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Mauffrey F, Bertelli C, Greub G, Grandbastien B, Senn L, Blanc DS. Plasmid diversity of Serratia marcescens and Klebsiella pneumoniae isolates involved in two carbapenem-resistant Enterobacteriaceae outbreaks in a Swiss hospital. Microbiol Spectr 2025:e0328424. [PMID: 40396774 DOI: 10.1128/spectrum.03284-24] [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: 01/06/2025] [Accepted: 04/09/2025] [Indexed: 05/22/2025] Open
Abstract
This study investigates two distinct carbapenemase-producing Enterobacteriaceae outbreaks involving patients and contaminated sink traps at the University Hospital of Lausanne. It focuses on the diversity and transmission dynamics of plasmids carrying carbapenemase genes. Between 2022 and 2023, 57 carbapenem-resistant Klebsiella pneumoniae and Serratia marcescens isolates were collected and analyzed. Core-genome MLST confirmed genetic similarity among isolates, linking the outbreaks to sink trap contamination. DNA extraction, sequencing (MinION/Illumina MiSeq), and assembly were performed, followed by ARG screening and plasmid typing. Plasmids were annotated, clustered, and compared using core SNP distances and structural analyses. Known plasmids were identified through PLSDB database matching. Eight MLST types were identified in K. pneumoniae and one (ST356) in S. marcescens. Analysis of 52 bla-carrying plasmids revealed 22 plasmid clusters, including 6 blaNDM-1 clusters in K. pneumoniae and 4 blaKPC-2 clusters in S. marcescens. Plasmids showed close relatedness within and across patient and environmental isolates, with core SNP distances ranging from 0 to 18. Some blaNDM-1 plasmids in K. pneumoniae clustered tightly, suggesting persistence and potential cross-contamination routes. The findings highlight sink traps as critical reservoirs for carbapenem-resistant Enterobacteriaceae and plasmids, promoting resistance gene spread across species. The observed plasmid diversity indicates transmission can occur independently of bacterial clonal spread, challenging traditional outbreak definitions. IMPORTANCE This research is critical in addressing the growing threat of antibiotic resistance, driven by the spread of resistance genes through plasmids. Plasmids, which can transfer between different bacteria, play a major role in spreading multidrug resistance, posing a serious challenge to healthcare systems worldwide. By highlighting how plasmids can move independently of bacterial spread, this study reveals the complexity of resistance transmission. It also underscores the importance of environmental reservoirs, such as hospital sink traps, in harboring and spreading resistant bacteria. These findings emphasize the need for better monitoring of plasmids and targeted infection control measures to prevent the spread of resistance genes and protect the effectiveness of current antibiotics.
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Affiliation(s)
- Florian Mauffrey
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Bruno Grandbastien
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurence Senn
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique S Blanc
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
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Ballaben AS, de Almeida OGG, Ferreira JC, de Oliveira Garcia D, Doi Y, Ernst RK, von Zeska Kress MR, Darini ALDC. Phenotypic and in silico characterization of carbapenem-resistant Serratia marcescens clinical strains. J Glob Antimicrob Resist 2025; 42:105-112. [PMID: 39984041 DOI: 10.1016/j.jgar.2025.02.013] [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: 09/30/2024] [Revised: 02/08/2025] [Accepted: 02/17/2025] [Indexed: 02/23/2025] Open
Abstract
BACKGROUND Serratia marcescens, an opportunistic nosocomial Gram-negative bacterium pathogen, has emerged as an important cause of healthcare-associated infections owing to its acquisition of antimicrobial resistance genes (ARGs) and virulence factor determinants. METHODS Four carbapenem-resistant S. marcescens strains were recovered from patients admitted to different hospitals in 2017 and 2018. We assessed the antimicrobial resistance and virulence context, as well as the genetic similarities of four Brazilian S. marcescens strains, and compared the genomes of these S. marcescens isolates with whole genome data of 428 S. marcescens strains available in the NCBI Reference Sequence. Antimicrobial susceptibility testing was performed by disk diffusion and broth microdilution methods according to CLSI recommendations. Whole genome sequencing was performed using Illumina NextSeq 250-bp paired-end sequencing for two isolates, Sm424 and Sm613, which presented representative phenotypes. RESULTS The pathogenicity of both sequenced strains was predicted using the Pathogen Finder tool. Both isolates carried efflux system genes (RND, SMR, MFS, ABC-family) and resistance genes (blaSTR-2, aac(6')-Ic, fos). Virulence factor genes involved in motility, regulation, capsule formation, acid resistance, and acriflavine resistance were also found. The Pathogen Finder tool predicted a > 71% probability of being a human pathogen for Sm424 and Sm613. CONCLUSION S. marcescens has shown increased adaptive, resistance, and pathogenic potential, being responsible for different nosocomial infections.
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Affiliation(s)
- Anelise Stella Ballaben
- Department of Agricultural and Environmental Biotechnology, Sao Paulo State University (UNESP), Faculty of Agricultural and Veterinary Sciences, Jaboticabal, Sao Paulo, Brazil; School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil.
| | - Otávio G G de Almeida
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Joseane Cristina Ferreira
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | | | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, MD, USA
| | - Marcia R von Zeska Kress
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Ana Lúcia da Costa Darini
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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Chen W, Li Z, Zheng J, Wang D, Gao S, Zhou W, Shen H, Zhang Y, Cao X. A comprehensive analysis of the epidemiological and genomic characteristics of global Serratia Marcescens. J Glob Antimicrob Resist 2025; 40:81-89. [PMID: 39631624 DOI: 10.1016/j.jgar.2024.11.013] [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: 07/08/2024] [Revised: 11/18/2024] [Accepted: 11/22/2024] [Indexed: 12/07/2024] Open
Abstract
BACKGROUND Serratia marcescens outbreaks present significant challenges in clinical treatment, necessitating a deeper understanding of its epidemiological and genomic traits. OBJECTIVE To analyse the epidemiological and genomic characteristics of S. marcescens at a global scale. METHODS High-quality genomes of S. marcescens were retrieved from NCBI and annotated using Prodigal. Antibiotic resistance genes (ARGs) were identified via Blastn, sequence types (STs) were determined with a proprietary tool, and phylogenetic analysis was conducted to explore evolutionary relationships. RESULTS The study analysed genomes from 33 countries, with major contributions from the USA (27.8%), UK (15.3%), Italy (14.7%), and Japan (10.7%). Human clinical samples accounted for 73.5% of the isolates, primarily from blood (44.8%) and sputum (19.3%). Eleven ARGs were identified, with sde being the most prevalent. Carbapenemase genes included blaSME, blaKPC, and blaNDM-1, though co-occurrence in individual strains was absent. Novel ARGs, including armA, rmtC, and fosA7.2, were reported. Among 855 genomes with identified STs, ST366, ST367, ST365, and ST423 were most common. Phylogenetic analysis highlighted significant genetic diversity and distinct evolutionary lineages. CONCLUSION Temporal analysis showed a genome peak in 2019, underscoring the global prevalence and adaptability of S. marcescens. The distribution of ARGs across diverse STs emphasizes horizontal gene transfer as a key driver of resistance. Judicious antibiotic use is essential to mitigate further resistance.
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Affiliation(s)
- Wenqin Chen
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, PR China
| | - Zheqian Li
- Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Jie Zheng
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, PR China
| | - Danwei Wang
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, PR China
| | - Shuo Gao
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, PR China
| | - Wanqing Zhou
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, PR China
| | - Han Shen
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, PR China
| | - Yan Zhang
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, PR China.
| | - Xiaoli Cao
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, PR China
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Guo Q, Zhao X, Ma J, Zhou Y, Gao F, Huang W, Sun L, Zhu S, Li L, Sun H, Jia W, Zhang H, Zhao D. Serratia marcescens outbreak in a neonatal intensive care unit associated with contaminated handwashing sinks. Indian J Med Microbiol 2024; 52:100741. [PMID: 39368552 DOI: 10.1016/j.ijmmb.2024.100741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 08/01/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024]
Abstract
PURPOSE This article describes the origin of a S. marcescens outbreak in a neonatal intensive care unit (NICU). MATERIALS AND METHODS A retrospective case-control study including 12 S. marcescens-positive and 22 S. marcescens-negative neonates in the NICU was performed to identify the source of the outbreak. S. marcescens isolates were collected during the outbreak and analyzed using whole-genome sequencing (WGS). IQ-Tree software, BEAST2 software package and SCOTTI software were used to construct a phylogenetic tree and a propagation path map. RESULTS The index case occurred on February 21st and outbreak ended on March 9th, 2021, affecting a total of 12 neonates (2 with S. marcescens infection and 10 with S. marcescens colonization). Multivariate logistic regression identified that the distance of <0.8 m between the bed unit and the sink (odds ratio [OR], 20.50; 95 % confidence interval [CI], 1.09-384.86), a large number of rotating nurses within a week (OR 2.58, 95 % CI, 1.09-6.11) and use of humidification water in the incubator (OR 189.70, 95 % CI, 2.76-13027.31) were significant increased risk factors for S. marcescens infection or colonization in the outbreak. WGS sifted out a predominant clone between contaminated handwashing sinks and patients, suggesting that cross-transmission was involved in the dissemination of S. marcescens. CONCLUSION Contaminated handwashing sinks can be a communication intermediary of S. marcescens infection or colonization of neonates in the NICU. A distance of <0.8 m between the bed unit and the sink, and a large number of rotating nurses might play important roles in this outbreak. Attention should be paid to sinks contamination and contact transmission to prevent outbreaks.
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Affiliation(s)
- Qiaozhi Guo
- Hospital Infection Control Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Xiaopeng Zhao
- Division of Neonatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Jingxiang Ma
- Hospital Infection Control Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Yi Zhou
- Hospital Infection Control Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Fei Gao
- Clinical Microbiology Experiments Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Wei Huang
- Antimicrobial Drug Screening Laboratory, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China.
| | - Li Sun
- Division of Neonatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Sufei Zhu
- Clinical Microbiology Experiments Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Lijuan Li
- Quality Control Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Huimin Sun
- Hospital Infection Control Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Wei Jia
- Medical Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
| | - Huayan Zhang
- Division of Neonatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China; Division of Neonatology, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Danyang Zhao
- Hospital Infection Control Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China.
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Van Goethem S, Xavier BB, Glupczynski Y, Berkell M, Willems P, Van Herendael B, Hoet K, Plaskie K, Van Brusselen D, Goossens H, Malhotra-Kumar S. Genomic epidemiological analysis of a single-centre polyclonal outbreak of Serratia marcescens, Belgium, 2022 to 2023. Euro Surveill 2024; 29:2400144. [PMID: 39611205 PMCID: PMC11605797 DOI: 10.2807/1560-7917.es.2024.29.48.2400144] [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: 03/04/2024] [Accepted: 06/10/2024] [Indexed: 11/30/2024] Open
Abstract
Serratia marcescens is an opportunistic pathogen with a propensity to cause nosocomial outbreaks, particularly in neonatal intensive care units (NICUs). We present a sustained outbreak spanning over 18 months (1 January 2022-29 August 2023) in a NICU in Antwerp, Belgium, affecting 61 neonates, identified through samples taken for diagnostic purposes and by rectal screening. Ten neonates were infected: five with lower respiratory tract infection, four with conjunctivitis and one fatal case with sepsis. In a logistic regression analysis, nursing in an incubator was significantly associated with acquisition of S. marcescens (odds ratio (OR): 2.99; 95% confidence interval (CI): 1.14-8.25; p < 0.05). Whole genome sequencing-based multilocus sequence typing (wgMLST) and core genome single nucleotide polymorphism (cgSNP) analysis of isolates from clinical (n = 4), screening (n = 52) and environmental samples (n = 8), identified eight clusters and five singletons not associated with the clusters. Although outbreak measures were successful in containing further spread within the ward during sudden surges when > 4 cases per week were identified (peak events), several peaks with different clonal clusters occurred. The emergence of similar outbreaks in Belgian hospitals underscores the need of continuous surveillance and NICU-specific infection prevention and control (IPC) measures.
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Affiliation(s)
- Sam Van Goethem
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
- ZAS Hospital Network, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
- ZAS Hospital Network, Antwerp, Belgium
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Matilda Berkell
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Philippe Willems
- Multidisciplinary Unit of Infectious Diseases, GZA (ZAS) Hospitals, Antwerp, Belgium
- Laboratory of Medical Microbiology, GZA (ZAS) Hospitals, Antwerp, Belgium
| | - Bruno Van Herendael
- Multidisciplinary Unit of Infectious Diseases, GZA (ZAS) Hospitals, Antwerp, Belgium
- Laboratory of Medical Microbiology, GZA (ZAS) Hospitals, Antwerp, Belgium
| | - Katrien Hoet
- Multidisciplinary Unit of Infectious Diseases, GZA (ZAS) Hospitals, Antwerp, Belgium
- Laboratory of Medical Microbiology, GZA (ZAS) Hospitals, Antwerp, Belgium
| | - Katleen Plaskie
- Multidisciplinary Unit of Infectious Diseases, GZA (ZAS) Hospitals, Antwerp, Belgium
- Department of Neonatology, GZA (ZAS) Hospitals, Antwerp, Belgium
| | - Daan Van Brusselen
- Multidisciplinary Unit of Infectious Diseases, GZA (ZAS) Hospitals, Antwerp, Belgium
- Department of Paediatrics, GZA (ZAS) Hospitals, Antwerp, Belgium
- Antwerp Paediatric Clinical Trial Network on vaccines and infectiology, University of Antwerp, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
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Tzialla C, Berardi A, Mondì V, on behalf of the Study Group of Neonatal Infectious Diseases. Outbreaks in the Neonatal Intensive Care Unit: Description and Management. Trop Med Infect Dis 2024; 9:212. [PMID: 39330901 PMCID: PMC11435871 DOI: 10.3390/tropicalmed9090212] [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: 07/31/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024] Open
Abstract
Healthcare settings, especially intensive care units, can provide an ideal environment for the transmission of pathogens and the onset of outbreaks. Many factors can contribute to the onset of an epidemic in a neonatal intensive care unit (NICU), including neonates' vulnerability to healthcare-associated infections, especially for those born preterm; facility design; frequent invasive procedures; and frequent contact with healthcare personnel. Outbreaks in NICUs are one of the most relevant problems because they are often caused by multidrug-resistant organisms associated with increased mortality and morbidity. The prompt identification of an outbreak, the subsequent investigation to identify the source of infection, the risk factors, the reinforcement of routine infection control measures, and the implementation of additional control measures are essential elements to contain an epidemic.
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Affiliation(s)
- Chryssoula Tzialla
- Neonatal and Pediatric Unit, Polo Ospedaliero Oltrepò, ASST Pavia, 27100 Pavia, Italy
| | - Alberto Berardi
- Neonatal Intensive Care Unit, University Hospital of Modena, 41124 Modena, Italy;
| | - Vito Mondì
- Neonatology and Neonatal Intensive Care Unit, Policlinico Casilino, 00169 Rome, Italy;
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Arora S, Myat Oo A, Shaik Ismail B, Poon WB, Lai D, Ko KKK, Wong HM, Tan KY, Aung MK, Conceicao E, Yang Y, Chan DYW, Sim JXY, Venkatachalam I, Lee LC, Ling ML. Rapid management of Serratia marcescens outbreak in neonatology unit in Singapore: Risk factors and infection control measures. Am J Infect Control 2024; 52:1084-1090. [PMID: 38761850 DOI: 10.1016/j.ajic.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND We describe the investigations for control of two consecutive Serratia marcescens outbreaks in neonatology unit of Singapore General Hospital. METHODS Epidemiological investigations, environmental sampling and risk-factors analysis were performed to guide infection control measures. Active surveillance sampling of nasopharyngeal aspirate and/or stool from neonates was conducted during both outbreaks. Whole-genome-sequencing was done to determine clonal links. Retrospective case-control study was conducted for second outbreak to identify risk factors for S marcescens acquisition. RESULTS In 2022, two genetically unrelated S marcescens outbreaks were managed involving five neonates in March 2022 (outbreak 1) and eight neonates in November 2022 (outbreak 2). A link to positive isolates from sinks in intensive care units and milk preparation room was identified during outbreak 1. Neonatal jaundice (aOR, 16.46; p-value= 0.023) and non-formula milk feeding (aOR, 13.88; p-value= 0.02) were identified as risk factors during second outbreak. Multiple interventions adopted were cohorting of positive cases, carriage-screening, enhanced environmental cleaning, and emphasis on alcohol-based handrubs for hand-hygiene. CONCLUSION The two outbreaks were likely due to infection prevention practices lapses and favourable environmental conditions. Nosocomial S marcescens outbreaks in neonatology units are difficult to control and require multidisciplinary approach with strict infection prevention measures to mitigate risk factors.
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Affiliation(s)
- Shalvi Arora
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore.
| | - Aung Myat Oo
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - Bushra Shaik Ismail
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - Woei Bing Poon
- Department of Neonatal and Developmental Medicine, Singapore General Hospital, Singapore, Singapore
| | - Deborah Lai
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore; Department of Molecular Pathology, Singapore General Hospital, Singapore, Singapore
| | - Karrie Kwan Ki Ko
- Department of Microbiology, Singapore General Hospital, Singapore, Singapore
| | - Hei Man Wong
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore; Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Kwee Yuen Tan
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - May Kyawt Aung
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - Edwin Conceicao
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - Yong Yang
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - Darius Yak Weng Chan
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - Jean Xiang Ying Sim
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore; Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Indumathi Venkatachalam
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore; Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Lai Chee Lee
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - Moi Lin Ling
- Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
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Inkster T. A narrative review and update on drain-related outbreaks. J Hosp Infect 2024; 151:33-44. [PMID: 38830539 DOI: 10.1016/j.jhin.2024.05.016] [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: 03/27/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Outbreaks linked to hospital drainage systems are well reported, and continue to present challenges to incident management teams. Such outbreaks can be protracted and complex, with multi-modal strategies being required for remediation. AIM To summarize recent drain-related outbreaks, investigate whether multi-modal control measures are being implemented, and determine any antecedent factors. METHODS Databases were searched for drain-related outbreaks over a 5-year period. Search terms employed included 'healthcare drainage outbreaks', 'drain outbreaks', 'drainage system outbreaks', 'sink outbreaks' and 'shower outbreaks'. Information was collected on country of origin, pathogens involved, unit affected, drain types, patient numbers, drainage system interventions, type of drain disinfectant, infection control interventions, typing method, outcomes and any antecedent factors. FINDINGS Nineteen drain-related outbreak studies were reviewed. The majority of incidents were due to carbapenemase-producing Enterobacterales, and were from critical care settings. Most (16/19) studies recognized the need for a multi-modal approach. Information on the success of interventions was not documented for all incidents, but 13/19 studies reported no further cases after control measures. Variation in the choice of agent and frequency of application exists with regards to drain disinfection. Seven studies discussed antecedent factors. CONCLUSION Despite drain-related outbreaks being reported for the last 24 years and review articles on the subject, outbreaks continue to pose significant challenges. There is currently no UK guidance on the management of drain-related outbreaks or the design of new buildings to mitigate the risk. Addressing the challenges from hospital drainage systems should be considered a priority by agencies and guidance developers.
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Affiliation(s)
- T Inkster
- Antimicrobial Resistance and Healthcare Associated Infection, Glasgow, UK.
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Liébana-Rodríguez M, Portillo-Calderón I, Fernández-Sierra MA, Delgado-Valverde M, Martín-Hita L, Gutiérrez-Fernández J. Nosocomial outbreak caused by Serratia marcescens in a neonatology intensive care unit in a regional hospital. Analysis and improvement proposals. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2024; 42:286-293. [PMID: 37331927 DOI: 10.1016/j.eimce.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/04/2023] [Indexed: 06/20/2023]
Abstract
OBJECTIVES Serratia marcescens (SM) may cause nosocomial outbreaks in Neonatal Intensive Care Units (NICU). We describe an outbreak of SM in a NICU and propose additional prevention and control recommendations. METHODS Between March 2019 and January 2020, samples were taken from patients in the NICU (rectal, pharyngeal, axillary and other locations) and from 15 taps and their sinks. Control measures were implemented including thorough cleaning of incubators, health education to staff and neonates'relatives, and use of single-dose containers. PFGE was performed in 19 isolates from patients and in 5 environmental samples. RESULTS From the first case in March 2019 to the detection of the outbreak, a month elapsed. Finally, 20 patients were infected and 5 colonized. 80% of infected neonates had conjunctivitis, 25% bacteremia, 15% pneumonia, 5% wound infection, and 5% urinary tract infection. Six neonates had two foci of infection. Among the 19 isolates studied, 18 presented the same pulsotype and only one of the isolates from the sinkhole showed a clonal relationship with those of the outbreak. Initial measures established were ineffective to control de outbreak and were implemented with exhaustive cleaning, use of individual eye drops, environmental sampling and changing sinks. CONCLUSION This outbreak presented a high number of neonates affected due to its late detection and torpid evolution. The microorganisms isolated from the neonates were related to an environmental isolate. Additional prevention and control measures are proposed, including routine weekly microbiological sampling.
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Affiliation(s)
- María Liébana-Rodríguez
- Departamento de Medicina Preventiva y Salud Pública, Hospital Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Ibs-Granada, Granada, Spain
| | - Inés Portillo-Calderón
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena. Instituto de Biomedicina de Sevilla (IBiS). Sevilla, Spain
| | - María Amelia Fernández-Sierra
- Departamento de Medicina Preventiva y Salud Pública, Hospital Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Ibs-Granada, Granada, Spain
| | - Mercedes Delgado-Valverde
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena. Instituto de Biomedicina de Sevilla (IBiS). Sevilla, Spain
| | - Lina Martín-Hita
- Departamento de Microbiología, Hospital Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada (Ibs-Granada), Granada, Spain
| | - José Gutiérrez-Fernández
- Departamento de Microbiología, Hospital Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada (Ibs-Granada), Granada, Spain; Departamento de Microbiología, Universidad de Granada-Instituto de Investigación Biosanitaria de Granada (Ibs-Granada), Granada, Spain.
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10
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Michel C, Echahidi F, Place S, Filippin L, Colombie V, Yin N, Martiny D, Vandenberg O, Piérard D, Hallin M. From Investigating a Case of Cellulitis to Exploring Nosocomial Infection Control of ST1 Legionella pneumophila Using Genomic Approaches. Microorganisms 2024; 12:857. [PMID: 38792686 PMCID: PMC11123157 DOI: 10.3390/microorganisms12050857] [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: 03/28/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Legionella pneumophila can cause a large panel of symptoms besides the classic pneumonia presentation. Here we present a case of fatal nosocomial cellulitis in an immunocompromised patient followed, a year later, by a second case of Legionnaires' disease in the same ward. While the first case was easily assumed as nosocomial based on the date of symptom onset, the second case required clear typing results to be assigned either as nosocomial and related to the same environmental source as the first case, or community acquired. To untangle this specific question, we applied core-genome multilocus typing (MLST), whole-genome single nucleotide polymorphism and whole-genome MLST methods to a collection of 36 Belgian and 41 international sequence-type 1 (ST1) isolates using both thresholds recommended in the literature and tailored threshold based on local epidemiological data. Based on the thresholds applied to cluster isolates together, the three methods gave different results and no firm conclusion about the nosocomial setting of the second case could been drawn. Our data highlight that despite promising results in the study of outbreaks and for large-scale epidemiological investigations, next-generation sequencing typing methods applied to ST1 outbreak investigation still need standardization regarding both wet-lab protocols and bioinformatics. A deeper evaluation of the L. pneumophila evolutionary clock is also required to increase our understanding of genomic differences between isolates sampled during a clinical infection and in the environment.
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Affiliation(s)
- Charlotte Michel
- Department of Microbiology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Fedoua Echahidi
- Department of Microbiology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Sammy Place
- Department of Internal Medicine and Infectious Diseases, EpiCURA Hospital, 7301 Hornu, Belgium
| | - Lorenzo Filippin
- Department of Internal Medicine and Infectious Diseases, EpiCURA Hospital, 7301 Hornu, Belgium
| | - Vincent Colombie
- Department of Internal Medicine and Infectious Diseases, EpiCURA Hospital, 7301 Hornu, Belgium
| | - Nicolas Yin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Faculty of Medicine and Pharmacy, Mons University, Chemin du Champ de Mars 37, 7000 Mons, Belgium
| | - Olivier Vandenberg
- Innovation and Business Development Unit, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Avenue Roosevelt 50, 1050 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Marie Hallin
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Avenue Roosevelt 50, 1050 Brussels, Belgium
- European Plotkin Institute for Vaccinology (EPIV), Université Libre de Bruxelles (ULB), Avenue Roosevelt 50, 1050 Brussels, Belgium
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11
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Kim S, Jung S, Lee DH, Chang CL, Bae M, Kim AR, Lee SJ, Lim S. Outbreak investigation of Serratia marcescens bloodstream infection in an obstetric ward for high-risk pregnant women. BMC Infect Dis 2024; 24:266. [PMID: 38418981 PMCID: PMC10900556 DOI: 10.1186/s12879-024-09134-1] [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: 11/07/2023] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Serratia marcescens is a gram-negative bacterium that is widespread in the environment. S. marcescens bacteremia can be fatal during pregnancy and cause persistent chorioamnionitis. This study reports an outbreak of Serratia marcescens bloodstream infection (BSI) among high-risk pregnant women in an obstetric ward. The purpose of this study is to report our experience with the usefulness of the ATP test in hospital environmental management and to confirm that bloodstream infections of patients with the same strain were correlated by WGS testing. METHODS This retrospective study collected the data of inpatients with S. marcescens bacteremia in obstetric ward for high-risk pregnant women from August 22, 2021, to October 14, 2021. We performed: an adenosine triphosphate (ATP) bioluminescence test in the environment with a high-contact area; environmental culture; on-site monitoring and staff education; and whole-genome sequencing (WGS) to evaluate genetic relationships among S. marcescens isolates. RESULTS S. marcescens BSI occurred in four consecutive patients. None of the patients had central venous catheters. An ATP bioluminescence test revealed that high-contact areas and areas for injection preparation were not clean (≥ 1000 relative light units). However, S. marcescens was not identified in the environmental cultures, likely due to intensive environmental cleaning and discarding of potentially contaminated specimens before the culture test. On-site monitoring and education were conducted for 1 month. There were no further reports of BSI until 6 months after the last patient was discharged. WGS performed on three isolates from three patients indicated that the isolated S. marcescens was likely from the same strain. CONCLUSIONS We controlled an S. marcescens outbreak by improving environmental cleaning as well as education of and behavior changes in healthcare workers. Using the ATP bioluminescence test can provide feedback on environmental cleaning and education. WGS played a role in determining the spread of BSI caused by the same strain.
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Affiliation(s)
- Seulki Kim
- Department of Internal Medicine, Division of Infectious Diseases, Pusan National University Yangsan Hospital, 20 Geumo-Ro, Mulgeum-Eup, Yangsan, 50612, Republic of Korea
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
| | - Sunah Jung
- Infection Prevention Department, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
| | - Dong Hyung Lee
- Department of Obstetrics and Gynecology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
- Department of Obstetrics & Gynecology, Pusan National University School of Medicine, Busan, Republic of Korea
| | - Chulhun L Chang
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
| | - Moonsuk Bae
- Department of Internal Medicine, Division of Infectious Diseases, Pusan National University Yangsan Hospital, 20 Geumo-Ro, Mulgeum-Eup, Yangsan, 50612, Republic of Korea
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
| | - A Reum Kim
- Department of Internal Medicine, Division of Infectious Diseases, Pusan National University Yangsan Hospital, 20 Geumo-Ro, Mulgeum-Eup, Yangsan, 50612, Republic of Korea
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
| | - Su Jin Lee
- Department of Internal Medicine, Division of Infectious Diseases, Pusan National University Yangsan Hospital, 20 Geumo-Ro, Mulgeum-Eup, Yangsan, 50612, Republic of Korea
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
| | - Seungjin Lim
- Department of Internal Medicine, Division of Infectious Diseases, Pusan National University Yangsan Hospital, 20 Geumo-Ro, Mulgeum-Eup, Yangsan, 50612, Republic of Korea.
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea.
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea.
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12
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Michel C, Argudín MDLA, Wautier M, Echahidi F, Prevost B, Vandenberg O, Martiny D, Hallin M. Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates. Access Microbiol 2024; 6:000649.v3. [PMID: 38482359 PMCID: PMC10928409 DOI: 10.1099/acmi.0.000649.v3] [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: 06/13/2023] [Accepted: 11/22/2023] [Indexed: 04/12/2024] Open
Abstract
Introduction Haemophilus influenzae (Hi) was long known as an easy-to-treat bacterium, but increasing resistance against beta-lactams and other critically important antibiotics is now a growing concern. We describe here the whole-genome sequencing (WGS) analysis of three non-typeable Hi isolates received in 2018-2019 by the Belgian National Reference Centre (NRC) for Haemophilus influenzae, as they presented an unusual multi-resistant profile. Methods All three isolates were sequenced by WGS and mapped to the reference isolate Hi Rd KW20. Shorten uptake signal sequences (USSs) known to be associated with homologous recombination were sought in ftsI, murE and murF genes, and inner partial sequences were compared against the blast nucleotide database to look for similarity with other Haemophilus species. Their antimicrobial resistance (AMR) genotype was studied. Core-genome multilocus sequence typing (MLST) was performed on the NTHi database pubMLST to place our isolates in the actual worldwide epidemiology. Results The isolates also harboured interspecies recombination patterns in the murF-murE-ftsI region involved in cell wall synthesis. The three isolates were multidrug resistant and two of them were also resistant to amoxicillin-clavulanic acid and showed a reduced susceptibility to meropenem. All three isolates belonged to the MLST clonal complex (CC) 422, and WGS revealed that the three were very similar. They harboured mobile genetic elements (carrying blaTEM-1B, mefA and msrD genes associated with resistance), mutations in gyrA and parC linked to fluoroquinolone resistance as well as remodelling events in ompP2 that might be related to lower carbapenem susceptibility. Conclusion The Hi evolution towards antimicrobial multiresistance (AMR) is a complex and poorly understood phenomenon, although probably linked to a large degree to the presence of USSs and exchange within the family Pasteurellaceae. To better understand the respective roles of clonal expansion, horizontal gene transfers, spontaneous mutations and interspecies genetic rearrangements in shaping Hi AMR, both analysis of Hi communities over time within individuals and worldwide monitoring of non-typeable Hi causing infections should be conducted.
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Affiliation(s)
- Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Maria De Los Angeles Argudín
- Department of Molecular Biology, Cliniques Universitaires Saint Luc (CUSL), Avenue Hippocrate 10, 1200, Brussels, Belgium
| | - Magali Wautier
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Fedoua Echahidi
- Department of Microbiology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Pleinlaan 2, 1050 Brussels, Belgium
| | - Benoit Prevost
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Olivier Vandenberg
- Innovation and Business Development Unit, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Avenue Roosevelt 50, 1050 Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Faculty of Medicine and Pharmacy, Mons University, Chemin du Champ de Mars 37, 7000 Mons, Belgium
| | - Marie Hallin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
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13
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Rodríguez-Villodres Á, Ortiz de la Rosa JM, Valencia-Martin R, Jiménez Parrilla F, Martín-Gutiérrez G, Márquez Patiño N, Perea Cruz E, Sánchez Jiménez MT, Pavón Delgado A, Cisneros JM, Lepe JA. Implementation of a PCR-based strategy to control an outbreak by Serratia marcescens in a Neonatal Intensive Care Unit. Ann Clin Microbiol Antimicrob 2023; 22:108. [PMID: 38082303 PMCID: PMC10714559 DOI: 10.1186/s12941-023-00657-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
OBJECTIVES To evaluate the clinical and epidemiological impact of a new molecular surveillance strategy based on qPCR to control an outbreak by Serratia marcescens in a Neonatal Intensive Care Unit (NICU). METHODS We design a specific qPCR for the detection of S. marcescens in rectal swabs of patients admitted to a NICU. We divided the surveillance study into two periods: (a) the pre-PCR, from the outbreak declaration to the qPCR introduction, and (b) the PCR period, from the introduction of the qPCR until the outbreak was solved. In all cases, S. marcescens isolates were recovered and their clonal relationship was analysed by PFGE. Control measures were implemented during the outbreak. Finally, the number of bloodstream infections (BSI) was investigated in order to evaluate the clinical impact of this molecular strategy. RESULTS Nineteen patients colonized/infected by S. marcescens were detected in the pre-PCR period (October 2020-April 2021). On the contrary, after the PCR implementation, 16 new patients were detected. The PFGE revealed 24 different pulsotypes belonging to 7 different clonal groups, that were not overlapping at the same time. Regarding the clinical impact, 18 months after the qPCR implementation, no more outbreaks by S. marcescens have been declared in the NICU of our hospital, and only 1 episode of BSI has occurred, compared with 11 BSI episodes declared previously to the outbreak control. CONCLUSIONS The implementation of this qPCR strategy has proved to be a useful tool to control the nosocomial spread of S. marcescens in the NICU.
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Affiliation(s)
- Ángel Rodríguez-Villodres
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, University Hospital Virgen del Rocío, Av. Manuel Siurot s/n, 41013, Seville, Spain.
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, Seville, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC). Instituto de Salud Carlos III, Madrid, Spain.
| | - José Manuel Ortiz de la Rosa
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, University Hospital Virgen del Rocío, Av. Manuel Siurot s/n, 41013, Seville, Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, Seville, Spain
| | - Raquel Valencia-Martin
- Clinical Unit of Preventive Medicine and Public Health, University Hospital Virgen del Rocío, Seville, Spain
- Department of Preventive Medicine, University of Seville, Seville, Spain
| | | | - Guillermo Martín-Gutiérrez
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, University Hospital Virgen del Rocío, Av. Manuel Siurot s/n, 41013, Seville, Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC). Instituto de Salud Carlos III, Madrid, Spain
| | - Natividad Márquez Patiño
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, University Hospital Virgen del Rocío, Av. Manuel Siurot s/n, 41013, Seville, Spain
| | - Estela Perea Cruz
- Clinical Unit of Preventive Medicine and Public Health, University Hospital Virgen del Rocío, Seville, Spain
| | | | | | - José Miguel Cisneros
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, University Hospital Virgen del Rocío, Av. Manuel Siurot s/n, 41013, Seville, Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC). Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Seville, Seville, Spain
| | - José Antonio Lepe
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, University Hospital Virgen del Rocío, Av. Manuel Siurot s/n, 41013, Seville, Spain
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC). Instituto de Salud Carlos III, Madrid, Spain
- Department of Microbiology, University of Seville, Seville, Spain
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14
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Liu X, Yan Z, Ye L, Wang K, Li J, Lin Y, Liao C, Liu Y, Li P, Du M. Genomic epidemiological investigation of an outbreak of Serratia marcescens neurosurgical site infections associated with contaminated haircutting toolkits in a hospital barber shop. J Hosp Infect 2023; 142:58-66. [PMID: 37774927 DOI: 10.1016/j.jhin.2023.09.013] [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: 07/19/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
Abstract
BACKGROUND Nine surgical site infections caused by Serratia marcescens were diagnosed in neurosurgical patients in a 3500-bed hospital between 2nd February and 6th April 2022. OBJECTIVE To trace the source of infections caused by S. marcescens to expedite termination of the outbreak and prevent future epidemics. METHODS A review of all surgical procedures and cultures yielding S. marcescens since February 2022 was conducted. Samples were collected from patients and environmental sources. S. marcescens isolates were characterized by antibiotic susceptibility testing. Whole-genome sequencing (WGS) was used to investigate genetic relationships. Resistance genes, virulence genes and plasmid replicons were identified. RESULTS S. marcescens was isolated from patients' puncture fluid, cerebrospinal fluid and other secretions, and was also cultured from the barbers' haircutting tools, including leather knives, slicker scrapers and razors. In total, 15 isolates were obtained from patients and eight isolates were obtained from haircutting tools. All isolates exhibited identical antibiotic resistance patterns. WGS revealed close clustering among the 23 isolates which differed significantly from previous strains. Three resistance genes and nine virulence-associated genes were detected in all isolates, and 19 of 23 isolates harboured an MOBP-type plasmid. The results confirmed an outbreak of S. marcescens, which was traced to contaminated haircutting tools in the hospital barber shop. The outbreak ended after extensive reinforcement of infection control procedures and re-education of the barbers. CONCLUSIONS These results highlight the risk of postoperative infections related to pre-operative skin preparation, and demonstrate the value of next-generation sequencing tools to expedite outbreak investigations.
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Affiliation(s)
- X Liu
- Chinese PLA Centre for Disease Control and Prevention, Beijing, China
| | - Z Yan
- Department of Disease Prevention and Control, The Second Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - L Ye
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - K Wang
- Chinese PLA Centre for Disease Control and Prevention, Beijing, China
| | - J Li
- Chinese PLA Centre for Disease Control and Prevention, Beijing, China
| | - Y Lin
- Chinese PLA Centre for Disease Control and Prevention, Beijing, China
| | - C Liao
- Chinese PLA Centre for Disease Control and Prevention, Beijing, China; School of Public Health, China Medical University, Shenyang, China
| | - Y Liu
- Department of Disease Prevention and Control, The First Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - P Li
- Chinese PLA Centre for Disease Control and Prevention, Beijing, China.
| | - M Du
- Department of Disease Prevention and Control, The First Medical Centre of Chinese PLA General Hospital, Beijing, China.
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15
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Chavignon M, Coignet L, Bonhomme M, Bergot M, Tristan A, Verhoeven P, Josse J, Laurent F, Butin M. Environmental Persistence of Staphylococcus capitis NRCS-A in Neonatal Intensive Care Units: Role of Biofilm Formation, Desiccation, and Disinfectant Tolerance. Microbiol Spectr 2022; 10:e0421522. [PMID: 36409142 PMCID: PMC9769769 DOI: 10.1128/spectrum.04215-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/23/2022] Open
Abstract
The clone Staphylococcus capitis NRCS-A is responsible for late-onset sepsis in neonatal intensive care units (NICUs) worldwide. Over time, this clone has evolved into three subgroups that are increasingly adapted to the NICU environment. This study aimed to decipher the mechanisms involved in NRCS-A persistence in NICUs. Twenty-six S. capitis strains belonging to each of the three NRCS-A clone subgroups and two other non-NRCS-A groups from neonates (alpha clone) or from adult patients ("other strains") were compared based on growth kinetics and ability to form biofilm as well as tolerance to desiccation and to different disinfectants. S. capitis biofilm formation was enhanced in rich medium and decreased under conditions of nutrient stress for all strains. However, under conditions of nutrient stress, NRCS-A strains presented an enhanced ability to adhere and form a thin biofilm containing more viable and culturable bacteria (mean 5.7 log10 CFU) than the strains from alpha clone (mean, 1.1 log10 CFU) and the "other strains" (mean, 4.2 log10 CFU) (P < 0.0001). The biofilm is composed of bacterial aggregates with a matrix mainly composed of polysaccharides. The NRCS-A clone also showed better persistence after a 48-h desiccation. However, disinfectant tolerance was not enhanced in the NRCS-A clone in comparison with that of strains from adult patients. In conclusion, the ability to form biofilm under nutrient stress and to survive desiccation are two major advantages for clone NRCS-A that could explain its ability to persist and settle in the specific environment of NICU settings. IMPORTANCE Neonatal intensive care units (NICUs) host extremely fragile newborns, including preterm neonates. These patients are very susceptible to nosocomial infections, with coagulase-negative staphylococci being the species most frequently involved. In particular, a Staphylococcus capitis clone named NRCS-A has emerged worldwide specifically in NICUs and is responsible for severe nosocomial sepsis in preterm neonates. This clone is specifically adapted to the NICU environment and is able to colonize and maintain on NICU surfaces. The present work explored the mechanisms involved in the persistence of the NRCS-A clone in the NICU environment despite strict hygiene measures. The ability to produce biofilm under nutritional stress and to resist desiccation appear to be the two main advantages of NRCS-A in comparison with other strains. These findings are pivotal to provide clues for subsequent development of targeted methods to combat NRCS-A and to stop its dissemination.
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Affiliation(s)
- Marie Chavignon
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Ludivine Coignet
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Mélanie Bonhomme
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Marine Bergot
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Anne Tristan
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Paul Verhoeven
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP (Groupe sur l’Immunité des Muqueuses et Agents Pathogènes), INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
- Department of Infectious Agents and Hygiene, University-Hospital of Saint-Etienne, Saint-Etienne, France
| | - Jérôme Josse
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Frédéric Laurent
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Marine Butin
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
- Service de Néonatologie et Réanimation Néonatale, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Bron, France
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16
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Yin L, Zhang PP, Wang W, Tang S, Deng SM, Jia AQ. 3-Phenylpropan-1-Amine Enhanced Susceptibility of Serratia marcescens to Ofloxacin by Occluding Quorum Sensing. Microbiol Spectr 2022; 10:e0182922. [PMID: 35972277 PMCID: PMC9603881 DOI: 10.1128/spectrum.01829-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/01/2022] [Indexed: 12/31/2022] Open
Abstract
Serratia marcescens (S. marcescens) is an environmental bacterium that causes infections with high morbidity and mortality. Notably, infections caused by multidrug-resistant S. marcescens have become a global public health issue. Therefore, the discovery of promising compounds to reduce the virulence of pathogens and restore antibiotic activity against multidrug-resistant bacteria is critical. Quorum sensing (QS) regulates virulence factors and biofilm formation of microorganisms to increase their pathogenicity and is, therefore, an important factor in the formation of multidrug resistance. In this study, we found that 3-phenylpropan-1-amine (3-PPA) inhibited S. marcescens NJ01 biofilm formation and virulence factors, including prodigiosin, protease, lipase, hemolysin, and swimming. The combination of 3-PPA (50.0 μg/mL) and ofloxacin (0.2 μg/mL) enhanced S. marcescens NJ01 sensitivity to ofloxacin. Based on crystalline violet staining, scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM), 3-PPA (50.0 μg/mL) reduced S. marcescens NJ01 biofilm formation by 48%. Quantitative real-time PCR (qRT-PCR) showed that 3-PPA regulated the expression of virulence- and biofilm-related genes fimA, fimC, bsmB, pigP, flhC, flhD, and sodB. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) indicated that 3-PPA affected intracellular metabolites of S. marcescens NJ01, leading to reduce metabolic activity. These results suggested that 3-PPA inhibits the pathogenicity of S. marcescens NJ01 by occluding QS. Thus, 3-PPA is feasible as an ofloxacin adjuvant to overcome multidrug-resistant S. marcescens and improve the treatment of intractable infections. IMPORTANCE Multidrug-resistant bacteria have become a major threat to global public health, leading to increased morbidity, mortality, and health care costs. Bacterial virulence factors and biofilms, which are regulated by quorum sensing (QS), are the primary causes of multidrug resistance. In this study, 3-PPA reduced virulence factors and eliminated biofilm formation by inhibiting QS in S. marcescens NJ01 bacteria, without affecting bacterial growth, thus restoring sensitivity to ofloxacin. Thus, the discovery of compounds that can restore antibiotic activity against bacteria is a promising strategy to mitigate multidrug resistance in pathogens.
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Affiliation(s)
- Lujun Yin
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
| | - Ping-Ping Zhang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Wei Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
| | - Shi Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Shi-Ming Deng
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Ai-Qun Jia
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
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17
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Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations. J Clin Microbiol 2022; 60:e0119622. [PMID: 36214584 PMCID: PMC9667775 DOI: 10.1128/jcm.01196-22] [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: 11/20/2022] Open
Abstract
Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of a S. marcescens cgMLST scheme is reported with the goal of enabling a standardized methodology and typing nomenclature. Four hundred ninety-one high-quality S. marcescens WGS data sets were extracted from public databases and-using the genomic sequence of NCBI reference strain S. marcescens Db11 (NZ_HG326223.1) as a starting point-all Db11 genes present in ≥97% data sets used to create a cgMLST scheme. The novel scheme was evaluated using WGS data from 24 outbreak investigations (n = 175 isolates) distributed over three continents. Analysis of Db11 genes within the 491 data sets identified 2,692 target genes present in ≥97% of genomes (mean, 99.1%; median, 99.9%). These genes formed the novel cgMLST scheme, covering 47.8% of nucleotides in the Db11 genome. Analyzing 175 isolates from 24 outbreaks using the novel scheme gave comparable results to previous typing efforts for both general groupings and allelic distances within clusters. In summary, a novel cgMLST scheme for S. marcescens was developed and evaluated. The scheme and its associated nomenclature will improve standardization of typing efforts for molecular surveillance and outbreak investigation, allowing better understanding of S. marcescens genomic epidemiology and facilitating interlaboratory comparisons.
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18
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Piccirilli A, Cherubini S, Brisdelli F, Fazii P, Stanziale A, Di Valerio S, Chiavaroli V, Principe L, Perilli M. Molecular Characterization by Whole-Genome Sequencing of Clinical and Environmental Serratia marcescens Strains Isolated during an Outbreak in a Neonatal Intensive Care Unit (NICU). Diagnostics (Basel) 2022; 12:diagnostics12092180. [PMID: 36140580 PMCID: PMC9498040 DOI: 10.3390/diagnostics12092180] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/27/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
The whole-genome sequencing (WGS) of eighteen S. marcescens clinical strains isolated from 18 newborns hospitalized in the Neonatal Intensive Care Unit (NICU) at Pescara Public Hospital, Italy, was compared with that of S. marcescens isolated from cradles surfaces in the same ward. The identical antibiotic resistance genes (ARGs) and virulence factors were found in both clinical and environmental S. marcescens strains. The aac(6′)-Ic, tetA(41), blaSRT-3, adeFGH, rsmA, and PBP3 (D350N) genes were identified in all strains. The SRT-3 enzyme, which exhibited 10 amino acid substitutions with respect to SST-1, the constitutive AmpC β-lactamase in S. marcescens, was partially purified and tested against some β-lactams. It showed a good activity against cefazolin. Both clinical and environmental S. marcescens strains exhibited susceptibility to all antibiotics tested, with the exception of amoxicillin/clavulanate.
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Affiliation(s)
- Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
- Correspondence: (A.P.); (M.P.); Tel.: +39-0862433489 (M.P.)
| | - Sabrina Cherubini
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Fabrizia Brisdelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Paolo Fazii
- Clinical Microbiology and Virology Unit, Pescara Public Hospital, 65122 Pescara, Italy
| | - Andrea Stanziale
- Clinical Microbiology and Virology Unit, Pescara Public Hospital, 65122 Pescara, Italy
| | - Susanna Di Valerio
- Neonatal Intensive Care Unit, Pescara Public Hospital, 65123 Pescara, Italy
| | - Valentina Chiavaroli
- Neonatal Intensive Care Unit, Pescara Public Hospital, 65123 Pescara, Italy
- Liggins Institute, The University of Auckland, Auckland 1141, New Zealand
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, “S. Giovanni di Dio” Hospital, 88900 Crotone, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
- Correspondence: (A.P.); (M.P.); Tel.: +39-0862433489 (M.P.)
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19
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Price V, Dunn SJ, Moran RA, Swindells J, McNally A. Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit. Microb Genom 2022; 8. [PMID: 35696727 PMCID: PMC9455706 DOI: 10.1099/mgen.0.000841] [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] [Indexed: 12/22/2022] Open
Abstract
In some neonatal units, the screening of isolates for antimicrobial-resistant organisms is a matter of routine, with theoretical benefits including the prevention or early detection of outbreaks. This study sought to use whole-genome sequencing (WGS) retrospectively to characterize the genomic epidemiology of Gram-negative organisms obtained from a screening programme in a 32-bed unit providing intensive, high-dependency and special care at City Hospital, Birmingham, UK, identifying occult transmission events and clinically important antimicrobial-resistance (AMR) genes. WGS was performed for 155 isolates collected from rectal and umbilical screening swabs over a 2 month period from 44 individual neonates. Genomic epidemiological analysis showed possible transmission events involving Escherichia coli, Enterobacter cloacae, Klebsiella oxytoca and Klebsiella pneumoniae not detected by routine screening, with eight putative clusters involving different individuals identified. Within phylogenetic clusters, the relatedness of organisms – as determined by the abundance of SNPs – varied widely, indicating that a variety of transmission routes may be implicated. While clinically important AMR genes were not present in the putative transmission clusters, our observation of suspected interspecies horizontal transfer of blaCTX-M-15 within individuals highlights the potential for their spread between organisms as well as individuals in this environment, with implications for surveillance. Our data show that WGS may reveal occult Gram-negative transmission events, demonstrating the potential of sequencing-based surveillance systems for nosocomial pathogens. Challenges remain in understanding how to utilize WGS surveillance to maximum effect in real-world settings.
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Affiliation(s)
- Vivien Price
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Steven J Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jonathan Swindells
- Black Country Pathology Service, Birmingham City Hospital, Dudley Road, Birmingham, West Midlands B18 7QH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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20
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Bolourchi N, Noori Goodarzi N, Giske CG, Nematzadeh S, Haririzadeh Jouriani F, Solgi H, Badmasti F. Comprehensive pan-genomic, resistome and virulome analysis of clinical OXA-48 producing carbapenem-resistant Serratia marcescens strains. Gene 2022; 822:146355. [PMID: 35189248 DOI: 10.1016/j.gene.2022.146355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/03/2022] [Accepted: 02/15/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly studied as the pathogens associated with hospital acquired infections. However, data on Serratia marcescens are not enough. S. marcescens is now becoming a propensity for its highly antimicrobial-resistant clinical infections. METHODS Four carbapenem-resistant S. marcescens (CR-SM) isolates were obtained from hospitalized patients through routine microbiological experiments. We assembled the isolates genomes using whole genome sequencing (WGS) and compared their resistome and virulome patterns. RESULTS The average length and CG content of chromosomes was 5.33 Mbp and 59.8%, respectively. The number of coding sequences (CDSs) ranged from 4,959 to 4,989. All strains had one single putative conjugative plasmid with IncL incompatibility (Inc) group. The strains harbored blaCTX-M-15, blaTEM-1 and blaSHV-134. All plamsids were positive for blaOXA-48. No blaNDM-1, blaKPC, blaVIM and blaIMP were identified. The blaSRT-2 and aac(6')-Ic genes were chromosomally-encoded. Class 1 integron was detected in strains P8, P11 and P14. The Escher_RCS47 and Salmon_SJ46 prophages played major role in plasmid-mediated carraige of extended spectrum β-lactamases (ESBLs). The CR-SM strains were equipt with typical virulence factors of oppotunistic pathogens including biofilm formation, adhesins, secretory systems and siderophores. The strains did not have ability to produce prodigiosin but were positive for chitinase and EstA. CONCLUSION The presence of conjugative plasmids harboring major β-lactamases within prophage and class 1 integron structures highlights the role of different mobile genetic elements (MGEs) in distribution of AMR factors and more specifically carbapenemases. More molecular studies are required to determine the status of carbapenem resistance in clinical starins. However, appropriate strategies to control the global dissemination of CR-SM are urgent.
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Affiliation(s)
- Negin Bolourchi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Narjes Noori Goodarzi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Shoeib Nematzadeh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | | | - Hamid Solgi
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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21
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Simões MF, Antunes A. Microbial Pathogenicity in Space. Pathogens 2021; 10:450. [PMID: 33918768 PMCID: PMC8069885 DOI: 10.3390/pathogens10040450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/04/2021] [Accepted: 04/08/2021] [Indexed: 12/25/2022] Open
Abstract
After a less dynamic period, space exploration is now booming. There has been a sharp increase in the number of current missions and also of those being planned for the near future. Microorganisms will be an inevitable component of these missions, mostly because they hitchhike, either attached to space technology, like spaceships or spacesuits, to organic matter and even to us (human microbiome), or to other life forms we carry on our missions. Basically, we never travel alone. Therefore, we need to have a clear understanding of how dangerous our "travel buddies" can be; given that, during space missions, our access to medical assistance and medical drugs will be very limited. Do we explore space together with pathogenic microorganisms? Do our hitchhikers adapt to the space conditions, as well as we do? Do they become pathogenic during that adaptation process? The current review intends to better clarify these questions in order to facilitate future activities in space. More technological advances are needed to guarantee the success of all missions and assure the reduction of any possible health and environmental risks for the astronauts and for the locations being explored.
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Affiliation(s)
- Marta Filipa Simões
- State Key Laboratory of Lunar and Planetary Sciences (SKLPlanets), Macau University of Science and Technology (MUST), Avenida Wai Long, Taipa, Macau, China;
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Macau, China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences (SKLPlanets), Macau University of Science and Technology (MUST), Avenida Wai Long, Taipa, Macau, China;
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Macau, China
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