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Additional file 1: Figure S1. Gene content dissimilarity among the Agrobacterium genomes. (A) and (B): principal coordinate analysis with and without the outgroup A. larrymoorei, respectively. The % variance explained by each axis is provided in parentheses. (C) and (D): hierarchical clustering with and without the outgroup A. larrymoorei, respectively. Figure S2. Global alignment of the linear chromosomes. Locations of T6SS-hcp operons and vgrG homologs are labeled. Figure S3. Logo plots of the putative protein domains identified among vgrG homologs. For each domain, the length and the number of homologs with the domain is labeled. Domain 1 is the only domain with a corresponding database entry (TIGR03361). Figure S4. Predicted structures of VgrG homologs. Regions are colored according to the scheme used in the domain analysis (Fig. 3). The chain D of PA0091 VgrG1 (PDB identifier: 4MTK) from Pseudomonas aeruginosa was selected as the template. The C-terminal parts that could not be confidently inferred are omitted. In all cases, the coverage (i.e., percentage of the sequence included in the structure prediction) are at least 75%, the sequence identity to the template is at least 30% and the confidence score is 100%. Figure S5. Maximum likelihood phylogenies of vgrG-associated domains. (A) Domain 1 (TIGR03361; VI_Rhs_Vgr super family), (B) Domain 2 (unknown function), and (C) Domain 3 (unknown function). Figure S6. Principal coordinate analysis of gene content among the putative pTi analyzed. Figure S7. Maximum likelihood phylogeny of pTi based on the concatenated alignment of shared single-copy genes. (A) All of the 20 pTi sequences analyzed; 21 core genes and 8534 aligned amino acid sites. (B) Excluding the two novel pTi; 40 core genes and 15,473 aligned amino acid sites, all branches received > 80% bootstrap support. Figure S8. Tomato tumor assay of strains 12D1, CFBP4996, and CFBP5473. Mock was inoculated with sterilized water as a negative control and strain C58 was included as a positive control. Strain 12D1 harbors a plasmid with opine transporter and catabolism genes but lacks vir regulon genes and identifiable T-DNA. CFBP4996 and CFBP5473 harbor novel types of putative tumor-inducing plasmids (pTi). (A) Tomato stems at three weeks after inoculation. Scale bar: 0.25 cm. (B) Weight distribution of five biological replicates (1-cm segments of the stem centered at the inoculation site). The letters indicate ANOVA results. Figure S9. Gene organization of the vir regulons on pTi. Syntenic regions are indicated by grey blocks. The virulence (vir) genes are highlighted in red, the conjugation (tra) genes are highlighted in yellow, and other genes are plotted in white.

BACKGROUND: Salmonella infection poses significant public health threat globally, especially in resource-limited countries. Emergence and spread of antibiotic resistant strains to fluoroquinolones have led to treatment failures and increased mortality in Salmonella infection. However, there is dearth of information regarding mechanisms of resistance to fluoroquinolones in Ghana. This study therefore sought to identify chromosomal mutations and plasmid-mediated resistance as possible mechanisms of fluoroquinolone resistance from clinical isolates in Ghana. METHODS: This was a retrospective study of archived isolates biobanked at Kumasi Centre for Collaborative Research in Tropical Medicine, Ghana. Isolates were obtained from blood, stool and oropharynx samples at two hospitals, between May, 2016 and January, 2018. Salmonella identification was done using standard microbiological protocols and antibiotic susceptibility testing performed by Kirby-Bauer disc diffusion method. Isolates with intermediate susceptibility and/or resistance to nalidixic acid and/or ciprofloxacin were selected and examined for chromosomal mutations by Sanger sequencing and plasmid-mediated resistance by PCR. RESULTS: Of 133 biobanked isolates cultured, 68 (51.1%) and 16 (12%) were identified as Salmonella Typhi and non-typhoidal Salmonella (NTS), respectively. Sequence analysis of gyrA gene revealed the presence of 5 different nonsynonymous mutations, with the most frequent mutation (Ile203Ser) occurring in 12 out of 13 isolates tested. Gyrase B (gyrB) gene had 1 nonsynonymous mutation in 3 out of 13 isolates, substituting phenylalanine with leucine at codon 601 (Phe601Leu). No mutation was observed in parC and parE genes. Two NTS isolates were found to harbour qnrS plasmid-mediated resistant gene of molecular size 550 bp with high ciprofloxacin MIC of 0.5 μg/ml. CONCLUSION: This study reports for the first time in Ghana plasmid-mediated fluoroquinolone resistant gene qnrS in Salmonella clinical isolates. Nonsynonymous mutations of gyrA and gyrB genes likely to confer Salmonella reduced susceptibility to ciprofloxacin were also reported.

The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of crops and industries. Xylella fastidiosa subspecies fastidiosa causes disease in grapevines (Pierce’s disease of grapevines, PD), a current problem in North America, Europe, and Asia. In this research, we studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in central Taiwan with a larger databased of 176 isolates from the US and two from Spain, the path of introduction into Taiwan was also investigated. Phylogenetic relationships, haplotype network, and genetic diversity analyses confirm that X. fastidiosa subsp. fastidiosa was recently introduced into Taiwan from the Southeast US (Georgia based on available data). Recent core genome recombination events were detected among introduced X. fastidiosa subsp. fastidiosa isolates in Taiwan. The events originated from an unknown donor not included in the current sampling, suggesting that higher sequence diversity exists in the region. Notably, no recombination events were detected between subsp. fastidiosa and Xylella taiwanensis. In summary, the results demonstrate that PD-causing X. fastidiosa population in Taiwan originated from the Southeast region of the US, and recombination occurs among isolates in Taiwan after invasion. This study will improve our understanding of the genetic diversity of PD-causing X. fastidiosa after invasion to a new region.&nbsp

Escherichia coli belonging to sequence type ST131 constitute a globally distributed pandemic lineage that causes multidrug-resistant extra-intestinal infections. ST131 E. coli frequently produce extended-spectrum β-lactamases (ESBLs), which confer resistance to many β-lactam antibiotics and make infections difficult to treat. We sequenced the genomes of 154 ESBL-producing E. coli clinical isolates belonging to the ST131 lineage from patients at the University of Pittsburgh Medical Center (UPMC) between 2004 and 2018. Isolates belonged to the well described ST131 clades A (8%), B (3%), C1 (33%), and C2 (54%). An additional four isolates belonged to another distinct subclade within clade C and encoded genomic characteristics that have not been previously described. Time-dated phylogenetic analysis estimated that the most recent common ancestor (MRCA) for all clade C isolates from UPMC emerged around 1989, consistent with previous studies. We identified multiple genes potentially under selection in clade C, including the cell wall assembly gene ftsI , the LPS biosynthesis gene arnC , and the yersiniabactin uptake receptor fyuA . Diverse ESBL genes belonging to the bla CTX-M , bla SHV , and bla TEM families were identified; these genes were found at varying numbers of loci and in variable numbers of copies across isolates. Analysis of ESBL flanking regions revealed diverse mobile elements that varied by ESBL type. Overall, our findings show that ST131 subclades C1 and C2 dominated and were stably maintained among patients in the same hospital and uncover possible signals of ongoing adaptation within the clade C ST131 lineage., Competing Interests: Competing Interests The authors have no relevant conflicts of interest to declare.