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Lê-Bury P, Echenique-Rivera H, Pizarro-Cerdá J, Dussurget O. Determinants of bacterial survival and proliferation in blood. FEMS Microbiol Rev 2024; 48:fuae013. [PMID: 38734892 PMCID: PMC11163986 DOI: 10.1093/femsre/fuae013] [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: 11/06/2023] [Revised: 04/29/2024] [Accepted: 05/10/2024] [Indexed: 05/13/2024] Open
Abstract
Bloodstream infection is a major public health concern associated with high mortality and high healthcare costs worldwide. Bacteremia can trigger fatal sepsis whose prevention, diagnosis, and management have been recognized as a global health priority by the World Health Organization. Additionally, infection control is increasingly threatened by antimicrobial resistance, which is the focus of global action plans in the framework of a One Health response. In-depth knowledge of the infection process is needed to develop efficient preventive and therapeutic measures. The pathogenesis of bloodstream infection is a dynamic process resulting from the invasion of the vascular system by bacteria, which finely regulate their metabolic pathways and virulence factors to overcome the blood immune defenses and proliferate. In this review, we highlight our current understanding of determinants of bacterial survival and proliferation in the bloodstream and discuss their interactions with the molecular and cellular components of blood.
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Affiliation(s)
- Pierre Lê-Bury
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Autoimmune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), 18 route du Panorama, 92260 Fontenay-aux-Roses, France
| | - Hebert Echenique-Rivera
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-146, 28 rue du Dr Roux, 75015 Paris, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, 28 rue du Dr Roux, 75015 Paris, France
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Long Q, Zhou W, Zhou H, Tang Y, Chen W, Liu Q, Bian X. Polyamine-containing natural products: structure, bioactivity, and biosynthesis. Nat Prod Rep 2024; 41:525-564. [PMID: 37873660 DOI: 10.1039/d2np00087c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Covering: 2005 to August, 2023Polyamine-containing natural products (NPs) have been isolated from a wide range of terrestrial and marine organisms and most of them exhibit remarkable and diverse activities, including antimicrobial, antiprotozoal, antiangiogenic, antitumor, antiviral, iron-chelating, anti-depressive, anti-inflammatory, insecticidal, antiobesity, and antioxidant properties. Their extraordinary activities and potential applications in human health and agriculture attract increasing numbers of studies on polyamine-containing NPs. In this review, we summarized the source, structure, classification, bioactivities and biosynthesis of polyamine-containing NPs, focusing on the biosynthetic mechanism of polyamine itself and representative polyamine alkaloids, polyamine-containing siderophores with catechol/hydroxamate/hydroxycarboxylate groups, nonribosomal peptide-(polyketide)-polyamine (NRP-(PK)-PA), and NRP-PK-long chain poly-fatty amine (lcPFAN) hybrid molecules.
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Affiliation(s)
- Qingshan Long
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Wen Zhou
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural, Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Ying Tang
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Wu Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.
| | - Qingshu Liu
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Musafer HK, Hussein NH, Kareem SM. Neonatal intensive care units: extended spectrum β-lactamase genes and biofilm formation by Serratia marcescens. Mol Biol Rep 2024; 51:167. [PMID: 38252349 DOI: 10.1007/s11033-023-09124-7] [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: 08/18/2023] [Accepted: 12/06/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND The increasing cases of bloodstream infections among children at neonatal intensive care units (NICUs) led this work to investigate biofilm production, antibiotics and the presence of ESβL genes in Serratia marcescens (S. marcescens) strains isolated from blood. METHODS Twenty S. marcescens strains were isolated and identified by the VITEK-2 system over 7 months from late 2022 to mid-2023 from Ibn Al-Balady Hospital in Baghdad. Kirby-Bauer test was used to measure antibiotic susceptibility. RESULTS The results revealed that 95% of twenty S. marcescens isolates were non-susceptible to Ampicillin and Amoxicillin-clavulanic. Furthermore, S. marcescens isolates showed a high sensitivity rate 70% toward Imipenem. All S. marcescens strains 100% were produced biofilm. This work clarifies that, out of 20 S. marcescens strains, 80% were harbored ESβL genes. The coexistence of blaTEM, blaCTX and blaSHV genes was shown in 43.75% of strains, while 56.25% of S. marcescens strains harbored single ES[Formula: see text]L genes. The biofilm values increase with the accuracy of EsβL genes. Phylogenetic analyses based on the sequence of blaCTX-M and blaTEM were done with closely related genes in the GenBank using MEGA6 software. CONCLUSIONS The distribution of blaTEM, blaCTX and blaSHV genes among local S. marcescens strains may be attributed to the indiscriminate use of antibiotics. The results confirmed the spread of ESβL genes in S. marcescens from blood infections among newborn infants.
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Affiliation(s)
- Hadeel K Musafer
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq.
| | - Nadheema H Hussein
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Sawsan M Kareem
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
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Ali F, Wu J, Kc D. A Sixty-Nine-Year-Old Female With Serratia marcescens Infection. Cureus 2023; 15:e49985. [PMID: 38179352 PMCID: PMC10766386 DOI: 10.7759/cureus.49985] [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: 07/14/2022] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Serratia marcescens is a bacterial pathogen that tends to cause opportunistic infections, mainly in immune-compromised patients. In this case, we present a 69-year-old female who presented to the emergency department (ED) at Mount Sinai Hospital in Chicago on February 11th, 2022, after a mechanical fall. She had a medical history of metastatic lung cancer treated with chemotherapy, hypertension, pulmonary embolism, polysubstance abuse, and chronic obstructive pulmonary disease (COPD). The patient was found to be positive for systemic inflammatory response syndrome (SIRS). The patient was then started on broad-spectrum antibiotics, including vancomycin and cefepime. Blood cultures were ordered and came back positive for Serratia marcescens. This patient had multiple factors for immune suppression, including metastatic lung cancer, chemotherapy, and polysubstance abuse. The infectious disease department was consulted for the blood culture results, and ceftriaxone was recommended. Later on, levofloxacin was recommended. Blood cultures were negative two days after being positive. Afterward, the patient was kept for monitoring until discharge. Serratia marcescens is found in several reservoirs in nature. Therefore, preventing contact with this pathogen in immune-compromised patients can be difficult. It is important to have a degree of clinical suspicion for opportunistic pathogens like Serratia marcescens whenever a patient with factors for immune compromise presents for any condition.
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Affiliation(s)
- Furkhan Ali
- Internal Medicine, Mount Sinai Hospital, Chicago, USA
| | - JinJin Wu
- Internal Medicine, Mount Sinai Hospital, Chicago, USA
| | - Dilip Kc
- Internal Medicine, Mount Sinai Hospital, Chicago, USA
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Ferguson D, Ryder R, Lunsford R, Dash A, Kamali A, Kimura A, Crandall J, Mukhopadhyay R, Dowless H, Ortiz N, Jue NK. Serratia marcescens Outbreak at a Correctional Facility: Environmental Sampling, Laboratory Analyses and Genomic Characterization to Assess Sources and Persistence. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6709. [PMID: 37681849 PMCID: PMC10487681 DOI: 10.3390/ijerph20176709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/12/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023]
Abstract
Serratia marcescens is an environmental bacterium and clinical pathogen that can cause an array of infections. We describe an environmental sampling and comparative genomics approach used to investigate a multi-year outbreak of S. marcescens at a correctional facility. Whole genome sequencing analysis revealed a predominant cluster of clonally related S. marcescens from nine patient cases and items associated with illicit drug use. Closely related strains found among items associated with case-patient cells and diluted Cell Block 64 (CB64), a quaternary ammonium disinfectant, and Break Out (BO), a multipurpose cleaner, highlighted their role as environmental reservoirs for S. marcescens in this outbreak. Comparative genomic analysis suggested outbreak strains were both persistent (identical strains found over long periods and in multiple locations of the correctional facility) and diverse (strains clustered with multiple global samples from NCBI database). No correlation was found between antimicrobial resistance (AMR) genes of outbreak strains; NCBI strains have more AMR genes. Principal component analysis (PCA) of virulence factors associated with persistence and infectivity indicated variation based on phylogroups, including the predominant cluster; identifiable variations among environmental versus clinical strains were not observed. Identification of multiple distinct genetic groups highlights the importance of putting epidemiological genomic studies in a proper genetic context.
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Affiliation(s)
- Donna Ferguson
- Public Health Laboratory, County of Monterey Health Department, Salinas, CA 93906, USA
| | - Rahil Ryder
- Public Health Laboratory, County of Monterey Health Department, Salinas, CA 93906, USA
| | - Rawni Lunsford
- Public Health Laboratory, County of Monterey Health Department, Salinas, CA 93906, USA
| | - Arie Dash
- Public Health Laboratory, County of Monterey Health Department, Salinas, CA 93906, USA
| | - Amanda Kamali
- Public Health, Medical Services Division, California Correctional Health Care Services, Elk Grove, CA 95758, USA
| | - Akiko Kimura
- Infectious Diseases Branch, Center for Infectious Diseases, California Department of Public Health, Richmond, CA 94804, USA
| | - John Crandall
- Microbial Diseases Laboratory Branch, Center for Laboratory Sciences, California Department of Public Health, Richmond, CA 94804, USA
| | - Rituparna Mukhopadhyay
- Microbial Diseases Laboratory Branch, Center for Laboratory Sciences, California Department of Public Health, Richmond, CA 94804, USA
| | - Heather Dowless
- Public Health, Medical Services Division, California Correctional Health Care Services, Elk Grove, CA 95758, USA
| | - Nancy Ortiz
- Infectious Diseases Branch, Center for Infectious Diseases, California Department of Public Health, Richmond, CA 94804, USA
| | - Nathaniel K. Jue
- Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, CA 93955, USA
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Pisco-Ortiz C, González-Almario A, Uribe-Gutiérrez L, Soto-Suárez M, Amaya-Gómez CV. Suppression of tomato wilt by cell-free supernatants of Acinetobacter baumannii isolates from wild cacao from the Colombian Amazon. World J Microbiol Biotechnol 2023; 39:297. [PMID: 37658991 PMCID: PMC10475004 DOI: 10.1007/s11274-023-03719-9] [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: 04/11/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023]
Abstract
Tomato vascular wilt caused by Fusarium oxysporum f. sp. lycopersici (Fol) is one of the most limiting diseases of this crop. The use of fungicides and varieties resistant to the pathogen has not provided adequate control of the disease. In this study, siderophore-producing bacteria isolated from wild cocoa trees from the Colombian Amazon were characterized to identify prominent strategies for plant protection. The isolates were taxonomically classified into five different genera. Eight of the fourteen were identified as bacteria of the Acinetobacter baumannii complex. Isolates CBIO024, CBIO086, CBIO117, CBIO123, and CBIO159 belonging to this complex showed the highest efficiency in siderophore synthesis, producing these molecules in a range of 91-129 µmol/L deferoxamine mesylate equivalents. A reduction in disease severity of up to 45% was obtained when plants were pretreated with CBIO117 siderophore-rich cell-free supernatant (SodSid). Regarding the mechanism of action that caused antagonistic activity against Fol, it was found that plants infected only with Fol and plants pretreated with SodSid CBIO117 and infected with Fol showed higher levels of PR1 and ERF1 gene expression than control plants. In contrast, MYC2 gene expression was not induced by the SodSid CBIO117 application. However, it was upregulated in plants infected with Fol and plants pretreated with SodSid CBIO117 and infected with the pathogen. In addition to the disease suppression exerted by SodSid CBIO117, the results suggest that the mechanism underlying this effect is related to an induction of systemic defense through the salicylic acid, ethylene, and priming defense via the jasmonic acid pathway.
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Affiliation(s)
- Carolina Pisco-Ortiz
- Centro de Investigación La Libertad, Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Villavicencio, Meta, Colombia
| | | | - Liz Uribe-Gutiérrez
- Centro de investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Mauricio Soto-Suárez
- Centro de investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Carol V Amaya-Gómez
- Centro de Investigación La Libertad, Corporación Colombiana de Investigación Agropecuaria - Agrosavia, Villavicencio, Meta, Colombia.
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O'Brien S, Culbert CT, Barraclough TG. Community composition drives siderophore dynamics in multispecies bacterial communities. BMC Ecol Evol 2023; 23:45. [PMID: 37658316 PMCID: PMC10472669 DOI: 10.1186/s12862-023-02152-8] [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: 11/29/2022] [Accepted: 08/17/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Intraspecific public goods are commonly shared within microbial populations, where the benefits of public goods are largely limited to closely related conspecifics. One example is the production of iron-scavenging siderophores that deliver iron to cells via specific cell envelope receptor and transport systems. Intraspecific social exploitation of siderophore producers is common, since non-producers avoid the costs of production but retain the cell envelope machinery for siderophore uptake. However, little is known about how interactions between species (i.e., interspecific interactions) can shape intraspecific public goods exploitation. Here, we predicted that strong competition for iron between species in diverse communities will increase costs of siderophore cooperation, and hence drive intraspecific exploitation. We examined how increasing microbial community species diversity shapes intraspecific social dynamics by monitoring the growth of siderophore producers and non-producers of the plant-growth promoting bacterium Pseudomonas fluorescens, embedded within tree-hole microbial communities ranging from 2 to 15 species. RESULTS We find, contrary to our prediction, that siderophore production is favoured at higher levels of community species richness, driven by increased likelihood of encountering key species that reduce the growth of siderophore non-producing (but not producing) strains of P. fluorescens. CONCLUSIONS Our results suggest that maintaining a diverse soil microbiota could partly contribute to the maintenance of siderophore production in natural communities.
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Affiliation(s)
- Siobhán O'Brien
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Christopher T Culbert
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
| | - Timothy G Barraclough
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
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Adedoyin FT, Sridhar BBM, Rosenzweig JA. Impact of metal exposure on environmentally isolated Serratia marcescens' growth, oxidative-stress resistance, biofilm formation, and proliferation in eukaryotic co-culture models. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 253:114677. [PMID: 36841082 DOI: 10.1016/j.ecoenv.2023.114677] [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: 07/13/2022] [Revised: 01/26/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Environmental metals can be noxious to the surrounding biota, indirectly impact freshwater habitats, and also impact microbiological communities. In this study, zinc (Zn) (55.5 mg/kg), manganese (Mn) (863.4 mg/kg) and lead (Pb) (17.5 mg/kg) levels measured in Houston watershed flood plain soil samples were higher than environmental agencies' thresholds. To investigate the effects of metal exposures, an environmentally isolated Serratia marcescens (SME), etiological agent of endocarditis and respiratory infections, and its reference strain (SMR) were exposed to Pb, Zn, and Mn, and subsequent oxidative stress responses and biofilm production were measured. Not surprisingly, SME was less sensitive to all 3 metal exposures than was SMR. Interestingly, SME produced increased biofilm and was more resistant to oxidative stress in the presence of Zn and Pb than SMR. In a 6 h lung infection model using BAES-2B cells, SME exhibited greater proliferation than SMR in all metal challenges. Similarly, in our HT29 gut infection model, SME out-proliferated SMR when challenged with Pb and Mn following the 6 h infection. Taken together, SME was better able to withstand environmental stressors than SMR, suggesting increased virulence potential of this opportunistic human pathogen.
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Affiliation(s)
- Folasade T Adedoyin
- Department of Environmental and Interdisciplinary Science, Texas Southern University, USA
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Liang Z, Shen J, Liu J, Sun X, Yang Y, Lv Y, Zheng J, Mou X, Li H, Ding X, Yang F. Prevalence and Characterization of Serratia marcescens Isolated from Clinical Bovine Mastitis Cases in Ningxia Hui Autonomous Region of China. Infect Drug Resist 2023; 16:2727-2735. [PMID: 37168514 PMCID: PMC10166088 DOI: 10.2147/idr.s408632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/15/2023] [Indexed: 05/13/2023] Open
Abstract
Purpose This study aimed to investigate the prevalence and genetic characterization of Serratia marcescens isolates from clinical bovine mastitis in Ningxia Hui Autonomous Region of China. Methods S. marcescens was identified by the polymerase-chain reaction of 16S rRNA gene and sequencing. Antimicrobial susceptibility was tested by the disk diffusion method. Genes of resistance and virulence were determined by the PCR. Results Overall, S. marcescens were confirmed from 32 of 2897 (1.1%) mastitis milk samples. These isolates showed high resistance to cefazolin (30/32, 93.8%) and chloramphenicol (28/32, 87.5%). A 12.5% (4/32) of the isolates displayed multidrug resistance (MDR). The most prevalent resistant genes found in S. marcescens were TEM (32/32, 100%) and CTX-M (24/32, 75.0%; CTX-M-15, 14/32, 43.8%; CTX-M-14, 8/32, 25.0%; CTX-M-65, 2/32, 6.3%) for extended-spectrum beta-lactamase, cmlA (28/32, 87.5%) and floR (16/32, 50.0%) for chloramphenicol resistance, SIM-1 (2/32, 6.3%) for carbapenemases, and sdeB (28/32, 87.5%), sdeY (26/32, 81.3%), sdeR (26/32, 81.3%) and sdeD (20/32, 62.5%) for efflux pumps. Moreover, all isolates carried virulence genes flhD, entB, and kpn, and most of them contained mrkD (30/32, 93.8%), ycfM (26/32, 81.3%), bsmB (26/32, 81.3%), pigP (26/32, 81.3%), kfu (24/32, 75.0%) and shlB (24/32, 75.0%). Conclusion To our knowledge, this is the first report of genetic determinants for antimicrobial resistance and virulence in S. marcescens isolated from bovine mastitis cases in China. These findings are useful for developing strategies for prevention and treatment of bovine mastitis caused by S. marcescens in China.
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Affiliation(s)
- Zeyi Liang
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Jiahao Shen
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Jing Liu
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Xu Sun
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Yayuan Yang
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Yanan Lv
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Juanshan Zheng
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Xiaoqing Mou
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Hongsheng Li
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Xuezhi Ding
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
| | - Feng Yang
- Key Laboratory of New Animal Drug Project of Gansu Province/Key Laboratory of Veterinary Pharmaceutics Discovery, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, Lanzhou, Gansu, 730050, People’s Republic of China
- Correspondence: Feng Yang; Xuezhi Ding, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Science, No. 335 Jiangouyan, Qilihe District, Lanzhou, Gansu, 730050, People’s Republic of China, Tel +86-931-2115262, Fax +86-931-2114180, Email ;
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First Genome Description of Providencia vermicola Isolate Bearing NDM-1 from Blood Culture. Microorganisms 2021; 9:microorganisms9081751. [PMID: 34442831 PMCID: PMC8398168 DOI: 10.3390/microorganisms9081751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/05/2021] [Accepted: 08/14/2021] [Indexed: 11/16/2022] Open
Abstract
In this paper, we describe the first complete genome sequence of Providencia vermicola species, a clinical multidrug-resistant strain harboring the New Delhi Metallo-β-lactamase-1 (NDM-1) gene, isolated at the Kinshasa University Teaching Hospital, in Democratic Republic of the Congo. Whole genome sequencing of an imipenem-resistant clinical Gram-negative P. vermicola P8538 isolate was performed using MiSeq and Gridion, and then complete genome analysis, plasmid search, resistome analysis, and comparative genomics were performed. Genome assembly resulted in a circular chromosome sequence of 4,280,811-bp and 40.80% GC and a circular plasmid (pPV8538_NDM-1) of 151,684-bp and 51.93%GC, which was identified in an Escherichia coli P8540 strain isolated in the same hospital. Interestingly, comparative genomic analysis revealed multiple sequences acquisition within the P. vermicola P8538 chromosome, including three complete prophages, a siderophore biosynthesis NRPS cluster, a Type VI secretion system (T6SS), a urease gene cluster, and a complete Type-I-F CRISPR-Cas3 system. Β-lactamase genes, including blaCMY-6 and blaNDM-1, were found on the recombinant plasmid pPV8538_NDM-1, in addition to other antibiotic resistance genes such as rmtC, aac6’-Ib3, aacA4, catA1, sul1, aac6’-Ib-cr, tetA, and tetB. Genome comparison with Providencia species revealed 82.95% of average nucleotide identity (ANI), with P. stuartii species exhibiting 90.79% of proteome similarity. We report the first complete genome of P. vermicola species and for the first time the presence of the blaNDM-1 gene in this species. This work highlights the need to improve surveillance and clinical practices in DR Congo in order to reduce or prevent the spread of such resistance.
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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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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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Pollet RM, Martin LM, Koropatkin NM. TonB-dependent transporters in the Bacteroidetes: Unique domain structures and potential functions. Mol Microbiol 2021; 115:490-501. [PMID: 33448497 DOI: 10.1111/mmi.14683] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/26/2022]
Abstract
The human gut microbiota endows the host with a wealth of metabolic functions central to health, one of which is the degradation and fermentation of complex carbohydrates. The Bacteroidetes are one of the dominant bacterial phyla of this community and possess an expanded capacity for glycan utilization. This is mediated via the coordinated expression of discrete polysaccharide utilization loci (PUL) that invariantly encode a TonB-dependent transporter (SusC) that works with a glycan-capturing lipoprotein (SusD). More broadly within Gram-negative bacteria, TonB-dependent transporters (TBDTs) are deployed for the uptake of not only sugars, but also more often for essential nutrients such as iron and vitamins. Here, we provide a comprehensive look at the repertoire of TBDTs found in the model gut symbiont Bacteroides thetaiotaomicron and the range of predicted functional domains associated with these transporters and SusD proteins for the uptake of both glycans and other nutrients. This atlas of the B. thetaiotaomicron TBDTs reveals that there are at least three distinct subtypes of these transporters encoded within its genome that are presumably regulated in different ways to tune nutrient uptake.
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Affiliation(s)
| | - Lauryn M Martin
- Department of Biology, Alcorn State University, Alcorn, MS, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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14
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Crits-Christoph A, Bhattacharya N, Olm MR, Song YS, Banfield JF. Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. Genome Res 2021; 31:239-250. [PMID: 33361114 PMCID: PMC7849407 DOI: 10.1101/gr.268169.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/16/2020] [Indexed: 12/27/2022]
Abstract
Biosynthetic gene clusters (BGCs) are operonic sets of microbial genes that synthesize specialized metabolites with diverse functions, including siderophores and antibiotics, which often require export to the extracellular environment. For this reason, genes for transport across cellular membranes are essential for the production of specialized metabolites and are often genomically colocalized with BGCs. Here, we conducted a comprehensive computational analysis of transporters associated with characterized BGCs. In addition to known exporters, in BGCs we found many importer-specific transmembrane domains that co-occur with substrate binding proteins possibly for uptake of siderophores or metabolic precursors. Machine learning models using transporter gene frequencies were predictive of known siderophore activity, molecular weights, and a measure of lipophilicity (log P) for corresponding BGC-synthesized metabolites. Transporter genes associated with BGCs were often equally or more predictive of metabolite features than biosynthetic genes. Given the importance of siderophores as pathogenicity factors, we used transporters specific for siderophore BGCs to identify both known and uncharacterized siderophore-like BGCs in genomes from metagenomes from the infant and adult gut microbiome. We find that 23% of microbial genomes from premature infant guts have siderophore-like BGCs, but only 3% of those assembled from adult gut microbiomes do. Although siderophore-like BGCs from the infant gut are predominantly associated with Enterobacteriaceae and Staphylococcus, siderophore-like BGCs can be identified from taxa in the adult gut microbiome that have rarely been recognized for siderophore production. Taken together, these results show that consideration of BGC-associated transporter genes can inform predictions of specialized metabolite structure and function.
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Affiliation(s)
- Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, Berkeley, California 94720, USA
| | - Nicholas Bhattacharya
- Department of Mathematics, University of California, Berkeley, California 94720, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University, California 94305, USA
| | - Yun S Song
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
- Department of Statistics, University of California, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, Berkeley, California 94720, USA
- Department of Microbiology and Immunology, Stanford University, California 94305, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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