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Vereecke N, Vandekerckhove A, Theuns S, Haesebrouck F, Boyen F. Whole genome sequencing to study antimicrobial resistance and RTX virulence genes in equine Actinobacillus isolates. Vet Res 2023; 54:33. [PMID: 37020296 PMCID: PMC10074821 DOI: 10.1186/s13567-023-01160-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/03/2023] [Indexed: 04/07/2023] Open
Abstract
Actinobacillus equuli is mostly associated with disease in horses and is most widely known as the causative agent of sleepy foal disease. Even though existing phenotypic tools such as biochemical tests, 16S rRNA gene sequencing, and Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) can be used to identify members of the Actinobacillus genus, these methods struggle to differentiate between certain species and do not allow strain, virulence, and antimicrobial susceptibility typing. Hence, we performed in-depth analysis of 24 equine Actinobacillus isolates using phenotypic identification and susceptibility testing on the one hand, and long-read nanopore whole genome sequencing on the other hand. This allowed to address strain divergence down to the whole genome single nucleotide polymorphism (SNP) level. While lowest resolution was observed for 16S rRNA gene classification, a new multi-locus sequence typing (MLST) scheme allowed proper classification up to the species level. Nevertheless, a SNP-level analysis was required to distinguish A. equuli subspecies equuli and haemolyticus. Our data provided first WGS data on Actinobacillus genomospecies 1, Actinobacillus genomospecies 2, and A. arthritidis, which allowed the identification of a new Actinobacillus genomospecies 1 field isolate. Also, in-depth characterization of RTX virulence genes provided information on the distribution, completeness, and potential complementary nature of the RTX gene operons within the Actinobacillus genus. Even though overall low prevalence of acquired resistance was observed, two plasmids were identified conferring resistance to penicillin-ampicillin-amoxicillin and chloramphenicol in one A. equuli strain. In conclusion our data delivered new insights in the use of long-read WGS in high resolution identification, virulence gene typing, and antimicrobial resistance (AMR) of equine Actinobacillus species.
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Affiliation(s)
- Nick Vereecke
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
- PathoSense BV, Lier, Belgium.
| | - Arlette Vandekerckhove
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | | | - Freddy Haesebrouck
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Filip Boyen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
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2
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Loy JD, Clawson ML, Adkins PRF, Middleton JR. Current and Emerging Diagnostic Approaches to Bacterial Diseases of Ruminants. Vet Clin North Am Food Anim Pract 2023; 39:93-114. [PMID: 36732002 DOI: 10.1016/j.cvfa.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The diagnostic approaches and methods to detect bacterial pathogens in ruminants are discussed, with a focus on cattle. Conventional diagnostic methods using culture, isolation, and characterization are being replaced or supplemented with new methods. These include molecular diagnostics such as real-time polymerase chain reaction and whole-genome sequencing. In addition, methods such as matrix-assisted laser desorption ionization-time-of-flight mass spectrometry enable rapid identification and enhanced pathogen characterization. These emerging diagnostic tools can greatly enhance the ability to detect and characterize pathogens, but performance and interpretation vary greatly across sample and pathogen types, disease syndromes, assay performance, and other factors.
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Affiliation(s)
- John Dustin Loy
- Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Michael L Clawson
- USDA, Agriculture Research Service US Meat Animal Research Center, Clay Center, NE, USA
| | - Pamela R F Adkins
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - John R Middleton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
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3
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Pandemic Clones of CTX-M-15 Producing Klebsiella pneumoniae ST15, ST147, and ST307 in Companion Parrots. Microorganisms 2022; 10:microorganisms10071412. [PMID: 35889131 PMCID: PMC9320316 DOI: 10.3390/microorganisms10071412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/22/2022] Open
Abstract
Psittacine birds are commonly kept as companion birds and the maintenance of these birds in captivity may represent a zoonotic risk and contribute to the propagation of multidrug-resistant and β-lactamase extended-spectrum (ESBLs)-producing pathogens. This study aimed to identify and characterize strains of the Klebsiella pneumoniae complex isolated from diseased psittacine birds, determining virulence and resistance profiles. K. pneumoniae strains were isolated from 16 birds (16/46). All strains carried more than three virulence genes, with a high frequency of fimH and kpn (93.75%), uge (87.52%), and irp-2 (81.25%) genes. The antimicrobial susceptibility revealed that 3/16 strains were ESBL producers. Genomic analysis revealed that CTX-M-15-positive strains belonged to sequence types (STs) ST15, ST147, and ST307, characterized as international clones associated with outbreaks of healthcare-associated infections (HAIs) worldwide.
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4
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Christensen H, Sajid SM, Bisgaard M, Magistrali CF, Massacci FR, Liman M, Menke T, Bischoff H, Olsen JE. Prediction of Pasteurella multocida serotypes based on whole genomic sequences. Vet Microbiol 2022; 271:109492. [PMID: 35714528 DOI: 10.1016/j.vetmic.2022.109492] [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: 01/31/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/01/2022]
Abstract
The serotypes of Pasteurella multocida were predicted based on whole genomic sequences (WGS) with specific genes of the capsular and liposaccharide (LPS) outer core polysaccharide regions as targets. A total of 56 strains were whole genomic sequenced and in addition all assembled genomes from NCBI were included for comparison. BIGSdb (Bacterial Isolate Genome Sequence Database) was installed on a Linux server and targets for capsular types A, B, D, E and F were defined as gene sequences of hyaD, bcbD, dcbF, ecbJ and fcbD, respectively and targets for LPS groups 1, 2, 3, 4, 5, 6, 7 and 8 were defined as gene sequences of pcgB, nctA, gatF, latB, rmlA, nctB, ppgB and natG, respectively. The serotypes of P. multocida were predicted from WGS by designating the capsular type and LPS group as well as subtype alleles to isolates. Comparisons between WGS predictions of capsular types and classical phenotypic typing showed correspondence in 87 % of cases whereas comparisons of WGS predictions of LPS groups to phenotypic typing corresponded for 82 % of the strains. In total 93 % and 94 % of the strains available with WGS could be capsular and LPS group typed, respectively. The server is free to access from https://ivsmlst.sund.ku.dk.
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Affiliation(s)
- Henrik Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Fredriksberg C, Denmark.
| | - Sajid Mahmood Sajid
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Fredriksberg C, Denmark; Department of Clinical Studies, Faculty of Veterinary and Animal Sciences, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | | | - Chiara Francesca Magistrali
- Research and Development Department, Istituto Zooprofilattico Sperimentale Umbria e Marche Togo Rosati, via G. Salvemini 1, 06126 Perugia, Italy
| | - Francesca Romana Massacci
- Research and Development Department, Istituto Zooprofilattico Sperimentale Umbria e Marche Togo Rosati, via G. Salvemini 1, 06126 Perugia, Italy
| | - Martin Liman
- AniCon Labor GmbH, Muehlenstraße 13, 49685 Hoeltinghausen, Germany
| | - Theresa Menke
- AniCon Labor GmbH, Muehlenstraße 13, 49685 Hoeltinghausen, Germany
| | - Henning Bischoff
- AniCon Labor GmbH, Muehlenstraße 13, 49685 Hoeltinghausen, Germany
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Fredriksberg C, Denmark
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Wielerella bovis gen. nov., sp. nov. a member of the family Neisseriaceae associated with bovine endocarditis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005387] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Seven bacterial strains isolated from bovine endocarditis in six animals from different geographic regions were investigated in a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences placed all seven isolates on a distinct, monophyletic cluster in the family
Neisseriaceae
with closest similarity to type strains of
Alysiella filiformis
(97.06 %) and
Kingella kingae
(96.34 %). Whole genome sequence analysis of isolates confirmed their species status, with an average nucleotide identity >96 % between isolates and <80 % to other type species of genera of
Neisseriaceae
while digital DNA–DNA hybridization values were >80 % and<18 %, respectively. The DNA G+C content was 42.5–43.0 mol%. Whole genome sequence based phylogeny showed the isolates being monophyletic and separated from established genera, thereby forming a new genus within the family
Neisseriaceae
. Similarly, analysis of MALDI-TOF MS reference spectra clustered the isolates close together and clearly separated from other genera, making this the method of choice for identification. Biochemical markers based on classical as well as commercial identification schemes allowed separation from closely related
Neisseriaceae
genera, even though the new taxon is biochemically not very active. Major fatty acids are C12 : 0, C14 : 0 and C16 : 0. The major quinone is ubiquinone Q-8. In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospholipid were predominant. We propose the novel genus Wielerella with the type species Wielerella bovis gen. nov., sp. nov. The type strain is CCUG 44465T (=DSM 113289T=JF 2483T) isolated post mortem from a cow with endocarditis in Switzerland.
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Virulence Genes Profile and Antimicrobial Susceptibility of Community-Acquired Bacterial Urinary Tract Infections in a Brazilian Hospital. Curr Microbiol 2021; 78:3913-3923. [PMID: 34522976 DOI: 10.1007/s00284-021-02650-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Urinary tract infections (UTI) are one of the most common diseases worldwide and Escherichia coli is the most common causative bacteria. Empirical treatment is challenging due to antimicrobial or multidrug-resistance. The aims of this study were to determine the uropathogens and their antimicrobial susceptibility profile, as well as to identify the phylogroups and virulence genes of E. coli strains, associated with community-acquired UTI in outpatients admitted at a Brazilian Hospital in southeast Brazil. In total, 47 bacterial strains were isolated from 47 patients, 44 women and 2 men (no gender record from one patient). The age of the patients whose urine culture were positive varied from 0 (less than one month) to 104 years. Most of the isolates were E. coli (41/47), followed by Klebsiella pneumoniae (2/47), Klebsiella variicola/Klebsiella aerogenes (1/47), Pseudomonas aeruginosa (1/47), Proteus mirabilis (1/47), and Citrobacter koseri (1/47). Most E. coli strains were classified as phylogroup B2 (15/41 = 36.59%) and B1 (12/41 = 29.27%) and the most common virulence genes among E. coli strains were fimH (31/41 = 75.61%), iutA (21/41 = 51.22%), and tratT (16/41 = 39.02%). Among the E. coli strains, 59% were multidrug-resistance and strains that were ampicillin, sulfamethoxazole/trimethoprim, or tetracycline-resistant exhibited more chance to be multidrug-resistance, with an odds ratio of 100.00 [95% confidence interval (CI) 9.44-1059.26], 22.50 (95% CI 3.95-128.30), and 12.83 (95% CI 2.68-61.45), respectively. Our results showed that E. coli was the main etiological agent identified and demonstrated high frequency of multidrug-resistance and virulence factors in bacterial strains isolated from UTIs.
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Prediction of Mannheimia haemolytica serotypes based on whole genomic sequences. Vet Microbiol 2021; 262:109232. [PMID: 34509701 DOI: 10.1016/j.vetmic.2021.109232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/02/2021] [Indexed: 11/24/2022]
Abstract
The aim of the investigation was to predict the serotypes of M. haemolytica based on whole genomic sequences with the capsular gene region as target. A total of 22 strains selected to have been serotyped and to represent all serotypes were investigated by whole genomic sequencing. The BIGSdb (Bacterial Isolate Genome Sequence Database) was downloaded and installed on a Linux server. Here the sequence database was setup with unique loci at serotype level. The server allows serotypes of M. haemolytica to be predicted from whole genomic sequences and the service is available to the public for free from https://ivsmlst.sund.root.ku.dk.
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8
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da Silva AP, Stoute S, Hauck R, Shivaprasad HL, Jerry C. A Case Report of Avian Malaria ( Plasmodium spp.) in Pen-Reared Pigeons ( Columba livia). Avian Dis 2021; 65:213-218. [PMID: 34412450 DOI: 10.1637/0005-2086-65.2.213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/22/2021] [Indexed: 11/05/2022]
Abstract
One dead 6-wk-old male racing pigeon (Columba livia) was submitted for postmortem evaluation after presenting with weight loss, anorexia, dry shanks, dehydration, and lethargy. The bird belonged to a confined flock with 12 other pigeons raised by a hobbyist. Two pigeons in the flock reportedly had died with a history of similar clinical signs. On gross examination, the liver and the spleen were diffusely dark brown to black. Histopathology revealed moderate to large amounts of anisotropic, intracytoplasmic black pigment, compatible with hemozoin, in the spleen, liver, lung, and kidneys, with small amounts in the heart and meninges of the brain. Marked plasmacytic infiltrates were observed in liver, lungs, heart, and kidneys. Blood smears from a clinically affected concomitant pigeon from the flock revealed numerous light-blue, round to oval, intraerythrocytic trophozoites and meronts suggestive of Plasmodium spp. PCR and sequencing tests were performed from spleen and ceca with fragments of the 18S ribosomal RNA and the mitochondrial cytochrome b (cytB) genes. Sequencing results confirmed the presence of Plasmodium in the affected pigeon. Although an exact genetic match could not be determined, the most similar species to the isolate from this study are Plasmodium relictum, Plasmodium matutinum, Plasmodium lutzi, and Plasmodium homocircumflexum.
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Affiliation(s)
- Ana P da Silva
- Turlock Branch, University of California, Davis, California Animal Health & Food Safety Laboratory System, Turlock, CA 95380
| | - Simone Stoute
- Turlock Branch, University of California, Davis, California Animal Health & Food Safety Laboratory System, Turlock, CA 95380
| | - Ruediger Hauck
- Department of Pathobiology and Department of Poultry Sciences, Auburn University, Auburn, AL 36849
| | - H L Shivaprasad
- Tulare Branch, University of California, Davis, California Animal Health & Food Safety Laboratory System, Tulare, CA 93274
| | - Carmen Jerry
- Turlock Branch, University of California, Davis, California Animal Health & Food Safety Laboratory System, Turlock, CA 95380,
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Christensen H, Kuhnert P, Foster G, Bisgaard M. Reclassification of [ Haemophilus] haemoglobinophilus as Canicola haemoglobinophilus gen. nov., comb. nov. including Bisgaard taxon 35. Int J Syst Evol Microbiol 2021; 71. [PMID: 34264807 DOI: 10.1099/ijsem.0.004881] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[Haemophilus] haemoglobinophilus and the unpublished Bisgaard taxon 35 are associated with respiratory and urogenital tract infections in dogs. A total of 21 strains including the type strain of [Haemophilus] haemoglobinophilus were included in the investigation. Strains of [Haemophilus] haemoglobinophilus and taxon 35 formed a monophyletic group demonstrating at least 97.8 and 96.5% similarities within the group based upon 16S rRNA and rpoB gene sequence comparisons, respectively. Glaesserella australis was the most closely related species to [Haemophilus] haemoglobinophilus and taxon 35 with 96.1 % 16S rRNA gene sequence similarity which is slightly higher than the 95 % separating most genera of the family Pasteurellaceae. However, the conserved protein sequence phylogeny documented a unique position of [Haemophilus] haemoglobinophilus with only 81 % identity to the most closely related species, genomospecies 1 of the genus Rodentibacter which is lower than the 85 % separating most genera of the family Pasteurellaceae. The conserved protein sequence identity to Haemophilus influenzae, the type species of the genus, was 77%, demonstrating that [Haemophilus] haemoglobinophilus is not properly classified as a member of the genus Haemophilus. On the basis of the phylogenetic comparisons, the taxa [Haemophilus] haemoglobinophilus and taxon 35 are proposed to be included with a novel genus Canicola with one species, Canicola haemoglobinophilus which is reclassified from [Haemophilus] haemoglobinophilus. Phenotypic characters obtained with isolates genetically approved to represent Canicola haemoglobinophilus were in accordance with those of the members of the family Pasteurellaceae, and the novel genus can be separated from most of the existing genera by a positive catalase reaction, lack of V-factor requirement for growth, lack of haemolysis of blood agar and negative Voges-Proskauer and urease tests. The novel genus cannot be separated by biochemical and physiological characteristics alone from the genera Aggregatibacter, Avibacterium, Frederiksenia and Spirabiliibacterium. However, MALDI-TOF mass spectroscopy and also RpoB amino acid signatures allowed a clear separation from these taxa, supporting the existence of a novel genus. The DNA G+C content is 37.0-37.8 mol% for the genus, based on the whole genomic sequences. The type strain of Canicola haemoglobinophilus is CCUG 3714T (=ATCC 19416T=NCTC 1659T) isolated in 1901 from the prepuce of a dog in Germany.
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Affiliation(s)
- Henrik Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 4 Stigbojlen, DK-1870 Frederiksberg C, Denmark
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggass-Strasse 122, CH-3001 Bern, Switzerland
| | - Geoffrey Foster
- SRUC Veterinary Service, An Lochran 10, Inverness Campus, Inverness, UK
| | - Magne Bisgaard
- Professor emeritus, Bisgaard Consulting, 40 Horsevænget, DK-4130 Viby Sjælland, Denmark
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10
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Payette F, Charlebois A, Fairbrother J, Beauchamp G, Leclere M. Nicoletella semolina in the airways of healthy horses and horses with severe asthma. J Vet Intern Med 2021; 35:1612-1619. [PMID: 33942932 PMCID: PMC8163135 DOI: 10.1111/jvim.16140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 04/10/2021] [Accepted: 04/16/2021] [Indexed: 12/31/2022] Open
Abstract
Background Nicoletella semolina was identified in the airways of horses and its low prevalence could be because of its difficult differentiation from other Pasteurellaceae. Objectives To develop a molecular method for the identification of N. semolina and to evaluate its prevalence in the mouth and the airways of healthy and severe asthmatic horses. Animals Six healthy and 6 severely asthmatic horses in phase I, 10 severely asthmatic horses in phase II, and 10 healthy horses in phase III. Methods Cohort (phases I and II) and cross‐sectional (phase III) studies. Quantitative polymerase chain reaction primers targeting the sodA gene were optimized. N. semolina was quantified in oral and nasal washes and in bronchoalveolar lavage fluid (BALF; phase I, sampled twice), in nasal washes and BALF (phase II, sampled twice), and in nasal washes (phase III). Results N. semolina was found in the nose of 5, 10, and 9 horses in phases I, II, and III, respectively (first sampling for phases I and II). Six BALF from 5 different horses were positive for N. semolina in phase II. In phase I, there was no significant difference in the nasal loads of healthy horses (median (range): 2.04 × 104 copies/mL (0‐2.44 × 105)) and asthmatic horses in exacerbation (3.75 × 102 (0‐4.84 × 106); Wilcoxon's rank sum test, P = .57). Conclusions and Clinical Importance N. semolina is commonly found in the airways of horses. The potential pathogenicity of N. semolina remains to be elucidated, but the molecular technique we developed will facilitate future studies.
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Affiliation(s)
- Flavie Payette
- Clinical Sciences Department, Faculté de Médecine VétérinaireUniversité de MontréalMontrealQuebecCanada
| | - Audrey Charlebois
- Clinical Sciences Department, Faculté de Médecine VétérinaireUniversité de MontréalMontrealQuebecCanada
| | - Julie‐Hélène Fairbrother
- Bacteriology Diagnostic Laboratory, Complexe de Diagnostic et d'Épidémiosurveillance Vétérinaires du Québec, Ministère de l'Agriculture, des Pêcheries et de l'Alimentation du Québec and Faculté de Médecine VétérinaireUniversité de MontréalMontrealQuebecCanada
| | - Guy Beauchamp
- Veterinary Biomedicine Department, Faculté de Médecine VétérinaireUniversité de MontréalMontrealQuebecCanada
| | - Mathilde Leclere
- Clinical Sciences Department, Faculté de Médecine VétérinaireUniversité de MontréalMontrealQuebecCanada
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11
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Hill V, Kuhnert P, Erb M, Machado RAR. Identification of Photorhabdus symbionts by MALDI-TOF MS. MICROBIOLOGY-SGM 2021; 166:522-530. [PMID: 32301690 DOI: 10.1099/mic.0.000905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Species of the bacterial genus Photorhabus live in a symbiotic relationship with Heterorhabditis entomopathogenic nematodes. Besides their use as biological control agents against agricultural pests, some Photorhabdus species are also a source of natural products and are of medical interest due to their ability to cause tissue infections and subcutaneous lesions in humans. Given the diversity of Photorhabdus species, rapid and reliable methods to resolve this genus to the species level are needed. In this study, we evaluated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Photorhabdus species. To this end, we established a collection of 54 isolates consisting of type strains and multiple field strains that belong to each of the validly described species and subspecies of this genus. Reference spectra for the strains were generated and used to complement a currently available database. The extended reference database was then used for identification based on the direct transfer sample preparation method and the protein fingerprint of single colonies. High-level discrimination of distantly related species was observed. However, lower discrimination was observed with some of the most closely related species and subspecies. Our results therefore suggest that MALDI-TOF MS can be used to correctly identify Photorhabdus strains at the genus and species level, but has limited resolution power for closely related species and subspecies. Our study demonstrates the suitability and limitations of MALDI-TOF-based identification methods for assessment of the taxonomic position and identification of Photorhabdus isolates.
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Affiliation(s)
- Virginia Hill
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland.,Institute of Plant Sciences, University of Bern, Switzerland
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Switzerland
| | - Ricardo A R Machado
- Experimental Biology Research Group, University of Neuchatel, Switzerland.,Institute of Plant Sciences, University of Bern, Switzerland
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12
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Wang X, Xu F, Ning K, Shen L, Qi X, Wang J. Construction and Application of MALDI-TOF Mass Spectrometry for the Detection of Haemophilus parasuis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5588855. [PMID: 33937398 PMCID: PMC8062181 DOI: 10.1155/2021/5588855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 01/02/2023]
Abstract
To construct a protein fingerprint database of Haemophilus parasuis (H. parasuis), thus improving its clinical diagnosis efficiency. A total of 15 H. parasuis standard strains were collected to establish a protein fingerprint database of H. parasuis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), and the effects of different culture media and culture time on the quality and identification results of the protein fingerprint were investigated. The results showed that tryptone soy agar (TSA) and tryptone soy broth (TSB) media and different incubation times had no significant effect on the characteristic peaks of the protein profiles. In addition, 18 clinical isolates were used to compare the identification results of the self-built protein fingerprint database, PCR detection, and basic database. Only one strain was identified in the original VITEK-MS system database, while the self-made protein fingerprint database of H. parasuis was 100% accurate for the detection of 18 clinical isolate strains. The protein fingerprint database of H. parasuis built by our laboratory is suitable for rapid clinical diagnosis of H. parasuis, due to its high accuracy, efficiency, and strong specificity.
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Affiliation(s)
- Xiaoxu Wang
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
| | - Feng Xu
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
| | - Kun Ning
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Liping Shen
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
| | - Xinyong Qi
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
| | - Jian Wang
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
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13
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Davies YM, Franco LS, Barbosa FB, Vanin CL, Gomes VTM, Moreno LZ, Barbosa MRF, Sato MIZ, Moreno AM, Knöbl T. Use of MALDI-TOF for identification and surveillance of gram-negative bacteria in captive wild psittacines. BRAZ J BIOL 2021; 82:e233523. [PMID: 33787713 DOI: 10.1590/1519-6984.233523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/08/2020] [Indexed: 11/22/2022] Open
Abstract
Microbiological studies of the sanitary and health status of psittacine birds that will be reintroduced is important in evaluating whether these animals act as carriers of pathogenic agents to other animals and humans. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a faster and more accurate method to identify bacteria than conventional microbiology methods. The aim of this study was to evaluate the health status of psittacines housed in captivity, by assessment of Gram-negative bacteria from fecal microbiota through MALDI- TOF MS identification. The results indicate high frequency of Gram-negative bacteria in feces (96.5%), especially from the Enterobacteriaceae family (88.7%). The most prevalent bacteria were Escherichia coli (39.0%), Proteus vulgaris (12.2%), Klebsiella spp. (12.1%) and Raoultella ornithinolytica (8.7%). Proteus hauseri, Citrobacter spp., Morganella morgannii, Providencia rettgeri, Enterobacter spp. and Escherichia hermannii were isolated with lower frequency. . All these agents are potentially pathogenic for parrots and can cause systemic infections in other animals and humans. These findings reinforce that MALDI- TOF MS proved to be a rapid and accurate method of identification of the microorganism and evaluation of the health status of psittacines, providing relevant data to assist decision-making regarding the sanitary protocols in wildlife centers, and possible future reintroduction of wild birds.
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Affiliation(s)
- Y M Davies
- Universidade de São Paulo - USP, Departamento de Patologia da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - L S Franco
- Universidade de São Paulo - USP, Departamento de Patologia da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - F B Barbosa
- Universidade de São Paulo - USP, Departamento de Patologia da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - C L Vanin
- Departamento de Fauna da Secretaria de Infraestrutura e Meio Ambiente do estado de São Paulo, São Paulo, SP, Brasil
| | - V T M Gomes
- Universidade de São Paulo - USP, Departamento de Medicina Veterinária Preventiva e Saúde Animal da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - L Z Moreno
- Universidade de São Paulo - USP, Departamento de Medicina Veterinária Preventiva e Saúde Animal da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - M R F Barbosa
- Companhia Ambiental do Estado de São Paulo - CETESB, São Paulo, SP, Brasil
| | - M I Z Sato
- Companhia Ambiental do Estado de São Paulo - CETESB, São Paulo, SP, Brasil
| | - A M Moreno
- Universidade de São Paulo - USP, Departamento de Medicina Veterinária Preventiva e Saúde Animal da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - T Knöbl
- Universidade de São Paulo - USP, Departamento de Patologia da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
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14
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Kuhnert P, Brodard I, Schönecker L, Akarsu H, Christensen H, Bisgaard M. Mannheimia pernigra sp. nov., isolated from bovine respiratory tract. Int J Syst Evol Microbiol 2021; 71. [PMID: 33470926 DOI: 10.1099/ijsem.0.004643] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Over a period of 1 year, 270 isolates identified as Taxon 39 of Bisgaard were obtained from the nasopharynx of veal calves at 11 epidemiologically independent Swiss fattening farms. Two isolates from each farm and the Australian Taxon 39 reference strain BNO311 were further characterized by genetic and phenotypic methods. Phylogenetic analysis of 16S rRNA and recN gene sequences placed the isolates in a single, distinct cluster within the genus Mannheimia. As to the rpoB gene, most isolates clustered together, but four strains formed a separate cluster close to Mannheimia varigena. Genome sequence analysis of isolates from both rpoB clusters confirmed their species status, with an average nucleotide identity (ANI) >98.9 % between isolates and <84 % to the closest species, M. varigena. Based upon whole genome sequences, the G+C content was determined as 39.1 mol%. Similarly, analysis of MALDI-TOF MS reference spectra clustered the isolates clearly separated from the other Mannheimia species, making this the method of choice for identification. In addition, numerous biochemical markers based on classical as well as commercial identification schemes were determined, allowing separation from other Mannheimia species and identification of the new taxon. Major fatty acids for strain 17CN0883T are C14 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. Major respiratory quinones are ubiquinone-7 and ubiquinone-8. We propose the name Mannheimia pernigra sp. nov. for former Taxon 39 of Bisgaard. The type strain is 17CN0883T (=CCUG 74657T=DSM 111153T) isolated from a veal calf in Switzerland.
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Affiliation(s)
- Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Isabelle Brodard
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Lutz Schönecker
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Hatice Akarsu
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, Stigbøjlen 4, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Magne Bisgaard
- Professor emeritus, Horsevænget 40, 4130 Viby Sjælland, Denmark
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15
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Ujvári B, Orbán B, Incze Z, Psáder R, Magyar T. Occurrence of Pasteurellaceae and Neisseriaceae bacteria in the pharyngeal and respiratory tract of dogs and cats - Short communication. Acta Vet Hung 2020; 68:231-235. [PMID: 33141116 DOI: 10.1556/004.2020.00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/13/2020] [Indexed: 11/19/2022]
Abstract
The occurrence of members of the Pasteurellaceae and Neisseriaceae families was studied in dogs and cats. A total of 110 nasal and pharyngeal swab samples from 47 dogs and 8 cats were collected. Most of the strains were identified by 16S rDNA sequencing, except Frederiksenia canicola and Pasteurella multocida where species-specific polymerase chain reactions were applied. The most frequently isolated species was F. canicola, which occurred only in dogs, mainly in the pharyngeal cavity. The second commonest bacterium, P. multocida was found in both types of samples and in both hosts. Other species from the family Pasteurellaceae, such as Haemophilus haemoglobinophilus, Pasteurella canis and P. dagmatis, were detected only in dogs. All isolated species belonging to the family Neisseriaceae, mainly representing Neisseria weaveri, were found only in the pharyngeal cavity. Neisseria weaveri and N. zoodegmatis could be detected in both hosts. Neisseria dumasiana and N. canis were isolated from dogs, while N. shayeganii only from a cat. For phylogenetic analysis, rpoB gene sequencing was performed, where the strains were on monophyletic branches and clearly separated from each other. In this study, recently described species such as F. canicola, N. shayeganii and N. dumasiana were detected that had never been isolated in Hungary before.
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Affiliation(s)
- Barbara Ujvári
- 1Institute for Veterinary Medical Research, Centre for Agricultural Research, P.O. Box 18, H-1581, Budapest, Hungary
| | - Bettina Orbán
- 1Institute for Veterinary Medical Research, Centre for Agricultural Research, P.O. Box 18, H-1581, Budapest, Hungary
| | - Zsuzsanna Incze
- 2Small Animal Clinic, University of Veterinary Medicine, Budapest, Hungary
| | - Roland Psáder
- 2Small Animal Clinic, University of Veterinary Medicine, Budapest, Hungary
| | - Tibor Magyar
- 1Institute for Veterinary Medical Research, Centre for Agricultural Research, P.O. Box 18, H-1581, Budapest, Hungary
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16
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Van Driessche L, De Neve C, Haesebrouck F, van Leenen K, Boyen F, Pardon B. Storage time and temperature affect the isolation rate of Mannheimia haemolytica and Pasteurella multocida from bovine bronchoalveolar lavage samples. BMC Vet Res 2020; 16:238. [PMID: 32660585 PMCID: PMC7359580 DOI: 10.1186/s12917-020-02456-7] [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: 10/02/2019] [Accepted: 07/06/2020] [Indexed: 11/18/2022] Open
Abstract
Background A microbiological diagnosis is essential to better target antimicrobial treatment, control and prevention of respiratory tract infections in cattle. Under field conditions, non-endoscopic broncho-alveolar lavage (nBAL) samples are increasingly collected. To what extent the highly variable turnaround time and storage temperatures between sampling and cultivation affect the isolation rate of bacterial pathogens is unknown. Therefore, the objective of this experimental study was to determine the effect of different storage temperatures (0 °C, 8 °C, 23 °C and 36 °C) and times (0,2,4,6,8,24,48 h) on the isolation rate and concentration of Pasteurellaceae in nBAL samples from clinically affected animals. Results At a storage temperature temperature of 36 °C isolation rates of Mannheimia haemolytica and Pasteurella multocida were significantly reduced 6 h and 48 h after sampling, respectively. At room temperature (23 °C), a decrease in M. haemolytica and P. multocida isolation rate was noticed, starting at 24 and 48 h after sampling, respectively, but only significant for P. multocida at 48 h. The presence of microbial contamination negatively affected the isolation of P. multocida in clinical nBAL samples, but not of M. haemolytica. Conclusion Optimal M. haemolytica and P. multocida isolation rates from clinical nBAL samples are obtained after storage at 0 °C or 8 °C, provided that the sample is cultivated within 24 h after sampling. The maximum period a sample can be stored without an effect on the M. haemolytica and P. multocida isolation success varies and is dependent on the storage temperature and the degree of microbial contamination.
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Affiliation(s)
- Laura Van Driessche
- Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
| | - Charlotte De Neve
- Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Katharina van Leenen
- Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Filip Boyen
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Bart Pardon
- Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
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17
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Kuhnert P, Brodard I, Alsaaod M, Steiner A, Stoffel MH, Jores J. Treponema phagedenis ( ex Noguchi 1912) Brumpt 1922 sp. nov., nom. rev., isolated from bovine digital dermatitis. Int J Syst Evol Microbiol 2020; 70:2115-2123. [PMID: 31999237 DOI: 10.1099/ijsem.0.004027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
'Treponema phagedenis' was originally described in 1912 by Noguchi but the name was not validly published and no type strain was designated. The taxon was not included in the Approved Lists of Bacterial Names and hence has no standing in nomenclature. Six Treponema strains positive in a 'T. phagedenis' phylogroup-specific PCR test were isolated from digital dermatitis (DD) lesions of cattle and further characterized and compared with the human strain 'T. phagedenis' ATCC 27087. Results of phenotypic and genotypic analyses including API ZYM, VITEK2, MALDI-TOF and electron microscopy, as well as whole genome sequence data, respectively, showed that they form a cluster of species identity. Moreover, this species identity was shared with 'T. phagedenis'-like strains reported in the literature to be regularly isolated from bovine DD. High average nucleotide identity values between the genomes of bovine and human 'T. phagedenis' were observed. Slight genomic as well as phenotypic variations allowed us to differentiate bovine from human isolates, indicating host adaptation. Based on the fact that this species is regularly isolated from bovine DD and that the name is well dispersed in the literature, we propose the species Treponema phagedenis sp. nov., nom. rev. The species can phenotypically and genetically be identified and is clearly separated from other Treponema species. The valid species designation will allow to further explore its role in bovine DD. The type strain for Treponema phagedenis sp. nov., nom. rev. is B43.1T (=DSM 110455T=NCTC 14362T) isolated from a bovine DD lesion in Switzerland.
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Affiliation(s)
- Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Isabelle Brodard
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Maher Alsaaod
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Adrian Steiner
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michael H Stoffel
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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18
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Kähl S, Maier T, Benga L, Fingas F, Baums CG. Differentiation of Rodentibacter pneumotropicus, Rodentibacter heylii and Muribacter muris by MALDI-TOF MS. J Microbiol Methods 2020; 169:105836. [PMID: 31917974 DOI: 10.1016/j.mimet.2020.105836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/04/2020] [Accepted: 01/05/2020] [Indexed: 10/25/2022]
Abstract
The pathogens Rodentibacter (R.) pneumotropicus and R. heylii as well as the commensal Muribacter (M.) muris are frequently isolated in mice. In this study, a MALDI-TOF MS database was extended with spectra of well characterized strains of these species. Compared to a multiplex PCR, all examined out-of-sample isolates were correctly identified.
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Affiliation(s)
- Sophie Kähl
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, University Leipzig, Leipzig, Germany
| | | | - Laurentiu Benga
- Central Unit for Animal Research and Animal Welfare Affairs, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany
| | | | - Christoph Georg Baums
- Institute of Bacteriology and Mycology, Faculty of Veterinary Medicine, University Leipzig, Leipzig, Germany.
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19
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Immunological and molecular techniques used for determination of serotypes in Pasteurellaceae. J Microbiol Methods 2020. [DOI: 10.1016/bs.mim.2020.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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20
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Rapid identification of respiratory bacterial pathogens from bronchoalveolar lavage fluid in cattle by MALDI-TOF MS. Sci Rep 2019; 9:18381. [PMID: 31804604 PMCID: PMC6895124 DOI: 10.1038/s41598-019-54599-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023] Open
Abstract
Respiratory tract infections are a major health problem and indication for antimicrobial use in cattle and in humans. Currently, most antimicrobial treatments are initiated without microbiological results, holding the risk of inappropriate first intention treatment. The main reason for this empirical treatment is the long turnaround time between sampling and availability of identification and susceptibility results. Therefore the objective of the present study was to develop a rapid identification procedure for pathogenic respiratory bacteria in bronchoalveolar lavage fluid (BALf) samples from cattle by MALDI-TOF MS, omitting the cultivation step on agar plates to reduce the turnaround time between sampling and identification of pathogens. The effects of two different liquid growth media and various concentrations of bacitracin were determined to allow optimal growth of Pasteurellaceae and minimise contamination. The best procedure was validated on 100 clinical BALf samples from cattle with conventional bacterial culture as reference test. A correct identification was obtained in 73% of the samples, with 59.1% sensitivity (Se) (47.2–71.0%) and 100% specificity (Sp) (100–100%) after only 6 hours of incubation. For pure and dominant culture samples, the procedure was able to correctly identify 79.2% of the pathogens, with a sensitivity (Se) of 60.5% (45.0–76.1%) and specificity (Sp) of 100% (100–100%). In mixed culture samples, containing ≥2 clinically relevant pathogens, one pathogen could be correctly identified in 57% of the samples with 57.1% Se (38.8–75.5%) and 100% Sp (100–100%). In conclusion, MALDI-TOF MS is a promising tool for rapid pathogen identification in BALf. This new technique drastically reduces turnaround time and may be a valuable decision support tool to rationalize antimicrobial use.
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21
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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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22
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Srečnik Š, Zdovc I, Javoršek U, Pirš T, Pavlica Z, Nemec A. Microbiological Aspects of Naturally Occurring Primary Endodontic Infections in Dogs. J Vet Dent 2019; 36:124-128. [PMID: 31542989 DOI: 10.1177/0898756419873639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Dental fractures are common in dogs, but data on microbiology of naturally occurring primary endodontic infections, and their relation to clinical and radiographic signs, are lacking. Samples were obtained from root canals of 32 periodontally healthy fractured teeth under aseptic conditions and immediately cultured for aerobic and anaerobic bacteria. Cultures were further identified by matrix-assisted laser desorption/ionization, time of flight technology. Sixty-one bacteria (30 bacterial species) were isolated from root canals; 54% were Gram-negative bacteria, 53% were facultative anaerobic, and 42% were anaerobic bacteria. Number of bacterial species in the root canals declined with the duration of fractures over 12 months. No statistically significant association was found between the number of bacterial species involved in the root canal infection and any of the clinical or radiographic signs of endodontic disease. Naturally occurring primary endodontic infections in dogs appear to be polymicrobial and involve only a selected number of opportunistic pathogen species.
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Affiliation(s)
- Špela Srečnik
- Dentistry and Oral Surgery Department, Veterinary Faculty, Small Animal Clinic, University of Ljubljana, Slovenia
| | - Irena Zdovc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Slovenia
| | - Urška Javoršek
- Dentistry and Oral Surgery Department, Veterinary Faculty, Small Animal Clinic, University of Ljubljana, Slovenia
| | - Tina Pirš
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Slovenia
| | - Zlatko Pavlica
- Dentistry and Oral Surgery Department, Veterinary Faculty, Small Animal Clinic, University of Ljubljana, Slovenia
| | - Ana Nemec
- Dentistry and Oral Surgery Department, Veterinary Faculty, Small Animal Clinic, University of Ljubljana, Slovenia
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23
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Is a Superior Diagnostic Tool for the Identification and Differentiation of Mycoplasmas Isolated from Animals. J Clin Microbiol 2019; 57:JCM.00316-19. [PMID: 31217275 DOI: 10.1128/jcm.00316-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/14/2019] [Indexed: 11/20/2022] Open
Abstract
In veterinary diagnostic laboratories, identification of mycoplasmas is achieved by demanding, cost-intensive, and time-consuming methods that rely on antigenic or genetic identification. Since matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) seems to represent a promising alternative to the currently practiced cumbersome diagnostics, we assessed its applicability for the identification of almost all mycoplasma species isolated from vertebrate animals so far. For generating main spectrum profiles (MSPs), the type strains of 98 Mycoplasma, 11 Acholeplasma, and 5 Ureaplasma species and, in the case of 69 species, 1 to 7 clinical isolates were used. To complete the database, 3 to 7 representatives of 23 undescribed Mycoplasma species isolated from livestock, companion animals, and wildlife were also analyzed. A large in-house library containing 530 MSPs was generated, and the diversity of spectra within a species was assessed by constructing dendrograms based on a similarity matrix. All strains of a given species formed cohesive clusters clearly distinct from all other species. In addition, phylogenetically closely related species also clustered closely but were separated accurately, indicating that the established database was highly robust, reproducible, and reliable. Further validation of the in-house mycoplasma library using 335 independent clinical isolates of 32 mycoplasma species confirmed the robustness of the established database by achieving reliable species identification with log scores of ≥1.80. In summary, MALDI-TOF MS proved to be an excellent method for the identification and differentiation of animal mycoplasmas, combining convenience, ease, speed, precision, and low running costs. Furthermore, this method is a powerful and supportive tool for the taxonomic resolution of animal mycoplasmas.
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Sinclair HA, Chapman P, Omaleki L, Bergh H, Turni C, Blackall P, Papacostas L, Braslins P, Sowden D, Nimmo GR. Identification of Lonepinella sp. in Koala Bite Wound Infections, Queensland, Australia. Emerg Infect Dis 2019; 25:153-156. [PMID: 30561297 PMCID: PMC6302581 DOI: 10.3201/eid2501.171359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report 3 cases of koala bite wound infection with Lonepinella koalarum–like bacteria requiring antimicrobial and surgical management. The pathogens could not be identified by standard tests. Phylogenetic analysis of 16S rRNA and housekeeping genes identified the genus. Clinicians should isolate bacteria and determine antimicrobial susceptibilities when managing these infections.
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25
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Uchida-Fujii E, Niwa H, Kinoshita Y, Nukada T. Actinobacillus species isolated from Japanese Thoroughbred racehorses in the last two decades. J Vet Med Sci 2019; 81:1234-1237. [PMID: 31292334 PMCID: PMC6785623 DOI: 10.1292/jvms.19-0192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Actinobacillus species are known to be pathogenic to horses. To clarify etiological agents of actinobacillosis in Japanese adult horses, 27 isolates from Japanese
Thoroughbred racehorses putatively identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry as Actinobacillus were further identified by
PCR of the A. equuli toxin gene, by CAMP test, and by 16S rRNA sequencing analysis. Actinobacillus equuli subsp. haemolyticus was isolated
most frequently (16/27) and was related to respiratory infections. Actinobacillus equuli subsp. equuli (4/27) was isolated from chronic cases or concomitant
with other bacterial infections. The remainder were A. pleuropneumoniae, unclassified Actinobacillus species and Pasteurella caballi.
Actinobacillus equuli including subsp. haemolyticus and subsp. equuli were the species most frequently isolated from equine
actinobacillosis in Japan.
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Affiliation(s)
- Eri Uchida-Fujii
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi 329-0412, Japan
| | - Hidekazu Niwa
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi 329-0412, Japan
| | - Yuta Kinoshita
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi 329-0412, Japan
| | - Toshio Nukada
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi 329-0412, Japan
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26
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Bokma J, Pardon B, Van Driessche L, Gille L, Deprez P, Haesebrouck F, Boyen F. Optimizing identification of Mycoplasma bovis by MALDI-TOF MS. Res Vet Sci 2019; 125:185-188. [PMID: 31252368 DOI: 10.1016/j.rvsc.2019.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 02/04/2023]
Abstract
Fast and accurate identification of Mycoplasma bovis in cattle samples is of great importance for rational treatment and control of pneumonia, arthritis and mastitis. However, which growth conditions will allow the fastest identification of M. bovis with MALDI-TOF MS remains unclear. Therefore, growth conditions and incubation time were investigated to optimize identification of M. bovis with MALDI-TOF MS and an in-house library was constructed. Nine different M. bovis strains were inoculated in triplicate in three liquid media (B1-3). Basic broth (B1) consisted of pleuropneumonia-like organism broth, enriched with 25% horse serum and 0.7% yeast extract. B2 and B3 were additionally supplemented with 0.5% pyruvate or 520 μg/mL ampicillin, respectively. Protein extraction was performed after 24, 48, 72, 96 and 120 h of incubation (37 °C, 5% CO2) and processed with Autoflex III smartbeam. Identification scores ≥1.7 were interpreted as reliable. The present study showed reliable identification of M. bovis with MALDI-TOF MS as early as 24 h after inoculation, and in broth supplemented with pyruvate, up to 120 h after inoculation. Serial dilutions showed improved survival of M. bovis in broth with pyruvate. The addition of ampicillin to prevent contamination, did not impair identification of M. bovis and state-of-the-art in-house libraries contributed to higher identification scores for M. bovis with MALDI-TOF MS.
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Affiliation(s)
- Jade Bokma
- Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Bart Pardon
- Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Laura Van Driessche
- Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Linde Gille
- Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Piet Deprez
- Department of Large Animal Internal Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Poultry diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Filip Boyen
- Department of Pathology, Bacteriology and Poultry diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
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27
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Miniero Davies Y, Xavier de Oliveira MG, Paulo Vieira Cunha M, Soares Franco L, Pulecio Santos SL, Zanolli Moreno L, Túlio de Moura Gomes V, Zanolli Sato MI, Schiavo Nardi M, Micke Moreno A, Becker Saidenberg A, Rose Marques de Sá L, Knöbl T. Edwardsiella tarda outbreak affecting fishes and aquatic birds in Brazil. Vet Q 2019; 38:99-105. [PMID: 30668277 PMCID: PMC6830998 DOI: 10.1080/01652176.2018.1540070] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Background:Edwardsiella tarda infections are frequent causes of severe outbreaks in the fish farming industry besides representing possible zoonotic risks. However, naturally occurring outbreaks that affect various species besides fishes are seldom described. Aim: To report an outbreak of acute mortality caused by E. tarda affecting multiple species that inhabited a natural pond in the state of São Paulo, Brazil. Materials and methods: Three adult tilapias, three Mallard ducks and one Snow egret were necropsied and subjected to further microbiological tests. Gross and microscopic lesions were documented. The antibiotic susceptibility and phylogenetic similarities among fish and avian strains were also determined. The E. tarda species was confirmed through MALDI-TOF, partial sodB sequencing and phylogenetic analysis. Results: Macroscopical findings between the three species included intestinal dilatation, mucosal hyperaemia and mucous to liquid contents. Common histopathology findings included acute enteritis, increased number of intraepithelial lymphocytes with bacteria adhered to the intestinal epithelium and lymphoid depletion in the spleen. E. tarda was isolated from several organs from all affected species. The phylogeny employing amplified fragment length polymorphism (AFLP) of eleven strains revealed high similarity (>90%) among the isolates regardless of the affected species or sampled organs. Ten isolates of E. tarda showed susceptibility to all tested antibiotics. Conclusions:E. tarda was identified as the cause of death of the species examined. Further studies would be necessary to determine the virulence of these strains and the possible risks regarding public health.
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Affiliation(s)
- Yamê Miniero Davies
- a Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | | | - Marcos Paulo Vieira Cunha
- a Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | - Leticia Soares Franco
- a Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | - Sandy Lorena Pulecio Santos
- a Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | - Luisa Zanolli Moreno
- b Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | - Vasco Túlio de Moura Gomes
- b Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | | | - Marcello Schiavo Nardi
- a Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | - Andrea Micke Moreno
- b Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | - Andre Becker Saidenberg
- a Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | - Lilian Rose Marques de Sá
- a Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
| | - Terezinha Knöbl
- a Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia da , Universidade de São Paulo , São Paulo , Brazil
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28
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Rapid detection of tetracycline resistance in bovine Pasteurella multocida isolates by MALDI Biotyper antibiotic susceptibility test rapid assay (MBT-ASTRA). Sci Rep 2018; 8:13599. [PMID: 30206239 PMCID: PMC6134125 DOI: 10.1038/s41598-018-31562-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/21/2018] [Indexed: 12/28/2022] Open
Abstract
Pasteurella multocida is notorious for its role as an opportunistic pathogen in infectious bronchopneumonia, the economically most important disease facing cattle industry and leading indication for antimicrobial therapy. To rationalize antimicrobial use, avoiding imprudent use of highly and critically important antimicrobials for human medicine, availability of a rapid antimicrobial susceptibility test is crucial. The objective of the present study was to design a MALDI Biotyper antibiotic susceptibility test rapid assay (MBT-ASTRA) procedure for tetracycline resistance detection in P. multocida. This procedure was validated on 100 clinical isolates with MIC-gradient strip test, and a comparison with disk diffusion was made. Sensitivity and specificity of the MBT-ASTRA procedure were 95.7% (95% confidence interval (CI) = 89.8–101.5) and 100% (95% CI = 100–100), respectively, classifying 98% of the isolates correctly after only three hours of incubation. Sensitivity and specificity of disk diffusion were 93.5% (95% CI = 86.3–100.6) and 96.3% (95% CI = 91.3–101.3) respectively, classifying 95% of the isolates correctly. In conclusion, this MBT-ASTRA procedure has all the potential to fulfil the need for a rapid and highly accurate tetracycline susceptibility testing in P. multocida to rationalize antimicrobial use in outbreaks of bronchopneumonia in cattle or other clinical presentations across species.
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29
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Whole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov. Int J Syst Evol Microbiol 2018; 68:2664-2681. [DOI: 10.1099/ijsem.0.002820] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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30
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Boot R, Nicklas W, Christensen H. Revised taxonomy and nomenclature of rodent Pasteurellaceae: Implications for monitoring. Lab Anim 2018; 52:300-303. [PMID: 29385897 DOI: 10.1177/0023677218754597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pasteurellosis is a well-recognized disease with similar pathology in all laboratory rodent species. Pasteurella pneumotropica is the most frequently mentioned member of the Pasteurellaceae isolated from mice and rats. Numerous other Pasteurellaceae taxa have been obtained from mice, rats, and other rodent species. Recently, rodent Pasteurellaceae have been submitted to comprehensive genetic and phenotypic (polyphasic) taxonomic studies. As a result they are now classed within six validly published new genera, namely Cricetibacter, Mesocricetibacter, Mannheimia, Muribacter, Necropsobacter, and Rodentibacter. All previously used names such as P. pneumotropica have become obsolete. The new classification forms a firm basis for the correct phenotypic identification of Pasteurellaceae from laboratory animals and for the selection of strains for pathogenicity studies. Consequences of taxonomic changes notably involve molecular methods used for the detection of Pasteurellaceae infection in laboratory animal colonies. Testing may be done using primer sets that detect all Pasteurellaceae taxa or sets developed to detect host-specific members of the family.
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Affiliation(s)
- R Boot
- 1 RIVM, Bilthoven, the Netherlands
| | | | - H Christensen
- 3 Department of Veterinary Disease Biology, University of Copenhagen, Denmark
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31
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Andrzejczuk S, Kosikowska U, Malm A, Chwiejczak E, Stepien-Pysniak D. Phenotypic diversity of Haemophilus influenzae and Haemophilus parainfluenzae isolates depending on origin and health condition. CURRENT ISSUES IN PHARMACY AND MEDICAL SCIENCES 2017. [DOI: 10.1515/cipms-2017-0018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background. Haemophili are common human microbiota representatives. The aim of our study was to investigate a diversity of Haemophilus spp. isolates selected from clinical specimens on the basis of biochemical characteristics, biotypes distribution, protein profiles and antimicrobial resistance. Results. A total of 893/1025 (87%) of haemophili isolates were identified: 260/1025 (25%) as H. influenzae and 633/1025 (62%) as H. parainfluenzae. Moreover, a group of 107/1025 (10%) isolates without species identification (with e.g. abnormal numerical profile) was described as Haemophilus spp. Within the H. influenzae isolates, biotypes II and III were in a great majority (92/893; 10%, each), whereas among H. parainfluenzae, the most commonly occurring was biotype I and II (301/893, 34% and 178/893, 20%, respectively). A similar prevalence of biotypes was obtained regardless of the patient’s age or health condition or the type of specimen. A production of beta-lactamases was shown in 46/893 (5%) haemophili, both H. influenzae (13/46, 28%) and H. parainfluenzae (33/46, 72%) isolates. On the basis of haemophili biochemical characteristics, the cluster analysis using the UPGMA method demonstrated a high degree of phenotypic similarity due to a small distances between isolates taken from both unhealthy children and adults. Conclusion. Based on biochemical characteristics, about 90% of haemophili clinical isolates representing human-specific respiratory microbiota were positively identified as H. influenzae and H. parainfluenzae. The same differences in biotypes and antimicrobial resistance among isolates selected from healthy people or from patients with chronic and recurrent diseases were detected.
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Affiliation(s)
- Sylwia Andrzejczuk
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki 1, 20-093 Lublin , Poland
| | - Urszula Kosikowska
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki 1, 20-093 Lublin , Poland
| | - Anna Malm
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki 1, 20-093 Lublin , Poland
| | - Edyta Chwiejczak
- Students Scientific Association at the Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki 1, 20-093 Lublin , Poland
| | - Dagmara Stepien-Pysniak
- Department of Veterinary Prevention and Birds Diseases, Institute of Biological Basis of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-950 Lublin , Poland
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32
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Oliveira MGX, Pressinotti LN, Carvalho GS, Oliveira MCV, Moreno LZ, Matajira CEC, Bergamo AS, Aleixo VM, Veiga AC, de Souza Corsino E, Christ APG, Sato MIZ, Moreno AM, Knöbl T. Arcobacter spp. in fecal samples from Brazilian farmed caimans (Caiman yacare, Daudin 1802). Trop Anim Health Prod 2017; 49:777-782. [DOI: 10.1007/s11250-017-1262-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 03/06/2017] [Indexed: 11/29/2022]
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33
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Bisgaard M, Xin D, Bertelsen MF, Bojesen AM, Christensen H. Prevalence of Taxa of Pasteurellaceae Among Populations of Healthy Captive Psittacine Birds. Avian Dis 2017; 61:102-106. [PMID: 28301245 DOI: 10.1637/11522-103016-reg] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sixty-two strains of Pasteurellaceae-like bacteria were isolated from the tracheas of 87 clinically healthy psittacine birds in two Danish zoos. The isolates were identified by a combination of rpoB and 16S rRNA gene sequencing and by matrix-assisted laser desorption-ionization time of flight. Twenty-eight strains belonged to the genus Volucribacter or were related to this genus and to the unnamed taxon 34 of Bisgaard, and 28 strains were related to the unnamed taxon 44 of Bisgaard. Four strains were identified as Pasteurella multocida , two isolates were classified with the related taxon 45 of Bisgaard, and a single isolate was classified as Pasteurella sp. The investigation documented an unrecognized reservoir of rarely reported and unclassified or unnamed species of Pasteurellaceae-like bacteria in psittacine birds. The results were in accordance with a recent report on isolation of Pasteurellaceae from diseased psittacine birds, and the investigation documented that the same taxa of Pasteurellaceae-like bacteria can be isolated from apparently healthy birds as well as from diseased birds.
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Affiliation(s)
| | - Di Xin
- B School of Life Science, Beijing Institute of Technology, Beijing 100081, People's Republic of China.,C Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - M F Bertelsen
- C Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark.,D Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - A M Bojesen
- C Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - H Christensen
- C Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
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34
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Matajira CEC, Moreno LZ, Gomes VTM, Silva APS, Mesquita RE, Doto DS, Calderaro FF, de Souza FN, Christ APG, Sato MIZ, Moreno AM. Evaluation of protein spectra cluster analysis for Streptococcus spp. identification from various swine clinical samples. J Vet Diagn Invest 2017; 29:245-249. [PMID: 28068884 DOI: 10.1177/1040638716686641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Traditional microbiological methods enable genus-level identification of Streptococcus spp. isolates. However, as the species of this genus show broad phenotypic variation, species-level identification or even differentiation within the genus is difficult. Herein we report the evaluation of protein spectra cluster analysis for the identification of Streptococcus species associated with disease in swine by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A total of 250 S. suis-like isolates obtained from pigs with clinical signs of encephalitis, arthritis, pneumonia, metritis, and urinary or septicemic infection were studied. The isolates came from pigs in different Brazilian states from 2001 to 2014. The MALDI-TOF MS analysis identified 86% (215 of 250) as S. suis and 14% (35 of 250) as S. alactolyticus, S. dysgalactiae, S. gallinaceus, S. gallolyticus, S. gordonii, S. henryi, S. hyointestinalis, S. hyovaginalis, S. mitis, S. oralis, S. pluranimalium, and S. sanguinis. The MALDI-TOF MS identification was confirmed in 99.2% of the isolates by 16S rDNA sequencing, with MALDI-TOF MS misidentifying 2 S. pluranimalium as S. hyovaginalis. Isolates were also tested by a biochemical automated system that correctly identified all isolates of 8 of the 10 species in the database. Neither the isolates of the 3 species not in the database ( S. gallinaceus, S. henryi, and S. hyovaginalis) nor the isolates of 2 species that were in the database ( S. oralis and S. pluranimalium) could be identified. The topology of the protein spectra cluster analysis appears to sustain the species phylogenetic similarities, further supporting identification by MALDI-TOF MS examination as a rapid and accurate alternative to 16S rDNA sequencing.
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Affiliation(s)
- Carlos E C Matajira
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Luisa Z Moreno
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Vasco T M Gomes
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Ana Paula S Silva
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Renan E Mesquita
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Daniela S Doto
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Franco F Calderaro
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Fernando N de Souza
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Ana Paula G Christ
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Maria Inês Z Sato
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
| | - Andrea M Moreno
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil (Matajira, Moreno, Gomes, Silva, Mesquita, Doto, Calderaro, de Souza, Moreno).,Environmental Company of São Paulo State, São Paulo, Brazil (Christ, Sato)
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35
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Molecular and antimicrobial susceptibility profiling of atypical Streptococcus species from porcine clinical specimens. INFECTION GENETICS AND EVOLUTION 2016; 44:376-381. [DOI: 10.1016/j.meegid.2016.07.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/28/2016] [Accepted: 07/31/2016] [Indexed: 11/20/2022]
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36
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Abstract
Histophilus somni is responsible for sporadic disease worldwide in cattle and, to a lesser extent, in small ruminants, bighorn sheep (Ovis canadensis), and North American bison (Bison bison). The importance of H. somni diseases can be attributed to improved clinical and laboratory recognition, combined with the growth in intensive management practices for cattle. Although outbreaks of bovine histophilosis can occur year-round, in northern and southern hemispheres, it is most frequent in late fall and early winter. Weather, stress, dietary changes, and comingling of cattle are likely to be major triggers for outbreaks. The most frequent clinical expressions of histophilosis include undifferentiated fever, fibrinosuppurative pneumonia, encephalitis-leptomeningitis, necrotizing myocarditis, and diffuse pleuritis. Neurological disease occurs either as thrombotic meningoencephalitis (TME) or as suppurative meningitis with ventriculitis. Acute myocarditis is characteristically necrotizing and generally involves one or both papillary muscles in the left ventricular myocardium. Biofilm-like aggregates of bacteria occur in capillaries and veins in myocardium, in the central nervous system, and on endocardial surfaces. H. somni is a component of bovine respiratory disease (BRD) complex. In our experience, it is most commonly diagnosed in subacute-to-chronic polymicrobial pulmonary infections in combination with Mannheimia haemolytica, Trueperella pyogenes, Pasteurella multocida, or Mycoplasma bovis. Other, less common forms of H. somni disease present as polyarthritis/tenosynovitis, abortion with placentitis and fetal septicemia, epididymitis-orchitis, and ocular infections. It is likely that H. somni is under-recognized clinically and diagnostically. Most state and provincial laboratories in North America rely on bacterial isolation to confirm infection. The use of more sensitive detection methods on field cases of histophilosis will help resolve the pathogenesis of H. somni in natural outbreaks, and whether the disease is as common elsewhere as it is in Canada.
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Puchalski A, Urban-Chmiel R, Dec M, Stęgierska D, Wernicki A. The use of MALDI-TOF mass spectrometry for rapid identification of Mannheimia haemolytica. J Vet Med Sci 2016; 78:1339-42. [PMID: 27109070 PMCID: PMC5053938 DOI: 10.1292/jvms.16-0087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Mannheimia haemolytica is the most important bacterial pathogen isolated
from cases of Bovine Respiratory Disease (BRD). Routine identification of these bacteria
is usually performed using phenotypic methods. Our study showed that MALDI-TOF MS is a
reliable alternative to these methods. All of the strains analyzed were identified as
M. haemolytica. The identification results were compared to those
obtained using conventional methods commonly used in microbiological diagnostics, based on
detection and analysis of biochemical properties of microorganisms. The degree of
agreement between the two methods for identifying M. haemolytica was
100%.
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Affiliation(s)
- Andrzej Puchalski
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland
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38
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Lau JSY, Omaleki L, Turni C, Barber SR, Browning GF, Francis MJ, Graham M, Korman TM. Human Wound Infection with Mannheimia glucosida following Lamb Bite. J Clin Microbiol 2015; 53:3374-6. [PMID: 26202121 PMCID: PMC4572521 DOI: 10.1128/jcm.01249-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/10/2015] [Indexed: 11/20/2022] Open
Abstract
Mannheimia spp. are veterinary pathogens that can cause mastitis and pneumonia in domestic cattle and sheep. While Mannheimia glucosida can be found as normal flora in oral and respiratory mucosa in sheep, there have been no reported cases of human infection with this organism.
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Affiliation(s)
- Jillian S Y Lau
- Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia
| | - Lida Omaleki
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
| | - Stuart Richard Barber
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Glenn Francis Browning
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Maryza Graham
- Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia Department of Microbiology, Monash Health, Clayton, Victoria, Australia
| | - Tony M Korman
- Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia Department of Microbiology, Monash Health, Clayton, Victoria, Australia Department of Medicine, Monash University, Clayton, Victoria, Australia
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Singhal N, Kumar M, Kanaujia PK, Virdi JS. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791. [PMID: 26300860 PMCID: PMC4525378 DOI: 10.3389/fmicb.2015.00791] [Citation(s) in RCA: 800] [Impact Index Per Article: 88.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 01/13/2023] Open
Abstract
Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.
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Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi New Delhi, India
| | - Pawan K Kanaujia
- Department of Microbiology, University of Delhi New Delhi, India
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40
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Evaluation of MALDI-ToF as a method for the identification of bacteria in the veterinary diagnostic laboratory. Res Vet Sci 2015; 101:42-9. [DOI: 10.1016/j.rvsc.2015.05.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/30/2015] [Accepted: 05/30/2015] [Indexed: 11/23/2022]
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Kuhnert P, Thomann A, Brodard I, Haefeli W, Korczak BM. Uruburuella testudinis sp. nov., isolated from tortoise (Testudo). Int J Syst Evol Microbiol 2015; 65:1251-1255. [PMID: 25634951 DOI: 10.1099/ijs.0.000089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic analysis was carried out on 11 uncommon Gram-stain-negative, non-motile, catalase- and oxidase-positive, but indole-negative, bacterial strains isolated from tortoises. Phenotypically and genetically they represented a homogeneous group of organisms most closely related to, but distinct from, Uruburuella suis. In a reconstructed 16S rRNA gene tree they clustered on a monophyletic branch next to U. suis with gene similarities between strains of 99.5-100%, and of up to 98.2% with U. suis . DNA-DNA hybridization indicated the organisms represented a novel species with only 40% DNA-DNA similarity with U. suis . Partial sequencing of rpoB resulted in two subclusters confirming the 16S rRNA gene phylogeny; both genes allowed clear separation and identification of the novel species. Furthermore, they could be unambiguously identified by matrix-assisted laser desorption ionization time-of-flight MS, where, again, they formed a highly homogeneous cluster separate from U. suis and other members of the family Neisseriaceae . The major fatty acids were C(16 : 0) and summed feature C(16 : 1)ω7c/iso-C(15 : 0) 2-OH. The DNA G+C content was 54.4 mol%. Based on phenotypic and genetic data we propose classifying these organisms as representatives of a novel species named Uruburuella testudinis sp. nov. The type strain is 07_OD624(T) ( = DSM 26510(T) = CCUG 63373(T)).
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Affiliation(s)
- Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Andreas Thomann
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Isabelle Brodard
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Bożena M Korczak
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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42
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Abstract
Species of the family Pasteurellaceae play an important role as primary or opportunistic, predominantly respiratory, pathogens in domestic and wild animals. Some of them cause severe disease with high economic losses in commercial animal husbandry. Hence, rapid and accurate differentiation of Pasteurellaceae is important and signifies a particular challenge to diagnostic laboratories. Identification and differentiation of Pasteurellaceae is mostly done using phenotypic tests or genetic identification based on sequence similarity of housekeeping genes, such as the rrs gene encoding the 16S ribosomal RNA (16S rRNA). Both approaches are time consuming, laborious, and costly, therefore often delaying the final diagnosis of disease or epidemics. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry represents an alternative rapid and reliable method for the differentiation of most members of the family Pasteurellaceae. It is able to differentiate within a few minutes the currently known 18 genera and most of the over 60 species and subspecies of Pasteurellaceae including many members encountered in veterinary diagnostic laboratories. A few closely related species and subspecies that cannot be discriminated by MALDI-TOF are easily identified further by complementary simple tests, such as hemolysis done simultaneously or routinely during pathogen isolation.
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Affiliation(s)
- Joachim Frey
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland,
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43
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Abstract
Histophilus somni was proposed in 2003 as a common name for bacteria that earlier had been called "Haemophilus somni", "Haemophilus agni", "Haemophilus somnifer", and "Histophilus ovis". The species is clearly separated from other species and genera within the family Pasteurellaceae. The species is phenotypically variable, but highly uniform regarding the 16S rDNA sequence. Whole-genome sequencing has revealed distinct genetic differences between a commensal and a pathogenic strain, particularly in regard to putative virulence factors. However, broad generalizations regarding the genetics of H. somni cannot be applied to the entire species until the genomes of additional strains are sequenced.
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Affiliation(s)
- Øystein Angen
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway.
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44
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Wragg P, Randall L, Whatmore AM. Comparison of Biolog GEN III MicroStation semi-automated bacterial identification system with matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S ribosomal RNA gene sequencing for the identification of bacteria of veterinary interest. J Microbiol Methods 2014; 105:16-21. [PMID: 25014253 DOI: 10.1016/j.mimet.2014.07.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 07/01/2014] [Accepted: 07/01/2014] [Indexed: 01/22/2023]
Abstract
Recent advances in phenotypic and chemotaxonomic methods have improved the ability of systems to resolve bacterial identities at the species level. Key to the effective use of these systems is the ability to draw upon databases which can be augmented with new data gleaned from atypical or novel isolates. In this study we compared the performance of the Biolog GEN III identification system (hereafter, GEN III) with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing in the identification of isolates of veterinary interest. The use of strains that had proven more difficult to identify by routine methods was designed to test the systems' abilities at the extremes of their performance range. Over an 18month period, 100 strains were analysed by all three methods. To highlight the importance of identification to species level, a weighted scoring system was devised to differentiate the capacity to identify at genus and species levels. The overall relative weighted scores were 0.869:0.781:0.769, achieved by 16S rRNA gene sequencing, GEN III and MALDI-TOF MS respectively, when compared to the 'gold standard'. Performance to the genus level was significantly better using 16S rRNA gene sequencing; however, performance to the species level was similar for all three systems.
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Affiliation(s)
- P Wragg
- Animal Health and Veterinary Laboratories Agency-Penrith Regional Laboratory, Penrith, Cumbria CA11 9RR, United Kingdom.
| | - L Randall
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, United Kingdom
| | - A M Whatmore
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, United Kingdom
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Masarikova M, Mrackova M, Sedlinska M. Application of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Identification of Stallion Semen Bacterial Contamination. J Equine Vet Sci 2014. [DOI: 10.1016/j.jevs.2014.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Alispahic M, Christensen H, Bisgaard M, Hess M, Hess C. MALDI-TOF mass spectrometry confirms difficulties in separating species of the Avibacterium genus. Avian Pathol 2014; 43:258-63. [PMID: 24802229 DOI: 10.1080/03079457.2014.916038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the present study a well-characterized strain collection (n = 33) of Avibacterium species was investigated by matrix-assisted laser desorption ionization-time-of flight mass spectrometry (MALDI-TOF MS). The robustness of the currently available reference database (Bruker Biotyper 3.0) was tested to determine the degree of identification of these strains. Reproducible signal patterns were obtained from all strains. However, identification of most strains was only possible at genus level. Furthermore, two strains could not be identified by this method. Based on their protein spectra profiles, a MALDI main spectra dendrogram was created to determine their relationship. Most strains were closely related-for example, 26 strains formed cluster 1 including the type strains of Avibacterium volantium, Avibacterium gallinarum, Avibacterium endocarditidis and Avibacterium avium-while Avibacterium paragallinarum biovars 1 and 2 formed cluster 2 and, finally, strain 55000 remained on its own. The present MALDI-TOF MS results confirm recent findings that only certain isolates of Av. paragallinarum represent a well-defined species within the genus Avibacterium, making a taxonomic revision essential. To improve identification of Avibacterium at species level by MALDI-TOF MS, relevant reference strains were included in the newly created database and results are presented. In conclusion, Av. paragallinarum can be identified by MALDI/Biotyper and not the other species of the genus.
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Affiliation(s)
- Merima Alispahic
- a Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health , University of Veterinary Medicine , Vienna , Austria
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47
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Korczak BM, Bisgaard M, Christensen H, Kuhnert P. Frederiksenia canicola gen. nov., sp. nov. isolated from dogs and human dog-bite wounds. Antonie van Leeuwenhoek 2014; 105:731-41. [DOI: 10.1007/s10482-014-0129-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/28/2014] [Indexed: 11/28/2022]
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Schröttner P, Schultz J, Rudolph W, Gunzer F, Thürmer A, Fitze G, Jacobs E. Actinobacillus equuli ssp. haemolyticus in a semi-occlusively treated horse bite wound in a 2-year-old girl. GERMAN MEDICAL SCIENCE : GMS E-JOURNAL 2013; 11:Doc14. [PMID: 24068980 PMCID: PMC3782719 DOI: 10.3205/000182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/16/2013] [Indexed: 11/30/2022]
Abstract
We report on the isolation of Actinobacillus equuli ssp. haemolyticus from wound smears of a 2-year-old girl who was admitted to the hospital due to partial amputation of the distal phalanx of her right middle finger caused by a horse bite. A. equuli typically causes diseases in horses and only very few reports describing human infections (mostly associated with wounds) are available in the literature. Interestingly, although the bacteria could be found in consecutive samples taken at different points in time, there were no signs of advancing infection or inflammation. Moreover, the fingertip regenerated after 74 days under semi-occlusive dressings with very pleasant results. For strain identification two automated systems were employed producing discrepant results: VITEK 2 described the pathogens as Pasteurella pneumotropica while MALDI-TOF MS analysis revealed A. equuli. Sequence analysis of 16S rDNA gene finally confirmed A. equuli ssp. haemolyticus as the isolated strain. The antimicrobial susceptibility testing was performed according to the CLSI criteria for Pasteurella spp. Additionally we conducted a test according to the EUCAST criteria.
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Affiliation(s)
- Percy Schröttner
- Faculty of Medicine, Institute of Medical Microbiology and Hygiene,Universitätsklinikum Carl-Gustav-Carus, Dresden, Germany
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Jores J, Fischer A, Sirand-Pugnet P, Thomann A, Liebler-Tenorio EM, Schnee C, Santana-Cruz I, Heller M, Frey J. Mycoplasma feriruminatoris sp. nov., a fast growing Mycoplasma species isolated from wild Caprinae. Syst Appl Microbiol 2013; 36:533-8. [PMID: 24016869 DOI: 10.1016/j.syapm.2013.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/26/2013] [Accepted: 07/31/2013] [Indexed: 11/26/2022]
Abstract
Five Mycoplasma strains from wild Caprinae were analyzed: four from Alpine ibex (Capra ibex) which died at the Berlin Zoo between 1993 and 1994, one from a Rocky Mountain goat collected in the USA prior to 1987. These five strains represented a population different from the populations belonging to the 'Mycoplasma mycoides cluster' as tested using multi locus sequence typing, Matrix-assisted laser desorption/ionization time of flight mass spectrometry analysis and DNA-DNA hybridization. Analysis of the 16S rRNA gene (rrs), genomic sequence based in silico as well as laboratory DNA-DNA hybridization, and the analysis of phenotypic traits in particular their exceptionally rapid growth all confirmed that they do not belong to any Mycoplasma species described to date. We therefore suggest these strains represent a novel species, for which we propose the name Mycoplasma feriruminatoris sp. nov. The type strain is G5847(T) (=DSM 26019(T)=NCTC 13622(T)) [corrected].
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Affiliation(s)
- Joerg Jores
- International Livestock Research Institute, PO Box 30709, 00100 Nairobi, Kenya.
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50
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Zangenah S, Güleryüz G, Boräng S, Ullberg M, Bergman P, Ozenci V. Identification of clinical Pasteurella isolates by MALDI-TOF -- a comparison with VITEK 2 and conventional microbiological methods. Diagn Microbiol Infect Dis 2013; 77:96-8. [PMID: 23886788 DOI: 10.1016/j.diagmicrobio.2013.06.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 06/02/2013] [Accepted: 06/14/2013] [Indexed: 11/27/2022]
Abstract
The aim of this study was to compare the performance of four methods that are widely used in the clinical microbiology laboratory for identification of Pasteurella species. The 4 methods evaluated were VITEK2, VITEK MS (BioMerieux), and Bruker Biotyper MS (Bruker) as well as traditional biochemical tests. Sequencing of the sodA gene was used as the reference method. Sixty-five isolates of Pasteurella spp. from 65 patients were analyzed. One Pasteurella multocida isolate from American Type Culture Collection (Manassas, VA, USA) was used as a reference. Traditional biochemical tests accurately identified 62/66 (94%) isolates. Both Bruker and Vitek matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identified 59/66 (89%) strains, but VITEK2 could only identify 32/66 (48.5%) isolates correctly. The mean time to identification using biochemical tests was 20 hours; VITEK2 took 6 hours and MALDI-TOF approximately 10 minutes. In conclusion, MALDI-TOF is a quick method, which accurately identified most isolates of Pasteurella to the species level. Thus, MALDI-TOF constitutes a valuable diagnostic tool in the clinical laboratory.
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Affiliation(s)
- Salah Zangenah
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Huddinge, Sweden; Department of Medicine, Centre for Infectious Medicine (CIM), Karolinska Institutet and Karolinska University Hospital, Huddinge, Sweden.
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