Draft Genome Sequences of Mycobacterium kansasii Strains 1010001454, 1010001458, 1010001468, 1010001493, 1010001495, and 1010001469, Isolated from Environmental Sources

Mycobacterium kansasii belongs to the nontuberculous mycobacteria (NTM) and causes opportunistic infections with both pulmonary and extrapulmonary manifestations. Here, we report the draft genome sequences of six environmental M. kansasii strains, designated 1010001495 (type I), 1010001469 (type II), 1010001468 (type III), 1010001458 (type IV), 1010001454 (type V), and 1010001493 (type V), originally isolated in five different European countries.The study was financed by the National Centre for Research and Development: “LIDER” Program (contract no. LIDER/044/457/L-4/12/NCBR/2013)

Stable population structure in Europe since the Iron Age, despite high mobility

Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000–3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire’s mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history

Zróżnicowanie genetyczne populacji ludzkich zamieszkujących teren dzisiejszej Polski we wczesnym średniowieczu

W ramach niniejszej rozprawy doktorskiej wykonano sekwencjonowanie NGS 120 genomów jądrowych, datowanych od epoki żelaza (n=2), poprzez okres rzymski (n=7) i wczesne średniowiecze (n=111) w Polsce. Materiały szkieletowe datowane na okres wczesnego średniowiecza obejmowały populacje reprezentujące: 1. „przeciętnych” mieszkańców Polski w okresie wczesnego średniowiecza - serie szkieletowe: Brześć Kujawski st. 5, Stary Brześć Kujawski Kolonia st. 3, Piotrów st. 1 (gm. Poddębice), Chełmno st. 20 (gm. Dąbie), Płock, Ostrowite st. 2 (gm. Chojnice), Sandomierz st. 1 i 7, 2. mieszkańców portowej osady handlowej na wyspie Wolin: Lubin st. 6, 3. prawdopodobną elitę wojskową państwa pierwszych Piastów, według dotychczasowych interpretacji archeologów przybyłą tu z terenu Rusi (Waregowie): Lutomiersk st. 1. Dodatkowo uwzględniono w analizie szkielety reprezentujące populacje zamieszkujące teren współczesnej Polski we wcześniejszych okresach archeologicznych: przedstawicieli kultury wielbarskiej z okresu rzymskiego (I-IV w. n.e., Weklice st. 7, gm. Elbląg) oraz kultury łużyckiej z wczesnej epoki żelaza (VIII-V w. p.n.e.) (stanowiska Kałdus pow. chełmiński i Boguszewo pow. grudziądzki w woj. kujawsko-pomorskim). Włączenie tych populacji miało na celu próbę odpowiedzi na pytanie o historię zasiedlenia ziem dzisiejszej Polski.EASI-Genomics this project has receied funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824110. Cyfrowe udostępnianie zasobów biomolekularnych i opisowych Biobanku i Katedry Antropologii Uniwersytetu Łódzkiego – charakterystyka populacji zamieszkujących tereny dzisiejszej Polski na przestrzeni dziejów. Platforma informacyjna eCzlowiek.pl. Finansowanie dla Młodych Naukowców 2018 r., Wydziału Biologii i Ochrony Środowiska. IDUB 2B111402000050.

In silico analysis of virulence associated genes in genomes of Escherichia coli strains causing colibacillosis in poultry

Introduction: Colibacillosis – the most common disease of poultry, is caused mainly by avian pathogenic Escherichia coli (APEC). However, thus far, no pattern to the molecular basis of the pathogenicity of these bacteria has been established beyond dispute. In this study, genomes of APEC were investigated to ascribe importance and explore the distribution of 16 genes recognised as their virulence factors

Genomic insights into the Mycobacterium kansasii complex : an update

Only very recently, has it been proposed that the hitherto existing Mycobacteriumkansasii subtypes (I–VI) should be elevated, each, to a species rank. Consequently, the former M. kansasii subtypes have been denominated as Mycobacterium kansasii (former type I), Mycobacterium persicum (II), Mycobacterium pseudokansasii (III), Mycobacterium innocens (V), and Mycobacterium attenuatum (VI). The present work extends the recently published findings by using a three-pronged computational strategy, based on the alignment fraction-average nucleotide identity, genome-to-genome distance, and core-genome phylogeny, yet essentially independent and much larger sample, and thus delivers a more refined and complete picture of the M. kansasii complex. Furthermore, five canonical taxonomic markers were used, i.e., 16S rRNA, hsp65, rpoB, and tuf genes, as well as the 16S-23S rRNA intergenic spacer region (ITS). The three major methods produced highly concordant results, corroborating the view that each M. kansasii subtype does represent a distinct species. This work not only consolidates the position of five of the currently erected species, but also provides a description of the sixth one, i.e., Mycobacterium ostraviense sp. nov. to replace the former subtype IV. By showing a close genetic relatedness, amonophyletic origin, and overlapping phenotypes, our findings support the recognition of the M. kansasii complex (MKC), accommodating all M. kansasii-derived species and Mycobacterium gastri. None of the most commonly used taxonomic markers was shown to accurately distinguish all the MKC species. Likewise, no species-specific phenotypic characteristics were found allowing for species differentiation within the complex, except the non-photochromogenicity of M. gastri. To distinguish, most reliably, between the MKC species, and between M. kansasii and M. persicum in particular, whole-genome-based approaches should be applied. In the absence of clear differences in the distribution of the virulence-associated region of difference 1 genes among the M. kansasii-derived species, the pathogenic potential of each of these species can only be speculatively assessed based on their prevalence among the clinically relevant population. Large-scale molecular epidemiological studies are needed to provide a better understanding of the clinical significance and pathobiology of the MKC species. The results of the in vitro drug susceptibility profiling emphasize the priority of rifampicin administration in the treatment of MKC-induced infections, while undermining the use of ethambutol, due to a high resistance to this drug

1 H -benzo[ d ]imidazole derivatives affect MmpL3 in Mycobacterium tuberculosis

International audienc

PPE51 Is Involved in the Uptake of Disaccharides by Mycobacterium tuberculosis

We have recently found that selected thio-disaccharides possess bactericidal effects against Mycobacterium tuberculosis but not against Escherichia coli or Staphylococcus aureus. Here, we selected spontaneous mutants displaying resistance against the investigated thio-glycoside. According to next-generation sequencing, four of six analyzed mutants which were resistant to high concentrations of the tested chemical carried nonsynonymous mutations in the gene encoding the PPE51 protein. The complementation of these mutants with an intact ppe51 gene returned their sensitivity to the wild-type level. The uptake of tritiated thio-glycoside was significantly more abundant in wild-type Mycobacterium tuberculosis compared to the strain carrying the mutated ppe51 gene. The ppe51 mutations or CRISPR-Cas9-mediated downregulation of PPE51 expression affected the growth of mutant strains on minimal media supplemented with disaccharides (maltose or lactose) but not with glycerol or glucose as the sole carbon and energy source. Taking the above into account, we postulate that PPE51 participates in the uptake of disaccharides by tubercle bacilli

Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis

Abstract Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston’s discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii

Stable population structure in Europe since the Iron Age, despite high mobility

International audienceAncient DNA research in the past decade has revealed that European populationstructure changed dramatically in the prehistoric period (14,000–3000 years before present, YBP),reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries.However, little is known about how population structure changed from the historical period onward(3000 YBP - present). To address this, we collected whole genomes from 204 individuals fromEurope and the Mediterranean, many of which are the first historical period genomes from theirregion (e.g. Armenia and France). We found that most regions show remarkable inter-individualheterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region wherethey were sampled, some indicating cross-Mediterranean contacts. Despite this high level ofmobility, overall population structure across western Eurasia is relatively stable through the historicalperiod up to the present, mirroring geography. We show that, under standard population geneticsmodels with local panmixia, the observed level of dispersal would lead to a collapse of populationstructure. Persistent population structure thus suggests a lower effective migration rate than indi-cated by the observed dispersal. We hypothesize that this phenomenon can be explained by exten-sive transient dispersal arising from drastically improved transportation networks and the RomanEmpire’s mobilization of people for trade, labor, and military. This work highlights the utility ofancient DNA in elucidating finer scale human population dynamics in recent history