title: It Is Not All about Single Nucleotide Polymorphisms: Comparison of Mobile Genetic Elements and Deletions in Listeria monocytogenes Genomes Links Cases of Hospital-Acquired Listeriosis to the Environmental Source.
abstract: The control of food-borne outbreaks caused by Listeria monocytogenes in humans relies on the timely identification of food or environmental sources and the differentiation of outbreak-related isolates from unrelated ones. This study illustrates the utility of whole-genome sequencing for examining the link between clinical and environmental isolates of L. monocytogenes associated with an outbreak of hospital-acquired listeriosis in Sydney, Australia. Comparative genomic analysis confirmed an epidemiological link between the three clinical and two environmental isolates. Single nucleotide polymorphism (SNP) analysis showed that only two SNPs separated the three human outbreak isolates, which differed by 19 to 20 SNPs from the environmental isolates and 71 to >10,000 SNPs from sporadic L. monocytogenes isolates. The chromosomes of all human outbreak isolates and the two suspected environmental isolates were syntenic. In contrast to the genomes of background sporadic isolates, all epidemiologically linked isolates contained two novel prophages and a previously unreported clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) locus subtype sequence. The mobile genetic element (MGE) profile of these isolates was distinct from that of the other serotype 1/2b reference strains and sporadic isolates. The identification of SNPs and clonally distinctive MGEs strengthened evidence to distinguish outbreak-related isolates of L. monocytogenes from cocirculating endemic strains.
authors: Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.
authors: Qinning
authors: Q
authors: Wang
authors: Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia Sydney Medical School-Westmead, The University of Sydney, Sydney, NSW, Australia.
authors: Nadine
authors: N
authors: Holmes
authors: Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia.
authors: Elena
authors: E
authors: Martinez
authors: NSW Enteric Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West, Sydney, NSW, Australia.
authors: Peter
authors: P
authors: Howard
authors: Marie Bashir Institute for Infectious Diseases and Biosecurity and School of Public Health, The University of Sydney, Sydney, NSW, Australia.
authors: Grant
authors: G
authors: Hill-Cawthorne
authors: Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, Australia Sydney Medical School-Westmead, The University of Sydney, Sydney, NSW, Australia NSW Enteric Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West, Sydney, NSW, Australia vitali.sintchenko@sydney.edu.au.
authors: Vitali
authors: V
authors: Sintchenko
mesh_terms: D000368:Aged; D001315:Australia / Q000453:epidemiology; D001483:Base Sequence; D003428:Cross Infection / Q000382:microbiology*; D004269:DNA, Bacterial / Q000235:genetics; D005260:Female; D005516:Food Microbiology; D005517:Foodborne Diseases / Q000382:microbiology; D016680:Genome, Bacterial / Q000235:genetics; D006760:Hospitalization; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008089:Listeria monocytogenes / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D008088:Listeriosis / Q000453:epidemiology* / Q000382:microbiology; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D058889:Molecular Typing; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D039002:Prophages / Q000235:genetics; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial