Stability, Entrapment and Variant Formation of Salmonella Genomic Island 1

Kiss, János; Nagy, Béla; Olasz, Ferenc

doi:10.1371/journal.pone.0032497

Cited by 39 publications

(94 citation statements)

References 40 publications

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“…We first examined whether homologous recombination between directly repeated elements of the original plasmids could lead to the observed phenotypes as it was described for SGI1 variants (28 IP40a derivatives, however, could not be formed this way due to the lack of extensive direct repeats around the resistance region.…”

Section: Resultsmentioning

confidence: 99%

“…The TG90F Ϫ recipient strain was derived from TG90 (27) by curing F=. Deletion derivatives were isolated by replica plating following 1 to 5 passages using TG1Nal (28) transconjugants harboring R16a, IP40a, or R55 under nonselective conditions (28). Mercury resistance of TG1Nal, TG1Nal/R16a, and TG1Nal/IP40a strains was tested as follows: cells were grown in LB until an optical density at 600 (OD 600 ) of approximately 0.8 was reached and serially diluted 10-fold to 10 7 , and then each dilution was dropped onto LB plates supplemented with 0, 2.5, 5, 10, 15, or 20 g/ml HgCl 2 and incubated overnight at 30°C.…”

Section: Methodsmentioning

confidence: 99%

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Characterization of Two Multidrug-Resistant IncA/C Plasmids from the 1960s by Using the MinION Sequencer Device

Szabó

Nagy

Wilk

et al. 2016

Antimicrob Agents Chemother

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Two A/C incompatibility group (IncA/C family) plasmids from the 1960s have been sequenced and classified into the A/C 2 type 1 group. R16a and IP40a contain novel antibiotic resistance islands and a complete GIsul2 genomic island not previously found in the family. In the 173.1-kb R16a, the 29.9-kb antibiotic resistance island (ARI) is located in a unique backbone position not utilized by ARIs. ARI R16a consists of Tn1, Tn6020, and Tn6333, harboring the resistance genes bla TEM-1D and aphA1b and a mer module, respectively; a truncated Tn5393 copy; and a gene cluster with unknown function. Plasmid IP40a is 170.4 kb in size and contains a 5.6-kb ARI inserted into the kfrA gene. ARI IP40a carrying bla TEM-1D and aphA1b genes is composed of Tn1 with a Tn6023 insertion. Additionally, IP40a harbors single IS2, IS186, and Tn1000 insertions scattered in the backbone; an IS150 copy in GIsul2; and a complete Tn6333 carrying a mer module at the position of ARI R16a . Loss of resistance markers in R16a, IP40a, and R55 was observed during stability tests. Every phenotypic change proved to be the result of recombination events involving mobile elements. Intramolecular transposition of IS copies that generated IP40a derivatives lacking large parts of the backbone could account for the formation of other family members, too. The MinION platform proved to be a valuable tool in bacterial genome sequencing since it generates long reads that span repetitive elements and facilitates full-length plasmid or chromosome assembly. Nanopore technology enables rapid characterization of large, low-copy-number plasmids and their rearrangement products.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Characterization of Two Multidrug-Resistant IncA/C Plasmids from the 1960s by Using the MinION Sequencer Device

Szabó

Nagy

Wilk

et al. 2016

Antimicrob Agents Chemother

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“…The mobility and stability of the SGI1 variants have previously been confirmed in S. enterica (6,19,20). Many SGI1 variants can be excised from the chromosome, and the resulting free circular form may be transferable with the helper plasmid (6,20).…”

mentioning

confidence: 81%

“…Many SGI1 variants can be excised from the chromosome, and the resulting free circular form may be transferable with the helper plasmid (6,20). The circular extrachromosomal form was detected in all four SGI1s after two rounds of PCR amplification by using the same circ1/2 primers (see Fig.…”

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confidence: 93%

Two Novel Salmonella Genomic Island 1 Variants in Proteus mirabilis Isolates from Swine Farms in China

Lei

Zhang

Liu

et al. 2015

Antimicrob Agents Chemother

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Four different Salmonella genomic island 1 (SGI1) variants, including two novel variants, were characterized in one Salmonella enterica serovar Rissen sequence type ST1917 isolate and three Proteus mirabilis isolates from swine farms in China. One novel variant was derived from SGI1-B with the backbone gene S021 disrupted by a 12.72-kb IS26 composite transposon containing the dfrA17-aadA5 cassettes and macrolide inactivation gene cluster mphA-mrx-mphR. The other one was an integron-free SGI1 and contained a 183-bp truncated S025 next to IS6100 and S044. Salmonella enterica is a zoonotic pathogen and is one of the primary causes of human infections worldwide. Salmonella genomic island 1 (SGI1) is an integrative 42.4-kb chromosomal element first identified in the multidrug resistance (MDR) S. enterica serovar Typhimurium phage type DT104 clone that has been epidemic among humans and domestic animals since the 1990s (1, 2). The MDR region in SGI1 is a complex In4-type class 1 integron (named In104) clustering five antibiotic resistance genes that confer resistance to ampicillin, chloramphenicol and florfenicol, streptomycin and spectinomycin, sulfonamides, and tetracycline (3). SGI1 was unexpectedly detected in a Proteus mirabilis clinical isolate in 2007 (4). Sequence analysis showed that SGI1 in S. enterica and P. mirabilis had the same chromosomal integration site, corresponding to the last 18 bp of the 3= end of the trmE (also named thdF) gene (5). It has been confirmed that SGI1 in S. enterica could be transferred by conjugation with the help of the IncA/C plasmid (6, 7).Many SGI1 variants result from the homologous recombination of gene cassettes within the MDR regions (3,(8)(9)(10)(11). A few variations in the SGI1 backbone are also described due to deletion, insertion, and transposition (3,9,10,(12)(13)(14)(15). Furthermore, several novel resistance genes, including the extended-spectrum ␤-lactamase (ESBL) gene bla VEB-6 and the fluoroquinolone resistance genes qnrA1 and qnrB2, have been reported in SGI1 (9, 11), suggesting that SGI1 could act as a mobilizable element to disseminate the critical resistance genes. In the present study, we characterized SGI1 among S. enterica and P. mirabilis isolates from swine farms in China.A total of 24 S. enterica and 61 P. mirabilis strains were isolated from samples of swine stools and diseased tissues in 35 swine farms from 16 provinces in China between May 2012 and February 2014. Antimicrobial susceptibility testing was performed by the disc diffusion method according to the CLSI guidelines (16). Primers used in this study are listed in Table S1 in the supplemental material. The left and right junctions of SGI1 were detected in one S. enterica serovar Rissen and three P. mirabilis strains. The multiple locus sequence typing for SGI1-containing S. Rissen strain Z4 showed that the types of the seven housekeeping genes, not reported to date, were 92 (aroC), 137 (dnaN), 8 (hemD), 524 (hisD), 206 (purE), 313 (sucA), and 330 (thrA). It was submitted to the website

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“…This alone enables a multidrug resistance phenotype, but the carriage of additional plasmids by SGI-1-containing strains is common (157). Interestingly, some plasmids have also been shown to enhance excision and variant formation of Salmonella genomic islands, such as the enhanced excision of SGI-1 by plasmids belonging to the IncA/C type (158,159). In addition to enhancing the excision of chromosomal islands, these plasmids may also harbor receptor sites for phage recognition.…”

Section: Role Of Plasmids In Salmonella Genome Evolutionmentioning

confidence: 99%

Salmonella Pathogenicity and Host Adaptation in Chicken-Associated Serovars

Foley

Johnson

Ricke

et al. 2013

Microbiol Mol Biol Rev

247

218

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SUMMARY Enteric pathogens such as Salmonella enterica cause significant morbidity and mortality. S. enterica serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts. S. enterica serovars such as S . Typhi, S . Dublin, and S . Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while S . Enteritidis and S . Typhimurium have broad host ranges. This review examines how S. enterica has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect. S . Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars. S. enterica serovars such as S . Kentucky and S . Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of Salmonella to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today.

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Stability, Entrapment and Variant Formation of Salmonella Genomic Island 1

Cited by 39 publications

References 40 publications

Characterization of Two Multidrug-Resistant IncA/C Plasmids from the 1960s by Using the MinION Sequencer Device

Characterization of Two Multidrug-Resistant IncA/C Plasmids from the 1960s by Using the MinION Sequencer Device

Two Novel Salmonella Genomic Island 1 Variants in Proteus mirabilis Isolates from Swine Farms in China

Salmonella Pathogenicity and Host Adaptation in Chicken-Associated Serovars

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