Genetic surveillance of endemic bovine Salmonella Infantis infection

Lindqvist, Nanna; Pelkonen, Sinikka

doi:10.1186/1751-0147-49-15

Cited by 15 publications

(10 citation statements)

References 13 publications

(18 reference statements)

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“…In the European Union (EU), S. Infantis has been the third most common serovar in humans since 2006 with a relative share between 1% and 2% (EFSA, 2019). Although this serovar is prevalent also in pigs and cattle (Rajic et al, 2005;Lindqvist and Pelkonen, 2007), poultry especially broiler and their products have been identified as one of the most important sources of human infection with S. Infantis (EFSA, 2019(EFSA, , 2020. In 2018, S. Infantis was the most frequently reported serovar in fowl in the EU (EFSA, 2019), accounting for 36.7% of all Salmonella isolates.…”

Section: Introductionmentioning

confidence: 99%

Emergence of Multidrug-Resistant Salmonella enterica Subspecies enterica Serovar Infantis of Multilocus Sequence Type 2283 in German Broiler Farms

et al. 2020

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During the last decade, Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) has become more prevalent across Europe with an increased capability to persist in broiler farms. In this study, we aimed to identify potential genetic causes for the increased emergence and longer persistence of S. Infantis in German poultry farms by high-throughput-sequencing. Broiler derived S. Infantis strains from two decades, the 1990s (n = 12) and the 2010s (n = 18), were examined phenotypically and genotypically to detect potential differences responsible for increased prevalence and persistence. S. Infantis organisms were characterized by serotyping and determining antimicrobial susceptibility using the microdilution method. Genotypic characteristics were analyzed by whole genome sequencing (WGS) to detect antimicrobial resistance and virulence genes as well as plasmids. To detect possible clonal relatedness within S. Infantis organisms, 17 accessible genomes from previous studies about emergent S. Infantis were downloaded and analyzed using complete genome sequence of SI119944 from Israel as reference. In contrast to the broiler derived antibioticsensitive S. Infantis strains from the 1990s, the majority of strains from the 2010s (15 out of 18) revealed a multidrug-resistance (MDR) phenotype that encodes for at least three antimicrobials families: aminoglycosides [ant(3")-Ia], sulfonamides (sul1), and tetracyclines [tet(A)]. Moreover, these MDR strains carry a virulence gene pattern missing in strains from the 1990s. It includes genes encoding for fimbriae clusters, the yersiniabactin siderophore, mercury and disinfectants resistance and toxin/antitoxin complexes. In depth genomic analysis confirmed that the 15 MDR strains from the 2010s carry a pESI-like megaplasmid with resistance and virulence gene patterns detected in the emerged S. Infantis strain SI119944 from Israel and clones inside and outside Europe. Genotyping analysis revealed two sequence types (STs) among the resistant strains from the 2010s, ST2283 (n = 13) and ST32 (n = 2). The sensitive strains from the 1990s, belong to sequence type ST32 (n = 10) and ST1032 (n = 2). Therefore,

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Section: Introductionmentioning

confidence: 99%

Emergence of Multidrug-Resistant Salmonella enterica Subspecies enterica Serovar Infantis of Multilocus Sequence Type 2283 in German Broiler Farms

et al. 2020

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“…Although epidemiological data would be needed to determine whether these clusters represent true single-source outbreaks, the observed patterns and the fact that four clusters represented PFGE types that were not identified outside a given cluster suggest that at least some of these clusters represent small outbreaks, possibly linked to localized sources, for example, restaurants (CDC, 2008b), group events where food is served (Camps et al, 2005), or even nonfood sources (CDC, 2008a). PFGE-based identification of single-source disease clusters and source tracking by PFGE is complicated by the fact that some PFGE types may be common and widely distributed (Woo, 2005;Lindqvist and Pelkonen, 2007). Identification of such a common PFGE type in multiple human or animal cases or among clinical cases and a possible source is more likely to be by chance and may sometimes not represent a causal relationship.…”

mentioning

confidence: 99%

Pulsed-Field Gel Electrophoresis Diversity of Human and Bovine ClinicalSalmonellaIsolates

Soyer

Alcaine

Schoonmaker-Bopp

et al. 2010

Foodborne Pathogens and Disease

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Pulsed-field gel electrophoresis (PFGE) characterization of 335 temporally and spatially matched clinical, bovine, and human Salmonella enterica subsp. enterica isolates revealed 167 XbaI PFGE patterns. These isolates were previously classified into 51 serotypes and 73 sequence types, as determined by multilocus sequence typing. Discriminatory power of PFGE (Simpson's index, D ¼ 0.991) was considerably higher than that of multilocus sequence typing (D ¼ 0.920) or serotyping (D ¼ 0.913). Although 128 PFGE types each only represented a single isolate, 8 PFGE types represented >4 isolates, including (i) three serotype Enteritidis and Heidelberg patterns that were only identified among human isolates, (ii) two PFGE patterns (each representing serotypes Bardo and Newport) that were significantly more common among bovine isolates as compared with human isolates; (iii) two PFGE types that each includes two serotypes (4,5,12:i:-and Typhimurium; Thompson and 1,7:-:1,5); and (iv) one PFGE type that includes eight Typhimurium isolates from humans and cattle. Characterization of isolates collected over multiple farm visits indicated that given specific PFGE types persisted over time on 11 farms. On an additional seven farms, isolates with a given sequence type represented multiple PFGE type, which typically only differed by <3 bands, suggesting PFGE type diversification during strain persistence. Sixteen PFGE types were isolated from 2 or more farms, including two widely distributed serotype Newport-associated PFGE types each found on 10 farms. In six instances two or three human isolates collected in the same county in the same or consecutive months represented the same subtypes, suggesting small human case clusters. PFGE-based characterization and surveillance of human and animal isolates can provide improved understanding of Salmonella diversity and epidemiology, including identification of possible host-associated and common, widely distributed PFGE types.

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“…This approach is capable to differentiates some of the strains classified as same phage types and serotypes (Landeras et al, 1996 ; Liebana et al, 2001 , 2002a , b , 2004 ; Clark et al, 2003 ). Nevertheless, researchers have reported that some different phage types strains yet revealed indistinguishable ribotypes (Fontana et al, 2003 ; Adaska et al, 2006 ; Lindqvist and Pelkonen, 2007 ), particularly when compared to PFGE (Eriksson et al, 2005 ). Comparisons of ribotyping with PFGE are unusual because it depends on what were the enzymes applied for digestion and the population characteristics studied (Jeoffreys et al, 2001 ; Liebana et al, 2001 ; Fontana et al, 2003 ).…”

Section: Genotypic Methodsmentioning

confidence: 99%

Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

2017

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Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST) has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models). Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.

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Genetic surveillance of endemic bovine Salmonella Infantis infection

Cited by 15 publications

References 13 publications

Emergence of Multidrug-Resistant Salmonella enterica Subspecies enterica Serovar Infantis of Multilocus Sequence Type 2283 in German Broiler Farms

Emergence of Multidrug-Resistant Salmonella enterica Subspecies enterica Serovar Infantis of Multilocus Sequence Type 2283 in German Broiler Farms

Pulsed-Field Gel Electrophoresis Diversity of Human and Bovine ClinicalSalmonellaIsolates

Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

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