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Petrin S, Tiengo A, Longo A, Furlan M, Marafin E, Zavagnin P, Orsini M, Losasso C, Barco L. Uncommon Salmonella Infantis Variants with Incomplete Antigenic Formula in the Poultry Food Chain, Italy. Emerg Infect Dis 2024; 30:795-799. [PMID: 38526241 PMCID: PMC10977818 DOI: 10.3201/eid3004.231074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Uncommon Salmonella Infantis variants displaying only flagellar antigens phenotypically showed identical incomplete antigenic formula but differed by molecular serotyping. Although most formed rough colonies, all shared antimicrobial resistances and the presence of usg gene with wild-type Salmonella Infantis. Moreover, they were undistinguishable wild-type Salmonella Infantis by whole-genome sequencing.
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Affiliation(s)
| | | | - Alessandra Longo
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Maddalena Furlan
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Elisa Marafin
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Paola Zavagnin
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Massimiliano Orsini
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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Petrin S, Orsini M, Massaro A, Olsen JE, Barco L, Losasso C. Phenotypic and genotypic antimicrobial resistance correlation and plasmid characterization in Salmonella spp. isolates from Italy reveal high heterogeneity among serovars. Front Public Health 2023; 11:1221351. [PMID: 37744490 PMCID: PMC10513437 DOI: 10.3389/fpubh.2023.1221351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction The spread of antimicrobial resistance among zoonotic pathogens such as Salmonella is a serious health threat, and mobile genetic elements (MGEs) carrying antimicrobial resistance genes favor this phenomenon. In this work, phenotypic antimicrobial resistance to commonly used antimicrobials was studied, and the antimicrobial resistance genes (ARGs) and plasmid replicons associated with the resistances were determined. Methods Eighty-eight Italian Salmonella enterica strains (n = 88), from human, animal and food sources, isolated between 2009 and 2019, were selected to represent serovars with different frequency of isolation in human cases of salmonellosis. The presence of plasmid replicons was also investigated. Results and discussion Resistances to sulphonamides (23.9%), ciprofloxacin (27.3%), ampicillin (29.5%), and tetracycline (32.9%) were the most found phenotypes. ARGs identified in the genomes correlated with the phenotypical results, with blaTEM-1B, sul1, sul2, tetA and tetB genes being frequently identified. Point mutations in gyrA and parC genes were also detected, in addition to many different aminoglycoside-modifying genes, which, however, did not cause phenotypic resistance to aminoglycosides. Many genomes presented plasmid replicons, however, only a limited number of ARGs were predicted to be located on the contigs carrying these replicons. As an expectation of this, multiple ARGs were identified on contigs with IncQ1 plasmid replicon in strains belonging to the monophasic variant of Salmonella Typhimurium. In general, high variability in ARGs and plasmid replicons content was observed among isolates, highlighting a high level of heterogeneity in Salmonella enterica. Irrespective of the serovar., many of the ARGs, especially those associated with critically and highly important antimicrobials for human medicine were located together with plasmid replicons, thus favoring their successful dissemination.
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Affiliation(s)
- Sara Petrin
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Massimiliano Orsini
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
| | - Andrea Massaro
- Applied Chemistry Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicenza, Italy
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lisa Barco
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
| | - Carmen Losasso
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, Legnaro, Italy
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Petrin S, Wijnands L, Benincà E, Mughini-Gras L, Delfgou-van Asch EHM, Villa L, Orsini M, Losasso C, Olsen JE, Barco L. Assessing phenotypic virulence of Salmonella enterica across serovars and sources. Front Microbiol 2023; 14:1184387. [PMID: 37346753 PMCID: PMC10279978 DOI: 10.3389/fmicb.2023.1184387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
Introduction Whole genome sequencing (WGS) is increasingly used for characterizing foodborne pathogens and it has become a standard typing technique for surveillance and research purposes. WGS data can help assessing microbial risks and defining risk mitigating strategies for foodborne pathogens, including Salmonella enterica. Methods To test the hypothesis that (combinations of) different genes can predict the probability of infection [P(inf)] given exposure to a certain pathogen strain, we determined P(inf) based on invasion potential of 87 S. enterica strains belonging to 15 serovars isolated from animals, foodstuffs and human patients, in an in vitro gastrointestinal tract (GIT) model system. These genomes were sequenced with WGS and screened for genes potentially involved in virulence. A random forest (RF) model was applied to assess whether P(inf) of a strain could be predicted based on the presence/absence of those genes. Moreover, the association between P(inf) and biofilm formation in different experimental conditions was assessed. Results and Discussion P(inf) values ranged from 6.7E-05 to 5.2E-01, showing variability both among and within serovars. P(inf) values also varied between isolation sources, but no unambiguous pattern was observed in the tested serovars. Interestingly, serovars causing the highest number of human infections did not show better ability to invade cells in the GIT model system, with strains belonging to other serovars displaying even higher infectivity. The RF model did not identify any virulence factor as significant P(inf) predictors. Significant associations of P(inf) with biofilm formation were found in all the different conditions for a limited number of serovars, indicating that the two phenotypes are governed by different mechanisms and that the ability to form biofilm does not correlate with the ability to invade epithelial cells. Other omics techniques therefore seem more promising as alternatives to identify genes associated with P(inf), and different hypotheses, such as gene expression rather than presence/absence, could be tested to explain phenotypic virulence [P(inf)].
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Affiliation(s)
- Sara Petrin
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lucas Wijnands
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Elisa Benincà
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Ellen H. M. Delfgou-van Asch
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Massimiliano Orsini
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - Carmen Losasso
- Microbial Ecology and Microrganisms Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lisa Barco
- WHOA and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
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Tiengo A, Orsini M, Petrin S, Losasso C, Longo A, Cento G, Ciot L, Ceruti R, Cibin V, Barco L. Whole-Genome Sequence of Salmonella enterica Serovar Bispebjerg from Turkey Reveals Its Pathogenic Potential. Microbiol Resour Announc 2023; 12:e0004323. [PMID: 37022181 DOI: 10.1128/mra.00043-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
We report the genome sequence of a Salmonella enterica subsp. enterica serovar Bispebjerg strain that was isolated from a turkey flock in 2011. The genome analysis of the strain, a rare and multihost serovar, revealed its pathogenic potential due to antimicrobial resistance and a plethora of Salmonella pathogenicity islands and virulence factors.
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Affiliation(s)
- Alessia Tiengo
- Italian National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Massimiliano Orsini
- Italian National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Sara Petrin
- Italian National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Carmen Losasso
- Italian National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Alessandra Longo
- Italian National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Giulia Cento
- Italian National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Laura Ciot
- Italian National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | | | - Veronica Cibin
- Epidemiology Department, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Lisa Barco
- Italian National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
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Peruzzo A, Vascellari M, Massaro A, Mancin M, Stefani A, Orsini M, Danesi P, Petrin S, Carminato A, Santoro MM, Speranza R, Losasso C, Capelli G. Giardia duodenalis Colonization Slightly Affects Gut Microbiota and Hematological Parameters in Clinically Healthy Dogs. Animals (Basel) 2023; 13:ani13060958. [PMID: 36978500 PMCID: PMC10044607 DOI: 10.3390/ani13060958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
Giardia duodenalis (Giardia) is a worldwide cause of acute diarrheal disease both in humans and animals. The primary aim of this study was to investigate possible variations in gut microbiota in a population of asymptomatic dogs (n = 31), naturally infected or not by Giardia. Gut microbiota and the hematological, biochemical, and fecal parameters related to intestinal function were investigated. Giardia infection was associated with a significant shift of beta diversity, showing a relevant reduction of Gammaproteobacteria and an increase of Fusobacteria in male-positive dogs if compared with negatives. A significant imbalance of different bacterial taxa, with particular reference to the Erysipelotrichales, Lactobacillales, Clostridiales, and Burkholderiales orders, was observed, with the first two being higher in Giardia-positive dogs. Giardia-positive males displayed significantly higher values of cCRP than negative males as well as positive females, supporting the presence of a pro-inflammatory state. Taken together, these results indicate that the presence of Giardia does not substantially modify the microbial ecology of the intestine nor the hematological markers of disease. Thus treatments against Giardia should be considered with caution in asymptomatic subjects.
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Affiliation(s)
- Arianna Peruzzo
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Marta Vascellari
- Laboratory of Histopathology, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Andrea Massaro
- Laboratory of Enhancement of Food Production, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Marzia Mancin
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Annalisa Stefani
- Laboratory of Animal Medicine, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Massimiliano Orsini
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Patrizia Danesi
- Laboratory of Parasitology, Mycology and Medical Entomology, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Sara Petrin
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Antonio Carminato
- Laboratory of Histopathology, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Michele Matteo Santoro
- Corso Allevamento e Addestramento Cinofili, Guardia di Finanza, 06061 Castiglione del Lago, Italy
| | - Roberto Speranza
- Corso Allevamento e Addestramento Cinofili, Guardia di Finanza, 06061 Castiglione del Lago, Italy
| | - Carmen Losasso
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
- Correspondence:
| | - Gioia Capelli
- Laboratory of Parasitology, Mycology and Medical Entomology, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
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Doni L, Oliveri C, Lasa A, Di Cesare A, Petrin S, Martinez-Urtaza J, Coman F, Richardson A, Vezzulli L. Large-scale impact of the 2016 Marine Heatwave on the plankton-associated microbial communities of the Great Barrier Reef (Australia). Mar Pollut Bull 2023; 188:114685. [PMID: 36739716 DOI: 10.1016/j.marpolbul.2023.114685] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
The Great Barrier Reef (GBR) is the world's largest coral ecosystem and is threatened by climate change. This study investigated the impact of the 2016 Marine Heatwave (MHW) on plankton associated microbial communities along a ∼800 km transect in the GBR. 16S rRNA gene metabarcoding of archived plankton samples collected from November 2014 to August 2016 in this region showed a significant increase in Planctomycetes and bacteria belonging to the genus Vibrio and Synechococcus during and after the heatwave. Notably, Droplet Digital PCR and targeted metagenomic analysis applied on samples collected four months after the MHW event revealed the presence of several potential pathogenic Vibrio species previously associated with diseases in aquatic animals. Overall, the 2016 MHW significantly impacted the surface picoplankton community and fostered the spread of potentially pathogenic bacteria across the GBR providing an additional threat for marine biodiversity in this area.
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Affiliation(s)
- Lapo Doni
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Corso Europa 26, 16132 Genoa, Italy
| | - Caterina Oliveri
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Corso Europa 26, 16132 Genoa, Italy
| | - Aide Lasa
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Corso Europa 26, 16132 Genoa, Italy; Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Departamento de Ecología y Biología Animal, Universidade de Vigo, 36310 Vigo, Spain
| | - Andrea Di Cesare
- Water Research Institute (IRSA) - MEG Molecular Ecology Group, CNR - National Research Council of Italy, Verbania 28922, Italy
| | - Sara Petrin
- Laboratory of Microbial ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro 35020, Italy
| | - Jaime Martinez-Urtaza
- Department of Genetics and Microbiology, Facultat de Biociéncies, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Frank Coman
- CSIRO Oceans and Atmosphere, EcoSciences Precinct, 41 Boggo Road, Dutton Park, Brisbane 4102, QLD, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere, BioSciences Precinct (QBP), St Lucia, QLD, Australia
| | - Anthony Richardson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Oceans and Atmosphere, BioSciences Precinct (QBP), St Lucia, QLD, Australia; Centre for Applications in Natural Resource Mathematics, School of Mathematics and Physics, University of Queensland, Saint Lucia 4072, QLD, Australia
| | - Luigi Vezzulli
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Corso Europa 26, 16132 Genoa, Italy.
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Petrin S, Mancin M, Losasso C, Deotto S, Olsen JE, Barco L. Effect of pH and Salinity on the Ability of Salmonella Serotypes to Form Biofilm. Front Microbiol 2022; 13:821679. [PMID: 35464965 PMCID: PMC9021792 DOI: 10.3389/fmicb.2022.821679] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/17/2022] [Indexed: 11/28/2022] Open
Abstract
Salmonella is a major cause of food-borne infections in Europe, and the majority of human infections are caused by only a few serotypes, among them are Salmonella enterica subsp. enterica serotype Enteritidis (hereafter Salmonella Enteritidis), Salmonella Typhimurium, and the monophasic variant of S. Typhimurium. The reason for this is not fully understood, but could include virulence factors as well as increased ability to transfer via the external environment. Formation of biofilm is considered an adaptation strategy used by bacteria to overcome environmental stresses. In order to assess the capability of different Salmonella serotypes to produce biofilm and establish whether this is affected by pH and salinity, 88 Salmonella isolates collected from animal, food, and human sources and belonging to 15 serotypes, including those most frequently responsible for human infections, were tested. Strains were grown in tryptic soy broth (TSB), TSB with 4% NaCl pH 4.5, TSB with 10% NaCl pH 4.5, TSB with 4% NaCl pH 7, or TSB with 10% NaCl pH 7, and biofilm production was assessed after 24 h at 37°C using crystal violet staining. A linear mixed effect model was applied to compare results from the different experimental conditions. Among the tested serotypes, S. Dublin showed the greatest ability to form biofilm even at pH 4.5, which inhibited biofilm production in the other tested serotypes. Salmonella Senftenberg and the monophasic variant of S. Typhimurium showed the highest biofilm production in TSB with 10% NaCl pH 7. In general, pH had a high influence on the ability to form biofilm, and most of the tested strains were not able to produce biofilm at pH 4.5. In contrast, salinity only had a limited influence on biofilm production. In general, serotypes causing the highest number of human infections showed a limited ability to produce biofilm in the tested conditions, indicating that biofilm formation is not a crucial factor in the success of these clones.
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Affiliation(s)
- Sara Petrin
- Microbial Ecology and Microorganisms Genomics Laboratory - SCS1, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Marzia Mancin
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Carmen Losasso
- Microbial Ecology and Microorganisms Genomics Laboratory - SCS1, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
- *Correspondence: Carmen Losasso,
| | - Silvia Deotto
- Clinical Diagnostics Laboratory - SCT4, Istituto Zooprofilattico Sperimentale delle Venezie, Basaldella di Campoformido, Italy
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lisa Barco
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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Petrin S, Orsini M, Mastrorilli E, Longo A, Cozza D, Olsen JE, Ricci A, Losasso C, Barco L. Identification and characterization of a spreadable IncI1 plasmid harbouring a bla CTX-M-15 gene in an Italian human isolate of Salmonella serovar Napoli. Plasmid 2021; 114:102566. [PMID: 33582117 DOI: 10.1016/j.plasmid.2021.102566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 10/22/2022]
Abstract
Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) ranks among the top serovars causing human infections in Italy, although not common in other European countries. Isolates are generally pan-susceptible or resistant to aminoglycosides only, however data on antimicrobial resistance genes in strains of S. Napoli are limited. Recently an isolate encoding resistance to third generation cephalosporins was reported. This study aimed to characterize plasmid-encoded cephalosporin resistance due to the blaCTX-M-15 gene in a human S. Napoli isolate in Italy, and to investigate plasmid stability over time. S. Napoli 16/174478 was confirmed to be ESBL-producing. The blaCTX-M-15 gene was shown to be located on an IncI1α plasmid of 90,272 bp (50.03 GC%) encoding for 107 coding sequences (CDS). The plasmid was successfully transferred by conjugation to an E. coli 1816 recipient strain (conjugation frequency 3.9 × 10-2 transconjugants per donor). Transconjugants were confirmed to carry the IncI1α plasmid, and to be ESBL-producing strains as well. Moreover, transconjugant colonies maintained the plasmid for up to 10 passages. The identification of S. Napoli isolates able to produce ESBLs is of great concern, as this pathogen is frequently associated with invasive infections and a higher risk of bacteraemia, and its reservoir has not yet been clearly identified.
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Affiliation(s)
- Sara Petrin
- Microbial Ecology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro (PD), Italy
| | - Massimiliano Orsini
- Microbial Ecology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro (PD), Italy
| | - Eleonora Mastrorilli
- Microbial Ecology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro (PD), Italy
| | - Alessandra Longo
- Microbial Ecology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro (PD), Italy
| | - Debora Cozza
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici (NA), Italy
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Antonia Ricci
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro (PD), Italy
| | - Carmen Losasso
- Microbial Ecology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro (PD), Italy.
| | - Lisa Barco
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro (PD), Italy
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Patuzzi I, Orsini M, Cibin V, Petrin S, Mastrorilli E, Tiengo A, Gobbo F, Catania S, Barco L, Ricci A, Losasso C. The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time. Microorganisms 2021; 9:221. [PMID: 33499060 PMCID: PMC7911313 DOI: 10.3390/microorganisms9020221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/27/2022] Open
Abstract
Campylobacter is the most frequent foodborne zoonotic bacteria worldwide, with chicken meat being overwhelmingly the most important reservoir for human infections. Control measures implemented at the farm level (i.e., biosecurity or vaccination), which have been successfully applied to limit other pathogens, such as Salmonella, have not been effective in reducing Campylobacter occurrence. Thus, new approaches are needed to fully understand the ecological interactions of Campylobacter with host animals to effectively comprehend its epidemiology. The objective of this study was to analyse longitudinally the gut microbiota composition of Campylobacter-infected and non-infected farms to identify any difference that could potentially be indicative of gut colonization by Campylobacter spp. Differences in the colonization rate and timing were observed at the farms that became positive for Campylobacter jejuni over the investigated time points, even though in positive tests, the occurrence of Campylobacter jejuni gut colonization was not observed before the second week of the life of the birds. Significant differences were observed in the abundances of specific bacterial taxa between the microbiota of individuals belonging to farms that became Campylobacter positive during the study and those who remained negative with particular reference to Bacteroidales and Clostridiales, respectively. Moreover, Campylobacter colonization dramatically influenced the microbiota richness, although to a different extent depending on the infection timing. Finally, a key role of Faecalibacterium and Lactobacillus genera on the Campylobacter microbial network was observed. Understanding the ecology of the Campylobacter interaction with host microbiota during infection could support novel approaches for broiler microbial barrier restoration. Therefore, evidence obtained through this study can be used to identify options to reduce the incidence of infection at a primary production level based on the targeted influence of the intestinal microbiota, thus helping develop new control strategies in order to mitigate the risk of human exposure to Campylobacter by chicken meat consumption.
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Affiliation(s)
- Ilaria Patuzzi
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Massimiliano Orsini
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Veronica Cibin
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Sara Petrin
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Eleonora Mastrorilli
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Alessia Tiengo
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Federica Gobbo
- Avian Pathology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (F.G.); (S.C.)
| | - Salvatore Catania
- Avian Pathology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (F.G.); (S.C.)
| | - Lisa Barco
- Experimental Microbiology Department, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy;
| | - Antonia Ricci
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Carmen Losasso
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
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El Hage R, Losasso C, Longo A, Petrin S, Ricci A, Mathieu F, Abi Khattar Z, El Rayess Y. Whole-genome characterisation of TEM-1 and CMY-2 β-lactamase-producing Salmonella Kentucky ST198 in Lebanese broiler chain. J Glob Antimicrob Resist 2020; 23:408-416. [DOI: 10.1016/j.jgar.2020.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/25/2020] [Accepted: 11/02/2020] [Indexed: 11/30/2022] Open
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Rota A, Corrò M, Patuzzi I, Milani C, Masia S, Mastrorilli E, Petrin S, Longo A, Del Carro A, Losasso C. Effect of sterilization on the canine vaginal microbiota: a pilot study. BMC Vet Res 2020; 16:455. [PMID: 33228646 PMCID: PMC7684734 DOI: 10.1186/s12917-020-02670-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Surgical sterilization is the most effective method of contraception for dogs. It also prevents pyometra and reduces the risk of mammary tumour development. However, this procedure also has negative effects, such as urinary incontinence. Steroid hormone deprivation following gonadectomy could also affect canine vaginal mucosa conditions and the microbial community colonizing the vaginal tract. This hypothesis was tested by comparing the vaginal cytology and microbial community of two groups of bitches, including 11 in anoestrus and 10 sterilized bitches (post-pubertal sterilization in the last 4 years). Bacteria were identified through metataxonomic analysis, amplifying the V3-V4 regions of 16S rRNA gene, and culturing methods. RESULTS Vaginal mucosa cytology was suggestive of dystrophic conditions in sterilized bitches, whereas a typical anoestrus pattern with parabasal and intermediate cells was appreciable in anoestrous animals. Metataxonomic analysis revealed large inter-individual variability. Salmonella, Mycoplasma and Staphylococcus were present in moderate quantities in almost all the samples in both groups. Mollicutes (class level) and Tenericutes (phylum level) were commonly present in moderate quantities in anoestrus samples, whereas these microbes were present at high levels in a single sample from the sterilized group. Based on culturing, a higher number of different species were isolated from the anoestrous bitches, and Mycoplasma canis was exclusively identified in an anoestrous bitch. Staphylococcus spp. was the most frequently isolated genus in both groups, followed by Streptococcus spp., and, among gram-negative bacteria, Escherichia spp. and Haemophilus spp. A comparison of the numbers of the most frequently isolated genera of bacteria from vaginal cultures of bitches revealed that Pasteurella and Proteus were the most frequently identified in sterilized animals based on metataxonomic analysis (p-value = 0.0497 and 0.0382, respectively), whereas Streptococcus was significantly and most frequently isolated from anoestrous bitches using culture methods (p value = 0.0436). CONCLUSIONS In this preliminary investigation, no global patterns of the vaginal bacteria community were noted that characterized the condition of the bitches; however, cytology suggested local modifications. Sterilization after puberty caused minimal alterations in the vaginal microbial community of bitches within 4 years after surgery.
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Affiliation(s)
- Ada Rota
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2-5, 10095, Grugliasco, Italy.
| | - Michela Corrò
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Ilaria Patuzzi
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Chiara Milani
- Department of Animal Medicine, Production and Health, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Stefania Masia
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Eleonora Mastrorilli
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Sara Petrin
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Alessandra Longo
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
| | - Angela Del Carro
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2-5, 10095, Grugliasco, Italy
| | - Carmen Losasso
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, PD, Italy
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Mastrorilli E, Petrin S, Orsini M, Longo A, Cozza D, Luzzi I, Ricci A, Barco L, Losasso C. Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017. BMC Genomics 2020; 21:202. [PMID: 32131727 PMCID: PMC7057659 DOI: 10.1186/s12864-020-6588-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/18/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated from humans and the environment, but neither the reservoir nor its route of infection are clearly defined. This serovar is characterized by high genomic diversity, and molecular evidences revealed important similarities with typhoidal serovars. RESULTS 179 S. Napoli genomes as well as 239 genomes of typhoidal and non-typhoidal serovars were analyzed in a comparative genomic study. Phylogenetic analysis and draft genome characterization in terms of Multi Locus Sequence Typing (MLST), plasmid replicons, Salmonella Pathogenicity Islands (SPIs), antimicrobial resistance genes (ARGs), phages, biocide and metal-tolerance genes confirm the high genetic variability of S. Napoli, also revealing a within-serovar phylogenetic structure more complex than previously known. Our work also confirms genomic similarity of S. Napoli to typhoidal serovars (S. Typhi and S. Paratyphi A), with S. Napoli samples clustering primarily according to ST, each being characterized by specific genomic traits. Moreover, two major subclades of S. Napoli can be clearly identified, with ST-474 being biphyletic. All STs span among isolation sources and years of isolation, highlighting the challenge this serovar poses to define its epidemiology and evolution. Altogether, S. Napoli strains carry less SPIs and less ARGs than other non-typhoidal serovars and seldom acquire plasmids. However, we here report the second case of an extended-spectrum β-lactamases (ESBLs) producing S. Napoli strain and the first cases of multidrug resistant (MDR) S. Napoli strains, all isolated from humans. CONCLUSIONS Our results provide evidence of genomic plasticity of S. Napoli, highlighting genomic similarity with typhoidal serovars and genomic features typical of non-typhoidal serovars, supporting the possibility of survival in different niches, both enteric and non-enteric. Presence of horizontally acquired ARGs and MDR profiles rises concerns regarding possible selective pressure exerted by human environment on this pathogen.
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Affiliation(s)
- Eleonora Mastrorilli
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
- Present address: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Sara Petrin
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| | - Massimiliano Orsini
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy.
| | - Alessandra Longo
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| | - Debora Cozza
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Ida Luzzi
- Istituto Superiore di Sanità, Rome, Italy
| | - Antonia Ricci
- Istituto Zooprofilattico Sperimentale delle Venezie, Food Safety Department, Legnaro, Italy
| | - Lisa Barco
- Istituto Zooprofilattico Sperimentale delle Venezie, Food Safety Department, Legnaro, Italy
| | - Carmen Losasso
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
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Petrin S, Patuzzi I, Di Cesare A, Tiengo A, Sette G, Biancotto G, Corno G, Drigo M, Losasso C, Cibin V. Evaluation and quantification of antimicrobial residues and antimicrobial resistance genes in two Italian swine farms. Environ Pollut 2019; 255:113183. [PMID: 31541814 DOI: 10.1016/j.envpol.2019.113183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/27/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances in bacteria. The occurrence of ARGs in Italian swine farming - which has specific characteristics - was investigated in order to explore resistance spread dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.
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Affiliation(s)
- Sara Petrin
- OU Microbial Ecology, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Ilaria Patuzzi
- OU Microbial Ecology, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | | | - Alessia Tiengo
- Food Pathogens and Antimicrobial Resistance Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Giovanni Sette
- Chemistry Department, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Giancarlo Biancotto
- Chemistry Department, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
| | - Gianluca Corno
- CNR-IRSA, Corso Tonolli, 50, 28922, Pallanza, Verbania, Italy
| | - Michele Drigo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Carmen Losasso
- OU Microbial Ecology, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy.
| | - Veronica Cibin
- Food Pathogens and Antimicrobial Resistance Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020, Legnaro, Italy
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Longo A, Losasso C, Vitulano F, Mastrorilli E, Turchetto S, Petrin S, Mantovani C, Dalla Pozza MC, Ramon E, Conedera G, Citterio CV, Ricci A, Barco L, Lettini AA. Insight into an outbreak of Salmonella Choleraesuis var. Kunzendorf in wild boars. Vet Microbiol 2019; 238:108423. [PMID: 31648730 DOI: 10.1016/j.vetmic.2019.108423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 10/26/2022]
Abstract
An unusual mortality of wild boars occurred in Italy from 2012 to 2015 due to Salmonella Choleraesuis infection. In order to confirm the occurrence of an outbreak of S. Choleraesuis in wild boars and to epidemically characterise the unique S. Choleraesuis biovar, a collection of isolates belonging to wild boars was investigated from the phenotypic, molecular and genomic points of view (PFGE and WGS). Moreover, the possibility of transmission to domestic pigs and humans, temporally and geographically close to the wild boar epidemic, was tested by also including in the panel isolates from infected domestic pigs and from one human case of infection. Wild boar isolates displayed a high genetic correlation, thus suggesting they are part of the same outbreak, with a common invasiveness potential. Conversely, no correlation between pig isolates and those from the other sources (wild boars and human) was found. However, the phylogenetic and PFGE analyses suggest a high degree of similarity between the human and the investigated wild boar outbreak isolates, implying the potential for the spread of Salmonella Choleraesuis among these species.
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Affiliation(s)
- Alessandra Longo
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Carmen Losasso
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy.
| | - Federica Vitulano
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Eleonora Mastrorilli
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Sara Turchetto
- SCT2 - Treviso, Belluno and Venezia - O.U. Eco-pathology, Istituto Zooprofilattico Sperimentale delle Venezie, Belluno, Italy
| | - Sara Petrin
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Claudio Mantovani
- Science Communication Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro PD, Italy
| | - Maria Cristina Dalla Pozza
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Elena Ramon
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Gabriella Conedera
- SCT4 - Friuli Venezia Giulia - Istituto Zooprofilattico Sperimentale delle Venezie, Pordenone, Italy
| | - Carlo V Citterio
- SCT2 - Treviso, Belluno and Venezia - O.U. Eco-pathology, Istituto Zooprofilattico Sperimentale delle Venezie, Belluno, Italy
| | - Antonia Ricci
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Lisa Barco
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Antonia Anna Lettini
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
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Longo A, Petrin S, Mastrorilli E, Tiengo A, Lettini AA, Barco L, Ricci A, Losasso C, Cibin V. Characterizing Salmonella enterica Serovar Choleraesuis, var. Kunzendorf: A Comparative Case Study. Front Vet Sci 2019; 6:316. [PMID: 31620457 PMCID: PMC6763558 DOI: 10.3389/fvets.2019.00316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/04/2019] [Indexed: 11/15/2022] Open
Abstract
Different Salmonella serovars generally display different antigenic formulae, but there are some exceptions. For instance, the same antigenic formula, 6,7:c:1,5, is shared by Salmonella enterica serovar, Paratyphi C, Typhisuis, and Choleraesuis. Moreover, three biotypes have been described within the S. Choleraesuis serovar. A distinction among such biotypes can only be based on biochemical behaviors (biotyping) posing serious concerns when rapid characterization is required. The study of an outbreak of severe epizootic salmonellosis in wild boars occurred in Italy between 2012 and 2014 and the typing of the isolates recovered from the outbreak were used to test different approaches for serovar identification. A number of 30 S. Choleraesuis var. Kunzendorf isolates from the outbreak were typed by means of four different methods to derive serovar and biotype: (i) slide agglutination method followed by biochemical tests, (ii) suspension array xMAP® Salmonella Serotyping Assay (SSA), (iii) whole genome sequencing (WGS) and data analysis using SeqSero tool, and (iv) WGS and data analysis using Salmonella TypeFinder tool. Slide agglutination, xMAP® SSA and WGS, followed by SeqSero analysis, are methods that infer the serovars according to the White-Kauffmann-Le Minor (WKL) scheme, based exclusively on antigens. Using these methods, isolates with incomplete antigenic formulae could be misleadingly excluded from an outbreak. On the contrary, WGS followed by Salmonella TypeFinder data analysis, which predicts the serotype on the basis of Multilocus sequence typing (MLST), might be able to cluster together isolates belonging to the same outbreak irrespective of the antigenic formula. Results suggest the benefit of routine use of a combination of in silico MLST and antigenic formula analysis to solve specific ambiguous case studies for outbreak investigation purposes.
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Affiliation(s)
| | | | | | | | | | | | | | - Carmen Losasso
- World Organisation for Animal Health (OIE), National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, Legnaro, Italy
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Petrin S, Longo A, Barco L, Cortini E, Peruzzo A, Antonelli P, Ramon E, Cibin V, Lettini AA, Ricci A, Losasso C. Different Resolution Power of Multilocus Variable-Number Tandem Repeat Analysis and Whole-Genome Sequencing in the Characterization of S. 1,4,[5],12:i:- Isolates. Foodborne Pathog Dis 2019; 16:558-561. [PMID: 30916593 DOI: 10.1089/fpd.2018.2563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica serovar 1,4,[5],12:i:- has emerged over the last two decades as one of the most common serovars causing human salmonellosis in Europe. It is supposed to originate from Salmonella enterica serovar Typhimurium due to antigenic and genotypic similarities between the two serovars. Due to the high level of similarity, the multilocus variable-number tandem repeat analysis (MLVA) protocol designed for Salmonella Typhimurium routine typing is commonly used also for the characterization of S. 1,4,[5],12:i. Nevertheless, the Salmonella Typhimurium-based MLVA protocol often shows poor discriminatory power for S. 1,4,[5],12:i. Indeed, only a limited number of MLVA profiles have been described for S. 1,4,[5],12:i:-. Moreover, based on the MLVA clustering, S. 1,4,[5],12:i:- is supposed to display high clonality. The aim of the present work was to assess whether the five loci of Salmonella Typhimurium investigated by MLVA are sufficiently accurate to correctly assign S. 1,4,[5],12:i:- isolates. For this purpose, 38 epidemiologically unrelated S. 1,4,[5],12:i:- were subjected to whole-genome sequencing. Isolates were selected among a collection of monophasic strains isolated in Italy from different sources over the period 2014-2016 and belonging to the five most commonly detected MLVA profiles. Results confirmed the possible clonality for S. 1,4,[5],12:i:- serovar in the light of the scarce difference observed in terms of single-nucleotide polymorphisms (SNPs) among investigated isolates. Nevertheless, unrelated isolates on the basis of the difference of SNP number were characterized as indistinguishable by MLVA profile, thus suggesting an insufficient resolution of MLVA. Hence, we can conclude that MLVA-based approach does not seem a valuable proxy to deepen into the epidemiological relationship among S. 1,4,[5],12:i:- isolates. These evidences can be useful to avoid incorrect assignment especially when surveillance data are used for outbreak investigations.
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Affiliation(s)
- Sara Petrin
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Alessandra Longo
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Lisa Barco
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Enzo Cortini
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Arianna Peruzzo
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Pietro Antonelli
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Elena Ramon
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Veronica Cibin
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Antonia Anna Lettini
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Antonia Ricci
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Carmen Losasso
- OIE and National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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Cibin V, Busetti M, Longo A, Petrin S, Knezevich A, Ricci A, Barco L, Losasso C. Whole Genome Sequencing of Salmonella Serovar Stanleyville from Two Italian Outbreaks Resulted in Unexpected Genomic Diversity Within and Between Outbreaks. Foodborne Pathog Dis 2019; 16:307-308. [PMID: 30615488 DOI: 10.1089/fpd.2018.2564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Veronica Cibin
- 1 National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Marina Busetti
- 2 Microbiology Unit, University Hospital of Trieste, Trieste, Italy
| | - Alessandra Longo
- 1 National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Sara Petrin
- 1 National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Anna Knezevich
- 2 Microbiology Unit, University Hospital of Trieste, Trieste, Italy
| | - Antonia Ricci
- 1 National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Lisa Barco
- 1 National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Carmen Losasso
- 1 National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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Di Cesare A, Petrin S, Fontaneto D, Losasso C, Eckert EM, Tassistro G, Borello A, Ricci A, Wilson WH, Pruzzo C, Vezzulli L. ddPCR applied on archived Continuous Plankton Recorder samples reveals long-term occurrence of class 1 integrons and a sulphonamide resistance gene in marine plankton communities. Environ Microbiol Rep 2018; 10:458-464. [PMID: 30022610 DOI: 10.1111/1758-2229.12665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/18/2018] [Accepted: 05/27/2018] [Indexed: 06/08/2023]
Abstract
Antibiotic resistance is a rising threat for human health. Although in clinical settings and terrestrial environments the rise of antibiotic resistant bacteria is well documented, their dissemination and spread in the marine environment, covering almost two-thirds of the Earth's surface, is still poorly understood. In this study, the presence and abundance of sulphonamide resistance gene (sul2) and class 1 integron-integrase gene (intI1), used as markers for the occurrence and spread of antibiotic resistance genes since the beginning of the antibiotic era, were investigated. Twenty-nine archived formalin-fixed samples, collected by the Continuous Plankton Recorder (CPR) survey in the Atlantic Ocean and North Sea from 1970 to 2011, were analysed using Droplet Digital PCR (ddPCR) applied for the first time on CPR samples. The two marker genes were present in a large fraction of the samples (48% for sul2 and 76% for intI1). In contrast, results from Real-Time PCR performed on the same samples greatly underestimate their occurrence (21% for sul2 and 52% for intI1). Overall, besides providing successful use of ddPCR for the molecular analysis of CPR samples, this study reveals long-term occurrence and spread of sul2 gene and class 1 integrons in the plankton-associated bacterial communities in the ocean.
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Affiliation(s)
- Andrea Di Cesare
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Sara Petrin
- O.U. Microbial Ecology, Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Diego Fontaneto
- Microbial Ecology Group (MEG), National Research Council - Institute of Ecosystem Study (CNR-ISE), Verbania, Italy
| | - Carmen Losasso
- O.U. Microbial Ecology, Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Ester M Eckert
- Microbial Ecology Group (MEG), National Research Council - Institute of Ecosystem Study (CNR-ISE), Verbania, Italy
| | - Giovanni Tassistro
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Alessio Borello
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Antonia Ricci
- O.U. Microbial Ecology, Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - William H Wilson
- CPR Survey, Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
| | - Carla Pruzzo
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Luigi Vezzulli
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
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Mastrorilli E, Pietrucci D, Barco L, Ammendola S, Petrin S, Longo A, Mantovani C, Battistoni A, Ricci A, Desideri A, Losasso C. A Comparative Genomic Analysis Provides Novel Insights Into the Ecological Success of the Monophasic Salmonella Serovar 4,[5],12:i:. Front Microbiol 2018; 9:715. [PMID: 29719530 PMCID: PMC5913373 DOI: 10.3389/fmicb.2018.00715] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 03/27/2018] [Indexed: 12/27/2022] Open
Abstract
Over the past decades, Salmonella 4,[5],12:i:- has rapidly emerged and it is isolated with high frequency in the swine food chain. Although many studies have documented the epidemiological success of this serovar, few investigations have tried to explain this phenomenon from a genetic perspective. Here a comparative whole-genome analysis of 50 epidemiologically unrelated S. 4,[5],12:i:-, isolated in Italy from 2010 to 2016 was performed, characterizing them in terms of genetic elements potentially conferring resistance, tolerance and persistence characteristics. Phylogenetic analyses indicated interesting distinctions among the investigated isolates. The most striking genetic trait characterizing the analyzed isolates is the widespread presence of heavy metals tolerance gene cassettes: most of the strains possess genes expected to confer resistance to copper and silver, whereas about half of the isolates also contain the mercury tolerance gene merA. A functional assay showed that these genes might be useful for preventing the toxic effects of metals, thus supporting the hypothesis that they can contribute to the success of S. 4,[5],12:i:- in farming environments. In addition, the analysis of the distribution of type II toxin-antitoxin families indicated that these elements are abundant in this serovar, suggesting that this is another factor that might favor its successful spread.
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Affiliation(s)
- Eleonora Mastrorilli
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Lisa Barco
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Serena Ammendola
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Sara Petrin
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Alessandra Longo
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Claudio Mantovani
- Science Communication Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Antonia Ricci
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Carmen Losasso
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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