Molecular characterization and phylogeny of Shiga toxin–producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing

Ferdous, Mithila; Friedrich, Alex; Grundmann, Hajo; Boer, Richard F. de; Croughs, P; Islam, Md. Atikul; Bergh, Marjolein Kluytmans-van den; Kooistra-Smid, A.M.D.; Rossen, John W. A.

doi:10.1016/j.cmi.2016.03.028

Cited by 63 publications

(72 citation statements)

References 38 publications

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“…MLST has been proposed as an adequate tool for producing genetic profiles for a vast number of isolates, especially under non-epidemic circumstances (Ferdous et al, 2016). In this study, a substantial genetic diversity was observed in 301 non-O157 STEC isolates collected from various sources.…”

Section: Discussionmentioning

confidence: 99%

Molecular and Phylogenetic Characterization of Non-O157 Shiga Toxin-Producing Escherichia coli Strains in China

Bai¹,

Xu³

et al. 2016

Front. Cell. Infect. Microbiol.

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Shiga toxin-producing Escherichia coli (STEC) causes diarrhea and hemorrhagic colitis with life-threatening complications, such as hemolytic uremic syndrome. The aim of this study was to assess the molecular epidemiologic features of non-O157 STEC strains from different resources in China and illustrate the role of animal reservoirs or animal-derived foodstuffs in human STEC infections. A collection of 301 non-O157 STEC isolates from domestic and wild animals (i.e., cattle, goat, pig, yak, pika, and antelope), raw meats (i.e., beef, pork, mutton, chicken, and duck), diarrheal patients, and healthy carriers in different regions of China were selected in this study. Of the 301 analyzed STEC isolates, 67 serogroups, and 118 serotypes were identified; this included some predominant serogroups associated with human disease, such as O26, O45, O103, O111, and O121. Eighteen different combinations of stx subtypes were found. Eleven isolates carried the intimin gene eae, 93 isolates contained ehxA, and 73 isolates carried astA. The prevalence of other putative adhesion genes saa, paa, efa1, and toxB was 28.90% (87), 6.98% (21), 2.31% (7), and 1% (3), respectively. The phylogenetic distribution of isolates was analyzed by multilocus sequence typing (MLST). Ninety-four sequence types were assigned across the 301 isolates. A subset of isolates recovered from yak and pika residing in the similar wild environments, Qinghai-Tibetan plateau, showed similar genetic profiles and more tendencies to cluster together. Isolates from goat and mutton exhibited close genetic relatedness with those from human-derived isolates, providing evidence that transmission may have occurred locally within intraspecies or interspecies, and importantly, from animal reservoirs, or raw meats to humans. Comparing isolates in this study with highly virulent strains by MLST, along with serotyping and virulence profiles, it is conceivable that some of isolates from goat, yak, or raw meats may have potential to cause human diseases.

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Section: Discussionmentioning

confidence: 99%

Molecular and Phylogenetic Characterization of Non-O157 Shiga Toxin-Producing Escherichia coli Strains in China

Bai¹,

Xu³

et al. 2016

Front. Cell. Infect. Microbiol.

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“…wgMLST was shown to have higher discriminatory power and typeability than in silico MLST. After the introduction of WGS as a typing tool with high potential, gene-by-gene comparison of WGS data has been applied successfully for several species in outbreak settings (22)(23)(24)(25)(26)(27). To our knowledge, this large multicenter study is the first to apply wgMLST for typing of Enterobacteriaceae in nonoutbreak settings and to include a comprehensive evaluation of its performance in a large collection of isolates without a clear epidemiological link.…”

Section: Discussionmentioning

confidence: 99%

“…Whole-genome multilocus sequence typing (wgMLST) is a WGS-based typing method that extends MLST to the genome level (20). Today, such gene-bygene comparison of WGS data has been applied successfully for several species in outbreak settings, but data for Enterobacteriaceae and nonoutbreak settings are still limited (22)(23)(24)(25)(26)(27). The aim of this study was to develop representative wgMLST schemes for the Citation Kluytmans-van den Bergh MFQ, Rossen JWA, Bruijning-Verhagen PCJ, Bonten MJM, Friedrich AW, Vandenbroucke-Grauls CMJE, Willems RJL, Kluytmans JAJW, on behalf of the SoM Study Group.…”

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confidence: 99%

“…However, sequence conservation in housekeeping genes limits its discriminatory power and thus its use in outbreak investigations (16)(17)(18). Whole-genome sequencing (WGS) has emerged as an ultimate typing tool that fits any bacterial species, study type, and laboratory (19)(20)(21)(22)(23)(24)(25)(26)(27). Knowledge of the sequence of the entire genome, rather than of only a few loci, has greatly increased the precision of molecular epidemiologic data and allows its use in infection control, where questions of similarity of isolates focus on recently diverged isolates.…”

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Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

et al. 2016

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e Molecular typing has become indispensable in the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings, but current methods are labor-intensive, are difficult to standardize, or have limited resolution. Whole-genome multilocus sequence typing (wgMLST) has emerged as a whole-genome sequencing (WGS)-based gene-by-gene typing method that may overcome these limitations and has been applied successfully for several species in outbreak settings. In this study, genus-, genetic-complex-, and species-specific wgMLST schemes were developed for Citrobacter spp., the Enterobacter cloacae complex, Escherichia coli, Klebsiella oxytoca, and Klebsiella pneumoniae and used to type a national collection of 1,798 extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) isolates obtained from patients in Dutch hospitals. Genus-, genetic-complex-, and species-specific thresholds for genetic distance that accurately distinguish between epidemiologically related and unrelated isolates were defined for Citrobacter spp., the E. cloacae complex, E. coli, and K. pneumoniae. wgMLST was shown to have higher discriminatory power and typeability than in silico MLST. In conclusion, the wgMLST schemes developed in this study facilitate high-resolution WGS-based typing of the most prevalent ESBL-producing species in clinical practice and may contribute to further elucidation of the complex epidemiology of antimicrobial-resistant Enterobacteriaceae. wgMLST opens up possibilities for the creation of a Web-accessible database for the global surveillance of ESBL-producing bacterial clones. The continuing global spread of extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) constitutes a major public health threat in both health care and community settings (1-4). Extended-spectrum beta-lactamases (ESBL) confer resistance to the majority of beta-lactam antibiotics, including third-generation cephalosporins, which limits the options for antimicrobial therapy and results in increased morbidity and mortality and health care costs (5, 6). Infection control guidelines recommend prevention of the spread of ESBL-E in health care settings (7,8). Molecular typing has become an important tool in infection control, as it enables the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings. Different molecular typing methods have been used, ranging from fingerprintbased methods, like pulsed-field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP), to sequencebased methods, like multilocus sequence typing (MLST) (9-11). Although widely adopted, PFGE is labor-intensive and difficult to standardize and has limited interlaboratory reproducibility (12)(13)(14). AFLP is less time-consuming than PFGE but may have lower discriminatory power for typing of Enterobacteriaceae (13, 15). MLST targets 7 or 8 housekeeping genes, depending on the Ent...

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“…coli has not only high serotype diversity but also high genome plasticity. About 1,200 genes define its conserved core genome, but the pan-genome contains more than 13,000 gene families, and the number is still growing (25)(26)(27). In STEC, this is in part due to several major virulence factors being located on transmissible genetic elements like plasmids, pathogenicity islands, or bacteriophages.…”

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confidence: 99%

The Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle

Barth

Menge

Eichhorn

et al. 2016

Appl Environ Microbiol

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Shiga toxin-producing Escherichia coli (STEC) strains can colonize cattle for several months and may, thus, serve as gene reservoirs for the genesis of highly virulent zoonotic enterohemorrhagic E. coli (EHEC). Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. IMPORTANCERuminants, especially cattle, are sources of food-borne infections by Shiga toxin-producing Escherichia coli (STEC) in humans. Some STEC strains persist in cattle for longer periods of time, while others are detected only sporadically. Persisting strains can serve as gene reservoirs that supply E. coli with virulence factors, thereby generating new outbreak strains. Attempts to reduce the human risk for acquiring STEC infections should therefore include strategies to control such persisting STEC strains. By analyzing representative genes of their core and accessory genomes, we show that bovine STEC with a persistent colonization type emerged independently from sporadically colonizing isolates and evolved in parallel evolutionary branches. However, persistent colonizing strains share similar sets of accessory genes. Defining the genetic patterns that distinguish persistent from sporadically colonizing STEC isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level.

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Molecular characterization and phylogeny of Shiga toxin–producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing

Cited by 63 publications

References 38 publications

Molecular and Phylogenetic Characterization of Non-O157 Shiga Toxin-Producing Escherichia coli Strains in China

Molecular and Phylogenetic Characterization of Non-O157 Shiga Toxin-Producing Escherichia coli Strains in China

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

The Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle

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