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Sevillano L, Herrera C, Valdes Á, de la Hoz Á, Cardeñoso L, Domingo D, Semiglia MA. First report of a carbapenemase OXA-48-producing Hafnia alvei clinical isolate. Access Microbiol 2023; 5:acmi000498.v3. [PMID: 37424558 PMCID: PMC10323787 DOI: 10.1099/acmi.0.000498.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/21/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Carbapenems are usually used in the treatment of infections caused by cephalosporin-resistant Enterobacterales ; however, the increase in carbapenem-resistant Enterobacterales (CRE) has become one of the most important problems in public health. Hafnia alvei is associated with intestinal and extraintestinal infections, especially in patients with any chronic disease or some type of immunosupression. H. alvei is resistant to first-generation aminopenicillins and cephalosporins owing to the β-lactamase (Amp C) in their chromosome; the only carbapenem-resistant Hafnia strain described until now was due to a lack of the OmpK36 protein that plays an important role in permeability to carbapenems. Case presentation We present the case of a 65-year-old male diagnosed with acute lithiasic cholecystitis. Culture of the biliary prosthesis yielded a OXA-48-producing H. alvei that was identified by MALDI-TOF (matrix-assisted laser desorption/ionization-time of flight) MS. Carbapenemase production was detected by immunochromatography and confirmed by sequencing. Conclusion To our knowledge, this is the first report of OXA-48-producing H. alvei probably obtained by horizontal transfer from Enterobacter cloacae OXA-48 isolated in previous samples.
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Affiliation(s)
- Laura Sevillano
- Servicio de Microbiología, Hospital Universitario de La Princesa, Madrid, Spain
| | - Cristhian Herrera
- Servicio de Microbiología, Hospital Universitario de La Princesa, Madrid, Spain
| | - Álvaro Valdes
- Servicio de Cirugía General y Digestivo, Hospital Universitario de La Princesa, C/Diego de León, 62. 28006, Madrid, Spain
| | - Ángela de la Hoz
- Servicio de Cirugía General y Digestivo, Hospital Universitario de La Princesa, C/Diego de León, 62. 28006, Madrid, Spain
| | - Laura Cardeñoso
- Servicio de Microbiología, Hospital Universitario de La Princesa, Madrid, Spain
| | - Diego Domingo
- Servicio de Microbiología, Hospital Universitario de La Princesa, Madrid, Spain
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2
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Yan C, Li X, Zhang G, Bi J, Hao H, Hou H. Quorum Sensing (QS)-regulated target predictions of Hafnia alvei H4 based on the joint application of genome and STRING database. Food Res Int 2022; 157:111356. [DOI: 10.1016/j.foodres.2022.111356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
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3
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Krahulcová M, Cverenkárová K, Olejníková P, Micajová B, Koreneková J, Bírošová L. Characterization of Antibiotic Resistant Coliform Bacteria and Resistance Genes Isolated from Samples of Smoothie Drinks and Raw Milk. Foods 2022; 11:foods11091324. [PMID: 35564047 PMCID: PMC9101137 DOI: 10.3390/foods11091324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
Raw foodstuffs have been marked as a healthier alternative in the context of nutrient content and are becoming more popular with consumers. Thermally untreated foods may represent a microbiological risk connected with the possible presence of antimicrobial resistance. The aim of this study was to prove that popular raw food beverages such as smoothies and raw milk may be a source of antibiotic-resistant coliform bacteria and resistant genes. The majority of antibiotic-resistant isolates (110) were identified as Enterobacter spp., Escherichia coli, and species of Klebsiella spp., predominantly β-lactam and chloramphenicol resistant. Multidrug resistance has been registered in one-third of resistants. Overproduction of efflux pumps was clarified in 8 different bacteria. The majority of resistant isolates were strong biofilm producers. Antibiotic resistance gene blaOXA was detected in 25% of isolates, especially in E. coli. Resistance genes blaTEM and blaSHV were detected in 19% and 14%, respectively. This is the first study to point out that popular raw drinks such as smoothies or raw milk, besides their nutrient benefits, could represent a reservoir of antibiotic-resistant bacteria as well as antibiotic resistance genes. According to this, raw drinks could contribute to the dissemination of antibiotic resistance in the human gastrointestinal tract and environment.
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Affiliation(s)
- Monika Krahulcová
- Department of Nutrition and Food Quality Assessment, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia; (K.C.); (B.M.); (J.K.); (L.B.)
- Correspondence: ; Tel.: +421-948-511-256
| | - Klára Cverenkárová
- Department of Nutrition and Food Quality Assessment, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia; (K.C.); (B.M.); (J.K.); (L.B.)
| | - Petra Olejníková
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia;
| | - Barbora Micajová
- Department of Nutrition and Food Quality Assessment, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia; (K.C.); (B.M.); (J.K.); (L.B.)
| | - Júlia Koreneková
- Department of Nutrition and Food Quality Assessment, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia; (K.C.); (B.M.); (J.K.); (L.B.)
| | - Lucia Bírošová
- Department of Nutrition and Food Quality Assessment, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia; (K.C.); (B.M.); (J.K.); (L.B.)
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4
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Mitchell M, Thornton L, Riley MA. Identifying more targeted antimicrobials active against select bacterial phytopathogens. J Appl Microbiol 2022; 132:4388-4399. [PMID: 35301784 DOI: 10.1111/jam.15531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/27/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022]
Abstract
AIMS Phytopathogens are a global threat to the world's food supply. Use of broad-spectrum bactericides and antibiotics to limit or eliminate bacterial infections is becoming less effective as levels of resistance increase, while concurrently becoming less desirable from an ecological perspective due to their collateral damage to beneficial members of plant and soil microbiomes. Bacteria produce numerous antimicrobials in addition to antibiotics, such as bacteriocins with their relatively narrow activity spectra, and inhibitory metabolic by-products, such as organic acids. There is interest in developing these naturally occurring antimicrobials for use as alternatives or supplements to antibiotics. METHODS AND RESULTS In this study, we investigate the inhibitory potential of 217 plant associated bacterial isolates from 44 species including plant pathogens, plant growth promoting rhizobacteria, and plant commensals. Over half of the isolates were found to produce antimicrobial substances, of which 68% were active against phytopathogens. Even more intriguing, 98% of phytopathogenic strains were sensitive to the compounds produced specifically by plant growth promoting rhizobacteria. CONCLUSION These data argue that plant-associated bacteria produce a broad range of antimicrobial substances, and that the substances produced preferentially target phytopathogenic bacteria. SIGNIFICANCE AND IMPACT OF STUDY There is a need for novel antimicrobials for use in agriculture. The methods presented here reveal the potential for simple phenotypic screening methods to provide a broad range of potential drug candidates.
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Affiliation(s)
| | - Logan Thornton
- Department of Biology, University of Massachusetts Amherst
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5
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Pan L, Li D, Sun Z, Lin W, Hong B, Qin W, Xu L, Liu W, Zhou Q, Wang F, Cai R, Qian M, Tong Y. First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism. Front Microbiol 2022; 12:754331. [PMID: 35211099 PMCID: PMC8861465 DOI: 10.3389/fmicb.2021.754331] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/20/2021] [Indexed: 01/25/2023] Open
Abstract
A unique lytic phage infecting Hafnia paralvei was isolated and identified. Hafnia phage Ca belongs to the family Autographiviridae, possessing an icosahedral head with a diameter of 55 nm and a short non-contractile tail. Unusually, the burst size of Hafnia phage Ca of 10,292 ± 1,097 plaque-forming units (PFUs)/cell is much larger than other dsDNA phages reported before. Compared to the genome of the related phage, Hafnia phage Ca genome contains extra genes including DNA mimic ocr, dGTP triphosphohydrolase inhibitor, endonuclease, endonuclease VII, and HNH homing endonuclease gene. Extraordinarily, the phage developed different sizes of plaques when a single plaque was picked out and inoculated on a double-layer Luria broth agar plate with its host. Furthermore, varied packaging tightness for the tails of Hafnia phage Ca was observed (tail length: 4.35–45.92 nm). Most of the tails appeared to be like a cone with appendages, some were dot-like, bun-like, table tennis racket handle-like, and ponytail-like. Although the complete genome of Hafnia phage Ca is 40,286 bp, an incomplete genome with a deletion of a 397-bp fragment, containing one ORF predicted as HNH homing endonuclease gene (HEG), was also found by high throughput sequencing. Most of the genome of the virus particles in large plaques is complete (>98%), while most of the genome of the virus particles in small plaques is incomplete (>98%), and the abundance of both of them in medium-sized plaques is similar (complete, 40%; incomplete, 60%). In an experiment to see if the phage could be protective to brocade carps intramuscularly injected with H. paralvei LY-23 and phage Ca, the protection rate of Hafnia phage Ca to brocade carp (Cyprinus aka Koi) against H. paralvei was 33.38% (0.01 < p < 0.05). This study highlights some new insights into the peculiar biological and genomic characteristics of phage.
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Affiliation(s)
- Lingting Pan
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhitong Sun
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wei Lin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Binxin Hong
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Weinan Qin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Lihua Xu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wencai Liu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qin Zhou
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Fei Wang
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Ruqian Cai
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Minhua Qian
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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6
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Pang Y, Wang S, Tao J, Wang J, Xue Z, Wang R. Mechanism of berberine hydrochloride interfering with biofilm formation of Hafnia alvei. Arch Microbiol 2022; 204:126. [PMID: 34997845 DOI: 10.1007/s00203-021-02617-8] [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: 09/20/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
Abstract
The mechanism of berberine hydrochloride (BBH) inhibiting the biofilm formation of Hafnia alvei was investigated in this study. The antibiofilm potential of BBH was evaluated by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) as well as crystal violet staining. The quorum-sensing (QS) inhibition was revealed by determination of QS-related genes expression and related signal molecules production using real-time quantitative PCR (RT-qPCR) and high performance liquid chromatography (HPLC). The binding of BBH to receptor proteins was simulated by molecular docking and molecular dynamics simulations. It was found that BBH at sub-minimum inhibitory concentrations (sub-MICs) significantly reduced the biofilm formation of H. alvei in a dose dependent manner. BBH inhibited the bacterial swimming motility, decreased the transcription of halI and halR genes, and reduced the production of signal molecule C14-HSL. It bound to HalR protein mainly through Van der Waals force and electrostatic interaction force. Based on these results, it was concluded that BBH inhibits the biofilm formation of H. alvei and the mechanism is related to its interference with QS through down-regulating the expression of halI and halR genes.
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Affiliation(s)
- Yuesheng Pang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Sha Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jiayue Tao
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jing Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zhe Xue
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, China.
| | - Rufeng Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China.
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7
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Phenotypic and molecular characterization of antimicrobial resistance in clinical species of Enterobacter, Serratia, and Hafnia in Northeast Iran. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
Hafnia alvei is a Gram-negative facultatively anaerobic bacillus that constitutes part of the human gut flora. Until recently, H. alvei strains could be mistakenly identified by conventional methods, miniaturisation or automatic systems as members of the Serratia, Escherichia, Citrobacter, Yokenella, Obesumbacterium or Salmonella genera. Consequently, molecular techniques were required for their definitive identification in the clinical laboratory. In addition, a new Hafnia species, H. paralvei, has recently appeared, which undoubtedly includes many of the strains reported in the literature as H. alvei. Alrhough H. alvei isolation from human clinical specimens remains uncommon, the development of drug resistance due to this species is emerging and it is likely that this organism will gain increasing importance in the future. Moreover, although H. alvei shares some virulence mechanisms with other Gram-negative enteropathogens, little is known about the factors that contribute to its pathogenesis in humans. The present article reviews the current identification methods, antimicrobial resistance and virulence factors of this bacterium.
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Affiliation(s)
- José Ramos-Vivas
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, España.
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9
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Begbey A, Guppy JH, Mohan C, Webster S. Hafnia alvei pneumonia: a rare cause of infection in the multimorbid or immunocompromised. BMJ Case Rep 2020; 13:13/12/e237061. [PMID: 33384344 PMCID: PMC7780556 DOI: 10.1136/bcr-2020-237061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Hafnia alvei is a rare, poorly understood commensal bacterium which has, on occasion, been shown to infect humans. We present two cases. The first patient presented with a 1-week history of dyspnoea, pleurisy and a productive cough, and the second with a prodrome of fatigue and night sweats. The former had a history of severe chronic obstructive pulmonary disease and the latter had a history of Crohn's disease. Both patients had underlying comorbidities and immunosuppression, but differed in presentation, radiological findings and recovery. This case series aims to remind readers of the broad differential of pathogens that can lead to disease in the immunocompromised and that one should not dismiss atypical cultured bacteria as commensal too hastily.
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Affiliation(s)
- Austin Begbey
- Respiratory Medicine, Tunbridge Wells Hospital, Tunbridge Wells, UK
| | | | - Chithra Mohan
- Respiratory Medicine, Tunbridge Wells Hospital, Tunbridge Wells, UK
| | - Simon Webster
- Respiratory Medicine, Tunbridge Wells Hospital, Tunbridge Wells, UK
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10
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Singh AK, Das S, Kumar S, Gajamer VR, Najar IN, Lepcha YD, Tiwari HK, Singh S. Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli. Front Microbiol 2020; 11:581072. [PMID: 33224119 PMCID: PMC7674312 DOI: 10.3389/fmicb.2020.581072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/18/2020] [Indexed: 12/25/2022] Open
Abstract
Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.
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Affiliation(s)
- Ashish Kumar Singh
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Saurav Das
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Santosh Kumar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Varsha Rani Gajamer
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Yangchen D. Lepcha
- State Institute of Rural Development (SIRD), Government of Sikkim, Gangtok, India
| | - Hare Krishna Tiwari
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Samer Singh
- Centre of Experimental Medicine and Surgery (CEMS), Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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11
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Zhang W, Chen Y, Shi Q, Hou B, Yang Q. Identification of bacteria associated with periapical abscesses of primary teeth by sequence analysis of 16S rDNA clone libraries. Microb Pathog 2019; 141:103954. [PMID: 31891793 DOI: 10.1016/j.micpath.2019.103954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/17/2019] [Accepted: 12/27/2019] [Indexed: 01/08/2023]
Abstract
OBJECTIVE This study aims to detect the predominant bacteria in acute periapical abscesses of primary teeth using culture-independent molecular methods based on 16S ribosomal DNA cloning. METHODS Purulent material was collected from nine children diagnosed with abscesses of endodontic origin. DNA was extracted and the 16S rRNA gene amplified with universal primer pairs 27F and 1492R. Amplified genes were cloned, sequenced by Applied Biosystems, and identified by comparison with known 16S rRNA gene sequences. RESULTS Bacterial DNA was present in all nine purulence samples. A total of 681 clones were classified into 8 phyla, 78 genera, and 125 species/phylotypes. The phyla were Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria, Tenericutes, Deinococcus-Thermus, and Spirochaetes. The most dominant genera were Streptococcus (13.3%), Fusobacterium (11.8%), Parvimonas (7.8%), Prevotella (6.7%), Sphingomonas (5.8%), and Hafnia (5.2%). Fusobacterium nucleatum (11.5%), Parvimonas micra (7.8%), Streptococcus intermedius (6.6%), Sphingomonas echinoides (5.3%), Hafnia alvei (5.2%), and Citrobacter freundii (4.9%) were the most common species/phylotypes. Among these species/phylotypes, F.nucleatum was the most prevalent (7/9). C. freundii, Carnobacterium maltaromaticum, and H. alvei were seldom detected species in acute periapical abscesses but had relatively high abundance and prevalence. CONCLUSION Acute periapical abscesses are polymicrobial with certain prevalent bacteria, especially anaerobic bacterium. The most predominant and prevalent bacteria of acute periapical abscesses in children was F. nucleatum.
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Affiliation(s)
- Wenwen Zhang
- Beijing Institute for Dental Research, Capital Medical University, School of Stomatology, Beijing, China
| | - Yuanyuan Chen
- Beijing Institute for Dental Research, Capital Medical University, School of Stomatology, Beijing, China
| | - Qing Shi
- Department of Pediatric Dentistry, Capital Medical University, School of Stomatology, Beijing, China
| | - Benxiang Hou
- Department of Endodontics, Capital Medical University, School of Stomatology, Beijing, China
| | - Qiubo Yang
- Beijing Institute for Dental Research, Capital Medical University, School of Stomatology, Beijing, China.
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12
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Yin Z, Yuan C, Du Y, Yang P, Qian C, Wei Y, Zhang S, Huang D, Liu B. Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity. BMC Genomics 2019; 20:768. [PMID: 31646960 PMCID: PMC6806506 DOI: 10.1186/s12864-019-6123-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/20/2019] [Indexed: 12/28/2022] Open
Abstract
Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.
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Affiliation(s)
- Zhiqiu Yin
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China.,TEDA institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomeics, TEDA college, Nankai university, Tianjin, People's Republic of China
| | - Chao Yuan
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China.,TEDA institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomeics, TEDA college, Nankai university, Tianjin, People's Republic of China
| | - Yuhui Du
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China.,TEDA institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomeics, TEDA college, Nankai university, Tianjin, People's Republic of China
| | - Pan Yang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China.,TEDA institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomeics, TEDA college, Nankai university, Tianjin, People's Republic of China
| | - Chengqian Qian
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China.,TEDA institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomeics, TEDA college, Nankai university, Tianjin, People's Republic of China
| | - Yi Wei
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China.,TEDA institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomeics, TEDA college, Nankai university, Tianjin, People's Republic of China
| | - Si Zhang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China.,TEDA institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Microbial Functional Genomeics, TEDA college, Nankai university, Tianjin, People's Republic of China
| | - Di Huang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China. .,TEDA institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China. .,Tianjin Key Laboratory of Microbial Functional Genomeics, TEDA college, Nankai university, Tianjin, People's Republic of China.
| | - Bin Liu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China. .,TEDA institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China. .,Tianjin Key Laboratory of Microbial Functional Genomeics, TEDA college, Nankai university, Tianjin, People's Republic of China.
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Milanowski M, Monedeiro F, Złoch M, Ratiu IA, Pomastowski P, Ligor T, De Martinis BS, Buszewski B. Profiling of VOCs released from different salivary bacteria treated with non-lethal concentrations of silver nitrate. Anal Biochem 2019; 578:36-44. [PMID: 31085164 DOI: 10.1016/j.ab.2019.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 01/03/2023]
Abstract
Considering the shortcomings related to antibiotics usage, the introduction of other bacteriostatic and bactericidal agents that present synergetic effects or standalone properties is urgently needed. AgNO3 is an important bactericidal agent, which imparts various functions on bacteria dependent on its concentration. Therefore, an understanding of its mechanisms of action in infinitesimal concentrations plays an important role which can ultimately lead to AgNO3 involvement in the pharmaceutical industry. The monitoring of VOC (volatile organic compound) profiles emitted by bacteria is a simple method to assess changes occurring in bacterial metabolism. In this study, VOCs of Hafnia alvei, Pseudomonas luteola and Staphylococcus warneri cultures were analyzed both in the absence and in the presence of three concentrations of AgNO3. Headspace solid-phase microextraction gas chromatography/mass spectrometry (HS-SPME-GC/MS) was employed for extraction and analysis. After supplementation with AgNO3, changes in the emitted fingerprints were investigated. Odorants associated with mouth-related and systemic diseases, like dimethyl trisulfide, indole (halitosis) and 2-hexanone (celiac disease), were also affected by addition of AgNO3. Statistical tests proved discrimination between obtained profiles with more that 90% variability. Moreover, physiological states of bacteria after dosage with various concentration of stressing agent were investigated and explained by the mechanisms of action.
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Affiliation(s)
- Maciej Milanowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str, 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str, 87-100, Toruń, Poland
| | - Fernanda Monedeiro
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str, 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str, 87-100, Toruń, Poland; Department of Chemistry, Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, CEP 14040-901, Ribeirão Preto, Brazil
| | - Michał Złoch
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str, 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str, 87-100, Toruń, Poland
| | - Ileana-Andreea Ratiu
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str, 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str, 87-100, Toruń, Poland; (d)Babeş-Bolyai University, Faculty of Chemistry and Chemical Engineering, 11 Arany Janos, RO-400028, Cluj-Napoca, Romania
| | - Paweł Pomastowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str, 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str, 87-100, Toruń, Poland
| | - Tomasz Ligor
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str, 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str, 87-100, Toruń, Poland
| | - Bruno S De Martinis
- Department of Chemistry, Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, CEP 14040-901, Ribeirão Preto, Brazil
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str, 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str, 87-100, Toruń, Poland.
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14
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Li T, He B, Mei Y, Wang D, Sun X, Li J. Inhibitory effect of vanillin on the virulence factors and biofilm formation of Hafnia alvei. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2018.12.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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