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Wang Y, Cai X, Hu S, Qin S, Wang Z, Cao Y, Hou C, Yang J, Zhou W. Comparative genomic analysis provides insight into the phylogeny and potential mechanisms of adaptive evolution of Sphingobacterium sp. CZ-2. Gene 2023; 855:147118. [PMID: 36521669 DOI: 10.1016/j.gene.2022.147118] [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: 07/13/2022] [Revised: 11/21/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Sphingobacterium is a class of Gram-negative, non-fermentative bacilli that have received widespread attention due to their broad ecological distribution and oil degradation ability, but are rarely involved in infections. In this manuscript, a novel Sphingobacterium strain isolated from wildfire-infected tobacco leaves was named Sphingobacterium sp. CZ-2. NGS and TGS sequencing results showed a whole genome of 3.92 Mb with 40.68 mol% GC content and containing 3,462 protein-coding genes, 9 rRNA-coding genes and 50 tRNA-coding genes. Phylogenetic analysis, ANI and dDDH calculations all supported that Sphingobacterium sp. CZ-2 represented a novel species of the genus Sphingobacterium. Analysis of the specific genes of Sphingobacterium sp. CZ-2 by comparative genomics revealed that metal transport proteins encoded by the troD and cusA genes could maintain the balance of heavy metal ion concentrations in the internal environment of bacteria and avoid heavy metal toxicity while meeting the needs of growth and reproduction, and transport proteins encoded by the malG gene could keep nutrients required for the survival of bacteria. Synteny and genome evolutionary analyses of Sphingobacterium strains implicated that the gene family contraction as a major process in genome evolution, with insertional sequences leading to mutations, deletions and reversals of genes that help bacteria to withstand complex environmental changes. Complete genome sequencing and systematic comparative genomic analysis will contribute new insights into the adaptive evolution of this novel species and the genus Sphingobacterium.
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Affiliation(s)
- Yongqiang Wang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Xunhui Cai
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shengnan Hu
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Sidong Qin
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Ziqi Wang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Yixiang Cao
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Chaoliang Hou
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Jiangshan Yang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Wei Zhou
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
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Chenalla NL, Ravindrachari M, Meenakshi M, Upender RG. An unusual cause of pyrexia of unknown origin with sepsis: A diagnostic challenge. Indian J Med Microbiol 2022; 43:36-38. [PMID: 36328828 DOI: 10.1016/j.ijmmb.2022.10.005] [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: 07/15/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022]
Abstract
Sphingobacterium species are ubiquitous and are abundant in nature and rarely involved in causing human infections. A 62-year-old man presented with recurrent episodes of high fever up to 40 °C accompanied by rigors, sweating, and malaise for the past 4 weeks. After a thorough workup, only elevated C-reactive protein with a leucocytosis was evident. Blood culture showed growth of Gram-negative bacilli which was identified as spingobacterium spiritivorum. Although S. spiritivorum is rare, with limited cases reported in the literature, it must be considered as a causative organism in patients with persistent fevers with sepsis.
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Affiliation(s)
| | - M Ravindrachari
- Department of Pulmonary Medicine, RVM Institute of Medical Sciences and Research Centre, Siddipet, Telangana, 502279, India.
| | - M Meenakshi
- Department of Microbiology, RVM Institute of Medical Sciences and Research Centre, Siddipet, Telangana, 502279, India.
| | - Reddy G Upender
- Department of Anaesthesia and Critical Care, Renee Hospital, Karimnagar, Telangana, 506001, India.
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Echefu G, Mahat R, Katragadda S, Reddy K. Sphingobacterium Spritivorum Associated With Spontaneous Bacterial Peritonitis in a Cirrhotic Patient With Gram-Positive Bacteremia. Cureus 2022; 14:e26053. [PMID: 35865420 PMCID: PMC9289197 DOI: 10.7759/cureus.26053] [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: 06/17/2022] [Indexed: 11/05/2022] Open
Abstract
Sphingobacterium spritivorum (SS) is a ubiquitous gram-negative organism and an uncommon cause of infection in humans. To our knowledge, there are no reported cases of this bacterium causing spontaneous bacterial peritonitis (SBP) in patients with cirrhosis. In this report, we discuss a case of a male patient in his late 60s who presented with severe sepsis from methicillin-resistant staphylococcus aureus (MRSA), in whom SS was subsequently identified via ascitic fluid culture. This unusual organism is known to have an innate resistance to multiple antibiotics and can cause life-threatening sepsis in cases of delayed or missed diagnosis. Clinicians should not be weighed down by anchoring bias and look for alternative, uncommon gram-negative organisms in cases of progressive sepsis in patients with ascites.
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Bansal S, Varshney S. Scrub Typhus Complicated by Rare Human Pathogen Sphingobacterium spiritivorum. Indian J Crit Care Med 2022; 26:742-744. [PMID: 35836642 PMCID: PMC9237151 DOI: 10.5005/jp-journals-10071-24254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sphingobacterium spiritivorum is a rare cause of human infections worldwide. After reviewing the literature, we could find only eight case reports to date. The majority of cases were of cellulitis and septicemia. Most of these patients were immunocompromised and the recovery rate was lesser. We present a case of a young female diagnosed with scrub typhus complicated by acute respiratory distress syndrome who developed septicemia and septic shock due to S. spiritivorum. She was managed with sensitive antibiotic levofloxacin, clinically improved, and discharged in satisfactory condition.
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Affiliation(s)
- Sonali Bansal
- Department of Critical Care, SPS Hospital, Ludhiana, Punjab, India
| | - Siddarth Varshney
- Department of Cardiology, CMC Hospital, Ludhiana, Punjab, India
- Siddarth Varshney, Department of Cardiology, CMC Hospital, Ludhiana, Punjab, India, Phone: +91 9045502542, e-mail:
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Sant' Anna D, Sampaio JLM, Sommaggio LRD, Mazzeo DEC, Marin-Morales MA, Marson FAL, Levy CE. The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates. Antonie van Leeuwenhoek 2019; 113:233-252. [PMID: 31560092 DOI: 10.1007/s10482-019-01333-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022]
Abstract
Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.
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Affiliation(s)
- Débora Sant' Anna
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, Barretos, São Paulo, Brazil.
| | - Jorge Luiz Mello Sampaio
- Microbiology Section, Fleury-Centers for Diagnostic Medicine, Av. General Waldomiro de Lima 508, São Paulo, 04344-070, Brazil
- Clinical Analysis and Toxicology Department, School of Pharmacy, University of São Paulo, Av. Professor Lineu Prestes, 580, Butantã, São Paulo, 05508-000, Brazil
| | - Lais Roberta Deroldo Sommaggio
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Dânia Elisa Christofoletti Mazzeo
- Department of Analytical Chemistry, Institute of Chemistry, São Paulo State University - Araraquara, Rua Professor Francisco Degni, 55, Araraquara, São Paulo, 14800-060, Brazil
| | - Maria Aparecida Marin-Morales
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Laboratory of Pulmonary Physiology, Center for Pediatrics Investigation, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Post-Graduate Program in Health Science, São Francisco University, Avenida São Francisco de Assis, 218, Cidade Universitária, Bragança Paulista, São Paulo, 12916-400, Brazil.
| | - Carlos Emílio Levy
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
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Nemoto D, Hitomi S, Moriyama Y, Iwamoto K, Saito K. Cellulitis Complicated with Bacteremia Due to Sphingobacterium Species: A Report of Two Cases and a Literature Review. Intern Med 2019; 58:2573-2576. [PMID: 31118372 PMCID: PMC6761337 DOI: 10.2169/internalmedicine.2178-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sphingobacterium species rarely cause human infection. We herein report two cases of cellulitis complicated with bacteremia due to this genus. The patients, both in their 70s and receiving corticosteroid therapy for their underlying diseases, had antecedent skin injuries in their affected limbs. The patients' symptoms improved promptly and completely with the administration of cefazolin, which did not inhibit the growth of isolated organisms at a concentration of 4 μg/mL.
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Affiliation(s)
- Daisuke Nemoto
- Department of Clinical Laboratories, University of Tsukuba Hospital, Japan
| | - Shigemi Hitomi
- Department of Infectious Diseases, University of Tsukuba Hospital, Japan
| | | | - Kazuyo Iwamoto
- Department of Dermatology, Tsuchiura Kyodo General Hospital, Japan
| | - Kazuhito Saito
- Department of Respiratory Diseases, Tsuchiura Kyodo General Hospital, Japan
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