Additional file 1: of Population structure and associated phenotypes of Salmonella enterica serovars Derby and Mbandaka overlap with host range

Strain information. Strain identifiers are used throughout the paper for convenience, the isolate number should be used to request culture material. For each strain the year and host of isolation are also displayed. (PDF 20 kb

Additional file 2: of Population structure and associated phenotypes of Salmonella enterica serovars Derby and Mbandaka overlap with host range

PCR primer sequences. PCR primer sequences for the amplification of SPI-1 and SPI-23 gene regions. The product length, start position and the genome from which the primers were designed is also shown. (PDF 28 kb

Data_Sheet_1_Geographical and temporal distribution of multidrug-resistant Salmonella Infantis in Europe and the Americas.zip

Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the “parasitic” pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids.</p

Frequency of gross lesions in thirty five piglets which died of septicaemia due to <i>Klebsiella pneumoniae</i>.

<p>Frequency of gross lesions in thirty five piglets which died of septicaemia due to <i>Klebsiella pneumoniae</i>.</p

Clinical details for English pig herds with outbreaks of septicaemia due to <i>Kpp</i> infection.

<p>Clinical details for English pig herds with outbreaks of septicaemia due to <i>Kpp</i> infection.</p

Clinical interventions and efficacy following the diagnosis of piglet septicaemia due to <i>Kpp</i>.

<p>Clinical interventions and efficacy following the diagnosis of piglet septicaemia due to <i>Kpp</i>.</p

BRIG analysis: Location of genomic regions unique to ST25 case isolates.

<p>The 3 phage sequences linked to <i>Kpp</i> ST25 isolates are highlighted with red bars. C, case; CR, case-related; cnda, contemporary non disease associated; H, historical.</p

Phylogenetic SNP tree analysis of <i>Klebsiella</i> genomes, using <i>Klebsiella pneumoniae</i> NTUH-K2044 as reference genome.

<p>Shaded isolates the ST25 case isolates. There were a total of 195803 SNP positions in the final dataset. Node colours indicate bootstrap support according to figure legend (Blue = low bootstrap support, Red = high bootstrap support).</p

Virulence gene analysis of 51 isolates from 1993 to 2011.

<p>Virulence gene analysis of 51 isolates from 1993 to 2011.</p

Emergence of <i>Klebsiella pneumoniae</i> subspecies <i>pneumoniae</i> as a cause of septicaemia in pigs in England - Fig 4

<p><b>(A) Gel picture showing electrophoretic separation of plasmids carried by 16 <i>Kpp</i> isolates</b>, migrating in 0.8% agarose (TBE), for 270 min at 150 v, 4°C, are shown. Yellow stars indicate location of pKPMC25 common to <i>Kpp</i> ST25 isolates. The plasmids in lane 1 and 21 are supercoiled DNA ladder. Lane 2, 12, 20 shows the reference plasmid bands from strain 39R861 (148 kb, 63 kb, 36 kb, genomic DNA band and 6.8 kb. Lane 3, 8–10 and 16–18 are <i>Kpp</i> ST25 isolates. Lanes 4–7, 11, 13–15 and 19 are non-ST25 <i>Kpp</i> isolates. (<b>B). Overview of pKPMC25 plasmid sequence features and comparison to closest matching plasmids</b>.</p