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Şimşek E, Kim K, Lu J, Silver A, Luo N, Lee CT, You L. A 'rich-get-richer' mechanism drives patchy dynamics and resistance evolution in antibiotic-treated bacteria. Mol Syst Biol 2024; 20:880-897. [PMID: 38877321 DOI: 10.1038/s44320-024-00046-5] [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: 11/19/2023] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/16/2024] Open
Abstract
Bacteria in nature often form surface-attached communities that initially comprise distinct subpopulations, or patches. For pathogens, these patches can form at infection sites, persist during antibiotic treatment, and develop into mature biofilms. Evidence suggests that patches can emerge due to heterogeneity in the growth environment and bacterial seeding, as well as cell-cell signaling. However, it is unclear how these factors contribute to patch formation and how patch formation might affect bacterial survival and evolution. Here, we demonstrate that a 'rich-get-richer' mechanism drives patch formation in bacteria exhibiting collective survival (CS) during antibiotic treatment. Modeling predicts that the seeding heterogeneity of these bacteria is amplified by local CS and global resource competition, leading to patch formation. Increasing the dose of a non-eradicating antibiotic treatment increases the degree of patchiness. Experimentally, we first demonstrated the mechanism using engineered Escherichia coli and then demonstrated its applicability to a pathogen, Pseudomonas aeruginosa. We further showed that the formation of P. aeruginosa patches promoted the evolution of antibiotic resistance. Our work provides new insights into population dynamics and resistance evolution during surface-attached bacterial growth.
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Affiliation(s)
- Emrah Şimşek
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Kyeri Kim
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Jia Lu
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Anita Silver
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Nan Luo
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Charlotte T Lee
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27708, USA.
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Du Z, Nakagawa A, Fang J, Ridwan R, Astuti WD, Sarwono KA, Sofyan A, Widyastuti Y, Cai Y. Cleaner anaerobic fermentation and greenhouse gas reduction of crop straw. Microbiol Spectr 2024; 12:e0052024. [PMID: 38832787 PMCID: PMC11218512 DOI: 10.1128/spectrum.00520-24] [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: 02/28/2024] [Accepted: 05/01/2024] [Indexed: 06/05/2024] Open
Abstract
Rice anaerobic fermentation is a significant source of greenhouse gas (GHG) emissions, and in order to efficiently utilize crop residue resources to reduce GHG emissions, rice straw anaerobic fermentation was regulated using lactic acid bacteria (LAB) inoculants (FG1 and TH14), grass medium (GM) to culture LAB, and Acremonim cellulolyticus (AC). Microbial community, GHG emission, dry matter (DM) loss, and anaerobic fermentation were analyzed using PacBio single-molecule real-time and anaerobic fermentation system. The epiphytic microbial diversity of fresh rice straw was extremely rich and contained certain nutrients and minerals. During ensiling, large amounts of GHG such as carbon dioxide are produced due to plant respiration, enzymatic hydrolysis reactions, and proliferation of aerobic bacteria, resulting in energy and DM loss. Addition of FG1, TH14, and AC alone improved anaerobic fermentation by decreasing pH and ammonia nitrogen content (P < 0.05) and increased lactic acid content (P < 0.05) when compared to the control, and GM showed the same additive effect as LAB inoculants. Microbial additives formed a co-occurrence microbial network system dominated by LAB, enhanced the biosynthesis of secondary metabolites, diversified the microbial metabolic environment and carbohydrate metabolic pathways, weakened the amino acid metabolic pathways, and made the anaerobic fermentation cleaner. This study is of great significance for the effective utilization of crop straw resources, the promotion of sustainable livestock production, and the reduction of GHG emissions.IMPORTANCETo effectively utilize crop by-product resources, we applied microbial additives to silage fermentation of fresh rice straw. Fresh rice straw is extremely rich in microbial diversity, which was significantly reduced after silage fermentation, and its nutrients were well preserved. Silage fermentation was improved by microbial additives, where the combination of cellulase and lactic acid bacteria acted as enzyme-bacteria synergists to promote lactic acid fermentation and inhibit the proliferation of harmful bacteria, such as protein degradation and gas production, thereby reducing GHG emissions and DM losses. The microbial additives accelerated the formation of a symbiotic microbial network system dominated by lactic acid bacteria, which regulated silage fermentation and improved microbial metabolic pathways for carbohydrates and amino acids, as well as biosynthesis of secondary metabolites.
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Affiliation(s)
- Zhumei Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Andressa Nakagawa
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | - Jiachen Fang
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Roni Ridwan
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Wulansih D. Astuti
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Ki A. Sarwono
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Ahmad Sofyan
- Research Center for Animal Husbandry, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Yantyati Widyastuti
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Yimin Cai
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
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Nanou C, Tzoraki M, Apostolidi DM, Metallinou D. Pantoea agglomerans Infection in Neonates: A Systematic Review of Case Reports. Cureus 2024; 16:e61704. [PMID: 38975398 PMCID: PMC11224779 DOI: 10.7759/cureus.61704] [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] [Accepted: 06/04/2024] [Indexed: 07/09/2024] Open
Abstract
Pantoea agglomerans, a gram-negative bacterium, has emerged as an opportunistic pathogen, particularly within neonatal healthcare settings. Initially perceived as an innocuous environmental contaminant, P. agglomerans has been increasingly implicated in a spectrum of clinical infections, including neonatal sepsis and bacteremia. This systematic review conducts an in-depth analysis of the clinical cases published in 2003-2023, elucidating the multifaceted clinical presentations and therapeutic challenges associated with P. agglomerans infections in neonates. In total, 11 case reports and case series of 45 neonates from eight different countries were included. Most of the infected patients (57.8%) were reported in Asian countries (Sri Lanka, India, Kuwait) and involved preterm neonates (64.4%) with extremely low to low birth weight, and concurrent medical conditions including co-infections in a few of them (15.6%). Blood was the main culture source of the pathogen, accounting for 42 cases (91.1%) whereas clinical presentations in neonates exhibited considerable heterogeneity, encompassing common symptoms such as feeding difficulties, respiratory distress, fever, lethargy, and sepsis. Neonatal survival largely depended on the infection's origin and the timing of diagnosis. Considering antibiotic susceptibility as a criterion for treatment selection led to a 74% survival rate. Usually, a combination of antibiotics was used. There were 11 neonatal deaths reported, leading to an estimated mortality rate of 24.4%. We conclude that outbreaks within neonatal intensive care units underscore the importance of stringent infection control practices and heightened surveillance, especially considering the rapid disease progression noted in the included studies. Enhanced awareness and understanding of the clinical and microbiological characteristics of P. agglomerans infections are paramount for optimizing outcomes and reducing the burden of disease in neonatal populations.
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Affiliation(s)
- Christina Nanou
- Department of Midwifery, School of Health and Care Sciences, University of West Attica, Athens, GRC
| | - Maria Tzoraki
- Medical School, National and Kapodistrian University of Athens, Athens, GRC
| | - Dimitra Maria Apostolidi
- Department of Midwifery, School of Health and Care Sciences, University of West Attica, Athens, GRC
| | - Dimitra Metallinou
- Department of Midwifery, School of Health and Care Sciences, University of West Attica, Athens, GRC
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He L, Huang R, Chen H, Zhao L, Zhang Z. Discovery and characterization of a novel pathogen Erwinia pyri sp. nov. associated with pear dieback: taxonomic insights and genomic analysis. Front Microbiol 2024; 15:1365685. [PMID: 38784818 PMCID: PMC11111954 DOI: 10.3389/fmicb.2024.1365685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
In 2022, a novel disease similar to pear fire blight was found in a pear orchard in Zhangye City, Gansu Province, China. The disease mainly damages the branches, leaves, and fruits of the plant. To identify the pathogen, tissue isolation and pathogenicity testing (inoculating the potential pathogen on healthy plant tissues) were conducted. Furthermore, a comprehensive analysis encompassing the pathogen's morphological, physiological, and biochemical characteristics and whole-genome sequencing was conducted. The results showed that among the eight isolates, the symptoms on the detached leaves and fruits inoculated with isolate DE2 were identical to those observed in the field. Verifying Koch's postulates confirmed that DE2 was the pathogenic bacterium that causes the disease. Based on a 16S rRNA phylogenetic tree, isolate DE2 belongs to the genus Erwinia. Biolog and API 20E results also indicated that isolate DE2 is an undescribed species of Erwinia. Isolate DE2 was negative for oxidase. Subsequently, the complete genome sequence of isolate DE2 was determined and compared to the complete genome sequences of 29 other Erwinia species based on digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses. The ANI and dDDH values between strain DE2 and Erwinia species were both below the species thresholds (ANI < 95-96%, dDDH<70%), suggesting that isolate DE2 is a new species of Erwinia. We will temporarily name strain DE2 as Erwinia pyri sp. nov. There were 548 predicted virulence factors in the genome of strain DE2, comprising 534 on the chromosome and 5 in the plasmids. The whole genome sequence of strain DE2 has been submitted to the NCBI database (ASM3075845v1) with accession number GCA_030758455.1. The strain DE2 has been preserved at the China Center for Type Culture Collection (CCTCC) under the deposit number CCTCC AB 2024080. This study represents the initial report of a potentially new bacterial species in the genus Erwinia that causes a novel pear dieback disease. The findings provide a valuable strain resource for the study of the genus Erwinia and establish a robust theoretical foundation for the prevention and control of emerging pear dieback diseases.
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Affiliation(s)
| | | | | | | | - Zhenfen Zhang
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Sino-U.S. Centers for Grazing Land Ecosystem Sustainability, Ministry of Science and Technology, Pratacultural College, Gansu Agricultural University, Lanzhou, China
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Efimochkina NR, Zinurova EE, Smotrina YV, Stetsenko VV, Polyanina AS, Markova YM, Sheveleva SA. Assessment of the Sensitivity of Foodborne Cronobacter spp. Strains and Other Enterobacteria to Temperature Stresses and Chlorine-Containing Biocides. Bull Exp Biol Med 2024; 177:98-103. [PMID: 38963599 DOI: 10.1007/s10517-024-06139-3] [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: 12/05/2023] [Indexed: 07/05/2024]
Abstract
We examined the effects of elevated temperatures and biocides on survivability of food isolates of Cronobacter spp. (C. sakazakii) and concomitant enterobacteriaceae obtained in microbiological control of infant nutrition products. Increased resistance of certain strains of Cronobacter, Enterobacter cloacae, and Pantoea spp. to thermal processing was revealed. Salmonella, Pantoea, and Cronobacter bacteria were least sensitive to antimicrobial action of chlorine-containing agents. The above properties varied in the strains of the same species. Specifically, only two of three examined isolates of Cronobacter spp. demonstrated lower sensitivity to heat in comparison with the enterobacterial test-cultures of other species.
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Affiliation(s)
- N R Efimochkina
- Federal Research Centre of Nutrition and Biotechnology, Moscow, Russia.
| | - E E Zinurova
- Federal Research Centre of Nutrition and Biotechnology, Moscow, Russia
| | - Yu V Smotrina
- Federal Research Centre of Nutrition and Biotechnology, Moscow, Russia
| | - V V Stetsenko
- Federal Research Centre of Nutrition and Biotechnology, Moscow, Russia
| | - A S Polyanina
- Federal Research Centre of Nutrition and Biotechnology, Moscow, Russia
| | - Yu M Markova
- Federal Research Centre of Nutrition and Biotechnology, Moscow, Russia
| | - S A Sheveleva
- Federal Research Centre of Nutrition and Biotechnology, Moscow, Russia
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Yan Y, Xu J, Huang W, Fan Y, Li Z, Tian M, Ma J, Lu X, Liang J. Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China. Microorganisms 2024; 12:911. [PMID: 38792738 PMCID: PMC11124135 DOI: 10.3390/microorganisms12050911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Microbial communities inhabiting sedimentary environments in river source regions serve as pivotal indicators of pristine river ecosystems. While the correlation between antibiotic resistome and pathogenicity with core gut bacteria in humans is well established, there exists a significant knowledge gap concerning the interaction of antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) with specific microbes in river source basins, often referred to as "terrestrial gut". Understanding the microbial composition, including bacteria and resident genetic elements such as ARGs, HPB, Mobile Genetic Elements (MGEs), and Virulence Factors (VFs), within natural habitats against the backdrop of global change, is imperative. To address this gap, an enrichment-based culturomics complementary along with metagenomics was conducted in this study to characterize the microbial biobank and provide preliminary ecological insights into profiling the dissemination of ARGs in the Lancang River Source Basin. Based on our findings, in the main stream of the Lancang River Source Basin, 674 strains of bacteria, comprising 540 strains under anaerobic conditions and 124 under aerobic conditions, were successfully isolated. Among these, 98 species were identified as known species, while 4 were potential novel species. Of these 98 species, 30 were HPB relevant to human health. Additionally, bacA and bacitracin emerged as the most abundant ARGs and antibiotics in this river, respectively. Furthermore, the risk assessment of ARGs predominantly indicated the lowest risk rank (Rank Ⅳ) in terms of endangering human health. In summary, enrichment-based culturomics proved effective in isolating rare and unknown bacteria, particularly under anaerobic conditions. The emergence of ARGs showed limited correlation with MGEs, indicating minimal threats to human health within the main stream of the Lancang River Source Basin.
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Affiliation(s)
- Yi Yan
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Jialiang Xu
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Wenmin Huang
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Yufeng Fan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Zhenpeng Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Mingkai Tian
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Jinsheng Ma
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Xin Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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Carobbi A, Leo K, Di Nepi S, Bosis E, Salomon D, Sessa G. PIX is an N-terminal delivery domain that defines a class of polymorphic T6SS effectors in Enterobacterales. Cell Rep 2024; 43:114015. [PMID: 38568810 DOI: 10.1016/j.celrep.2024.114015] [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: 07/18/2023] [Revised: 02/13/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
The type VI secretion system (T6SS), a widespread protein delivery apparatus, plays a role in bacterial competition by delivering toxic effectors into neighboring cells. Identifying new T6SS effectors and deciphering the mechanism that governs their secretion remain major challenges. Here, we report two orphan antibacterial T6SS effectors in the pathogen Pantoea agglomerans (Pa). These effectors share an N-terminal domain, Pantoea type six (PIX), that defines a widespread class of polymorphic T6SS effectors in Enterobacterales. We show that the PIX domain is necessary and sufficient for T6SS-mediated effector secretion and that PIX binds to a specialized Pa VgrG protein outside its C-terminal toxic domain. Our findings underline the importance of identifying and characterizing delivery domains in polymorphic toxin classes as a tool to reveal effectors and shed light on effector delivery mechanisms.
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Affiliation(s)
- Andrea Carobbi
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel; School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ksenia Leo
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel; School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Simone Di Nepi
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Guido Sessa
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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Ajeeb TT, Gonzalez E, Solomons NW, Vossenaar M, Koski KG. Human milk microbiome: associations with maternal diet and infant growth. Front Nutr 2024; 11:1341777. [PMID: 38529196 PMCID: PMC10962684 DOI: 10.3389/fnut.2024.1341777] [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: 11/20/2023] [Accepted: 02/22/2024] [Indexed: 03/27/2024] Open
Abstract
Introduction Ingestion of human milk (HM) is identified as a significant factor associated with early infant gut microbial colonization, which has been associated with infant health and development. Maternal diet has been associated with the HM microbiome (HMM). However, a few studies have explored the associations among maternal diet, HMM, and infant growth during the first 6 months of lactation. Methods For this cross-sectional study, Mam-Mayan mother-infant dyads (n = 64) were recruited from 8 rural communities in the Western Highlands of Guatemala at two stages of lactation: early (6-46 days postpartum, n = 29) or late (109-184 days postpartum, n = 35). Recruited mothers had vaginally delivered singleton births, had no subclinical mastitis or antibiotic treatments, and breastfed their infants. Data collected at both stages of lactation included two 24-h recalls, milk samples, and infant growth status indicators: head-circumference-for-age-z-score (HCAZ), length-for-age-z-score (LAZ), and weight-for-age-z-score (WAZ). Infants were divided into subgroups: normal weight (WAZ ≥ -1SD) and mildly underweight (WAZ < -1SD), non-stunted (LAZ ≥ -1.5SD) and mildly stunted (LAZ < -1.5SD), and normal head-circumference (HCAZ ≥ -1SD) and smaller head-circumference (HCAZ < -1SD). HMM was identified using 16S rRNA gene sequencing; amplicon analysis was performed with the high-resolution ANCHOR pipeline, and DESeq2 identified the differentially abundant (DA) HMM at the species-level between infant growth groups (FDR < 0.05) in both early and late lactation. Results Using both cluster and univariate analyses, we identified (a) positive correlations between infant growth clusters and maternal dietary clusters, (b) both positive and negative associations among maternal macronutrient and micronutrient intakes with the HMM at the species level and (c) distinct correlations between HMM DA taxa with maternal nutrient intakes and infant z-scores that differed between breast-fed infants experiencing growth faltering and normal growth in early and late lactation. Conclusion Collectively, these findings provide important evidence of the potential influence of maternal diet on the early-life growth of breastfed infants via modulation of the HMM.
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Affiliation(s)
- Tamara T. Ajeeb
- School of Human Nutrition, McGill University, Montreal, QC, Canada
- Department of Clinical Nutrition, College of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill Genome Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Noel W. Solomons
- Center for Studies of Sensory Impairment, Aging and Metabolism (CeSSIAM), Guatemala City, Guatemala
| | - Marieke Vossenaar
- Center for Studies of Sensory Impairment, Aging and Metabolism (CeSSIAM), Guatemala City, Guatemala
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Delik E, Eroğlu B, Tefon-Öztürk BE. Evaluation of the in vitro effects of concentrations of antibiotics on three Enterobacteriaceae isolates. World J Microbiol Biotechnol 2024; 40:73. [PMID: 38240926 PMCID: PMC10799096 DOI: 10.1007/s11274-023-03877-w] [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: 11/21/2023] [Accepted: 12/17/2023] [Indexed: 01/22/2024]
Abstract
Due to the misuse and overuse of antibiotics, bacteria are now exposed to sub-minimum inhibitory concentrations (sub-MICs) of antibiotics in various environments. In recent years, exposure of bacteria to sub-MICs of antibiotics has led to the widespread emergence of antibiotic-resistant bacteria. In this study, three bacterial species from the Enterobacteriaceae family (Raoultella ornithinolytica, Pantoea agglomerans and Klebsiella quasivariicola) were isolated from water. The antibiotic susceptibility of these bacteria to 16 antibiotics was then investigated. The effects of sub-MICs of four selected antibiotics (kanamycin, chloramphenicol, meropenem, and ciprofloxacin) on the growth, biofilm formation, surface polysaccharide production, siderophore production, morphology, and expression of the translational/transcriptional regulatory transformer gene rfaH of these bacteria were analysed. The MICs of kanamycin, chloramphenicol, meropenem, and ciprofloxacin were determined to be 1, 2, 0.03 and 0.03 µg/mL for R. ornithinolytica; 0.6, 6, 0.03 and 0.05 µg/mL for P. agglomerans; and 2, 5, 0.04 and 0.2 µg/mL for K. quasivariicola. The growth kinetics and biofilm formation ability decreased for all three isolates at sub-MICs. The surface polysaccharides of R. ornithinolytica and P. agglomerans increased at sub-MICs. There was no significant change in the siderophore activities of the bacterial isolates, with the exception of MIC/2 meropenem in R. ornithinolytica and MIC/2 kanamycin in K. quasivariicola. It was observed that the sub-MICs of meropenem and ciprofloxacin caused significant changes in bacterial morphology. In addition, the expression of rfaH in R. ornithinolytica and K. quasivariicola increased with the sub-MICs of the selected antibiotics.
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Affiliation(s)
- Eda Delik
- Biology Department, Faculty of Science, Akdeniz University, 07070, Antalya, Turkey
| | - Berfin Eroğlu
- Biology Department, Faculty of Science, Akdeniz University, 07070, Antalya, Turkey
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10
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Haley E, Luke N, Mathur M, Festa RA, Wang J, Jiang Y, Anderson LA, Baunoch D. The Prevalence and Association of Different Uropathogens Detected by M-PCR with Infection-Associated Urine Biomarkers in Urinary Tract Infections. Res Rep Urol 2024; 16:19-29. [PMID: 38221993 PMCID: PMC10787514 DOI: 10.2147/rru.s443361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/16/2023] [Indexed: 01/16/2024] Open
Abstract
Background Many emerging uropathogens are currently identified by multiplex polymerase chain reaction (M-PCR) in suspected UTI cases. Standard urine culture (SUC) has significantly lower detection rates, raising questions about whether these organisms are associated with UTIs and truly cause inflammation. Objective To determine if microbes detected by M-PCR were likely causative of UTI by measuring inflammatory biomarkers in the urine of symptomatic patients. Design Setting and Participants Midstream voided urine was collected from subjects ≥60 years presenting to urology clinics with symptoms of UTI (n = 1132) between 01/2023 and 05/2023. Microbe detection was by M-PCR and inflammation-associated biomarker (neutrophil gelatinase-associated lipocalin, interleukin 8, and interleukin 1β) was by enzyme-linked immunosorbent assay. Biomarker positivity was measured against individual and groups of organisms, E. coli and non-E. coli cases, emerging uropathogens, monomicrobial and polymicrobial cases. Outcome Measurements and Statistical Analysis Distributions were compared using 2-sample Wilcoxon Rank Sum test with 2-tailed p-values < 0.05 considered statistically significant. Results and Limitations M-PCR was positive in 823 (72.7%) specimens with 28 of 30 (93%) microorganisms/groups detected. Twenty-six of twenty-eight detected microorganisms/groups (93%) had ≥2 biomarkers positive in >66% of cases. Both non-E. coli cases and E. coli cases had significant biomarker positivity (p < 0.05). Limitations were that a few organisms had low prevalence making inferences about their individual significance difficult. Conclusion The majority of microorganisms identified by M-PCR were associated with active inflammation measured by biomarker positivity, indicating they are likely causative of UTIs in symptomatic patients. This includes emerging uropathogens frequently not detected by standard urine culture.
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Affiliation(s)
- Emery Haley
- Department of Clinical Research, Pathnostics, Irvine, CA, USA
| | - Natalie Luke
- Department of Clinical Research, Pathnostics, Irvine, CA, USA
| | - Mohit Mathur
- Department of Medical Affairs, Pathnostics, Irvine, CA, USA
| | - Richard A Festa
- Department of Research and Development, Pathnostics, Irvine, CA, USA
| | - Jimin Wang
- Department of Statistical Analysis, Stat4Ward, Pittsburgh, PA, USA
| | - Yan Jiang
- Department of Statistical Analysis, Stat4Ward, Pittsburgh, PA, USA
| | - Lori A Anderson
- L.Anderson Diagnostic Market Access Consulting, San Diego, CA, USA
| | - David Baunoch
- Department of Research and Development, Pathnostics, Irvine, CA, USA
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Casale R, Boattini M, Bianco G, Comini S, Corcione S, Garazzino S, Silvestro E, De Rosa FG, Cavallo R, Costa C. Bloodstream Infections by Pantoea Species: Clinical and Microbiological Findings from a Retrospective Study, Italy, 2018-2023. Antibiotics (Basel) 2023; 12:1723. [PMID: 38136757 PMCID: PMC10740582 DOI: 10.3390/antibiotics12121723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
(1) Background: The widespread use of MALDI-TOF coupled to mass spectrometry has improved diagnostic accuracy by identifying uncommon bacteria. Among Enterobacterales, Pantoea species have been seen to be implicated in several human infections, but their clinical and microbiological framework is currently based on a few anecdotal reports. (2) Methods: We conducted this five-year (2018-2023) single-center study aimed at investigating the prevalence and clinical and microbiological findings of Pantoea species bloodstream infections. (3) Results: Among the 4996 bloodstream infection Gram-negative isolates collected during the study period, Pantoea species accounted for 0.4% (n = 19) of isolates from 19 different patients, 5 of them being pediatric cases. Among Pantoea species isolates, P. agglomerans was the most frequently detected (45%; n = 9) followed by P. eucrina (30%; n = 6) and P. septica (15%; n = 3). Malignancy (35.7%) in adults and malignancy (40%) and cerebrovascular disease following meconium aspiration (40%) in pediatric patients as comorbidities and shivering and/or fever following parenteral infusion (36.8%) as a symptom/sign of Pantoea species bloodstream infection onset were the most frequently observed clinical features. Among adults, primary bloodstream infection was the most frequent (50%), whereas among pediatric patients, the most commonly identified sources of infection were catheter-related (40%) and the respiratory tract (40%). Overall, Pantoea species bloodstream infection isolates displayed high susceptibility to all the antibiotics except for ampicillin (63.2%), fosfomycin (73.7%), and piperacillin/tazobactam (84.2%). Targeted antibiotic treatment was prescribed as monotherapy for adults (71.4%) and combination therapy for pediatric patients (60%). The most prescribed antibiotic regimens were piperacillin/tazobactam (21.4%) in adults and meropenem- (40%) and aminoglycoside-containing (40%) antibiotics in pediatric patients. The overall 28-day all-cause mortality rate was 5.3% (n = 1). (4) Conclusions: The prevalence and 28-day mortality rate of Pantoea species bloodstream infections were low. The prescription of targeted therapy including broad-spectrum antibiotics could indicate an underestimation of the specific involvement of the Pantoea species in the onset of the disease, warranting further studies defining their pathogenic potential.
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Affiliation(s)
- Roberto Casale
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
| | - Matteo Boattini
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
- Lisbon Academic Medical Centre, 1649-028 Lisbon, Portugal
| | - Gabriele Bianco
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
| | - Sara Comini
- Operative Unit of Clinical Pathology, Carlo Urbani Hospital, 60035 Jesi, Italy
| | - Silvia Corcione
- Department of Medical Sciences, Infectious Diseases, University of Turin, 10124 Turin, Italy
| | - Silvia Garazzino
- Infectious Diseases Unit, Department of Pediatric and Public Health Sciences, Regina Margherita Children’s Hospital, 10126 Turin, Italy
| | - Erika Silvestro
- Infectious Diseases Unit, Department of Pediatric and Public Health Sciences, Regina Margherita Children’s Hospital, 10126 Turin, Italy
| | - Francesco Giuseppe De Rosa
- Department of Medical Sciences, Infectious Diseases, University of Turin, 10124 Turin, Italy
- Unit of Infectious Diseases, Cardinal Massaia Hospital, 14100 Asti, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
| | - Cristina Costa
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
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12
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Shetty S, Kamble A, Singh H. Insights into the Potential Role of Plasmids in the Versatility of the Genus Pantoea. Mol Biotechnol 2023:10.1007/s12033-023-00960-3. [PMID: 38007817 DOI: 10.1007/s12033-023-00960-3] [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: 06/16/2023] [Accepted: 10/23/2023] [Indexed: 11/28/2023]
Abstract
In the past two decades, 25 different species of the genus Pantoea within the Enterobacteriaceae family, have been isolated from different environmental niches. These species have a wide range of biological roles. Versatility in functions and hosts indicate that this genus has undergone extensive genetic diversification, which can be attributed to the different extra-chromosomal genetic elements or plasmids found across this genus. We have analyzed the functions of these plasmids and categorized them into four major groups for a better understanding of their future applications. The first and second group includes plasmids that contribute to genetic diversification and pathogenicity, respectively. The third group comprises cryptic plasmids of Pantoea. The last group includes plasmids that play a role in the metabolic versatility of the genus Pantoea. We have analyzed the data available up to May 2023 from two databases (viz; NCBI and PLSDB). In our analysis we have found a vast gap in knowledge. Complete gene annotations are available for only a few of the plasmids. This review highlights these challenges as an avenue for future research.
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Affiliation(s)
- Srinidhi Shetty
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, 400056, India
| | - Asmita Kamble
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, 400056, India
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, 400056, India.
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13
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Zhang Y, Fan Y, Zhan Y, Wang H, Li X, Wang H, Feng T, Shi L, Wang J, Wang H, Lu Z. Genomic characterization of Pantoea anthophila strain UI705 causing urinary tract infections in China. Front Cell Infect Microbiol 2023; 13:1208473. [PMID: 37520438 PMCID: PMC10375405 DOI: 10.3389/fcimb.2023.1208473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Pantoea anthophila (P. anthophila) is a Gram-negative bacterium initially isolated from Impatiens balsamina in India. P. anthophila has been characterized with low pathogenicity, and no human infections caused by this organism have been reported yet. We report the first case of urinary tract infection caused by P. anthophila in a 73-year-old man after bladder cancer surgery. Methods The bacterial isolate gained from urine was named UI705 and identified as P. anthophila by MALDI-TOF mass spectrometry. The genome sequencing and analysis were performed to further characterize the pathogenesis of the clinical isolate. Result and discussion To the best of our knowledge, this is the first report of human infection caused by P. anthophila in China. The draft genome sequence of P. anthophila UI705 provides a fundamental resource for subsequent investigation of its virulence factors, antibiotic resistance, host-pathogen interactions, and comparative genomics of genus Pantoea.
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Affiliation(s)
- Yingmiao Zhang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Fan
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhan
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Department of Medical Laboratory, Shiyan Hospital of Integrated Traditional and Western Medicine, Shiyan, China
| | - Xun Li
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tian Feng
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lifeng Shi
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongxin Lu
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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14
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Miura K, Tanaka M, Date M, Ito M, Mizuno N, Mizuno K. Comparison of bacterial profiles in human milk from mothers of term and preterm infants. Int Breastfeed J 2023; 18:29. [PMID: 37291566 DOI: 10.1186/s13006-023-00563-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/14/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Reducing the disposal of donated human milk (HM) is important for efficient management of human milk banks (HMBs). The presence of bacteria growth is the main factor that contributes to the disposal of donated HM. The bacterial profile in HM is suspected to differ between term and preterm mothers, with HM from preterm mothers containing more bacteria. Thus, elucidation of the causes of bacterial growth in preterm and term HM may help to reduce the disposal of donated preterm HM. This study compared the bacterial profiles of HM between mothers of term infants and mothers of preterm infants. METHODS This pilot study was conducted in the first Japanese HMB, which was initiated in 2017. This study analyzed 214 human milk samples (term: 75, preterm: 139) donated by 47 registered donors (term: 31, preterm: 16) from January to November 2021. Bacterial culture results in term and preterm HM were retrospectively reviewed in May 2022. Differences in total bacterial count and bacterial species count per batch were analyzed using the Mann-Whitney U test. Bacterial loads were analyzed using the Chi-square test or Fisher's exact test. RESULTS The disposal rate did not significantly differ between term and preterm groups (p = 0.77), but the total amount of disposal was greater in the preterm group (p < 0.01). Coagulase-negative Staphylococci, Staphylococcus aureus, and Pseudomonas fluorescens were frequently found in both types of HM. Serratia liquefaciens (p < 0.001) and two other bacteria were present in term HM; a total of five types of bacteria, including Enterococcus faecalis and Enterobacter aerogenes (p < 0.001) were present in preterm HM. The median (interquartile range) total bacterial counts were 3,930 (435-23,365) colony-forming units (CFU)/mL for term HM and 26,700 (4,050-334,650) CFU/mL for preterm HM (p < 0.001). CONCLUSIONS This study revealed that HM from preterm mothers had a higher total bacterial count and different types of bacteria than HM from term mothers. Additionally, preterm infants can receive nosocomial-infection-causing bacteria in the NICU through their mother's milk. Enhanced hygiene instructions for preterm mothers may reduce the disposal of valuable preterm human milk, along with the risk of HM pathogen transmission to infants in NICUs.
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Affiliation(s)
- Kumiko Miura
- The Nippon Foundation Human Milk Bank, Nihonbashi-koamicho Square Building 1F, 17-10 Nihonbashi-koamicho, Chuo-ku, Tokyo, 103-0016, Japan
- Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu-shi, Oita, 879-5593, Japan
| | - Miori Tanaka
- The Nippon Foundation Human Milk Bank, Nihonbashi-koamicho Square Building 1F, 17-10 Nihonbashi-koamicho, Chuo-ku, Tokyo, 103-0016, Japan
| | - Midori Date
- The Nippon Foundation Human Milk Bank, Nihonbashi-koamicho Square Building 1F, 17-10 Nihonbashi-koamicho, Chuo-ku, Tokyo, 103-0016, Japan
| | - Mizuho Ito
- The Nippon Foundation Human Milk Bank, Nihonbashi-koamicho Square Building 1F, 17-10 Nihonbashi-koamicho, Chuo-ku, Tokyo, 103-0016, Japan
| | - Noriko Mizuno
- Japan Human Milk Bank Association, 4-4 Nihonbashi-Hisamatsucho, Chuo-ku, Tokyo, 103-8480, Japan
| | - Katsumi Mizuno
- The Nippon Foundation Human Milk Bank, Nihonbashi-koamicho Square Building 1F, 17-10 Nihonbashi-koamicho, Chuo-ku, Tokyo, 103-0016, Japan.
- Japan Human Milk Bank Association, 4-4 Nihonbashi-Hisamatsucho, Chuo-ku, Tokyo, 103-8480, Japan.
- Department of Pediatrics, Showa University of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8666, Japan.
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15
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Susanto M, Dunning J, Chew R. Pantoea abscess mimicking sarcoma in a HTLV-1-infected Indigenous Australian man: Case report and literature review. Clin Case Rep 2023; 11:e7351. [PMID: 37215972 PMCID: PMC10196424 DOI: 10.1002/ccr3.7351] [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: 10/07/2022] [Revised: 11/11/2022] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Gram-negative bacteria of the genus Pantoea are emerging bacterial causes of diverse sporadic and outbreak-linked infections. Chronic Pantoea abscesses are unusual and may give rise to a differential diagnosis of malignancy. Foreign body retention and host immune defects may be risk factors for such chronic infections.
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Affiliation(s)
- Maja Susanto
- Infectious Diseases UnitRedcliffe HospitalRedcliffeQueenslandAustralia
| | - Jacki Dunning
- Department of SurgeryAlice Springs HospitalAlice SpringsNorthern TerritoryAustralia
| | - Rusheng Chew
- Infectious Diseases UnitAlice Springs HospitalAlice SpringsNorthern TerritoryAustralia
- Faculty of MedicineUniversity of QueenslandBrisbaneQueenslandAustralia
- Centre for Tropical Medicine and Global HealthUniversity of OxfordOxfordUK
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16
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Belykh OI, Sorokovikova EG, Tomberg IV, Fedorova GA, Kuzmin AV, Krasnopeev AY, Suslova MY, Potapov SA, Belykh TI, Norovsuren J, Galachyants AD, Tikhonova IV. Water Quality, Toxicity and Diversity of Planktonic and Benthic Cyanobacteria in Pristine Ancient Lake Khubsugul (Hövsgöl), Mongolia. Toxins (Basel) 2023; 15:toxins15030213. [PMID: 36977104 PMCID: PMC10053237 DOI: 10.3390/toxins15030213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
For the first time, microcystin-producing cyanobacteria have been detected in Khubsugul, which is ancient, pristine and one of the world’s largest lakes. The microcystin synthetase genes belonged to the genera Nostoc, Microcystis and possibly Snowella spp. No microcystins were found in the water of the lake. Using the HPLC-HRMS/TOF, five microcystin congeners were identified in biofilms from stony substrates sampled in the coastal zone. The concentration of microcystins in biofilms was low: 41.95 µg g−1 d. wt. by ELISA and 55.8 µg g−1 d. wt. using HPLC. The taxonomic composition of planktonic and benthic cyanobacterial communities was determined by means of microscopy and high-throughput sequencing of 16S rDNA amplicons. Nostocales cyanobacteria dominated benthos of Lake Khubsugul and Synechococcales—plankton. The abundance of cyanobacteria was low both in plankton and benthos; there was no mass development of cyanobacteria. Hydrochemical and microbiological analyses showed that the water in the lake was clean; the number of faecal microorganisms was significantly below the acceptable guideline values. Hydrochemical and hydrophysical parameters, and the concentration of chlorophyll a, were low and within the range of values recorded in the 1970s to 1990s, and corresponded to the oligotrophic state of the lake. There were no signs of anthropogenic eutrophication of the lake and no conditions for the cyanobacterial blooms.
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Affiliation(s)
- Olga I. Belykh
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
- Correspondence: (O.I.B.); (E.G.S.)
| | - Ekaterina G. Sorokovikova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
- Correspondence: (O.I.B.); (E.G.S.)
| | - Irina V. Tomberg
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Galina A. Fedorova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Anton V. Kuzmin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Andrey Yu. Krasnopeev
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Maria Yu. Suslova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Sergey A. Potapov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Tatiana I. Belykh
- Institute for Culture, Social Communication and Information Technology, Baikal State University, 11 Lenin Str., Irkutsk 664003, Russia
| | - Jadambaa Norovsuren
- Institute of Biology of the Mongolian Academy of Sciences, 54B Peace Avenue, Bayanzurkh District, Ulaanbaatar 13330, Mongolia
| | - Agnia D. Galachyants
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
| | - Irina V. Tikhonova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Str., Irkutsk 664033, Russia
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Zrelovs N, Jansons J, Kazaka T, Kazaks A, Dislers A. Three Phages One Host: Isolation and Characterization of Pantoea agglomerans Phages from a Grasshopper Specimen. Int J Mol Sci 2023; 24:ijms24031820. [PMID: 36768143 PMCID: PMC9915841 DOI: 10.3390/ijms24031820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
The bacterial genus Pantoea comprises species found in a variety of different environmental sources. Pantoea spp. are often recovered from plant material and are capable of both benefitting the plants and acting like phytopathogens. Some species of Pantoea (including P. agglomerans) are considered opportunistic human pathogens capable of causing various infections in immunocompromised subjects. In this study, a strain of P. agglomerans (identified by 16S rRNA gene sequencing) was isolated from a dead specimen of an unidentified Latvian grasshopper species. The retrieved strain of P. agglomerans was then used as a host for the potential retrieval of phages from the same source material. After rounds of plaque purification and propagation, three high-titer lysates corresponding to putatively distinct phages were acquired. Transmission electron microscopy revealed that one of the phages was a myophage with an unusual morphology, while the two others were typical podophages. Whole-genome sequencing (WGS) was performed for each of these isolated phages. Genome de novo assembly and subsequent functional annotation confirmed that three different strictly lytic phages were isolated. Elaborate genomic characterization of the acquired phages was performed to elucidate their place within the so-far-uncovered phage diversity.
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Merla C, Mileto I, Gaiarsa S, Achille C, Ghirardello S, Corbella M, Baldanti F, Cambieri P. Surveillance in a Neonatal Intensive Care Unit Allowed the Isolation of a Strain of VIM-Producing Pantoea brenneri. Antibiotics (Basel) 2023; 12:antibiotics12010098. [PMID: 36671299 PMCID: PMC9854652 DOI: 10.3390/antibiotics12010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/22/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023] Open
Abstract
Here, we describe the isolation of a strain of the genus Pantoea encoding a VIM carbapenemase, the first to our knowledge. The strain, isolated from a rectal swab of a 10-day-old newborn admitted to a neonatal intensive care unit (NICU), was identified through whole-genome sequencing analyses as Pantoea brenneri. The strain harbored the carbapenemases gene blaVIM-1. The prompt application of contact measures and the isolation of the newborn prevented the dissemination of VIM-producing P. brenneri and of the plasmid carrying the VIM-1 gene to other newborns.
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Affiliation(s)
- Cristina Merla
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Irene Mileto
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
- Scuola di Specializzazione in Microbiologia e Virologia, Università degli Studi di Pavia, 27100 Pavia, Italy
| | - Stefano Gaiarsa
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Cristian Achille
- Neonatologia e Terapia Intensiva Neonatale, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Stefano Ghirardello
- Neonatologia e Terapia Intensiva Neonatale, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marta Corbella
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
- Correspondence:
| | - Fausto Baldanti
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
- Department of Clinical: Surgical, Diagnostic and Pediatric Sciences, Università degli Studi di Pavia, 27100 Pavia, Italy
| | - Patrizia Cambieri
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Dahm S, Lee G, Cleland H, Menezes H, Ng S. The use of carbon dioxide and intense pulsed light laser for the treatment of hypertrophic burn scars: A case series. Scars Burn Heal 2023; 9:20595131231202103. [PMID: 38022893 PMCID: PMC10655654 DOI: 10.1177/20595131231202103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Introduction Hypertrophic scarring is a common and debilitating consequence of burn scars. While there is limited evidence for current treatment options, laser therapy has been shown to be effective, low risk and minimally invasive. This study assesses the use of carbon dioxide lasers and intense pulsed light devices in the treatment of hypertrophic burn scars. Methods In this case series, patients were recruited from a hypertrophic burn scar waitlist and completed a Patient and Observer Scar Assessment Scale prior to and six weeks after laser therapy. The Nordlys (intense pulsed light) and CO2RE (carbon dioxide) systems from Candela Medical were used, with a range of settings used depending on the assessment of the burn scar. The differences between scores were calculated for the total Patient and Observer Scar Assessment Scale score, pain, itch, colour, stiffness, thickness, irregularity and the overall opinion of the scar. Statistical analysis was completed using a paired, two-tailed student T test. Results A total of 31 patients were recruited for this trial with a range of scar locations, surface areas and mechanism of burn injury. The calculated difference in mean showed a significant reduction for the overall Patient and Observer Scar Assessment Scale score (1.93, p < 0.0001), pain (1.39, p = 0.0002), itch (1.84, p = 0.0002), colour (1.97, p < 0.0001), stiffness (2.47, p < 0.0001), thickness (2.1, p < 0.0001), irregularity (1.89, p < 0.0001) and overall opinion (1.58, p = 0.0003). Conclusion Current management options for hypertrophic scarring have limited evidence. Laser therapy presents a minimally invasive procedure that can be completed under topical anaesthetic and has shown to be effective following a single treatment of combined carbon dioxide laser and intense pulsed light device therapy. Lay Summary Many people will suffer a burn injury throughout their life and up to almost 3 out of 4 people with burn injuries will suffer from hypertrophic scars (a thickened, red and itchy scar). These scars cause distress both due to their appearance and their reduction of function, particularly over a joint or muscle. Laser therapy, in which different wave lengths of light (pulsed light) or gas (carbon dioxide) target the scar, has been found to be effective and have minimal side effects in the management of hypertrophic scars. While individual lasers have been assessed and found to be effective and low risk, the combined use of multiple lasers on the same scar has not been extensively studied. We studied the effectiveness of both light and gas laser therapies on hypertrophic scars. Patients with hypertrophic scars completed a questionnaire that focused on their perspective of their scar (pain, itch, stiffness, thickness, irregularity, overall opinion) prior to the treatment. The patients then underwent laser therapy (with local anaesthetic gel) with either pulsed light and/or carbon dioxide (gas) laser. The type of laser used was decided by the clinician performing the therapy depending on scar location and thickness. Patients then re-completed the subjective survey six weeks following the laser therapy, and the results compared. We learnt that laser therapy (both light, gas and a combination of both) are effective (and low risk) in reducing the subjective burden of the scar for the patient.
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Affiliation(s)
- Sophia Dahm
- Victorian Adult Burns Service, Alfred Hospital, Melbourne, Australia
| | - Geoffrey Lee
- Victorian Adult Burns Service, Alfred Hospital, Melbourne, Australia
| | - Heather Cleland
- Victorian Adult Burns Service, Alfred Hospital, Melbourne, Australia
| | - Hana Menezes
- Victorian Adult Burns Service, Alfred Hospital, Melbourne, Australia
| | - Sally Ng
- Victorian Adult Burns Service, Alfred Hospital, Melbourne, Australia
- Department of Plastic and Reconstructive Surgery, Austin Health, Melbourne, Australia
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20
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Grami E, Laadouze I, Ben Tiba S, Hafiane A, Sealey KS, Saidi N. Isolation, Characterization, and Comparative Genomic Analysis of vB_Pd_C23, a Novel Bacteriophage of Pantoea dispersa. Curr Microbiol 2022; 80:52. [PMID: 36562822 DOI: 10.1007/s00284-022-03152-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Pantoea bacteria species cause human animal infections, and contribute to soil and aquatic environmental pollution. A novel bacteriophage, vB_Pd_C23 was isolated from a Tunisian wastewater system and represents the first new phage infecting P. dispersa. Lysis kinetics, electron microscopy, and genomic analyses revealed that the vB_Pd_C23 phage has a head diameter of 50 nm and contractile tail dimensions of 100 nm by 23 nm; vB_Pd_C23 has a linear double-stranded DNA genome consisting of 44,714-bp and 49.66% GC-content. Predicted functions were assigned to 75 open reading frames (ORFs) encoding proteins and one tRNA, the annotation revealed that 21 ORFs encode for unique proteins of yet unknown function with no reliable homologies. This indicates that the new species vB_Pd_C23 exhibits novel viral genes. Phylogenetic analysis along with comparative analyses generating nucleotide identity and similarity of vB_Pd_C23 whole genome suggests that the phage is a candidate for a new genus within the Caudoviricetes Class. The characteristics of this phage could not be attributed to any previous genera recognized by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Emna Grami
- Centre de Recherches et des Technologies des Eaux (CERTE), Laboratoire Eaux, Membranes et Biotechnologies de L'Environnement (LR18CERTE04), Technopark of Borj Cedria, BP 273, 8020, Soliman, Tunisia.,Faculté des Sciences de Bizerte, Université de Carthage, 7021, Carthage, Tunisia
| | - Imen Laadouze
- Centre de Recherches et des Technologies des Eaux (CERTE), Laboratoire Eaux, Membranes et Biotechnologies de L'Environnement (LR18CERTE04), Technopark of Borj Cedria, BP 273, 8020, Soliman, Tunisia.,Faculté des Sciences de Bizerte, Université de Carthage, 7021, Carthage, Tunisia
| | - Saoussen Ben Tiba
- Faculté des Sciences de Bizerte, Université de Carthage, 7021, Carthage, Tunisia
| | - Amor Hafiane
- Centre de Recherches et des Technologies des Eaux (CERTE), Laboratoire Eaux, Membranes et Biotechnologies de L'Environnement (LR18CERTE04), Technopark of Borj Cedria, BP 273, 8020, Soliman, Tunisia
| | | | - Neila Saidi
- Centre de Recherches et des Technologies des Eaux (CERTE), Laboratoire Eaux, Membranes et Biotechnologies de L'Environnement (LR18CERTE04), Technopark of Borj Cedria, BP 273, 8020, Soliman, Tunisia.
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Wicaksono WA, Buko A, Kusstatscher P, Cernava T, Sinkkonen A, Laitinen OH, Virtanen SM, Hyöty H, Berg G. Impact of Cultivation and Origin on the Fruit Microbiome of Apples and Blueberries and Implications for the Exposome. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02157-8. [PMID: 36542126 DOI: 10.1007/s00248-022-02157-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Vegetables and fruits are a crucial part of the planetary health diet, directly affecting human health and the gut microbiome. The objective of our study was to understand the variability of the fruit (apple and blueberry) microbiome in the frame of the exposome concept. The study covered two fruit-bearing woody species, apple and blueberry, two countries of origin (Austria and Finland), and two fruit production methods (naturally grown and horticultural). Microbial abundance, diversity, and community structures were significantly different for apples and blueberries and strongly influenced by the growing system (naturally grown or horticultural) and country of origin (Austria or Finland). Our results indicated that bacterial communities are more responsive towards these factors than fungal communities. We found that fruits grown in the wild and within home gardens generally carry a higher microbial diversity, while commercial horticulture homogenized the microbiome independent of the country of origin. This can be explained by horticultural management, including pesticide use and post-harvest treatments. Specific taxonomic indicators were identified for each group, i.e., for horticultural apples: Pseudomonas, Ralstonia, and Stenotrophomonas. Interestingly, Ralstonia was also found to be enriched in horticultural blueberries in comparison to such that were home and wildly grown. Our study showed that the origin of fruits can strongly influence the diversity and composition of their microbiome, which means that we are exposed to different microorganisms by eating fruits from different origins. Thus, the fruit microbiome needs to be considered an important but relatively unexplored external exposomic factor.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Aisa Buko
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Aki Sinkkonen
- Natural Resources Institute Finland Luke, Turku, Finland
| | - Olli H Laitinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Suvi M Virtanen
- Health and Well-Being Promotion Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Faculty of Social Sciences, Unit of Health Sciences, Tampere University, Tampere, Finland
- Research, Development and Innovation Center, Tampere University Hospital, Tampere, Finland
- Center for Child Health Research, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany.
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Cross-Over Pathogenic Bacteria Detected in Infected Tomatoes ( Solanum lycopersicum L.) and Peppers ( Capsicum annuum L.) in Bulgaria. Pathogens 2022; 11:pathogens11121507. [PMID: 36558841 PMCID: PMC9783152 DOI: 10.3390/pathogens11121507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
The ability of certain human pathogens to adapt to plants without losing their virulence toward people is a major concern today. Thus, the aim of the present work was the investigation of the presence of cross-over pathogenic bacteria in infected tomato and pepper plants. The objects of the study were 21 samples from seven different parts of the plants and three from tomato rhizosphere. In total, 26 strains were isolated, identified by MALDI-TOF, and phenotypically characterized. The PCR amplification of the rpoB gene was applied as an approach for the rapid detection of cross-over pathogens in plant samples. A great bacterial diversity was revealed from tomato samples as nine species were identified (Leclercia adecarboxylata, Pseudesherichia vulneris, Enterobacter cancerogenus, Enterobacter cloacae, Enterobacter bugandensis, Acinetobacter calcoaceticus, Pantoea agglomerans, Pantoea ananatis, and Pectobacterium carotovorum). Polymicrobial contaminations were observed in samples T2 (tomato flower) and T10 (tomato fruit). Five species were identified from pepper samples (P. agglomerans, L. adecarboxylata, Pseudomonas sp., Pseudomonas putida, and Enterococcus sp.). Antibiotic resistance patterns were assigned in accordance with EFSA recommendations. All isolates showed varying resistance to the tested antibiotics. The genetic basis for the phenotypic antibiotic resistance was not revealed. No genes for the virulence factors were found among the population. To our knowledge, this is the first overall investigation of tomato and pepper cross-over pathogenic bacterial populations in Bulgaria.
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Ajeeb TT, Gonzalez E, Solomons NW, Koski KG. Human milk microbial species are associated with infant head-circumference during early and late lactation in Guatemalan mother-infant dyads. Front Microbiol 2022; 13:908845. [PMID: 36466698 PMCID: PMC9709448 DOI: 10.3389/fmicb.2022.908845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/10/2022] [Indexed: 08/27/2023] Open
Abstract
Human milk contains abundant commensal bacteria that colonize and establish the infant's gut microbiome but the association between the milk microbiome and head circumference during infancy has not been explored. For this cross-sectional study, head-circumference-for-age-z-scores (HCAZ) of vaginally delivered breastfed infants were collected from 62 unrelated Mam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala during two stages of lactation, 'early' (6-46 days postpartum, n = 29) or 'late' (109-184 days postpartum, n = 33). At each stage of lactation, infants were divided into HCAZ ≥ -1 SD (early: n = 18; late: n = 14) and HCAZ < -1 SD (early: n = 11; late: n = 19). Milk microbiome communities were assessed using 16S ribosomal RNA gene sequencing and DESeq2 was used to compare the differential abundance (DA) of human milk microbiota with infant HCAZ subgroups at both stages of lactations. A total of 503 ESVs annotated 256 putative species across the 64 human milk samples. Alpha-diversity using Chao index uncovered a difference in microbial community richness between HCAZ ≥ -1 SD and HCAZ < -1 SD groups at late lactation (p = 0.045) but not at early lactation. In contrast, Canonical Analysis of Principal Coordinates identified significant differences between HCAZ ≥ -1 SD and HCAZ < -1 SD at both stages of lactation (p = 0.003); moreover, 26 milk microbial taxa differed in relative abundance (FDR < 0.05) between HCAZ ≥ -1 SD and HCAZ < -1 SD, with 13 differentially abundant at each lactation stage. Most species in the HCAZ ≥ -1 SD group were Streptococcus species from the Firmicutes phylum which are considered human colonizers associated with human milk whereas the HCAZ < -1 SD group at late lactation had more differentially abundant taxa associated with environmentally and 'potentially opportunistic' species belonging to the Actinobacteria genus. These findings suggest possible associations between brain growth of breastfed infants and the milk microbiome during lactation. Importantly, these data provide the first evidence of cross talk between the human milk microbiome and the infant brain that requires further investigation.
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Affiliation(s)
- Tamara T. Ajeeb
- School of Human Nutrition, McGill University, Montréal, QC, Canada
- Department of Clinical Nutrition, College of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill Genome Centre, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada
| | - Noel W. Solomons
- Center for Studies of Sensory Impairment, Aging and Metabolism (CeSSIAM), Guatemala City, Guatemala
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Sulja A, Pothier JF, Blom J, Moretti C, Buonaurio R, Rezzonico F, Smits THM. Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734. BMC Genomics 2022; 23:742. [DOI: 10.1186/s12864-022-08966-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractPantoea agglomerans DAPP-PG 734 was isolated as endophyte from knots (tumors) caused by Pseudomonas savastanoi pv. savastanoi DAPP-PG 722 in olive trees. To understand the plant pathogen-endophyte interaction on a genomic level, the whole genome of P. agglomerans DAPP-PG 734 was sequenced and annotated. The complete genome had a total size of 5′396′424 bp, containing one circular chromosome and four large circular plasmids. The aim of this study was to identify genomic features that could play a potential role in the interaction between P. agglomerans DAPP-PG 734 and P. savastanoi pv. savastanoi DAPP-PG 722. For this purpose, a comparative genomic analysis between the genome of P. agglomerans DAPP-PG 734 and those of related Pantoea spp. was carried out. In P. agglomerans DAPP-PG 734, gene clusters for the synthesis of the Hrp-1 type III secretion system (T3SS), type VI secretion systems (T6SS) and autoinducer, which could play an important role in a plant-pathogenic community enhancing knot formation in olive trees, were identified. Additional gene clusters for the biosynthesis of two different antibiotics, namely dapdiamide E and antibiotic B025670, which were found in regions between integrative conjugative elements (ICE), were observed. The in-depth analysis of the whole genome suggested a characterization of the P. agglomerans DAPP-PG 734 isolate as endophytic bacterium with biocontrol activity rather than as a plant pathogen.
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Lorenzi AS, Bonatelli ML, Chia MA, Peressim L, Quecine MC. Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook. Microorganisms 2022; 10:microorganisms10102072. [PMID: 36296348 PMCID: PMC9610544 DOI: 10.3390/microorganisms10102072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 12/01/2022] Open
Abstract
Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct or indirect mechanisms. Members of this genus contribute to plant growth mainly by increasing the supply of nitrogen, solubilizing ammonia and inorganic phosphate, and producing phytohormones (e.g., auxins). Several other studies have shown the potential of strains of Pantoea spp. to induce systemic resistance and protection against pests and pathogenic microorganisms in cultivated plants. Strains of the species Pantoea agglomerans deserve attention as a pest and phytopathogen control agent. Several of them also possess a biotechnological potential for therapeutic purposes (e.g., immunomodulators) and are implicated in human infections. Thus, the differentiation between the harmful and beneficial strains of P. agglomerans is mandatory to apply this bacterium safely as a biofertilizer or biocontroller. This review specifically evaluates the potential of the strain-associated features of P. agglomerans for bioprospecting and agricultural applications through its biological versatility as well as clarifying its potential animal and human health risks from a genomic point of view.
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Affiliation(s)
- Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Maria Letícia Bonatelli
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH—UFZ, 04318 Leipzig, Germany
| | - Mathias Ahii Chia
- Department of Botany, Ahmadu Bello University, Zaria 810211, Nigeria
| | - Leonardo Peressim
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, USP, Piracicaba 13418-900, SP, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, USP, Piracicaba 13418-900, SP, Brazil
- Correspondence:
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Mustapha SS, Ibrahim M, Aliyu S, Abdulkadir I. Enterobacter agglomerans, an uncommon cause of community-acquired bacterial infection in neonates. J Trop Pediatr 2022; 68:6760803. [PMID: 36228308 DOI: 10.1093/tropej/fmac085] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Enterobacter agglomerans formerly termed Erwina herbicola but now called Pantonea agglomerans is a ubiquitous gram-negative bacterium that rarely causes mild and opportunistic infection in humans. Sources of infection are myriad causing both local and systemic disease across all systems of the body. Infection is often fulminant and fatal in neonates. We aim to report another facet of the infection as seen in our centre. Of the 248 neonates recruited into the study, 94 had bacteria isolated from their blood, eight (8.5%) of whom had E. agglomerans sepsis. Infection was acquired from the community though its source could not be determined. The clinical features were non-specific running a mild course. Toxic granulation, elevated immature polymorph count and procalcitonin level was found in 50% and 75% of the neonates. Isolate was sensitive to most tested antibiotics, showing 100% sensitivity to gentamicin and ciprofloxacin and the survival rate was excellent (87.5%).
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Affiliation(s)
| | - Mohammed Ibrahim
- Department of Medical Microbiology, Immunology Federal Teaching Hospital, Gombeand, Zaria
| | - Shamsudin Aliyu
- Department of Medical Microbiology, Ahmadu Bello University, Zaria
| | - Isa Abdulkadir
- Department of Paediatrics, Ahmadu Bello University, Zaria, Zaria
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Mateus C, Martins AR, Toscano C, Matias P, Branco P. Pantoea in Peritoneal Dialysis: A Rare Cause of Peritonitis. Cureus 2022; 14:e26878. [PMID: 35978740 PMCID: PMC9375850 DOI: 10.7759/cureus.26878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2022] [Indexed: 12/02/2022] Open
Abstract
Peritonitis is the most common complication of peritoneal dialysis (PD) and an important cause of PD failure. There are numerous etiological agents, mostly bacteria. Pantoea spp is a rare cause of peritonitis. We describe three cases of Pantoea peritonitis in three PD patients. Previous reports have identified risk factors such as close contact with plants and animals. We review the typical clinical presentation and prognosis. It is fulcral to teach patients about the risks regarding proximity to plants and animals to prevent this type of infection.
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Sun H, Schnürer A, Müller B, Mößnang B, Lebuhn M, Makarewicz O. Uncovering antimicrobial resistance in three agricultural biogas plants using plant-based substrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154556. [PMID: 35306061 DOI: 10.1016/j.scitotenv.2022.154556] [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: 12/20/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Antimicrobial resistance (AMR) is becoming an increasing global concern and the anaerobic digestion (AD) process represents a potential transmission route when digestates are used as fertilizing agents. AMR contaminants, e.g. antibiotic-resistant bacteria (ARB) and plasmid-mediated antibiotic resistance genes (ARGs) have been found in different substrates and AD systems, but not yet been investigated in plant-based substrates. AMR transfer from soils to vegetable microbiomes has been observed, and thus crop material potentially represents a so far neglected AMR load in agricultural AD processes, contributing to AMR spread. In order to test this hypothesis, this study examined the AMR situation throughout the process of three biogas plants using plant-based substrates only, or a mixture of plant-based and manure substrates. The evaluation included a combination of culture-independent and -dependent methods, i.e., identification of ARGs, plasmids, and pathogenic bacteria by DNA arrays, and phylogenetic classification of bacterial isolates and their phenotypic resistance pattern. To our knowledge, this is the first study on AMR in plant-based substrates and the corresponding biogas plant. The results showed that the bacterial community isolated from the investigated substrates and the AD processing facilities were mainly Gram-positive Bacillus spp. Apart from Pantoea agglomerans, no other Gram-negative species were found, either by bacteria culturing or by DNA typing array. In contrast, the presence of ARGs and plasmids clearly indicated the existence of Gram-negative pathogenic bacteria, in both substrate and AD process. Compared with substrates, digestates had lower levels of ARGs, plasmids, and culturable ARB. Thus, digestate could pose a lower risk of spreading AMR than substrates per se. In conclusion, plant-based substrates are associated with AMR, including culturable Gram-positive ARB and Gram-negative pathogenic bacteria-associated ARGs and plasmids. Thus, the AMR load from plant-based substrates should be taken into consideration in agricultural biogas processing.
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Affiliation(s)
- He Sun
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, BioCenter, Box 7025, SE-750 07 Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, BioCenter, Box 7025, SE-750 07 Uppsala, Sweden.
| | - Bettina Müller
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, BioCenter, Box 7025, SE-750 07 Uppsala, Sweden
| | - Bettina Mößnang
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Lange Point 6, 85354 Freising, Germany
| | - Michael Lebuhn
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Lange Point 6, 85354 Freising, Germany
| | - Oliwia Makarewicz
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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Yuvarajan S, Hameed A, Bhagwath Arun A, Kanekar S, Rekha PD. Urease-negative uropathogen Kalamiella piersonii YU22 metabolizes urea by urea carboxylase and allophanate hydrolase enzyme system. Microbiol Res 2022; 263:127142. [DOI: 10.1016/j.micres.2022.127142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
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Cobo F, González A, Pérez-Carrasco V, García-Salcedo JA. Pantoea stewartii: A new pathogen as a cause of bacteremia? ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:278-280. [PMID: 35260365 DOI: 10.1016/j.eimce.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/05/2021] [Accepted: 03/16/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Fernando Cobo
- Servicio de Microbiología e Instituto de Investigación Biosanitaria ibs. GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain.
| | - Adrián González
- Servicio de Microbiología e Instituto de Investigación Biosanitaria ibs. GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Virginia Pérez-Carrasco
- GENYO, Centro de Investigación Genómica y oncológica Pfizer/Universidad de Granada/Gobierno Regional de Andalucía, Granada, Spain
| | - José A García-Salcedo
- Servicio de Microbiología e Instituto de Investigación Biosanitaria ibs. GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain; GENYO, Centro de Investigación Genómica y oncológica Pfizer/Universidad de Granada/Gobierno Regional de Andalucía, Granada, Spain
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Xiang LG, Wang HC, Wang F, Cai LT, Li WH, Hsiang T, Yu ZH. Analysis of Phyllosphere Microorganisms and Potential Pathogens of Tobacco Leaves. Front Microbiol 2022; 13:843389. [PMID: 35572673 PMCID: PMC9100574 DOI: 10.3389/fmicb.2022.843389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
In the tobacco phyllosphere, some of the microbes may have detrimental effects on plant health, while many may be neutral or even beneficial. Some cannot be cultivated, so culture-independent methods are needed to explore microbial diversity. In this study, both metagenetic analysis and traditional culture-dependent methods were used on asymptomatic healthy leaves and symptomatic diseased leaves of tobacco plants. In the culture-independent analysis, asymptomatic leaves had higher microbial diversity and richness than symptomatic leaves. Both asymptomatic and symptomatic leaves contained several potentially pathogenic bacterial and fungal genera. The putative bacterial pathogens, such as species of Pseudomonas, Pantoea, or Ralstonia, and putative fungal pathogens, such as species of Phoma, Cladosporium, Alternaria, Fusarium, Corynespora, and Epicoccum, had a higher relative abundance in symptomatic leaves than asymptomatic leaves. FUNGuild analysis indicated that the foliar fungal community also included endophytes, saprotrophs, epiphytes, parasites, and endosymbionts. PICRUSt analysis showed that the dominant functions of the bacterial community in a symptomatic leaf were cellular processes and environmental information processing. In the other five foliar samples, the dominant functions of the bacterial community were genetic information processing, metabolism, and organismal systems. In the traditional culture-dependent method, 47 fungal strains were isolated from 60 symptomatic tobacco leaf fragments bearing leaf spots. Among them, 21 strains of Colletotrichum (29%), Xylariaceae (14%), Corynespora (14%), Pestalotiopsis (10%), Alternaria (10%), Epicoccum (10%), Byssosphaeria (5%), Phoma (5%), and Diaporthe (5%) all fulfilled Koch’s postulates and were found to cause disease on detached tobacco leaves in artificial inoculation tests. Symptoms on detached leaves caused by three strains of Corynespora cassiicola in artificial inoculation tests were similar to the original disease symptoms in the tobacco field. This study showed that the combined application of culture-dependent and independent methods could give comprehensive insights into microbial composition that each method alone did not reveal.
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Affiliation(s)
- Li-Gang Xiang
- College of Agriculture, Yangtze University, Jingzhou, China
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Han-Cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- *Correspondence: Han-Cheng Wang,
| | - Feng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Feng Wang,
| | - Liu-Ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Wen-Hong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Zhi-He Yu
- College of Life Sciences, Yangtze University, Jingzhou, China
- Zhi-He Yu,
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32
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Successful Treatment of Pantoea agglomerans Bacteremia Using Oral Antibiotics. Case Rep Infect Dis 2022; 2022:6136265. [PMID: 35502196 PMCID: PMC9056224 DOI: 10.1155/2022/6136265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022] Open
Abstract
A 30-year-old female with a medical history of gastrointestinal reflux and intravenous methamphetamine use was admitted to the hospital with complaints of fever and chills. Pantoae agglomerans was isolated in one out of two blood cultures. Although information was limited about the duration and efficacy of oral antibiotics to treat this type of infection, the patient recovered with oral antibiotic treatment following a short course of intravenous antibiotics.
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Seo DW, Yum SJ, Lee HR, Kim SM, Jeong HG. Microbiota Analysis and Microbiological Hazard Assessment in Chinese Chive ( Allium tuberosum Rottler) Depending on Retail Types. J Microbiol Biotechnol 2022; 32:195-204. [PMID: 34949749 PMCID: PMC9628847 DOI: 10.4014/jmb.2112.12013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022]
Abstract
Chinese chive (Allium tuberosum Rottler) has potential risks associated with pathogenic bacterial contamination as it is usually consumed raw. In this study, we investigated the microbiota of Chinese chives purchased from traditional markets and grocery stores in March (Spring) and June (Summer) 2017. Differences in bacterial diversity were observed, and the microbial composition varied across sampling times and sites. In June, potential pathogenic genera, such as Escherichia, Enterobacter, and Pantoea, accounted for a high proportion of the microbiota in samples purchased from the traditional market. A large number of pathogenic bacteria (Acinetobacter lwoffii, Bacillus cereus, Klebsiella pneumoniae, and Serratia marcescens) were detected in the June samples at a relatively high rate. In addition, the influence of the washing treatment on Chinese chive microbiota was analyzed. After storage at 26°C, the washing treatment accelerated the growth of enterohemorrhagic Escherichia coli (EHEC) because it caused dynamic shifts in Chinese chive indigenous microbiota. These results expand our knowledge of the microbiota in Chinese chives and provide data for the prediction and prevention of food-borne illnesses.
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Affiliation(s)
- Dong Woo Seo
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Su-jin Yum
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Heoun Reoul Lee
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Seung Min Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Hee Gon Jeong
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea,Corresponding author Phone: +82-42-821-6726 E-mail:
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Shrestha B, K C N, Bastola C, Jahir T, Risal R, Thapa S, Enriquez D, Schmidt F. Pantoea agglomerans: An Elusive Contributor to Chronic Obstructive Pulmonary Disease Exacerbation. Cureus 2021; 13:e18562. [PMID: 34760410 PMCID: PMC8571802 DOI: 10.7759/cureus.18562] [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] [Accepted: 10/06/2021] [Indexed: 12/23/2022] Open
Abstract
The ubiquitously present gram-negative bacteria Pantoea agglomerans is not a commonly known human pathogen. Recently, increasing recognition of the species as a human pathogen has led to controversy as limited documented cases of P.agglomerans bacteremia and infections have been reported in the literature, with most cases reported among immunocompromised patients or the pediatric population. Here, we present the case of a 54-year-old female with P. agglomerans and Enterococcus faecium bacteremia along with chronic obstructive pulmonary disease.
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Affiliation(s)
- Binav Shrestha
- Pulmonary Medicine, Interfaith Medical Center, Brooklyn, USA
| | - Nabin K C
- Internal Medicine, Interfaith Medical Center, Brooklyn, USA
| | | | - Tahmina Jahir
- Pulmonary Medicine, Interfaith Medical Center, Brooklyn, USA
| | - Ruby Risal
- Pulmonary Medicine, Interfaith Medical Center, Brooklyn, USA
| | - Shivani Thapa
- Internal Medicine, Interfaith Medical Center, Brooklyn, USA
| | - Danilo Enriquez
- Pulmonary Medicine, Interfaith Medical Center, Brooklyn, USA
| | - Frances Schmidt
- Pulmonary Medicine, Interfaith Medical Center, Brooklyn, USA
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Toys in the Playrooms of Children’s Hospitals: A Potential Source of Nosocomial Bacterial Infections? CHILDREN 2021; 8:children8100914. [PMID: 34682179 PMCID: PMC8534795 DOI: 10.3390/children8100914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022]
Abstract
Pediatric patients are more susceptible and vulnerable to nosocomial infections, in part because of their nascent and developing immune system and in part due to certain congenital conditions. Consequently, we found limited literature that investigated and reported children’s toys in hospital playrooms as potential reservoirs of pathogenic microbes. Hence, in the present study, we aimed to investigate toys as potential vectors for nosocomial infections in children’s hospitals. Microbiological samples from 120 toys were collected between April 2018 and November 2018. The specimens were cultivated on suitable cultivation agars for 24–72 h at 37 °C and CFU/cm2 (colony forming units) was determined. Antibiotic susceptibility testing was performed using disc diffusion and E-tests. Our results indicate that 84% of samples were contaminated with different microbes. Four distinct genera and thirty-seven species of bacteria were identified. The most frequently isolated pathogen was Sphingomonas paucimobilis (>603 CFU/cm2). Most of the identified microorganisms were members of normal human microbiota. Although Staphylococcus aureus and Acinetobacter baumannii were identified, CFU/cm2 was relatively low and they were found to be sensitive to antibiotics. Additionally, plastic toys showed the highest average CFU/cm2 of 91.9. Our results bolster the need for adoption and strict enforcement of proper disinfection techniques for toys in the hospital playrooms.
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Huang J, Mi J, Yan Q, Wen X, Zhou S, Wang Y, Ma B, Zou Y, Liao X, Wu Y. Animal manures application increases the abundances of antibiotic resistance genes in soil-lettuce system associated with shared bacterial distributions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147667. [PMID: 34004530 DOI: 10.1016/j.scitotenv.2021.147667] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
An increasing amount of animal manures is being used in agriculture, and the effect of animal manures application on the abundance of antibiotics resistance genes (ARGs) in soil-plant system has attracted widespread attention. However, the impacts of animal manures application on the various types of bacterial distribution that occur in soil-lettuce system are unclear. To address this topic, the effects of poultry manure, swine manure or chemical fertilizer application on ARG abundance and the distribution of shared bacteria were investigated in this study. In a lettuce pot experiment, 13 ARGs and 2 MGEs were quantified by qPCR, and bacterial communities in the soil, lettuce endosphere and lettuce phyllosphere were analysed by 16S rRNA sequence analysis. The results showed that the application of poultry or swine manure significantly increased ARG abundance in the soil, a result attributed mainly to increases in the abundances of tetG and tetC. The application of poultry manure, swine manure and chemical fertilizer significantly increased ARG abundance in the lettuce endosphere, and tetG abundance was significantly increased in the poultry and swine manure groups. However, animal manures application did not significantly increase ARG abundance in the lettuce phyllosphere. Flavobacteriaceae, Sphingomonadaceae and 11 other bacterial families were the shared bacteria in the soil, lettuce endosphere, and phyllosphere. The Streptomycetaceae and Methylobacteriaceae were significantly positively correlated with intI1 in both the soil and endosphere. Chemical fertilizer application increased both the proportions of Sphingomonadaceae and tetX abundance, which were positively correlated in the endosphere. Comamonadaceae and Flavobacteriaceae were not detected in the lettuce endosphere under swine manure application. Cu was related to Flavobacteriaceae in the lettuce endosphere. Overall, poultry and swine manure application significantly increased ARG abundance in the soil-lettuce system, which might be due to the shared bacterial distribution.
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Affiliation(s)
- Jielan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Qiufan Yan
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Shizheng Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China.
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Agarwal G, Choudhary D, Stice SP, Myers BK, Gitaitis RD, Venter SN, Kvitko BH, Dutta B. Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion. Front Microbiol 2021; 12:684756. [PMID: 34489883 PMCID: PMC8417944 DOI: 10.3389/fmicb.2021.684756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the 'alt' gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.
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Affiliation(s)
- Gaurav Agarwal
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Divya Choudhary
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Shaun P Stice
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Brendon K Myers
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Ronald D Gitaitis
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
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Complete Genome Sequence of Pantoea agglomerans ASB05 Using Illumina and PacBio Sequencing. Microbiol Resour Announc 2021; 10:e0050121. [PMID: 34323608 PMCID: PMC8320467 DOI: 10.1128/mra.00501-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the complete genome sequence of Pantoea agglomerans ASB05 and three associated plasmids, generated using a combination of the Illumina and PacBio platforms. P. agglomerans ASB05 was isolated from fresh cherries purchased in Albany, CA, in 2016.
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Changes in physico-chemical characteristics and viable bacterial communities during fermentation of alfalfa silages inoculated with Lactobacillus plantarum. World J Microbiol Biotechnol 2021; 37:127. [PMID: 34181131 DOI: 10.1007/s11274-021-03095-2] [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: 07/11/2020] [Accepted: 06/18/2021] [Indexed: 10/21/2022]
Abstract
This study investigated the effect of inoculating Lactobacillus (L.) plantarum PS-8 in fermentation of alfalfa silages. We monitored the fermentation characteristics and bacterial population dynamics during the ensiling process. PacBio single molecule real time sequencing was combined with propidium monoazide (PMA) treatment to monitor the viable microbiota dynamics. We found that inoculating L. plantarum PS-8 may improve the silage quality by accelerating acidification, reducing the amounts of clostridia, coliform bacteria, molds and yeasts, elevating the protein and organic acid contents (except butyrate), and enhancing lactic acid bacteria (LAB) while suppressing harmful microorganisms. Some significant differential abundant taxa were found between the PMA-treated and non-treated microbiota. For example, the relative abundances of L. brevis, L. plantarum, and Pediococcus pentosaceus were significantly higher in the PMA-treated group than the non-PMA-treated group, suggesting obvious differences between the viable and non-viable microbiota. It would thus be necessary to distinguish between the viable and non-viable microbial communities to further understand their physiological contribution in silage fermentation. By tracking the dynamics of viable microbiota in relation with changes in the physico-chemical parameters, our study provided novel insights into the beneficial effects of inoculating L. plantarum PS-8 in silage fermentation and the physiological function of the viable bacterial communities.
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Jo Y, Back CG, Kim KH, Chu H, Lee JH, Moh SH, Cho WK. Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits. Int J Mol Sci 2021; 22:6202. [PMID: 34201359 PMCID: PMC8227054 DOI: 10.3390/ijms22126202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/05/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022] Open
Abstract
Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study.
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Affiliation(s)
- Yeonhwa Jo
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (K.-H.K.)
| | - Chang-Gi Back
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 55365, Korea;
| | - Kook-Hyung Kim
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (K.-H.K.)
| | - Hyosub Chu
- R&D Division, BERTIS Inc., Seongnam-si 13605, Korea;
| | - Jeong Hun Lee
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (J.H.L.); (S.H.M.)
| | - Sang Hyun Moh
- Anti-Aging Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; (J.H.L.); (S.H.M.)
| | - Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (K.-H.K.)
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A Case of Nosocomial Outbreak of Pantoea agglomerans Related to Parenteral Nutrition Procedures. Healthcare (Basel) 2021; 9:healthcare9060684. [PMID: 34200170 PMCID: PMC8226852 DOI: 10.3390/healthcare9060684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022] Open
Abstract
Pantoea agglomerans is a Gram-negative bacterium that infrequently infects humans. Most reports involving it are about infections in soft tissues or bone/joint infections caused by contamination from soil or penetrating trauma by vegetation, such as thorns and splinters. More frequently, it is found as an opportunistic pathogen in immunocompromised patients. It is not rare to find reports of bacteremia and sepsis from contamination of intravenous fluid, parenteral nutrition, blood products and anesthetic agents-that is, through contamination of medical devices and products. We reported a bacterial infection epidemic occurred in 2011 in a hospital in middle Italy which involved different hospital wards; Pantoea agglomerans was isolated from blood cultures of all infected patients and the source of infection was identified in contaminated parenteral nutrition prepared from the local pharmacy.
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Roeder HA, Fuller B, Scoular S. Septic Shock Caused by Rahnella aquatilis Bacteremia in an Immunocompetent Adult. AMERICAN JOURNAL OF CASE REPORTS 2021; 22:e930888. [PMID: 33861730 PMCID: PMC8057651 DOI: 10.12659/ajcr.930888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Patient: Male, 37-year-old Final Diagnosis: Septic shock Symptoms: Fever • rigors Medication: — Clinical Procedure: — Specialty: Infectious Diseases
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Affiliation(s)
- Heidi A Roeder
- Department of Clinical Pharmacy, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
| | - Benjamin Fuller
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sarah Scoular
- Department of Clinical Pharmacy, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
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Cobo F, González A, Pérez-Carrasco V, García-Salcedo JA. Pantoea stewartii: A new pathogen as a cause of bacteremia? Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00079-3. [PMID: 33858706 DOI: 10.1016/j.eimc.2021.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/05/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Affiliation(s)
- Fernando Cobo
- Servicio de Microbiología e Instituto de Investigación Biosanitaria ibs. GRANADA, Hospital Universitario Virgen de las Nieves, Granada, España.
| | - Adrián González
- Servicio de Microbiología e Instituto de Investigación Biosanitaria ibs. GRANADA, Hospital Universitario Virgen de las Nieves, Granada, España
| | - Virginia Pérez-Carrasco
- GENYO, Centro de Investigación Genómica y oncológica Pfizer/Universidad de Granada/Gobierno Regional de Andalucía, Granada, España
| | - José A García-Salcedo
- Servicio de Microbiología e Instituto de Investigación Biosanitaria ibs. GRANADA, Hospital Universitario Virgen de las Nieves, Granada, España; GENYO, Centro de Investigación Genómica y oncológica Pfizer/Universidad de Granada/Gobierno Regional de Andalucía, Granada, España
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Draft Genome Sequence of the Putative Endophytic Bacterium Pantoea agglomerans R6, Associated with Lactuca serriola from South Africa. Microbiol Resour Announc 2021; 10:10/10/e00023-21. [PMID: 33707320 PMCID: PMC7953283 DOI: 10.1128/mra.00023-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the draft genome sequence (∼4.7 Mb) of the endopyhtic bacterium Pantoea agglomerans strain R6, which was isolated from surface-sterilized roots of Lactuca serriola (prickly lettuce).
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Vale AP, Shubin L, Cummins J, Leonard FC, Barry G. Detection of bla OXA-1, bla TEM-1, and Virulence Factors in E. coli Isolated From Seals. Front Vet Sci 2021; 8:583759. [PMID: 33763460 PMCID: PMC7982830 DOI: 10.3389/fvets.2021.583759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
Marine mammals are frequently considered good sentinels for human, animal and environmental health due to their long lifespan, coastal habitat, and characteristics as top chain predators. Using a One Health approach, marine mammals can provide information that helps to enhance the understanding of the health of the marine and coastal environment. Antimicrobial resistance (AMR) is the quintessential One Health problem that poses a well-recognised threat to human, animal, and ecosystem health worldwide. Treated and untreated sewage, hospital waste and agricultural run-off are often responsible for the spread of AMR in marine and freshwater ecosystems. Rescued seals (n = 25) were used as sentinels to investigate the levels of AMR in the Irish coastal ecosystem. Faecal swabs were collected from these animals and bacterial isolates (E. coli and cefotaxime-resistant non-E. coli) from each swab were selected for further investigation. E. coli isolates were characterised in terms of phylogenetic group typing, AMR, and virulence factors. All E. coli isolates investigated in this study (n = 39) were ampicillin resistant while 26 (66.6%) were multi-drug resistant (MDR). Resistance genes bla OXA-1 and bla TEM-1 were detected in 16/39 and 6/39 isolates, respectively. Additionally, virulence factors associated with adhesion (sfa, papA, and papC) and siderophores (fyuA and iutA) were identified. An additional 19 faecal cefotaxime-resistant non-E. coli isolates were investigated for the presence of β-lactamase encoding genes. These isolates were identified as presumptive Leclercia, Pantoea and Enterobacter, however, none were positive for the presence of the genes investigated. To the authors knowledge this is the first study reporting the detection of bla OXA-1 and bla TEM-1 in phocid faecal E. coli in Europe. These results highlight the importance of marine mammals as sentinels for the presence and spread of AMR in the marine and coastal environment.
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Affiliation(s)
- Ana P Vale
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Lynae Shubin
- School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Juliana Cummins
- Central Veterinary Research Laboratory, Backweston Laboratory Complex, Celbridge, Ireland
| | - Finola C Leonard
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Gerald Barry
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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Inhibition of Pantoea agglomerans contamination of fresh-cut jackfruit by exposure to weak organic acid vapors. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Alpiste FO, Ezquerra GM, Pujol RM. Wound infection by Pantoea agglomerans after penetrating plant injury. Indian J Dermatol Venereol Leprol 2021; 88:633-635. [PMID: 33666040 DOI: 10.25259/ijdvl_1069_19] [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: 12/01/2019] [Accepted: 05/01/2020] [Indexed: 11/04/2022]
Abstract
Pantoea agglomerans is a ubiquitous gram-negative bacterium that has been linked to skin and joint infections secondary to plant injuries. Herein we report a 58-year-old woman who presented with 2 erythematous nodules with purulent discharge on the anterior aspect of the right leg that developed after a penetrating plant injury. The patient was initially treated with amoxicillin-clavulanic acid, cloxacillin and clindamycin without improvement. P. agglomerans was isolated from both exudate and skin biopsy cultures. Healing of the lesions was achieved after the spontaneous release of a retained plant fragment and treatment with cotrimoxazole. Identification of P. agglomerans in persistent exudative lesions should alert the clinician regarding a possible previous plant injury and retained vegetal fragments. Conventional antibiotic treatment and the extraction of retained foreign bodies usually lead to complete resolution.
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Affiliation(s)
- Ferran Olmos Alpiste
- Department of Dermatology, Hospital del Mar - Parc de Salut Mar, Barcelona, Spain
| | | | - Ramon M Pujol
- Department of Dermatology, Hospital del Mar - Parc de Salut Mar, Barcelona, Spain
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48
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Koester T, Kusano T, Eijer H, Escher R, Waldegg G. Septic arthritis of the knee due to Pantoea agglomerans: look for the thorn. J Bone Jt Infect 2021; 6:51-55. [PMID: 33552878 PMCID: PMC7852405 DOI: 10.5194/jbji-6-51-2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/08/2020] [Indexed: 11/30/2022] Open
Abstract
We report on a patient with septic arthritis of the knee with Pantoea agglomerans after a penetrating black locust thorn injury. Antibiotics alone or in combination with an arthroscopy may be insufficient for achieving
source control. Accurate medical history and open debridement with a search
for a thorn fragment are key to successful treatment.
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Affiliation(s)
- Tobias Koester
- Department of Orthopedics and Traumatology, Emmental Hospital, Burgdorf, Switzerland
| | - Taro Kusano
- Department of Orthopedics and Traumatology, Emmental Hospital, Burgdorf, Switzerland
| | - Henk Eijer
- Department of Orthopedics and Traumatology, Emmental Hospital, Burgdorf, Switzerland
| | - Robert Escher
- Department of Internal Medicine and Infectious Diseases, Emmental Hospital, Burgdorf, Switzerland
| | - Gabriel Waldegg
- Department of Internal Medicine and Infectious Diseases, Emmental Hospital, Burgdorf, Switzerland
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Abstract
Pantoea is a plant pathogen infrequently reported to cause opportunistic bloodstream infections. This gram-negative bacillus is a rare cause of hospital-acquired infections in newborn infants with high mortality. Since the creation of the new genus Pantoea in 1989, the evidence base available to neonatal health care providers is limited. Most of the available literature consists of case reports and case series. This review aims to consolidate the current reported literature on Pantoea infections, focusing on newborn infants and the neonatal intensive care unit (NICU). Prematurity and the associated relative immunocompromised state are major risk factors for hospital-acquired infections due to Pantoea in newborn infants. Recent advances in molecular biology have improved our understanding of the cross-kingdom pathogenesis exhibited by Pantoea. Respiratory symptoms and association with central venous lines are the most common clinical presentation of Pantoea bacteremia in newborn infants. Early institution of appropriate antibiotic therapy against this organism could be lifesaving. Therefore, it is critical for neonatologists to understand the clinical spectrum of Pantoea infections in NICUs.
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Affiliation(s)
- Srinivasan Mani
- Pediatrics/Neonatology, State University of New York, Buffalo, USA
| | - Jayasree Nair
- Pediatrics/Neonatology, State University of New York, Buffalo, USA
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Tsilifis C, Pareja-Cebrian L. Neonatal Thoracic Infection with Mixta. Infect Prev Pract 2021; 3:100114. [PMID: 34368734 PMCID: PMC8335919 DOI: 10.1016/j.infpip.2021.100114] [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: 09/24/2020] [Accepted: 01/06/2021] [Indexed: 11/05/2022] Open
Abstract
The Erwiniaceae are a family of gram-negative, aerobic coliforms which are pathogenic to a number of plants. Recently described within this family are the Pantoea, strains of which have been associated with infection in immunocompromised children and post-surgical meningitis but also colonisation of a healthy human subject's gastrointestinal tract, as well as a variety of agricultural diseases. In 2015, a further clade of this family was established as the genus Mixta. In this case report, we describe infection of the pleural space and lung parenchyma with members of Mixta in a term neonate following an anastomic leak post-primary repair of congenital trache-oesophageal fistula, causing a respiratory and cardiovascular deterioration. Mixta were identified by MALDI-TOF. The child made a full recovery with use of intravenous piperacillin-tazobactam. The Mixta genus must be added to a list of opportunistic pathogens responsible for infection following perforation of the gastrointestinal tract.
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Affiliation(s)
- Christo Tsilifis
- Paediatric Immunology and Infectious Diseases, Great North Children's Hospital, Royal Victoria Infirmary, Newcastle Upon Tyne, United Kingdom.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Lucia Pareja-Cebrian
- Department of Microbiology and Virology, Royal Victoria Infirmary, Newcastle Upon Tyne, United Kingdom
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