An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation

Bloodstream infections by Salmonella enterica serovar Typhimurium constitute a major health burden in sub-Saharan Africa (SSA). These invasive non-typhoidal (iNTS) infections are dominated by isolates of the antibiotic resistance-associated sequence type (ST) 313. Here, we report emergence of ST313 sublineage II.1 in the Democratic Republic of the Congo. Sublineage II.1 exhibits extensive drug resistance, involving a combination of multidrug resistance, extended spectrum β-lactamase production and azithromycin resistance. ST313 lineage II.1 isolates harbour an IncHI2 plasmid we name pSTm-ST313-II.1, with one isolate also exhibiting decreased ciprofloxacin susceptibility. Whole genome sequencing reveals that ST313 II.1 isolates have accumulated genetic signatures potentially associated with altered pathogenicity and host adaptation, related to changes observed in biofilm formation and metabolic capacity. Sublineage II.1 emerged at the beginning of the 21st century and is involved in on-going outbreaks. Our data provide evidence of further evolution within the ST313 clade associated with iNTS in SSA. Invasive non-typhoidal Salmonella (iNTS) infections are dominated by antibiotic resistant isolates of the sequence type (ST) 313. Here, the authors identify the ST313 sublineage II.1 in the Democratic Republic of the Congo exhibiting extensive drug resistance and genetic signatures potentially associated with host adaptation.

[1]  G. Dougan,et al.  Salmonella enterica serovar Typhi Producing CTX-M-15 Extended Spectrum β-Lactamase in the Democratic Republic of the Congo. , 2017, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[2]  N. Wheeler,et al.  Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica , 2017, bioRxiv.

[3]  J. Jacobs,et al.  Antimicrobial Resistance in Invasive Non-typhoid Salmonella from the Democratic Republic of the Congo: Emergence of Decreased Fluoroquinolone Susceptibility and Extended-spectrum Beta Lactamases , 2013, PLoS neglected tropical diseases.

[4]  Jacqueline A. Keane,et al.  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins , 2014, Nucleic acids research.

[5]  G. Muth,et al.  Conjugative DNA transfer in Streptomyces by TraB: is one protein enough? , 2012, FEMS microbiology letters.

[6]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[7]  Julian Parkhill,et al.  Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data , 2016, bioRxiv.

[8]  G. Dougan,et al.  Dysregulated Humoral Immunity to Nontyphoidal Salmonella in HIV-Infected African Adults , 2010, Science.

[9]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[10]  F. Fang,et al.  Loss of Multicellular Behavior in Epidemic African Nontyphoidal Salmonella enterica Serovar Typhimurium ST313 Strain D23580 , 2016, mBio.

[11]  T. Wallis,et al.  Flagellar Phase Variation of Salmonella enterica Serovar Typhimurium Contributes to Virulence in the Murine Typhoid Infection Model but Does Not InfluenceSalmonella-Induced Enteropathogenesis , 2001, Infection and Immunity.

[12]  F. Weill,et al.  Invasive Salmonella enterica Serotype Typhimurium Infections, Democratic Republic of the Congo, 2007–2011 , 2014, Emerging infectious diseases.

[13]  Fabian Rivera-Chávez,et al.  Salmonella Uses Energy Taxis to Benefit from Intestinal Inflammation , 2013, PLoS pathogens.

[14]  A. Bäumler,et al.  Comparative Analysis of Salmonella Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut , 2014, mBio.

[15]  Benjamin Hofner,et al.  opm: an R package for analysing OmniLog® phenotype microarray data , 2013, Bioinform..

[16]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[17]  S. West,et al.  Azithromycin to Reduce Childhood Mortality in Sub-Saharan Africa , 2018 .

[18]  N. P. H. Lan,et al.  New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam , 2018, mBio.

[19]  Gemma C. Langridge,et al.  Patterns of genome evolution that have accompanied host adaptation in Salmonella , 2014, Proceedings of the National Academy of Sciences.

[20]  J. Casadesús,et al.  Roles of the Outer Membrane Protein AsmA of Salmonella enterica in the Control of marRAB Expression and Invasion of Epithelial Cells , 2009, Journal of bacteriology.

[21]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[22]  Nicola K. Petty,et al.  BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons , 2011, BMC Genomics.

[23]  M. Gilmour,et al.  The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics. , 2004, Plasmid.

[24]  J. Logsdon,et al.  Do Salmonella carry spare tyres? , 2008, Trends in microbiology.

[25]  J. Crump,et al.  Global Burden of Invasive Nontyphoidal Salmonella Disease, 2010 , 2015, Emerging infectious diseases.

[26]  Andrew C. Pawlowski,et al.  The Comprehensive Antibiotic Resistance Database , 2013, Antimicrobial Agents and Chemotherapy.

[27]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[28]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[29]  G. Dougan,et al.  Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. , 2009, Genome research.

[30]  S. Kariuki,et al.  Invasive multidrug-resistant non-typhoidal Salmonella infections in Africa: zoonotic or anthroponotic transmission? , 2006, Journal of medical microbiology.

[31]  A. Drummond,et al.  Bayesian inference of population size history from multiple loci , 2008, BMC Evolutionary Biology.

[32]  S. West,et al.  Mass azithromycin distribution for reducing childhood mortality in sub-Saharan Africa , 2018, The New England journal of medicine.

[33]  S. Clare,et al.  Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa , 2015, PLoS neglected tropical diseases.

[34]  J. Wain,et al.  Intra-continental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa , 2012, Nature Genetics.

[35]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[36]  T. Hothorn,et al.  Simultaneous Inference in General Parametric Models , 2008, Biometrical journal. Biometrische Zeitschrift.

[37]  Julian Parkhill,et al.  ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads , 2017, bioRxiv.

[38]  Dong Xie,et al.  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..

[39]  Simon R. Harris,et al.  SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments , 2016, bioRxiv.

[40]  Gemma C. Langridge,et al.  Ceftriaxone-Resistant Salmonella enterica Serotype Typhimurium Sequence Type 313 from Kenyan Patients Is Associated with the blaCTX-M-15 Gene on a Novel IncHI2 Plasmid , 2015, Antimicrobial Agents and Chemotherapy.

[41]  Amy K. Cain,et al.  Drug Resistance in Salmonella enterica ser. Typhimurium Bloodstream Infection, Malawi , 2014, Emerging infectious diseases.

[42]  R. Kingsley,et al.  Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants , 2018, Infection and Immunity.

[43]  Nicholas A Feasey,et al.  Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa , 2012, The Lancet.

[44]  J. Wain,et al.  Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005–2010 , 2016, Emerging infectious diseases.

[45]  U. Römling,et al.  Characterization of the rdar morphotype, a multicellular behaviour in Enterobacteriaceae , 2005, Cellular and Molecular Life Sciences CMLS.

[46]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[47]  C. Gomes,et al.  Macrolide resistance mechanisms in Enterobacteriaceae: Focus on azithromycin , 2016, Critical reviews in microbiology.

[48]  Paul P. Gardner,et al.  A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes , 2016, bioRxiv.

[49]  K. Hokamp,et al.  Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella , 2018, Proceedings of the National Academy of Sciences.

[50]  J. Crump,et al.  Community-acquired bloodstream infections in Africa: a systematic review and meta-analysis. , 2010, The Lancet. Infectious diseases.

[51]  F. Weill,et al.  Prevalence and characterization of extended-spectrum β-lactamase-producing clinical Salmonella enterica isolates in Dakar, Senegal, from 1999 to 2009. , 2014, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[52]  M. Falagas,et al.  Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. , 2012, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[53]  Justin Zobel,et al.  SRST2: Rapid genomic surveillance for public health and hospital microbiology labs , 2014, bioRxiv.

[54]  G. Ramachandran,et al.  Invasive Salmonella Typhimurium ST313 with Naturally Attenuated Flagellin Elicits Reduced Inflammation and Replicates within Macrophages , 2015, PLoS neglected tropical diseases.

[55]  Khalil Abudahab,et al.  Microreact: visualizing and sharing data for genomic epidemiology and phylogeography , 2016, Microbial genomics.

[56]  J. Crump,et al.  A Perspective on Invasive Salmonella Disease in Africa. , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[57]  Samuel Kariuki,et al.  Epidemiology and Genomics of Invasive Nontyphoidal Salmonella Infections in Kenya. , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[58]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[59]  J. Hinton,et al.  Invasive Non-Typhoidal Salmonella Typhimurium ST313 Are Not Host-Restricted and Have an Invasive Phenotype in Experimentally Infected Chickens , 2013, PLoS neglected tropical diseases.

[60]  S. Kariuki,et al.  Characterisation of community acquired non-typhoidal Salmonella from bacteraemia and diarrhoeal infections in children admitted to hospital in Nairobi, Kenya , 2006, BMC Microbiology.

[61]  M. Ouellette,et al.  Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. , 2017, The Lancet. Infectious diseases.

[62]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[63]  G. Dougan,et al.  Genotypic Homogeneity of Multidrug Resistant S. Typhimurium Infecting Distinct Adult and Childhood Susceptibility Groups in Blantyre, Malawi , 2012, PloS one.

[64]  J. Muyembe,et al.  Invasive Salmonella Infections at Multiple Surveillance Sites in the Democratic Republic of the Congo, 2011-2014. , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[65]  Rekha R Meyer,et al.  Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid , 2004, Nature Genetics.

[66]  Allan R. Wilks,et al.  Constructing a Geographical Database , 1997 .

[67]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[68]  A. Driessen,et al.  Distribution and Physiology of ABC-Type Transporters Contributing to Multidrug Resistance in Bacteria , 2007, Microbiology and Molecular Biology Reviews.

[69]  G. Ramachandran,et al.  Poor biofilm-forming ability and long-term survival of invasive Salmonella Typhimurium ST313. , 2016, Pathogens and disease.

[70]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[71]  S. Nair,et al.  Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins , 2018, mBio.

[72]  Christopher M. Parry,et al.  Antimicrobial Resistance , and Antimicrobial Management of Invasive Salmonella Infections , 2015 .

[73]  F. Aarestrup,et al.  Genomics of an emerging clone of Salmonella serovar Typhimurium ST313 from Nigeria and the Democratic Republic of Congo. , 2013, Journal of infection in developing countries.

[74]  Jacqueline A. Keane,et al.  Circlator: automated circularization of genome assemblies using long sequencing reads , 2015, Genome Biology.

[75]  J. Jacobs,et al.  Microbiological, clinical and molecular findings of non-typhoidal Salmonella bloodstream infections associated with malaria, Oriental Province, Democratic Republic of the Congo , 2016, BMC Infectious Diseases.