversity encoding metallo-beta-lactamases comprising blaNDM-1. The heterogeneity of resistance patterns of S. marcescens lineages elucidated herein highlights the relevance of surveillance programs, using whole-genome sequencing, to provide insights into the molecular epidemiology of carbapenemase producing strains of this species.
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25
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Wang X, Xiao W, Li L, Jing M, Sun M, Chang Y, Qu Y, Jiang Y, Xu Q. Analysis of the molecular characteristics of a blaKPC-2-harbouring untypeable plasmid in Serratia marcescens. Int Microbiol 2021; 25:237-244. [PMID: 34232406 DOI: 10.1007/s10123-021-00172-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Serratia marcescens has attracted increasing attention worldwide as a neglected opportunistic pathogen of public health concern, especially due to its antimicrobial resistance features, which usually cause nosocomial infections in immunocompromised or critically ill patients. METHODS In our study, four carbapenem-resistant Serratia marcescens (CRSM) clinical isolates were characterized in our hospital from February 2018 to May 2018. The conjugation experiment confirmed the transferability of the carbapenem resistance gene. The types of carbapenem resistance genes were detected by PCR. The homology of the strains was analysed by pulsed field gel electrophoresis (PFGE). The characteristics of the plasmid and environment of carbapenem resistance genes were analysed after whole genome sequencing was performed. Then, we compared the amino acid sequence of the replication initiation protein and constructed a dendrogram by the neighbour-joining method. RESULTS All four isolates showed carbapenem resistance conferred by a blaKPC-2-harbouring plasmid. They had exactly the same bands confirmed by PFGE and were defined as the homologous strains. The blaKPC-2 genes in all of the isolates were located in a 42,742 bp plasmid, which was located in the core region of antibiotic resistance and was composed of Tn3 family transposons, recombinant enzyme genes, ISKpn6 and ISKpn27. The core region of antibiotic resistance formed a 'Tn3-ISKpn6-blaKPC-ISKpn27-Tn3' structure, which was an independent region as a movable element belonging to transposon Tn6296 and its derivatives. The plasmid had a similar skeleton to incX6 plasmids and a similar amino acid sequence to the replication initiation protein. The plasmid was defined as an untypeable blaKPC-2-harbouring plasmid named the 'IncX6-like' plasmid. CONCLUSION The four CRSM isolates were mainly clonally disseminated with a blaKPC-2-harbouring plasmid in our hospital. The pKPC-2-HENAN1602 plasmid (CP047392) in our study was first reported in Serratia marcescens, which belongs to an untypeable group named the 'IncX6-like' plasmid. The carbapenem-resistant gene structure surrounding blaKPC-2 as a sole accessory module can be acquired by horizontal gene transfer and might lead to serious nosocomial infection.
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Affiliation(s)
- Xiaokun Wang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Weiqiang Xiao
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Lu Li
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Min Jing
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Mingyue Sun
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Yanmin Chang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Yuanye Qu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Yu Jiang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Qingxia Xu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China. .,Department of Zhengzhou Key Laboratory of Digestive Tumor Markers, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China.
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Abstract
Gram-negative bacteremia is a devastating public health threat, with high mortality in vulnerable populations and significant costs to the global economy. Concerningly, rates of both Gram-negative bacteremia and antimicrobial resistance in the causative species are increasing. Gram-negative bacteremia develops in three phases. First, bacteria invade or colonize initial sites of infection. Second, bacteria overcome host barriers, such as immune responses, and disseminate from initial body sites to the bloodstream. Third, bacteria adapt to survive in the blood and blood-filtering organs. To develop new therapies, it is critical to define species-specific and multispecies fitness factors required for bacteremia in model systems that are relevant to human infection. A small subset of species is responsible for the majority of Gram-negative bacteremia cases, including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii The few bacteremia fitness factors identified in these prominent Gram-negative species demonstrate shared and unique pathogenic mechanisms at each phase of bacteremia progression. Capsule production, adhesins, and metabolic flexibility are common mediators, whereas only some species utilize toxins. This review provides an overview of Gram-negative bacteremia, compares animal models for bacteremia, and discusses prevalent Gram-negative bacteremia species.
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Affiliation(s)
- Caitlyn L Holmes
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mark T Anderson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Harry L T Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Michael A Bachman
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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27
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González-Montalvo MA, Tavares-Carreón F, González GM, Villanueva-Lozano H, García-Romero I, Zomosa-Signoret VC, Valvano MA, Andrade A. Defining chaperone-usher fimbriae repertoire in Serratia marcescens. Microb Pathog 2021; 154:104857. [PMID: 33762200 DOI: 10.1016/j.micpath.2021.104857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/12/2021] [Indexed: 11/28/2022]
Abstract
Chaperone-usher (CU) fimbriae are surface organelles particularly prevalent among the Enterobacteriaceae. Mainly associated to their adhesive properties, CU fimbriae play key roles in biofilm formation and host cell interactions. Little is known about the fimbriome composition of the opportunistic human pathogen Serratia marcescens. Here, by using a search based on consensus fimbrial usher protein (FUP) sequences, we identified 421 FUPs across 39 S. marcescens genomes. Further analysis of the FUP-containing loci allowed us to classify them into 20 conserved CU operons, 6 of which form the S. marcescens core CU fimbriome. A new systematic nomenclature is proposed according to FUP sequence phylogeny. We also established an in vivo transcriptional assay comparing CU promoter expression between an environmental and a clinical isolate of S. marcescens, which revealed that promoters from 3 core CU operons (referred as fgov, fpo, and fps) are predominantly expressed in the two strains and might represent key core adhesion appendages contributing to S. marcescens pathogenesis.
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Affiliation(s)
- Martín A González-Montalvo
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología, Monterrey, Nuevo León, 64460, Mexico
| | - Faviola Tavares-Carreón
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, 66455, Mexico
| | - Gloria M González
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología, Monterrey, Nuevo León, 64460, Mexico
| | - Hiram Villanueva-Lozano
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología, Monterrey, Nuevo León, 64460, Mexico
| | - Inmaculada García-Romero
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - Viviana C Zomosa-Signoret
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Bioquímica y Medicina Molecular, Monterrey, Nuevo León, 64460, Mexico
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - Angel Andrade
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología, Monterrey, Nuevo León, 64460, Mexico.
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28
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The ABC-Type Efflux Pump MacAB Is Involved in Protection of Serratia marcescens against Aminoglycoside Antibiotics, Polymyxins, and Oxidative Stress. mSphere 2021; 6:6/2/e00033-21. [PMID: 33692192 PMCID: PMC8546677 DOI: 10.1128/msphere.00033-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Serratia marcescens is an emerging pathogen with increasing clinical importance due to its intrinsic resistance to several classes of antibiotics. The chromosomally encoded drug efflux pumps contribute to antibiotic resistance and represent a major challenge for the treatment of bacterial infections. The ABC-type efflux pump MacAB was previously linked to macrolide resistance in Escherichia coli and Salmonella enterica serovar Typhimurium. The role of the MacAB homolog in antibiotic resistance of S. marcescens is currently unknown. We found that an S. marcescens mutant lacking the MacAB pump did not show increased sensitivity to the macrolide antibiotic erythromycin but was significantly more sensitive to aminoglycoside antibiotics and polymyxins. We also showed that, in addition to its role in drug efflux, the MacAB efflux pump is required for swimming motility and biofilm formation. We propose that the motility defect of the ΔmacAB mutant is due, at least in part, to the loss of functional flagella on the bacterial surface. Furthermore, we found that the promoter of the MacAB efflux pump was active during the initial hours of growth in laboratory medium and that its activity was further elevated in the presence of hydrogen peroxide. Finally, we demonstrate a complete loss of ΔmacAB mutant viability in the presence of peroxide, which is fully restored by complementation. Thus, the S. marcescens MacAB efflux pump is essential for survival during oxidative stress and is involved in protection from polymyxins and aminoglycoside antibiotics. IMPORTANCE The opportunistic pathogen Serratia marcescens can cause urinary tract infections, respiratory infections, meningitis, and sepsis in immunocompromised individuals. These infections are challenging to treat due to the intrinsic resistance of S. marcescens to an extensive array of antibiotics. Efflux pumps play a crucial role in protection of bacteria from antimicrobials. The MacAB efflux pump, previously linked to efflux of macrolides in Escherichia coli and protection from oxidative stress in Salmonella enterica serovar Typhimurium, is not characterized in S. marcescens. We show the role of the MacAB efflux pump in S. marcescens protection from aminoglycoside antibiotics and polymyxins, modulation of bacterial motility, and biofilm formation, and we illustrate the essential role for this pump in bacterial survival during oxidative stress. Our findings make the MacAB efflux pump an attractive target for inhibition to gain control over S. marcescens infections.
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Cosic A, Leitner E, Petternel C, Galler H, Reinthaler FF, Herzog-Obereder KA, Tatscher E, Raffl S, Feierl G, Högenauer C, Zechner EL, Kienesberger S. Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping. Front Microbiol 2021; 12:692453. [PMID: 34276625 PMCID: PMC8283571 DOI: 10.3389/fmicb.2021.692453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/28/2021] [Indexed: 02/03/2023] Open
Abstract
Members of the Klebsiella oxytoca species complex (KoSC) are emerging human pathogens causing infections of increasing significance especially in healthcare settings. KoSC strains are affiliated with distinct phylogroups based on genetic variation at the beta-lactamase gene (bla OXY) and it has been proposed that each major phylogroup represents a unique species. However, since the typing methods applied in clinical settings cannot differentiate every species within the complex, existing clinical, epidemiological and DNA sequence data is frequently misclassified. Here we systematically examined the phylogenetic relationship of KoSC strains to evaluate robustness of existing typing methods and to provide a simple typing strategy for KoSC members that cannot be differentiated biochemically. Initial analysis of a collection of K. oxytoca, K. michiganensis, K. pasteurii, and K. grimontii strains of environmental origin showed robust correlation of core phylogeny and blaOXY grouping. Moreover, we identified species-specific accessory gene loci for these strains. Extension of species correlation using database entries initially failed. However, assessment of average nucleotide identities (ANI) and phylogenetic validations showed that nearly one third of isolates in public databases have been misidentified. Reclassification resulted in a robust reference strain set for reliable species identification of new isolates or for retyping of strains previously analyzed by multi-locus sequence typing (MLST). Finally, we show convergence of ANI, core gene phylogeny, and accessory gene content for available KoSC genomes. We conclude that also the monophyletic members K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii can be simply differentiated by a PCR strategy targeting bla OXY and accessory genes defined here.
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Affiliation(s)
- Amar Cosic
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christian Petternel
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Herbert Galler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Franz F. Reinthaler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Kathrin A. Herzog-Obereder
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Elisabeth Tatscher
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Sandra Raffl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Gebhard Feierl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- BioTechMed-Graz, Graz, Austria
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Ellen L. Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- *Correspondence: Sabine Kienesberger,
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Is there a widespread clone of Serratia marcescens producing outbreaks worldwide? J Hosp Infect 2020; 108:7-14. [PMID: 33181279 DOI: 10.1016/j.jhin.2020.10.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND Serratia marcescens frequently causes outbreaks in healthcare settings. There are few studies using high-throughput sequencing (HTS) that analyse S. marcescens outbreaks. We present the analysis of two outbreaks in neonatal intensive care units (NICUs) in hospitals from the Comunitat Valenciana (CV, Spain) and the impact of using different reference genomes. METHODS DNA from cultured isolates was extracted and sequenced by HTS using Illumina NextSeq. Reads were mapped against two reference genomes, strains UMH9 and Db11, and the unmapped fraction of the genomes was assembled to fully genetically characterize the isolates. FINDINGS Isolates from the first outbreak were identical to the UMH9 reference, an unrelated isolate obtained three years earlier in the USA. This did not occur when the Db11 strain, a standard reference for S. marcescens, was used as the reference for mapping. To check whether UMH9 was a widely distributed clone spreading in the CV, the second outbreak isolates were mapped against this reference. They were not closely related to this strain, and this outbreak could be defined as such regardless of the reference used for mapping the reads. CONCLUSIONS The choice of the reference for genomic analysis of outbreaks is a critical decision. In the case of the first outbreak, this choice changed the interpretation of the results drastically, allowing or preventing the definition of the outbreak according to the reference used. Although HTS is a powerful tool for epidemiological analysis, it is still essential to collect microbiological and epidemiological data for the correct interpretation of the results.
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The Serratia marcescens Siderophore Serratiochelin Is Necessary for Full Virulence during Bloodstream Infection. Infect Immun 2020; 88:IAI.00117-20. [PMID: 32393508 DOI: 10.1128/iai.00117-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
Serratia marcescens is a bacterium frequently found in the environment, but over the last several decades it has evolved into a concerning clinical pathogen, causing fatal bacteremia. To establish such infections, pathogens require specific nutrients; one very limited but essential nutrient is iron. We sought to characterize the iron acquisition systems in S. marcescens isolate UMH9, which was recovered from a clinical bloodstream infection. Using RNA sequencing (RNA-seq), we identified two predicted siderophore gene clusters (cbs and sch) that were regulated by iron. Mutants were constructed to delete each iron acquisition locus individually and in conjunction, generating both single and double mutants for the putative siderophore systems. Mutants lacking the sch gene cluster lost their iron-chelating ability as quantified by the chrome azurol S (CAS) assay, whereas the cbs mutant retained wild-type activity. Mass spectrometry-based analysis identified the chelating siderophore to be serratiochelin, a siderophore previously identified in Serratia plymuthica Serratiochelin-producing mutants also displayed a decreased growth rate under iron-limited conditions created by dipyridyl added to LB medium. Additionally, mutants lacking serratiochelin were significantly outcompeted during cochallenge with wild-type UMH9 in the kidneys and spleen after inoculation via the tail vein in a bacteremia mouse model. This result was further confirmed by an independent challenge, suggesting that serratiochelin is required for full S. marcescens pathogenesis in the bloodstream. Nine other clinical isolates have at least 90% protein identity to the UMH9 serratiochelin system; therefore, our results are broadly applicable to emerging clinical isolates of S. marcescens causing bacteremia.
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Bacteriological Study of Electronic Devices Used by Healthcare Workers at Ruhengeri Referral Hospital. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5872929. [PMID: 32685504 PMCID: PMC7330630 DOI: 10.1155/2020/5872929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/05/2020] [Indexed: 01/31/2023]
Abstract
Electronic devices have become one of the most essential accessories being used in hospitals. Those devices increase the communication and contact making healthcare delivery more efficient and quality service oriented. The study was designed to collect reliable information about the spreading of pathogens through electronic devices especially in sensitive departments. The objectives of this study were to evaluate the bacterial colonization of electronic devices and determine the effectiveness of disinfection with alcohol 70% (w/v) to reduce the bacterial colonization of electronic devices. It was a cross-sectional study where samples were collected by means of moistened swabs in sterile saline solution from 30 electronic devices used by healthcare workers at Ruhengeri Referral Hospital within four different units: maternity, neonathology, intensive care, and theater room. To evaluate the effects of disinfection using 70% isopropyl alcohol, the second sample collection was carried out after decontamination with 70% isopropyl alcohol. Samples were analyzed in the microbiology lab of INES-Ruhengeri. The result showed that Staphylococcus aureus was the most predominant with 22.5%. Lactobacillus and Citrobacter spp. were 12.5%; Pseudomonas aeruginosa, coagulase-negative Staphylococci, and Serratia marcescens were 10%; Escherichia coli was 7.5%; Klebsiella spp. and Providencia spp. were at 5%. The lowest prevalence was 2.5% of Enterobacter spp. and Salmonella spp. The threat of dissemination of isolated microorganisms is valid, since all devices evaluated in this study showed bacterial contamination of species associated to hospital-acquired infections. Special care should be taken when using electronic devices in healthcare settings in addition to disinfection to reduce the risk of transmission of bacterial agents. Further studies should evaluate the antibiotic susceptibility for better conclusive results since all isolated bacteria in this study were subjected to high resistance and were associated with nosocomial infections.
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The contest of microbial pigeon neighbors: Interspecies competition between Serratia marcescens and the human pathogen Cryptococcus neoformans. Fungal Biol 2020; 124:629-638. [PMID: 32540186 DOI: 10.1016/j.funbio.2020.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Accepted: 03/10/2020] [Indexed: 11/21/2022]
Abstract
In nature, microorganisms often exhibit competitive behavior for nutrients and limited space, allowing them to alter the virulence determinants of pathogens. The human pathogenic yeast Cryptococcus neoformans can be found organized in biofilms, a complex community composed of an extracellular matrix which confers protection against predation. The aim of this study was to evaluate and characterize antagonistic interactions between two cohabiting microorganisms: C. neoformans and the bacteria Serratia marcescens. The interaction of S. marcescens with C. neoformans expressed a negative effect on biofilm formation, polysaccharide capsule, production of urease, and melanization of the yeast. These findings evidence that competition in mixed communities can result in dominance by one species, with direct impact on the physiological modulation of virulence determinants. Such an approach is key for understating the response of communities to the presence of competitors and, ultimately, rationally designing communities to prevent and treat certain diseases.
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Naidoo Y, Valverde A, Cason ED, Pierneef RE, Cowan DA. A clinically important, plasmid-borne antibiotic resistance gene (β-lactamase TEM-116) present in desert soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 719:137497. [PMID: 32114220 DOI: 10.1016/j.scitotenv.2020.137497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
The exhaustive use of antibiotics in humans, animal farming and other agricultural practices has resulted in the frequent appearance of antibiotic resistant bacteria in human-impacted habitats. However, antibiotic resistance in natural (less-impacted) habitats is less understood. Using shotgun metagenomics we analysed soils from relatively low anthropogenic impact sites across the Namib Desert. We report the presence of a clinically significant extended spectrum β-lactamase (TEM-116), on a ColE1-like plasmid also carrying a metal resistance gene (arsC). The co-occurrence of resistance to antimicrobial drugs and metals encoded on a single mobile genetic element increases the probability of dissemination of these resistance determinants and the potential selection of multiple resistance mechanisms. In addition, the presence of a P7 entero-bacteriophage on the same plasmid, may represent a new vehicle for the propagation of TEM-116 in these soil communities. These findings highlight the role of the environment in the One Health initiative.
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Affiliation(s)
- Yashini Naidoo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa
| | - Angel Valverde
- Department of Microbial, Biochemical and Food Technology, University of the Free State, Nelson Mandela Drive, Bloemfontein 9300, South Africa
| | - Errol D Cason
- Department of Animal, Wildlife and Grassland Science, University of the Free State, Nelson Mandela Drive, Bloemfontein 9300, South Africa
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria 0110, South Africa
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa.
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Ferreira RL, Rezende GS, Damas MSF, Oliveira-Silva M, Pitondo-Silva A, Brito MCA, Leonardecz E, de Góes FR, Campanini EB, Malavazi I, da Cunha AF, Pranchevicius MCDS. Characterization of KPC-Producing Serratia marcescens in an Intensive Care Unit of a Brazilian Tertiary Hospital. Front Microbiol 2020; 11:956. [PMID: 32670210 PMCID: PMC7326048 DOI: 10.3389/fmicb.2020.00956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Serratia marcescens has emerged as an important opportunistic pathogen responsible for nosocomial and severe infections. Here, we determined phenotypic and molecular characteristics of 54 S. marcescens isolates obtained from patient samples from intensive-care-unit (ICU) and neonatal intensive-care-unit (NIUC) of a Brazilian tertiary hospital. All isolates were resistant to beta-lactam group antibiotics, and 92.6% (50/54) were not susceptible to tigecycline. Furthermore, 96.3% showed intrinsic resistance to polymyxin E (colistin), a last-resort antibiotic for the treatment of infections caused by MDR (multidrug-resistant) Gram-negative bacteria. In contrast, high susceptibility to other antibiotics such as fluoroquinolones (81.5%), and to aminoglycosides (as gentamicin 81.5%, and amikacin 85.2%) was found. Of all isolates, 24.1% were classified as MDR. The presence of resistance and virulence genes were examined by PCR and sequencing. All isolates carried KPC-carbapenemase (blaKPC) and extended spectrum beta-lactamase blaTEM genes, 14.8% carried blaOXA–1, and 16.7% carried blaCTX–M–1group genes, suggesting that bacterial resistance to β-lactam antibiotics found may be associated with these genes. The genes SdeB/HasF and SdeY/HasF that are associated with efflux pump mediated drug extrusion to fluoroquinolones and tigecycline, respectively, were found in 88.9%. The aac(6′)-Ib-cr variant gene that can simultaneously induce resistance to aminoglycoside and fluoroquinolone was present in 24.1% of the isolates. Notably, the virulence genes to (i) pore-forming toxin (ShlA); (ii) phospholipase with hemolytic and cytolytic activities (PhlA); (iii) flagellar transcriptional regulator (FlhD); and (iv) positive regulator of prodigiosin and serratamolide production (PigP) were present in 98.2%. The genetic relationship among the isolates determined by ERIC-PCR demonstrated that the vast majority of isolates were grouped in a single cluster with 86.4% genetic similarity. In addition, many isolates showed 100% genetic similarity to each other, suggesting that the S. marcescens that circulate in this ICU are closely related. Our results suggest that the antimicrobial resistance to many drugs currently used to treat ICU and NIUC patients, associated with the high frequency of resistance and virulence genes is a worrisome phenomenon. Our findings emphasize the importance of active surveillance plans for infection control and to prevent dissemination of these strains.
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Affiliation(s)
- Roumayne L Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Graziela S Rezende
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | | | - Mariana Oliveira-Silva
- Programas de Pós-graduação em Odontologia e Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, Brazil
| | - André Pitondo-Silva
- Programas de Pós-graduação em Odontologia e Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Márcia C A Brito
- Laboratório Central de Saúde Pública do Tocantins, Palmas, Brazil
| | - Eduardo Leonardecz
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Fabiana R de Góes
- Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, São Carlos, Brazil
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Anderson F da Cunha
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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Saralegui C, Ponce-Alonso M, Pérez-Viso B, Moles Alegre L, Escribano E, Lázaro-Perona F, Lanza VF, de Pipaón MS, Rodríguez JM, Baquero F, Del Campo R. Genomics of Serratia marcescens Isolates Causing Outbreaks in the Same Pediatric Unit 47 Years Apart: Position in an Updated Phylogeny of the Species. Front Microbiol 2020; 11:451. [PMID: 32296400 PMCID: PMC7136904 DOI: 10.3389/fmicb.2020.00451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
The first documented nosocomial outbreak caused by Serratia marcescens in Spain occurred in 1969 at the neonatal intensive care unit (NICU) of the tertiary La Paz Children's Hospital in Madrid, Spain, and based on the available phenotyping techniques at this time, it was considered as a monoclonal outbreak. Only 47 years later, another S. marcescens outbreak of an equivalent dimension occurred at the same NICU. The aim of the present study was to study isolates from these historical and contemporary outbreaks by phenotypic analysis and whole-genome sequencing techniques and to position these strains along with 444 publicly available S. marcescens genomes, separately comparing core genome and accessory genome contents. Clades inferred by both approaches showed high correlation, indicating that core and accessory genomes seem to evolve in the same manner for S. marcescens. Nine S. marcescens clusters were identified, and isolates were grouped in two of them according to sampling year. One exception was isolate 13F-69, the most genetically distant strain, located in a different cluster. Categorical functions in the annotated accessory genes of both collections were preserved among all isolates. No significant differences in frequency of insertion sequences in historical (0.18-0.20)-excluding the outlier strain-versus contemporary isolates (0.11-0.19) were found despite the expected resting effect. The most dissimilar isolate, 13F-69, contains a highly preserved plasmid previously described in Bordetella bronchiseptica. This strain exhibited a few antibiotic resistance genes not resulting in a resistant phenotype, suggesting the value of gene down expression in adaptation to long-term starvation.
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Affiliation(s)
- Claudia Saralegui
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Red Española de Investigación en Patología Infecciosa, Madrid, Spain
| | - Manuel Ponce-Alonso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Red Española de Investigación en Patología Infecciosa, Madrid, Spain
| | - Blanca Pérez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Laura Moles Alegre
- Unidad de Esclerosis Múltiple, Instituto de Investigación Sanitaria Biodonostia, Donostia-San Sebastián, Spain
| | - Esperanza Escribano
- Servicio de Neonatología, Hospital Universitario La Paz, and Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Val F Lanza
- Unidad de Bioinformática del IRYCIS, Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
| | - Miguel Sáenz de Pipaón
- Servicio de Neonatología, Hospital Universitario La Paz, and Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Miguel Rodríguez
- Departamento de Nutrición y Ciencia de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
| | - Rosa Del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Red Española de Investigación en Patología Infecciosa, Madrid, Spain
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Vanhove M, Sicard A, Ezennia J, Leviten N, Almeida RPP. Population structure and adaptation of a bacterial pathogen in California grapevines. Environ Microbiol 2020; 22:2625-2638. [PMID: 32114707 DOI: 10.1111/1462-2920.14965] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/03/2020] [Accepted: 02/26/2020] [Indexed: 12/30/2022]
Abstract
Xylella fastidiosa subsp. fastidiosa causes Pierce's disease of grapevine (PD) and has been present in California for over a century. A singly introduced genotype spread across the state causing large outbreaks and damaging the grapevine industry. This study presents 122 X. fastidiosa subsp. fastidiosa genomes from symptomatic grapevines, and explores pathogen genetic diversity associated with PD in California. A total of 5218 single-nucleotide polymorphisms (SNPs) were found in the dataset. Strong population genetic structure was found; isolates split into five genetic clusters divided into two lineages. The core/soft-core genome constituted 41.2% of the total genome, emphasizing the high genetic variability of X. fastidiosa genomes. An ecological niche model was performed to estimate the environmental niche of the pathogen within California and to identify key climatic factors involved in dispersal. A landscape genomic approach was undertaken aiming to link local adaptation to climatic factors. A total of 18 non-synonymous polymorphisms found to be under selective pressures were correlated with at least one environmental variable highlighting the role of temperature, precipitation and elevation on X. fastidiosa adaptation to grapevines in California. Finally, the contribution to virulence of three of the genes under positive selective pressure and of one recombinant gene was studied by reverse genetics.
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Affiliation(s)
- Mathieu Vanhove
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Anne Sicard
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Jeffery Ezennia
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Nina Leviten
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
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Quezada-Aguiluz M, Lincopan N, Cerdeira L, Fuga B, Silva F, Barrera B, Cifuentes M, Bello-Toledo H, Opazo-Capurro A, González-Rocha G. Draft genome sequence of a multidrug-resistant KPC-2 and SRT-2 co-producing Serratia marcescens strain isolated from a hospitalised patient in Chile. J Glob Antimicrob Resist 2020; 21:1-2. [PMID: 32061814 DOI: 10.1016/j.jgar.2020.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/21/2020] [Accepted: 02/06/2020] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Serratia marcescens is a neglected opportunistic pathogen of public-health concern, especially due to its antimicrobial resistance features. Here we report the draft genome sequence of the first KPC-2 and SRT-2 co-producing S. marcescens strain (UCO-366) recovered from a catheter tip culture of a hospitalised patient in Santiago, Chile, in 2014. METHODS Whole genomic DNA of strain UCO-366 was extracted and was sequenced using an Illumina NextSeq platform. De novo genome assembly was performed using Unicycler v.0.4.0 and the genome was annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.4.8. Genomic features were analysed using bioinformatic tools available at the Center for Genomic Epidemiology, the Comprehensive Antibiotic Resistance Database (CARD) and Pathosystems Resource Integration Center (PATRIC). RESULTS The genome size of strain UCO-366 was 5 267 357bp, with a G+C content of 59.7% and comprising 5299 coding sequences (CDS), 42 tRNAs and 115 pseudogenes. The genome of UCO-366 also included an IncL/M plasmid. The resistome comprised various antimicrobial resistance genes (ARGs) conferring resistance to carbapenems, cephalosporins, aminoglycosides, sulfonamides, chloramphenicol, rifampicin and fluoroquinolones. Importantly, S. marcescens UCO-366 harboured blaKPC-2 and blaSRT-2, representing the first description of these β-lactamase genes in this species in Chile. CONCLUSION Here we report the genome of the first KPC-positive multidrug-resistant S. marcescens strain identified in Chile, which co-harboured several ARGs. The genome sequence of S. marcescens UCO-366 provides an insight into the antimicrobial resistance characteristics of this species in this country and offers important data for further genomic studies on this critical priority pathogen.
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Affiliation(s)
- Mario Quezada-Aguiluz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Francisco Silva
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Boris Barrera
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Marcela Cifuentes
- Comité de Prevención y Control de Infecciones Asociadas a la Atención de Salud y Epidemiología Hospitalaria, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile
| | - Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile.
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile
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Gilbert R, Torres M, Clemens R, Hateley S, Hosamani R, Wade W, Bhattacharya S. Spaceflight and simulated microgravity conditions increase virulence of Serratia marcescens in the Drosophila melanogaster infection model. NPJ Microgravity 2020; 6:4. [PMID: 32047838 PMCID: PMC7000411 DOI: 10.1038/s41526-019-0091-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022] Open
Abstract
While it has been shown that astronauts suffer immune disorders after spaceflight, the underlying causes are still poorly understood and there are many variables to consider when investigating the immune system in a complex environment. Additionally, there is growing evidence that suggests that not only is the immune system being altered, but the pathogens that infect the host are significantly influenced by spaceflight and ground-based spaceflight conditions. In this study, we demonstrate that Serratia marcescens (strain Db11) was significantly more lethal to Drosophila melanogaster after growth on the International Space Station than ground-based controls, but the increased virulence phenotype of S. marcescens did not persist after the bacterial cultures were passaged on the ground. Increased virulence was also observed in bacteria that were grown in simulated microgravity conditions on the ground using the rotating wall vessel. Increased virulence of the space-flown bacteria was similar in magnitude between wild-type flies and those that were mutants for the well-characterized immune pathways Imd and Toll, suggesting that changes to the host immune system after infection are likely not a major factor contributing towards increased susceptibility of ground-reared flies infected with space-flown bacteria. Characterization of the bacteria shows that at later timepoints spaceflight bacteria grew at a greater rate than ground controls in vitro, and in the host. These results suggest complex physiological changes occurring in pathogenic bacteria in space environments, and there may be novel mechanisms mediating these physiological effects that need to be characterized.
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Affiliation(s)
- Rachel Gilbert
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA USA
| | - Medaya Torres
- 2FILMSS/Bionetics, NASA Ames Research Center, Moffett Field, CA USA
| | - Rachel Clemens
- 2FILMSS/Bionetics, NASA Ames Research Center, Moffett Field, CA USA
| | - Shannon Hateley
- 3Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Ravikumar Hosamani
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA USA
| | - William Wade
- 2FILMSS/Bionetics, NASA Ames Research Center, Moffett Field, CA USA
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Friman MJ, Eklund MH, Pitkälä AH, Rajala-Schultz PJ, Rantala MHJ. Description of two Serratia marcescens associated mastitis outbreaks in Finnish dairy farms and a review of literature. Acta Vet Scand 2019; 61:54. [PMID: 31727124 PMCID: PMC6857314 DOI: 10.1186/s13028-019-0488-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 10/27/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Infection with Serratia spp. have been associated with mastitis outbreaks in dairy cattle herds. Environmental contamination or a point source, like a teat dip product, have often been observed to be potential sources of such outbreaks. We describe two Serratia marcescens associated mastitis outbreaks associated with a contaminated teat dip containing a tertiary alkyl amine, n,n-bis (3-aminopropyl) dodecylamine in two dairy cattle farms in Finland. S. marcescens strains isolated from milk and environmental samples were identified by the MALDI-TOF method. RESULTS Six specimens (n = 19) on Herd 1 and all specimens (n = 9) on Herd 2 were positive for S. marcescens. Positive specimens were from mastitis milk and teat dip liquid and equipment. Bacteria were not isolated from the unopened teat dip canister. The same clone of S. marcescens was isolated from milk samples and teat dip samples within the farms. Pulsed field gel electrophoresis results to the S. marcescens isolates from these two different herds were tested with unweighted pair-group method using arithmetic average clustering analysis. The isolates were not same clone in both herds, because similarity in that test was only 75% when cut-off value to similarity is 85%. CONCLUSIONS Our investigation showed that the post milking teat dip and/or temporary containers were contaminated with S. marcescens and these were most likely the sources for new mastitis cases. The negative result from the unopened teat dip canister and positive results from refillable containers demonstrated that the product itself was not contaminated with S. marcescens at the production unit, but became contaminated at the farm level.
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Affiliation(s)
- Mari Johanna Friman
- Department of Veterinary Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Paroninkuja 20, 04920 Saarentaus, Mäntsälä, Finland
| | - Marjut Hannele Eklund
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, PO Box 57, 00014 Helsinki, Finland
| | - Anna Helena Pitkälä
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, PO Box 57, 00014 Helsinki, Finland
| | - Päivi Johanna Rajala-Schultz
- Department of Veterinary Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Paroninkuja 20, 04920 Saarentaus, Mäntsälä, Finland
| | - Merja Hilma Johanna Rantala
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, PO Box 57, 00014 Helsinki, Finland
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Karkey A, Joshi N, Chalise S, Joshi S, Shrestha S, Thi Nguyen TN, Dongol S, Basnyat B, Baker S, Boinett CJ. Outbreaks of Serratia marcescens and Serratia rubidaea bacteremia in a central Kathmandu hospital following the 2015 earthquakes. Trans R Soc Trop Med Hyg 2019; 112:467-472. [PMID: 30107587 PMCID: PMC6181195 DOI: 10.1093/trstmh/try077] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/30/2018] [Indexed: 12/12/2022] Open
Abstract
Background Human infections with Serratia spp. are generally limited to Serratia marcescens and the Serratia liquefaciens complex. There is little data regarding the infections caused by the remaining Serratia spp., as they are seldom isolated from clinical specimens. Methods In this health care setting in Kathmandu, Nepal routine blood culture is performed on all febrile patients with a temperature >38°C or when there is clinical suspicion of bacteremia. During 2015 we atypically isolated and identified several Serratia spp. We extracted clinical data from these cases and performed whole genome sequencing on all isolates using a MiSeq system (Ilumina, San Diego, CA, USA). Results Between June and November 2015, we identified eight patients with suspected bacteremia that produced a positive blood culture for Serratia spp., six Serratia rubidaea and five Serratia marcescens. The S. rubidaea were isolated from three neonates and were concentrated in the neonatal intensive care unit between June and July 2015. All patients were severely ill and one patient died. Whole genome sequencing confirmed that six Nepalese S. rubidaea sequences were identical and indicative of a single-source outbreak. Conclusions Despite extensive screening we were unable to identify the source of the outbreak, but the inferred timeline suggested that these atypical infections were associated with the aftermath of two massive earthquakes. We speculate that deficits in hygienic behavior, combined with a lack of standard infection control, in the post-earthquake emergency situation contributed to these unusual Serratia spp. outbreaks.
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Affiliation(s)
- Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Satdobato, Lagankhel Rd, Patan, Kathmandu, Nepal.,Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine and Research Building, Oxford University, Old Campus Road, Roosevelt Drive, Headington, Oxford, UK
| | - Niva Joshi
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Satdobato, Lagankhel Rd, Patan, Kathmandu, Nepal
| | - Shiva Chalise
- Patan Academy of Health Sciences, Department of Paediatrics, Patan Hospital, Satdobato Lagankhel Rd, Patan, Kathmandu, Nepal
| | - Suchita Joshi
- Patan Academy of Health Sciences, Department of Paediatrics, Patan Hospital, Satdobato Lagankhel Rd, Patan, Kathmandu, Nepal
| | - Shrijana Shrestha
- Patan Academy of Health Sciences, Department of Paediatrics, Patan Hospital, Satdobato Lagankhel Rd, Patan, Kathmandu, Nepal
| | - To Nguyen Thi Nguyen
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Quan 5, Ho Chi Minh City, Vietnam
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Satdobato, Lagankhel Rd, Patan, Kathmandu, Nepal
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Satdobato, Lagankhel Rd, Patan, Kathmandu, Nepal.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine and Research Building, Oxford University, Old Campus Road, Roosevelt Drive, Headington, Oxford, UK
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine and Research Building, Oxford University, Old Campus Road, Roosevelt Drive, Headington, Oxford, UK.,Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, UK
| | - Christine J Boinett
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine and Research Building, Oxford University, Old Campus Road, Roosevelt Drive, Headington, Oxford, UK
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Moles L, Gómez M, Moroder E, Jiménez E, Escuder D, Bustos G, Melgar A, Villa J, Del Campo R, Chaves F, Rodríguez JM. Serratia marcescens colonization in preterm neonates during their neonatal intensive care unit stay. Antimicrob Resist Infect Control 2019; 8:135. [PMID: 31413826 PMCID: PMC6688303 DOI: 10.1186/s13756-019-0584-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 07/24/2019] [Indexed: 11/23/2022] Open
Abstract
Background Nosocomial sepsis is the main problem that preterms have to face during their stay at neonatal intensive care units (NICU). Serratia marcescens is an emerging cause of preterm sepsis but its epidemiology is still largely unknown. Consequently, the aims of this study were to know the rate of preterms colonized by S. marcescens during their stay at the NICU and the characteristics and evolution of the S. marcescens population, including the susceptibility to clinically relevant antibiotics. Methods Twenty-six preterm infants born with a gestational age ≤ 32 weeks and/or weigh ≤1500 g were included in the study. Samples of meconium and feces (n = 92) were collected during their first month of life of the infants, together with feeding samples after their pass through enteral feeding tubes (n = 37). Samples were inoculated on MacConkey agar plates. The isolates identified as S. marcescens were genotyped using RAPD and PFGE; and antibiotics susceptibility was performed in a Vitek 2 system. Results A total of 179 S. marcescens isolates were obtained from the samples. PFGE profiling and cluster analysis allowed the classification of the isolates into 7 different S. marcescens clones. PFGE patterns 1 and 3 were the dominant strains in the fecal samples colonizing 31 and 35% of the infants, respectively. Those isolates causing bacteremia in two infants clustered in PFGE pattern 3. Conclusion S. marcescens is a bacterial species closely associated to the NICU environment. It can be frequently isolated from preterm’s feces although only some genetic lineages seem to be associated to sepsis. Enteral feeding tubes act as important reservoirs to keep the S. marcescens population in the NICU. Trial registration The local ethic committee approved this trial with the reference 09/157.
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Affiliation(s)
- Laura Moles
- 1Department of Nutrition and Food Science, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Marta Gómez
- 1Department of Nutrition and Food Science, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040 Madrid, Spain.,Servicio de Pediatría Hospital Francesc de Borja, Gandía, Valencia, Spain
| | - Elena Moroder
- 1Department of Nutrition and Food Science, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Esther Jiménez
- 1Department of Nutrition and Food Science, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Diana Escuder
- 3Servicio de Neonatología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Gerardo Bustos
- 3Servicio de Neonatología, Hospital Universitario 12 de Octubre, Madrid, Spain.,4Red de Salud Materno-Infantil y del Desarrollo (SAMID), Instituto Carlos III, Madrid, Spain
| | - Ana Melgar
- 3Servicio de Neonatología, Hospital Universitario 12 de Octubre, Madrid, Spain.,4Red de Salud Materno-Infantil y del Desarrollo (SAMID), Instituto Carlos III, Madrid, Spain
| | - Jeniffer Villa
- 5Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Rosa Del Campo
- 6Servicio de Microbiología y Parasitología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias, Madrid, Spain
| | - Fernando Chaves
- 5Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Juan M Rodríguez
- 1Department of Nutrition and Food Science, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040 Madrid, Spain
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Genome analysis of urease positive Serratia marcescens, co-producing SRT-2 and AAC(6′)-Ic with multidrug efflux pumps for antimicrobial resistance. Genomics 2019; 111:653-660. [DOI: 10.1016/j.ygeno.2018.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 12/13/2017] [Accepted: 04/03/2018] [Indexed: 11/22/2022]
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Gajdács M, Urbán E. Resistance Trends and Epidemiology of Citrobacter- Enterobacter- Serratia in Urinary Tract Infections of Inpatients and Outpatients (RECESUTI): A 10-Year Survey. MEDICINA (KAUNAS, LITHUANIA) 2019; 55:E285. [PMID: 31216725 PMCID: PMC6630883 DOI: 10.3390/medicina55060285] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 12/17/2022]
Abstract
Background and objectives: Urinary tract infections (UTIs) are the third most common infections in humans, representing a significant factor of morbidity, both among outpatients and inpatients. The pathogenic role of Citrobacter, Enterobacter, and Serratia species (CES bacteria) has been described in UTIs. CES bacteria present a therapeutic challenge due to the various intrinsic and acquired resistance mechanisms they possess. Materials and Methods: The aim of this study was to assess and compare the resistance trends and epidemiology of CES pathogens in UTIs (RECESUTI) in inpatients and outpatients during a 10-year study period. To evaluate the resistance trends of isolated strains, several antibiotics were chosen as indicator drugs based on local utilization data. 578 CES isolates were obtained from inpatients and 554 from outpatients, representing 2.57 ± 0.41% of all positive urine samples for outpatients and 3.02 ± 0.40% for inpatients. E. cloacae was the most prevalent species. Results: The ratio of resistant strains to most of the indicator drugs was higher in the inpatient group and lower in the second half of the study period. ESBL-producing isolates were detected in 0-9.75% from outpatient and 0-29.09% from inpatient samples. Conclusions: Resistance developments of CES bacteria, coupled with their intrinsic non-susceptibility to several antibiotics, severely limits the number of therapeutic alternatives, especially for outpatients.
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Affiliation(s)
- Márió Gajdács
- Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, Eötvös utca 6., 6720 Szeged, Hungary.
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Semmelweis utca 6., 6725 Szeged, Hungary.
| | - Edit Urbán
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Semmelweis utca 6., 6725 Szeged, Hungary.
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Raymond F, Boissinot M, Ouameur AA, Déraspe M, Plante PL, Kpanou SR, Bérubé È, Huletsky A, Roy PH, Ouellette M, Bergeron MG, Corbeil J. Culture-enriched human gut microbiomes reveal core and accessory resistance genes. MICROBIOME 2019; 7:56. [PMID: 30953542 PMCID: PMC6451232 DOI: 10.1186/s40168-019-0669-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/20/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer. RESULTS Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements. CONCLUSION Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.
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Affiliation(s)
- Frédéric Raymond
- École de nutrition, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec City, Canada.
- Institut sur la nutrition et les aliments fonctionnels, Québec, Canada.
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Amin Ahmed Ouameur
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Maxime Déraspe
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Centre de recherche en données massives, Université Laval, Québec City, Canada
| | - Pier-Luc Plante
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Centre de recherche en données massives, Université Laval, Québec City, Canada
| | - Sewagnouin Rogia Kpanou
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Centre de recherche en données massives, Université Laval, Québec City, Canada
| | - Ève Bérubé
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Ann Huletsky
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Paul H Roy
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Département de Microbiologie, Infectiologie et d'Immunologie, Faculté de Médecine, Université Laval, Québec City, Canada
| | - Michel G Bergeron
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Département de Microbiologie, Infectiologie et d'Immunologie, Faculté de Médecine, Université Laval, Québec City, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
- Centre de recherche en données massives, Université Laval, Québec City, Canada
- Département de médecine moléculaire, Faculté de Médecine, Université Laval, Québec City, Canada
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Serratia marcescens Infections in Neonatal Intensive Care Units (NICUs). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16040610. [PMID: 30791509 PMCID: PMC6406414 DOI: 10.3390/ijerph16040610] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 01/21/2023]
Abstract
Serratia marcescens belongs to the family Enterobacteriaceae, which is commonly found in water, soil, animals, insects, plants. Although S. marcescens displays relatively low virulence, it causes nosocomial infections and outbreaks in severely immunocompromised or critically ill patients, particularly in settings such as intensive care units (ICUs), especially neonatal units (NICUs). This microorganism gives rise to a wide range of clinical manifestations in newborns: from asymptomatic colonization to keratitis, conjunctivitis, urinary tract infections, pneumonia, surgical wound infections, sepsis, bloodstream infection and meningitis. The most frequent site of infection is the bloodstream, followed by the respiratory apparatus and the gastrointestinal tract. Strains of S. marcescens involved in epidemic events have frequently proved to be multi-resistant. Indeed, this species displays intrinsic resistance to several classes of antibiotics. Often, the specific source of the infection cannot be identified. However, the contaminated hands of healthcare workers are believed to be a major vehicle of its transmission. In neonatal intensive care units, colonized or infected newborns are the main potential source of S. marcescens, particularly in the respiratory apparatus, but also in the gastrointestinal tract. The early identification of colonized or infected patients and the prompt implementation of infection control measures, particularly rigorous hand hygiene and contact precautions, are essential in order to curb the spread of infection.
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Abreo E, Altier N. Pangenome of Serratia marcescens strains from nosocomial and environmental origins reveals different populations and the links between them. Sci Rep 2019; 9:46. [PMID: 30631083 PMCID: PMC6328595 DOI: 10.1038/s41598-018-37118-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022] Open
Abstract
Serratia marcescens is a Gram-negative bacterial species that can be found in a wide range of environments like soil, water and plant surfaces, while it is also known as an opportunistic human pathogen in hospitals and as a plant growth promoting bacteria (PGPR) in crops. We have used a pangenome-based approach, based on publicly available genomes, to apply whole genome multilocus sequence type schemes to assess whether there is an association between source and genotype, aiming at differentiating between isolates from nosocomial sources and the environment, and between strains reported as PGPR from other environmental strains. Most genomes from a nosocomial setting and environmental origin could be assigned to the proposed nosocomial or environmental MLSTs, which is indicative of an association between source and genotype. The fact that a few genomes from a nosocomial source showed an environmental MLST suggests that a minority of nosocomial strains have recently derived from the environment. PGPR strains were assigned to different environmental types and clades but only one clade comprised strains accumulating a low number of known virulence and antibiotic resistance determinants and was exclusively from environmental sources. This clade is envisaged as a group of promissory MLSTs for selecting prospective PGPR strains.
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Affiliation(s)
- Eduardo Abreo
- Laboratorio de Bioproducción, Plataforma de Bioinsumos, INIA Uruguay, Ruta 48 Km 10, Canelones, Uruguay.
| | - Nora Altier
- Laboratorio de Bioproducción, Plataforma de Bioinsumos, INIA Uruguay, Ruta 48 Km 10, Canelones, Uruguay
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Hawken SE, Snitkin ES. Genomic epidemiology of multidrug-resistant Gram-negative organisms. Ann N Y Acad Sci 2019; 1435:39-56. [PMID: 29604079 PMCID: PMC6167210 DOI: 10.1111/nyas.13672] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 02/13/2018] [Accepted: 02/17/2018] [Indexed: 12/12/2022]
Abstract
The emergence and spread of antibiotic-resistant Gram-negative bacteria (rGNB) across global healthcare networks presents a significant threat to public health. As the number of effective antibiotics available to treat these resistant organisms dwindles, it is essential that we devise more effective strategies for controlling their proliferation. Recently, whole-genome sequencing has emerged as a disruptive technology that has transformed our understanding of the evolution and epidemiology of diverse rGNB species, and it has the potential to guide strategies for controlling the evolution and spread of resistance. Here, we review specific areas in which genomics has already made a significant impact, including outbreak investigations, regional epidemiology, clinical diagnostics, resistance evolution, and the study of epidemic lineages. While highlighting early successes, we also point to the next steps needed to translate this technology into strategies to improve public health and clinical medicine.
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Affiliation(s)
- Shawn E Hawken
- Department of Microbiology and Immunology, University of Michigan Medical School, Michigan, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Michigan, USA
- Division of Infectious Diseases/Department of Medicine, University of Michigan Medical School, Michigan, USA
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Moradigaravand D, Palm M, Farewell A, Mustonen V, Warringer J, Parts L. Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data. PLoS Comput Biol 2018; 14:e1006258. [PMID: 30550564 PMCID: PMC6310291 DOI: 10.1371/journal.pcbi.1006258] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/28/2018] [Accepted: 11/18/2018] [Indexed: 12/17/2022] Open
Abstract
The emergence of microbial antibiotic resistance is a global health threat. In clinical settings, the key to controlling spread of resistant strains is accurate and rapid detection. As traditional culture-based methods are time consuming, genetic approaches have recently been developed for this task. The detection of antibiotic resistance is typically made by measuring a few known determinants previously identified from genome sequencing, and thus requires the prior knowledge of its biological mechanisms. To overcome this limitation, we employed machine learning models to predict resistance to 11 compounds across four classes of antibiotics from existing and novel whole genome sequences of 1936 E. coli strains. We considered a range of methods, and examined population structure, isolation year, gene content, and polymorphism information as predictors. Gradient boosted decision trees consistently outperformed alternative models with an average accuracy of 0.91 on held-out data (range 0.81-0.97). While the best models most frequently employed gene content, an average accuracy score of 0.79 could be obtained using population structure information alone. Single nucleotide variation data were less useful, and significantly improved prediction only for two antibiotics, including ciprofloxacin. These results demonstrate that antibiotic resistance in E. coli can be accurately predicted from whole genome sequences without a priori knowledge of mechanisms, and that both genomic and epidemiological data can be informative. This paves way to integrating machine learning approaches into diagnostic tools in the clinic.
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Affiliation(s)
- Danesh Moradigaravand
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Martin Palm
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research at the University of Gothenburg, Gothenburg, Sweden
| | - Anne Farewell
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research at the University of Gothenburg, Gothenburg, Sweden
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology HIIT, Helsinki, Finland
| | - Jonas Warringer
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research at the University of Gothenburg, Gothenburg, Sweden
| | - Leopold Parts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Department of Computer Science, University of Tartu, Tartu, Estonia
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Dhusia K, Raja K, Thomas PPM, Yadav PK, Ramteke PW. Molecular dynamics simulation analysis of conessine against multi drug resistant Serratia marcescens. INFECTION GENETICS AND EVOLUTION 2018; 67:101-111. [PMID: 30396000 DOI: 10.1016/j.meegid.2018.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/02/2018] [Accepted: 11/01/2018] [Indexed: 10/27/2022]
Abstract
Ornithine decarboxylase (ODC) is an immediate precursor of polyamine biosynthesis in Serratia marcescens and a potential target for inhibition of its growth. We predicted the 3D structural conformation of ODC enzyme and validated it using MDS in our previous study. In this current study, the potential inhibitors of ODC were obtained by virtual screening of potential inhibitors from ZINC database and studied in depth for their different binding pose. Among the ten virtually screened inhibitors, Conessine exhibited the best binding with ODC and its inhibition property was studied further by MDS studies. The natural compound conessine is isolated from plant Holarrhena antidysenterica and it is studied against ODC of Serratia marcenses for its inhibitory potentials. This revealed unforeseen twisted position in root mean square fluctuation (RMSF) and ODC modelled conformation that influenced ligand binding. Both predicted model and ligand bound model were compared and found to be stable with Root Mean Square Deviation (RMSD) of approximately 7 nm and 0.25 nm to that of crystallographic structure over simulation time of 55 ns and 70 ns respectively. This work paves the way for future development of new drugs against nosocomial diseases caused by Serratia marcescens.
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Affiliation(s)
- Kalyani Dhusia
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, U.P., India
| | - Kalpana Raja
- Department of Dermatology, University of Michigan Medical School, Ann arbor, MI 48109, USA
| | - Pierre Paul Michel Thomas
- Institute of Public Health Genomics, Genetics and Cell Biology cluster, GROW Research School for Oncology and Developmental Biology, Maastricht University, the Netherlands
| | - Pramod K Yadav
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, U.P., India
| | - Pramod W Ramteke
- Department of Biological Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, U.P., India.
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