Genomic Characterization of the Three Balkan Livestock Guardian Dogs

Mateja Janeš; Minja Zorc; Maja Ferenčaković; Ino Curik; Peter Dovč; Vlatka Cubric-Curik

doi:10.3390/su13042289

Genomic Characterization of the Three Balkan Livestock Guardian Dogs

Sustainability ◽

10.3390/su13042289 ◽

2021 ◽

Vol 13 (4) ◽

pp. 2289

Author(s):

Mateja Janeš ◽

Minja Zorc ◽

Maja Ferenčaković ◽

Ino Curik ◽

Peter Dovč ◽

...

Keyword(s):

Conservation Management ◽

Diversity Management ◽

Genomic Diversity ◽

Mountainous Areas ◽

Autosomal Snps ◽

The Balkans ◽

Gray Wolves ◽

Low Diversity ◽

Genomic Characterization

Balkan Livestock Guardian Dogs (LGD) were bred to help protect sheep flocks in sparsely populated, remote mountainous areas in the Balkans. The aim of this study was genomic characterization (107,403 autosomal SNPs) of the three LGD breeds from the Balkans (Karst Shepherd, Sharplanina Dog, and Tornjak). Our analyses were performed on 44 dogs representing three Balkan LGD breeds, as well as on 79 publicly available genotypes representing eight other LGD breeds, 70 individuals representing seven popular breeds, and 18 gray wolves. The results of multivariate, phylogenetic, clustering (STRUCTURE), and FST differentiation analyses showed that the three Balkan LGD breeds are genetically distinct populations. While the Sharplanina Dog and Tornjak are closely related to other LGD breeds, the Karst Shepherd is a slightly genetically distinct population with estimated influence from German Shepard (Treemix analysis). Estimated genomic diversity was high with low inbreeding in Sharplanina Dog (Ho = 0.315, He = 0.315, and FROH>2Mb = 0.020) and Tornjak (Ho = 0.301, He = 0.301, and FROH>2Mb = 0.033) breeds. Low diversity and high inbreeding were estimated in Karst Shepherds (Ho = 0.241, He = 0.222, and FROH>2Mb = 0.087), indicating the need for proper diversity management. The obtained results will help in the conservation management of Balkan LGD dogs as an essential part of the specific grazing biocultural system and its sustainable maintenance.

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Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

Microorganisms ◽

10.3390/microorganisms9081612 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1612

Author(s):

Werner Ruppitsch ◽

Andjela Nisic ◽

Patrick Hyden ◽

Adriana Cabal ◽

Jasmin Sucher ◽

...

Keyword(s):

Genetic Diversity ◽

Safety Evaluation ◽

Gene Clusters ◽

Northern Region ◽

Genomic Diversity ◽

High Genetic Diversity ◽

Pathogenic Factors ◽

Flavor Development ◽

Genomic Characterization

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

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One year of SARS-CoV-2: Genomic characterization of COVID-19 outbreak in Qatar

10.1101/2021.05.19.21257433 ◽

2021 ◽

Author(s):

Fatiha M. Benslimane ◽

Hebah A. AlKhatib ◽

Ola Al-Jamal ◽

Dana Albatesh ◽

Sonia Boughattas ◽

...

Keyword(s):

International Travel ◽

Genomic Diversity ◽

Whole Genome ◽

Genome Sequences ◽

Short Period ◽

National Response ◽

Genomic Characterization ◽

One Year ◽

Local Transmission

The state of Qatar has emerged as a major transit hub connecting all parts of the globe, making it as a hotspot for infectious disease introduction and providing an ideal setting to monitor the emergence and spread of variants. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population's genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number in the mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. This raises the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor SARS-CoV-2 profile and re-emergence in Qatar.

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Genomic characterization of 16S rRNA methyltransferase-producing Escherichia coli isolates from the Parisian area, France

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa105 ◽

2020 ◽

Vol 75 (7) ◽

pp. 1726-1735 ◽

Cited By ~ 2

Author(s):

François Caméléna ◽

Florence Morel ◽

Manel Merimèche ◽

Jean-Winoc Decousser ◽

Hervé Jacquier ◽

...

Keyword(s):

Escherichia Coli ◽

16S Rrna ◽

Genomic Diversity ◽

Health Concern ◽

M Gene ◽

Genetic Environment ◽

E Coli ◽

Genomic Characterization ◽

High Level

Abstract Background The resistance to all aminoglycosides (AGs) conferred by 16S rRNA methyltransferase enzymes (16S-RMTases) is a major public health concern. Objectives To characterize the resistance genotype, its genetic environment and plasmid support, and the phylogenetic relatedness of 16S-RMTase-producing Escherichia coli from France. Methods We screened 137 E. coli isolates resistant to all clinically relevant AGs from nine Parisian hospitals for 16S-RMTases. WGS was performed on clinical isolates with high-level AG resistance (MIC ≥256 mg/L) and their transformants. Results Thirty of the 137 AG-resistant E. coli produced 16S-RMTases: 11 ArmA, 18 RmtB and 1 RmtC. The 16S-RMTase producers were also resistant to third-generation cephalosporins (90% due to a blaCTX-M gene), co-trimoxazole, fluoroquinolones and carbapenems (blaNDM and blaVIM genes) in 97%, 83%, 70% and 10% of cases, respectively. Phylogenomic diversity was high in ArmA producers, with 10 different STs, but a similar genetic environment, with the Tn1548 transposon carried by a plasmid closely related to pCTX-M-3 in 6/11 isolates. Conversely, RmtB producers belonged to 12 STs, the most frequent being ST405 and ST complex (STc) 10 (four and four isolates, respectively). The rmtB gene was carried by IncF plasmids in 10 isolates and was found in different genetic environments. The rmtC gene was carried by the pNDM-US plasmid. Conclusions ArmA and RmtB are the predominant 16S-RMTases in France, but their spread follows two different patterns: (i) dissemination of a conserved genetic support carrying armA in E. coli with high levels of genomic diversity; and (ii) various genetic environments surrounding rmtB in clonally related E. coli.

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One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.768883 ◽

2021 ◽

Vol 11 ◽

Author(s):

Fatiha M. Benslimane ◽

Hebah A. Al Khatib ◽

Ola Al-Jamal ◽

Dana Albatesh ◽

Sonia Boughattas ◽

...

Keyword(s):

International Travel ◽

Genomic Diversity ◽

Diverse Population ◽

Genome Sequences ◽

Short Period ◽

National Response ◽

Genomic Characterization ◽

One Year ◽

Local Transmission

Qatar, a country with a strong health system and a diverse population consisting mainly of expatriate residents, has experienced two large waves of COVID-19 outbreak. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population’s genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number of mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. These findings raise the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor the SARS-CoV-2 profile and re-emergence in Qatar.

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Genomic Characterization of Two Shiga Toxin–Converting Bacteriophages Induced From Environmental Shiga Toxin–Producing Escherichia coli

Frontiers in Microbiology ◽

10.3389/fmicb.2021.587696 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yujie Zhang ◽

Yen-Te Liao ◽

Alexandra Salvador ◽

Vivian C. H. Wu

Keyword(s):

Escherichia Coli ◽

Phylogenetic Analysis ◽

Dna Sequences ◽

Shiga Toxin ◽

Genomic Diversity ◽

Whole Genome ◽

E Coli ◽

Uremic Syndrome ◽

Genomic Characterization

Shiga toxin (Stx), encoded by stx genes located in prophage sequences, is the major agent responsible for the pathogenicity of Shiga toxin-producing Escherichia coli (STEC) and is closely associated with the development of hemolytic uremic syndrome (HUS). Although numerous Stx prophage sequences have been reported as part of STEC bacterial genomes, the information about the genomic characterization of Stx-converting bacteriophages induced from STEC strains is relatively scarce. The objectives of this study were to genomically characterize two Stx-converting phages induced from environmental STEC strains and to evaluate their correlations with published Stx-converting phages and STEC strains of different origins. The Stx1-converting phage Lys8385Vzw and the Stx2-converting phage Lys19259Vzw were induced from E. coli O103:H11 (RM8385) and E. coli O157:H7 (RM19259), respectively. Whole-genome sequencing of these phages was conducted on a MiSeq sequencer for genomic characterization. Phylogenetic analysis and comparative genomics were performed to determine the correlations between these two Stx-converting phages, 13 reference Stx-converting phages, and 10 reference STEC genomes carrying closely related Stx prophages. Both Stx-converting phages Lys8385Vzw and Lys19259Vzw had double-stranded DNA, with genome sizes of 50,953 and 61,072 bp, respectively. Approximately 40% of the annotated coding DNA sequences with the predicted functions were likely associated with the fitness for both phages and their bacterial hosts. The whole-genome–based phylogenetic analysis of these two Stx-converting phages and 13 reference Stx-converting phages revealed that the 15 Stx-converting phages were divided into three distinct clusters, and those from E. coli O157:H7, in particular, were distributed in each cluster, demonstrating the high genomic diversity of these Stx-converting phages. The genomes of Stx-converting phage Lys8385Vzw and Lys19259Vzw shared a high-nucleotide similarity with the prophage sequences of the selected STEC isolates from the clinical and environmental origin. The findings demonstrate the genomic diversity of Stx-converting phages induced from different STEC strains and provide valuable insights into the dissemination of stx genes among E. coli population via the lysogenization of Stx-converting phages.

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