Comparative Genome Analysis of Hungarian and Global Strains of Salmonella Infantis.

INTRODUCTION: The emergence and spread of new strains of zoonotic bacteria, such as multidrug resistant (MDR) Salmonella Infantis, represent a growing health risk for humans in and outside Europe due to foodborne infections of poultry meat origin. OBJECTIVES: In order to understand genome relations of S. Infantis strains from Hungary and from different geographic regions, we performed a comprehensive genome analysis of nine Hungarian and 67 globally selected strains of S. Infantis and 26 Salmonella strains representing 13 non-Infantis serovars. RESULTS: Analyses of whole-, and accessory genomes, showed that almost all S. Infantis strains were separated from the non-Infantis serovars. S. Infantis strains from Hungary formed subclusters based on their time of isolation. In whole genome sequence analysis, the Swiss strains of S. Infantis were closely related to each other and clustered together with subclusters of strains from Hungary, Japan, Italy, United States, and Israel. The accessory genome analysis revealed that the Swiss strains were distinct from most of the strains investigated, including the Hungarian ones. Analysis of the cloud genes offered the most detailed insight into the genetic distance and relationship of S. Infantis strains confirming that the Swiss and Hungarian strains belonged to different lineages. As expected, core genome analysis provided the least discriminatory power for analysis of S. Infantis. Genomic sequences of nine strains from Brazil, Israel, Mexico, Nigeria, and Senegal (deposited as S. Infantis) proved to be outliers from the S. Infantis clade. They were predicted to be Salmonella Rissen, Salmonella Ouakarm, Salmonella Kentucky, Salmonella Thompson, and Salmonella enterica subsp. diarizonae. CONCLUSION: Accessory genome of S. Infantis showed the highest diversity suggesting a faster evolution than that of the whole genomes contributing to the emergence of multiple genetic variants of S. Infantis worldwide. Accordingly, in spite of the comprehensive analysis of several genomic characteristics, no epidemiologic links between these S. Infantis strains from different countries could be established. It is also concluded that several strains originally designated as S. Infantis need in databanks reclassification.

Abundance of mobile genetic elements in an Acinetobacter lwoffii strain isolated from Transylvanian honey sample.

Based on phylogenetic analyses, strain M2a isolated from honey, an unexpected source of acinetobacters, was classified as Acinetobacter lwoffii. The genome of this strain is strikingly crowded with mobile genetic elements. It harbours more than 250 IS elements of 15 IS-families, several unit and compound transposons and 15 different plasmids. These IS elements, including 30 newly identified ones, could be classified into at least 53 IS species. Regarding the plasmids, 13 of the 15 belong to the Rep-3 superfamily and only one plasmid, belonging to the "Low-GC" family, possesses a seemingly complete conjugative system. The other plasmids, with one exception, have a mobilization region of common pattern, consisting of the divergent mobA/mobL-family and mobS-, mobC- or traD-like genes separated by an oriT-like sequence. Although two plasmids of M2a are almost identical to those of A. lwoffi strains isolated from gold mine or Pleistocene sediments, most of them have no close relatives. The presence of numerous plasmid-borne and chromosomal metal resistance determinants suggests that M2a previously has also evolved in a metal-polluted environment. The numerous, possibly transferable, plasmids and the outstanding number of transposable elements may reflect the high potential of M2a for rapid evolution.

Two Draft Genome Sequences of Sphingobacterium sp. Strains Isolated from Honey.

Here, we report two annotated draft genome sequences of Sphingobacterium sp. strains isolated from honey. The genomes of strains 1.A.4 and 1.A.5 show a limited similarity to each other and to genomes of other Sphingobacterium species, indicating that these isolates may represent new species.

Draft Genome Sequences of Saccharibacter sp. Strains 3.A.1 and M18 Isolated from Honey and a Honey Bee (Apis mellifera) Stomach.

The annotated draft genome sequences of two recent Saccharibacter sp. strains isolated from honey and a honey bee stomach in 2014 are reported here. Currently, two Saccharibacter whole-genome sequences are available in databases; thus, the sequences of our new isolates will contribute to a better understanding of Saccharibacter genomes.

Genome Sequences of Salmonella enterica subsp. enterica Serovar Infantis Strains from Hungary Representing Two Peak Incidence Periods in Three Decades.

Four strains of Salmonella enterica subsp. enterica serovar Infantis isolated from humans (1980 to 1982) and broiler chickens (2016) have been sequenced. They represent the early and recent peak incidences of this serovar in Hungary. Genome sequences of these isolates provide comparative data on the evolution and rise of an endemic S Infantis clone in Hungary.

Genome Sequences of Multidrug-Resistant Salmonella enterica subsp. enterica Serovar Infantis Strains from Broiler Chicks in Hungary.

Three strains of Salmonella enterica serovar Infantis isolated from healthy broiler chickens from 2012 to 2013 have been sequenced. Comparison of these and previously published S Infantis genome sequences of broiler origin in 1996 and 2004 will provide new insight into the genome evolution and recent spread of S Infantis in poultry.

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

Two A/C incompatibility group (IncA/C family) plasmids from the 1960s have been sequenced and classified into the A/C2 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. ARIR16a consists of Tn1, Tn6020, and Tn6333, harboring the resistance genes blaTEM-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. ARIIP40a carrying blaTEM-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 ARIR16a 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.