High-Quality Draft Genome Sequences for Four Drug-Resistant or Outbreak-Associated Shigella sonnei Strains Generated with PacBio Sequencing and Whole-Genome Maps

Lindsey, Rebecca L.; Batra, Dhwani; Rowe, Lori A.; Loparev, Vladimir N.; Juieng, Phalasy; Garcia-Toledo, Lisley; Bicknese, Amelia; Stripling, Devon; Martin, Haley; Chen, Jessica; Strockbine, Nancy; Trees, Eija

doi:10.1128/genomea.00906-17

Cited by 3 publications

(3 citation statements)

References 2 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Pacific BioSciences sequencing was completed as previously described (Lindsey et al, 2017). Briefly, E. coli genomic DNA was extracted according to the manufacturer's protocol (Archive Pure, 5 Prime, Gaithersburg, MD).…”

Section: Sequencingmentioning

confidence: 99%

The Virulence of Escherichia coli O157:H7 Isolates in Mice Depends on Shiga Toxin Type 2a (Stx2a)-Induction and High Levels of Stx2a in Stool

Hauser

Atitkar

Petro

et al. 2020

Front. Cell. Infect. Microbiol.

Self Cite

View full text Add to dashboard Cite

In this study we compared nine Shiga toxin (Stx)-producing Escherichia coli O157:H7 patient isolates for Stx levels, stx-phage insertion site(s), and pathogenicity in a streptomycin (Str)-treated mouse model. The strains encoded stx 2a , stx 1a and stx 2a , or stx 2a and stx 2c. All of the strains elaborated 10 5-10 6 cytotoxic doses 50% (CD 50) into the supernatant after growth in vitro as measured on Vero cells, and showed variable levels of increased toxin production after growth with sub-inhibitory levels of ciprofloxacin (Cip). The stx 2a +stx 2c + isolates were 90-100% lethal for Str-treated BALB/c mice, though one isolate, JH2013, had a delayed time-to-death. The stx 2a + isolate was avirulent. Both an stx 2a and a recA deletion mutant of one of the stx 2a +stx 2c + strains, JH2010, exhibited at least a three-log decrease in cytotoxicity in vitro and both were avirulent in the mice. Stool from Str-treated mice infected with the highly virulent isolates were 10-to 100-fold more cytotoxic than feces from mice infected with the clinical isolate, JH2012, that made only Stx2a. Taken together these findings demonstrate that the stx 2a-phage from JH2010 induces to higher levels in vivo than does the phage from JH2012. The stx 1a +stx 2a + clinical isolates were avirulent and neutralization of Stx1 in stool from mice infected with those strains indicated that the toxin produced in vivo was primarily Stx1a. Treatment of mice infected with Stx1a+Stx2a+ isolates with Cip resulted in an increase in Stx2a production in vivo and lethality in the mice. Our data suggest that high levels of Stx2a in stool are predictive of virulence in mice.

show abstract

Section: Sequencingmentioning

confidence: 99%

The Virulence of Escherichia coli O157:H7 Isolates in Mice Depends on Shiga Toxin Type 2a (Stx2a)-Induction and High Levels of Stx2a in Stool

Hauser

Atitkar

Petro

et al. 2020

Front. Cell. Infect. Microbiol.

Self Cite

View full text Add to dashboard Cite

show abstract

“…A trimethoprim/sulfamethoxazole-resistant Shigella isolate was first reported in Japan [ 19 , 20 ], followed by the emergence of diverse resistant Shigella types [ 21 , 22 ]. Previous studies reported a frequent resistance to some of the commonly used antibiotics, such as ampicillin and tetracyclines, worldwide [ 23 – 25 ]. Recently, the resistance to quinolones and cephalosporins was reported as well [ 12 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

Dominant serotype distribution and antimicrobial resistance profile of Shigella spp. in Xinjiang, China

et al. 2018

View full text Add to dashboard Cite

Shigella represents one of the major diarrhea-inducing pathogens threatening public health, but its prevalence and antimicrobial resistance profile in Xinjiang Uygur Autonomous region, China, remains unclear. We conducted comprehensive investigation of Shigella serotype distribution and antimicrobial resistance pattern in Xinjiang, identifying 458 Shigella isolates between 2008 to 2014. Shigella flexneri was identified as predominant species, and several S. flexneri serotypes were isolated, including atypical serotypes 1c, 2c, and 4s. Dominant S. flexneri serotypes were 2a, 1b, 2b, and Xv, different from those generally dominant in China. A hybrid serotype pattern was observed, which included the major Chinese serotypes (2a, Xv) and those predominant in Pakistan (1b, 2b). Shigella sonnei was shown to have a lower frequency compared with that generally observed in China, but an increasing trend of infections associated with this pathogen was observed. Furthermore, a high frequency of drug resistance and different Shigella antimicrobial resistance patterns were demonstrated as well, including very severe resistance phenotypes, such as multidrug resistance and resistance to frontline antibiotics. Seventy-five cephalosporin-resistant Shigella isolates were frequently identified with the resistance determinants that can undergo horizontal transfer, such as blaOXA, blaTEM, blaCTX-M, and integrons, facilitating the development of cephalosporin resistance among Shigella subtypes. Additionally, genetic analyses demonstrated that all 86 quinolone-resistant S. flexneri isolates possess 3–4 mutation sites in quinolone resistance-determining regions, primarily contributing to their resistance to quinolone. However, S. sonnei isolates were not shown to be quinolone resistant. Co-resistance to cephalosporins and quinolones was detected in 17 S. flexneri isolates, and these isolates were additionally multidrug resistant and carried β-lactamase genes and quinolone-resistance determinants. As is demonstrated in this study, dominant serotypes of Shigella were distributed in unique trend with dangerous drug resistance patterns. Novel strategies are urgently required to prevent the development of drug resistance among diarrhea-inducing pathogens.

show abstract

“…We proceeded to validate our predictions experimentally by evaluating growth requirements of the predicted auxotrophs. We were able to obtain six E. coli (61)(62)(63)(64), three Yersinia (65), three Salmonella (66,67), three Shigella (68,69), and one Klebsiella (70) strain (Fig. 6).…”

Section: Experimental Validation Of Auxotrophies Highlight Technologicalmentioning

confidence: 99%

Metabolic and genetic basis for auxotrophies in Gram-negative species

Seif

Choudhary

Hefner

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Auxotrophies constrain the interactions of bacteria with their environment, but are often difficult to identify. Here, we develop an algorithm (AuxoFind) using genome-scale metabolic reconstruction to predict auxotrophies and apply it to a series of available genome sequences of over 1,300 Gram-negative strains. We identify 54 auxotrophs, along with the corresponding metabolic and genetic basis, using a pangenome approach, and highlight auxotrophies conferring a fitness advantage in vivo. We show that the metabolic basis of auxotrophy is species-dependent and varies with 1) pathway structure, 2) enzyme promiscuity, and 3) network redundancy. Various levels of complexity constitute the genetic basis, including 1) deleterious single-nucleotide polymorphisms (SNPs), in-frame indels, and deletions; 2) single/multigene deletion; and 3) movement of mobile genetic elements (including prophages) combined with genomic rearrangements. Fourteen out of 19 predictions agree with experimental evidence, with the remaining cases highlighting shortcomings of sequencing, assembly, annotation, and reconstruction that prevent predictions of auxotrophies. We thus develop a framework to identify the metabolic and genetic basis for auxotrophies in Gram-negatives.

show abstract

High-Quality Draft Genome Sequences for Four Drug-Resistant or Outbreak-Associated Shigella sonnei Strains Generated with PacBio Sequencing and Whole-Genome Maps

Abstract: Drug-resistant Shigella sonnei poses a clinical and public health challenge. We report here the high-quality draft whole-genome sequences of four outbreak-associated S. sonnei isolates; three were resistant to two or more antibiotics, and one was resistant to streptomycin only.

Cited by 3 publications

References 2 publications

The Virulence of Escherichia coli O157:H7 Isolates in Mice Depends on Shiga Toxin Type 2a (Stx2a)-Induction and High Levels of Stx2a in Stool

The Virulence of Escherichia coli O157:H7 Isolates in Mice Depends on Shiga Toxin Type 2a (Stx2a)-Induction and High Levels of Stx2a in Stool

Dominant serotype distribution and antimicrobial resistance profile of Shigella spp. in Xinjiang, China

Metabolic and genetic basis for auxotrophies in Gram-negative species

Contact Info

Product

Resources

About