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Leishmania tropica is one of the main causative agents of cutaneous leishmaniasis (CL). Population structures of L. tropica appear to be genetically highly diverse. However, the relationship between L. tropica strains genomic diversity, protein coding gene evolution and biogeography are still poorly understood. In this study, we sequenced the genomes of three new clinical L. tropica isolates, two derived from a recent outbreak of CL in camps hosting Syrian refugees in Lebanon and one historical isolate from Azerbaijan to further refine comparative genome analyses. In silico multilocus microsatellite typing (MLMT) was performed to integrate the current diversity of genome sequence data in the wider available MLMT genetic population framework. Single nucleotide polymorphism (SNPs), gene copy number variations (CNVs) and chromosome ploidy were investigated across the available 18 L. tropica genomes with a main focus on protein coding genes. MLMT divided the strains in three populations that broadly correlated with their geographical distribution but not populations defined by SNPs. Unique SNPs profiles divided the 18 strains into five populations based on principal component analysis. Gene ontology enrichment analysis of the protein coding genes with population specific SNPs profiles revealed various biological processes, including iron acquisition, sterols synthesis and drug resistance. This study further highlights the complex links between L. tropica important genomic heterogeneity and the parasite broad geographic distribution. Unique sequence features in protein coding genes identified in distinct populations reveal potential novel markers that could be exploited for the development of more accurate typing schemes to further improve our knowledge of the evolution and epidemiology of the parasite as well as highlighting protein variants of potential functional importance underlying L. tropica specific biology., Competing Interests: The authors have declared that no competing interests exist.

Objectives: The rapid emergence of carbapenem-resistant Acinetobacter baumannii is a global health concern. A comparative genomic analysis was performed on two ST85 A. baumannii strains harboring bla NDM-1 and bla OXA-94 collected in Lebanon from Syrian Civil War victims., Methods: Genome sequencing data of ACMH-6200 and ACMH-6201 were used for in silico extraction of multilocus sequence types (MLST), resistance genes, and virulence factors. Plasmids were genetically mapped in silico and using PCR-based replicon typing (PBRT). The genetic environment of bla NDM-1 and bla OXA-94 was determined, and whole-genome single nucleotide polymorphism (wgSNP) analysis in comparison with 41 publicly available A. baumannii genomes was performed., Results: Tn125 carrying bla NDM-1 was truncated by the insertion of ISAba14 downstream of dct, generating ΔTn125. bla OXA-94 was upstream of ISAba13 and ISAba17. Resistance to ceftazidime could be attributed to AmpC cephalosporinase encoded by bla ADC-25 , and to bla NDM-1 on plasmids . GyrA (S83L) and ParC (S80L) substitutions conferred resistance to fluoroquinolones. wgSNP analysis separated the isolates based on their sequence types., Conclusions: The role of refugees in the transmission of antimicrobial resistance in developing countries is understudied. As such, this study sheds light on the correlation between population mobility and the importation of drug-resistant pathogens. It also highlights the manifold mechanisms underlying antibiotic resistance in A. baumannii., (Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.)