Genomic Portrait of the Evolution and Epidemic Spread of a Recently Emerged Multidrug-Resistant Shigella flexneri Clone in China

Zhang, Nan; Lan, Ruiting; Sun, Qiang; Wang, Jianping; Wang, Yiting; Zhang, Jin; Yu, Deshan; Hu, Wanfu; Hu, Shoukui; Dai, Hongyue; Du, Pengcheng; Wang, Haiyin; Xu, Jianguo

doi:10.1128/jcm.02669-13

Cited by 22 publications

(26 citation statements)

References 39 publications

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“…The properties and the statistics of the genome are summarized in Additional file 1: Table S1. The resulting genomic size of strain SP1 was similar to previous studies within the range of 4.1–4.8 M bp [31, 32]. Similarly, CDSs numbers were close to the previous publication [31].…”

Section: Resultssupporting

confidence: 89%

Genome sequence of Shigella flexneri strain SP1, a diarrheal isolate that encodes an extended-spectrum β-lactamase (ESBL)

Shen

Fan

Guo

et al. 2017

Ann Clin Microbiol Antimicrob

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BackgroundShigellosis is the most common cause of gastrointestinal infections in developing countries. In China, the species most frequently responsible for shigellosis is Shigella flexneri. S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on biochemical and serological properties. Moreover, increasing numbers of ESBL-producing Shigella strains have been isolated from clinical samples. Despite this, only a few cases of ESBL-producing Shigella have been described in China. Therefore, a better understanding of ESBL-producing Shigella from a genomic standpoint is required. In this study, a S. flexneri type 1a isolate SP1 harboring blaCTX-M-14, which was recovered from the patient with diarrhea, was subjected to whole genome sequencing.ResultsThe draft genome assembly of S. flexneri strain SP1 consisted of 4,592,345 bp with a G+C content of 50.46%. RAST analysis revealed the genome contained 4798 coding sequences (CDSs) and 100 RNA-encoding genes. We detected one incomplete prophage and six candidate CRISPR loci in the genome. In vitro antimicrobial susceptibility testing demonstrated that strain SP1 is resistant to ampicillin, amoxicillin/clavulanic acid, cefazolin, ceftriaxone and trimethoprim. In silico analysis detected genes mediating resistance to aminoglycosides, β-lactams, phenicol, tetracycline, sulphonamides, and trimethoprim. The bla CTX-M-14 gene was located on an IncFII2 plasmid. A series of virulence factors were identified in the genome.ConclusionsIn this study, we report the whole genome sequence of a blaCTX-M-14-encoding S. flexneri strain SP1. Dozens of resistance determinants were detected in the genome and may be responsible for the multidrug-resistance of this strain, although further confirmation studies are warranted. Numerous virulence factors identified in the strain suggest that isolate SP1 is potential pathogenic. The availability of the genome sequence and comparative analysis with other S. flexneri strains provides the basis to further address the evolution of drug resistance mechanisms and pathogenicity in S. flexneri.Electronic supplementary materialThe online version of this article (doi:10.1186/s12941-017-0212-2) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 89%

Genome sequence of Shigella flexneri strain SP1, a diarrheal isolate that encodes an extended-spectrum β-lactamase (ESBL)

Shen

Fan

Guo

et al. 2017

Ann Clin Microbiol Antimicrob

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“…Wholegenome sequencing of 59 isolates of 14 serotypes indicated that ST91 arose around 1993 by acquiring multidrug resistance and had spread across China within a decade. These findings further suggest that multidrug resistance is the key selective pressure for the emergence of the S. flexneri epidemic clone and that Shigella epidemics in China were caused by a combination of local expansion and inter-regional spread of serotype Xv [60]. The data together underscore challenges to the current vaccine development and control strategies for shigellosis [45].…”

Section: S Suis St7 Emerged and Spread In Chinamentioning

confidence: 84%

Landscape of emerging and re-emerging infectious diseases in China: impact of ecology, climate, and behavior

Liu

et al. 2018

Front. Med.

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For the past several decades, the infectious disease profile in China has been shifting with rapid developments in social and economic aspects, environment, quality of food, water, housing, and public health infrastructure. Notably, 5 notifiable infectious diseases have been almost eradicated, and the incidence of 18 additional notifiable infectious diseases has been significantly reduced. Unexpectedly, the incidence of over 10 notifiable infectious diseases, including HIV, brucellosis, syphilis, and dengue fever, has been increasing. Nevertheless, frequent infectious disease outbreaks/events have been reported almost every year, and imported infectious diseases have increased since 2015. New pathogens and over 100 new genotypes or serotypes of known pathogens have been identified. Some infectious diseases seem to be exacerbated by various factors, including rapid urbanization, large numbers of migrant workers, changes in climate, ecology, and policies, such as returning farmland to forests. This review summarizes the current experiences and lessons from China in managing emerging and re-emerging infectious diseases, especially the effects of ecology, climate, and behavior, which should have merits in helping other countries to control and prevent infectious diseases.

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“…To determine whether the nonsense mutation in fimB is present in all S . flexneri strains, we analyzed results of two WGS projects, one encompassing 59 strains covering 14 serotypes (1a, 1b, 1d, 2a, 2b, 3a, 3b, 4a, 4av, 4b, X, Xv, Y and Yv) isolated from different provinces of China between 1997 and 2006 [ 40 ] and the other encompassing the 16 type strains covering all the established serotypes (1a, 1b, 1c, 2a, 2b, 3a, 3b, 3c, 4a, 4b, 5a, 5b, 6, X, Y and E1037) isolated from various regions between 1949 and 1972 and held at Public Health England (PHE) [ 41 ], as well as the sequence of the S . flexneri 2a strain NCTC1 isolated from a English soldier on the Western front in 1915 [ 37 ].…”

Section: Resultsmentioning

confidence: 99%

“…flexneri Chilean clinical isolates and the survey of the genome sequences and WGS results of over 80 S . flexneri strains from various origins [ 37 ], [ 40 ]- [ 41 ] indicated that the very same mutation in fimB is present in all S . flexneri strains, except strains of serotype 6.…”

Section: Discussionmentioning

confidence: 99%

“…flexneri CDC 796–83 (serotype 6), AERO01000069.1; S . flexneri collection of 59 strains covering 14 serotypes (1a, 1b, 1d, 2a, 2b, 3a, 3b, 4a, 4av, 4b, X, Xv, Y and Yv), AZOG00000000.1 to AZQM00000000.1 [ 40 ]; S . flexneri collection of the 16 type strains covering all the established serotypes (1a, 1b, 1c, 2a, 2b, 3a, 3b, 3c, 4a, 4b, 5a, 5b, 6, X, Y and E1037), ERS088060-ERS088076 [ 41 ]; S .…”

Section: Methodsmentioning

confidence: 99%

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Distinct Mutations Led to Inactivation of Type 1 Fimbriae Expression in Shigella spp.

et al. 2015

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Shigella spp. are responsible for bacillary dysentery in humans. The acquisition or the modification of the virulence plasmid encoding factors promoting entry of bacteria into and dissemination within epithelial cells was a critical step in the evolution of these bacteria from their Escherichia coli ancestor(s). Incorporation of genomic islands (GI) and gene inactivation also shaped interactions between these pathogens and their human host. Sequence analysis of the GI inserted next to the leuX tRNA gene in S. boydii, S. dysenteriae, S. flexneri, S. sonnei and enteroinvasive E. coli (EIEC) suggests that this region initially carried the fec, yjhATS and fim gene clusters. The fim cluster encoding type I fimbriae is systematically inactivated in both reference strains and clinical isolates and distinct mutations are responsible for this inactivation in at least three phylogenetic groups. To investigate consequences of the presence of fimbriae on the outcome of the interaction of Shigella with host cells, we used a S. flexneri strain harboring a plasmid encoding the E. coli fim operon. Production of fimbriae by this recombinant strain increased the ability of bacteria to adhere to and enter into epithelial cells and had no effect on their ability to disseminate from cell to cell. The observations that production of type I fimbriae increases invasion of epithelial cells and that independent mutations abolish fimbriae production in Shigella suggest that these mutations correspond to pathoadaptive events.

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Genomic Portrait of the Evolution and Epidemic Spread of a Recently Emerged Multidrug-Resistant Shigella flexneri Clone in China

Cited by 22 publications

References 39 publications

Genome sequence of Shigella flexneri strain SP1, a diarrheal isolate that encodes an extended-spectrum β-lactamase (ESBL)

Genome sequence of Shigella flexneri strain SP1, a diarrheal isolate that encodes an extended-spectrum β-lactamase (ESBL)

Landscape of emerging and re-emerging infectious diseases in China: impact of ecology, climate, and behavior

Distinct Mutations Led to Inactivation of Type 1 Fimbriae Expression in Shigella spp.

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