Strain-specific Recovery of S. sonnei from Artificially Contaminated Baby Carrots: Enhancing Food-safety Investigations with a Customized Shigella Detection Method Based on Genomically predicted Antibiotic Resistance Traits.

Shigella spp. are Gram-negative gastrointestinal bacterial pathogens that cause bacillary dysentery or shigellosis in humans. Isolation of Shigella from outbreak-associated foods is often problematic due to the lack of selectivity of cultural enrichment broths. To facilitate Shigella recovery from foods, we have developed strain-specific enrichment media based on the genomically-predicted antimicrobial resistance (AMR) features of an outbreak-associated Shigella sonnei strain harboring resistance genes for streptomycin (STR) and trimethoprim (TMP). To assess performance of the method, baby carrots were artificially contaminated with the S. sonnei strain at low (2.4 CFU), medium (23.5 CFU), and high levels (235 CFU) along with 10-fold higher levels of a Shigella-inhibiting Escherichia coli strain. The target S. sonnei strain was successfully recovered from artificially-contaminated baby carrots when enriched in modified Tryptone Soya Broth (mTSB) supplemented with TMP, whereas Shigella was not recovered from Shigella broth (SB) or SB supplemented with STR. Quantitative PCR analysis indicated that supplementation of the enrichment broths with TMP or STR increased the relative proportion of S. sonnei in enrichment cultures, except at the lowest inoculation level for STR. Microbiome profiling of the baby carrot enrichment cultures conducted by 16S rRNA gene sequencing indicated that both SB-STR and mTSB-TMP repressed the growth of competing Enterobacteriaceae in the enrichment cultures, relative to SB without supplementation. Overall, improved Shigella recovery was achieved with the addition of the appropriate custom selective agent during cultural enrichments demonstrating that genomically informed custom selective enrichment of Shigella could be a valuable tool for supporting future foodborne shigellosis outbreak investigations.

Overcoming Microbial Inhibition of S. Sonnei Through the Exploitation of Genomically Predicted Antibiotic Resistance Profiles for the Development of Food Enrichment Media.

Linking outbreaks of Shigella spp. to specific foods is challenging due to poor selectivity of current enrichment media. We have previously shown that enrichment media, tailored to the genomically-predicted antimicrobial resistance (AMR) of Shiga toxigenic E. coli strains, enhances their isolation from foods. This study investigates the application of this approach for Shigella isolation. The AMR gene profiles of 21,908 published S. sonnei genomes indicated a high prevalence of genes conferring resistance to streptomycin (aadA, aph(3″)-Ib, aph(6)-Id, 92.8%), sulfonamides (sul1, sul2, 74.8%), and/or trimethoprim (dfrA, 96.2%). Genomic analysis and antibiotic susceptibility testing conducted with a panel of 17 outbreak-associated S. sonnei strains confirmed the correlation of AMR gene detection with resistance phenotypes. Supplementation of Shigella Broth (SB) with up to 400 µg/mL of trimethoprim or sulfadiazine did not suppress the growth of sensitive strains, whereas 100 µg/mL of streptomycin increased the selectivity of this broth. All three antibiotics increased the selectivity of modified Tryptone Soya Broth (mTSB). Based on these results, supplemented media formulations were developed and assessed by measuring the relative growth of S. sonnei in cultures coinoculated with a strain of bacteriocin-producing E. coli that is inhibitory to Shigella growth. S. sonnei was not recovered from cocultures grown in SB or mTSB without antibiotics. In contrast, media supplemented with streptomycin at 50 and 100 µg/mL, trimethoprim at 25 and 50 µg/mL, and sulfadiazine at 100 µg/mL increased the relative proportion of S. sonnei in postenrichment cultures. The enhanced recovery of resistant S. sonnei strains achieved in this study indicates that, in cases where genomic data are available for clinical S. sonnei isolates, customization of selective enrichment media based on AMR gene detection could be a valuable tool for supporting the investigation of foodborne shigellosis outbreaks.

Rapid emergence of extensively drug-resistant Shigella sonnei in France.

Shigella sonnei, the main cause of bacillary dysentery in high-income countries, has become increasingly resistant to antibiotics. We monitored the antimicrobial susceptibility of 7121 S. sonnei isolates collected in France between 2005 and 2021. We detected a dramatic increase in the proportion of isolates simultaneously resistant to ciprofloxacin (CIP), third-generation cephalosporins (3GCs) and azithromycin (AZM) from 2015. Our genomic analysis of 164 such extensively drug-resistant (XDR) isolates identified 13 different clusters within CIP-resistant sublineage 3.6.1, which was selected in South Asia ∼15 years ago. AZM resistance was subsequently acquired, principally through IncFII (pKSR100-like) plasmids. The last step in the development of the XDR phenotype involved various extended-spectrum beta-lactamase genes (blaCTX-M-3, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaCTX-M-134) carried by different plasmids (IncFII, IncI1, IncB/O/K/Z) or even integrated into the chromosome, and encoding resistance to 3GCs. This rapid emergence of XDR S. sonnei, including an international epidemic strain, is alarming, and good laboratory-based surveillance of shigellosis will be crucial for informed decision-making and appropriate public health action.

The Effect of Mutation in Lipopolysaccharide Biosynthesis on Bacterial Fitness.

This paper presents the genome sequence of a Shigella sonnei mutant strain (S. sonnei 4351) and the effect of mutation in lipopolysaccharide biosynthesis on bacterial fitness. Lipopolysaccharides are the major component of the outer leaflet of the Gram-negative outer membrane. We report here a frameshift mutation of the gene gmhD in the genome of S. sonnei 4351. The mutation results in a lack of epimerization of the core heptose while we also found increased thermosensitivity, abnormal cell division, and increased susceptibility to erythromycin and cefalexin compared to the S. sonnei 4303. Comparative genomic analysis supplemented with structural data helps us to understand the effect of specific mutations on the virulence of the bacteria and may provide an opportunity to study the effect of short lipopolysaccharides.

Shigella sonnei, an emerging multidrug-resistant sexually transmitted pathogen in Franche-Comté, France.

Shigella sonnei (S. sonnei) is sometimes sexually transmitted. Men, who have sex with men (MSM), may have sexual behaviours different from heterosexual population, and thus may be at risk for S. sonnei infection. We describe three cases of multidrug-resistant S. sonnei in MSM (one HIV-infected patient and two patients receiving pre-exposure prophylaxis against HIV). S. sonnei was isolated from stool specimens and all patients were successfully treated with parenteral third-generation cephalosporins following laboratory confirmation that the isolates were resistant to azithromycin. Two men (patients 2 and 3) were linked epidemiologically. These cases highlight the emergence of this pathogen and its association with some sexual behaviours among MSM in Franche-Comté, France.

Therapeutic target identification via differential genome analysis of antibiotic resistant Shigella sonnei and inhibitor evaluation against a selected drug target.

Shigella sonnei has been implicated in bloody diarrhea (accompanied by abdominal pain and fever) and is an emerging pathogen of concern, especially in developing countries. The major means of transmission is the fecal-oral route while sexual transmission has also been reported. In children, the impact might be stunted growth due to life-threatening illness. Resistance has been reported in this species for several types of antibiotics. In this study, we retrieved the antibiotic-resistant labeled whole genome sequences of the species from the PATRIC database and performed a pan-genome analysis to filter out core genes. Antibiotic resistance was studied in the core, accessory and unique genome. Core genes were utilized as seed substance for essentiality analysis and drug candidate assignment. Product of the gene aroG, i.e. chorismate biosynthetic process 3-deoxy-7-phosphoheptulonate synthase enzyme, responsible for aromatic amino acid family biosynthetic process, was taken for further downstream processing. Natural product libraries of flavonoids (n = 178), ZINC database derived inhibitor compounds of the 3-deoxy-7-phosphoheptulonate synthase enzyme (n = 112), and streptomycin compounds (n = 737) were docked to find out potent inhibitors, followed by dynamics simulation of 50 ns each for top compounds.. Physicochemical and ADMET profiling of the top compounds was done to analyze their safety for consumption. We propose that the top compounds: Phytoene from Streptomycin library and ZINC000036444158 (synonym:1,16-bis[(dihydroxyphosphinyl)oxy]hexadecane) from 3-deoxy-7-phosphoheptulonate synthase inhibitor library of ZINC database (and used as a control in this study) should be tested in vitro against Shigella sonnei, to fully determine their efficacy. This could add to the drying pipeline of potent drug molecules against emerging pathogens.

Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia.

Conventional disease surveillance for shigellosis in developing country settings relies on serotyping and low-resolution molecular typing, which fails to contextualise the evolutionary history of the genus. Here, we interrogated a collection of 1,804 Shigella whole genome sequences from organisms isolated in four continental Southeast Asian countries (Thailand, Vietnam, Laos, and Cambodia) over three decades to characterise the evolution of both S. flexneri and S. sonnei. We show that S. sonnei and each major S. flexneri serotype are comprised of genetically diverse populations, the majority of which were likely introduced into Southeast Asia in the 1970s-1990s. Intranational and regional dissemination allowed widespread propagation of both species across the region. Our data indicate that the epidemiology of S. sonnei and the major S. flexneri serotypes were characterised by frequent clonal replacement events, coinciding with changing susceptibility patterns against contemporaneous antimicrobials. We conclude that adaptation to antimicrobial pressure was pivotal to the recent evolutionary trajectory of Shigella in Southeast Asia.

Shigella sonnei: virulence and antibiotic resistance.

Shigella sonnei is the emerging pathogen globally, as it is the second common infectious species of shigellosis (bloody diarrhoea) in low- and middle-income countries (LMICs) and the leading one in developed world. The multifactorial processes and novel mechanisms have been identified in S. sonnei, that are collectively playing apart a substantial role in increasing its prevalence, while replacing the S. flexneri and other Gram-negative gut pathogens niche occupancy. Recently, studies suggest that due to improvement in sanitation S. sonnei has reduced cross-immunization from Plesiomonas shigelliodes (having same O-antigen as S. sonnei) and also found to outcompete the two major species of Enterobacteriaceae family (Shigella flexneri and Escherichia coli), due to encoding of type VI secretion system (T6SS). This review aimed to highlight S. sonnei as an emerging pathogen in the light of recent research with pondering aspects on its epidemiology, transmission, and pathogenic mechanisms. Additionally, this paper aimed to review S. sonnei disease pattern and related complications, symptoms, and laboratory diagnostic techniques. Furthermore, the available treatment reigns and antibiotic-resistance patterns of S. sonnei are also discussed, as the ciprofloxacin and fluoroquinolone-resistant S. sonnei has already intensified the global spread and burden of antimicrobial resistance. In last, prevention and controlling strategies are briefed to limit and tackle S. sonnei and possible future areas are also explored that needed more research to unravel the hidden mysteries surrounding S. sonnei.

Comparative genome analysis of 12 Shigella sonnei strains: virulence, resistance, and their interactions.

Shigellosis is a highly infectious disease that is mainly transmitted via fecal-oral contact of the bacteria Shigella. Four species have been identified in Shigella genus, among which Shigella flexneri is used to be the most prevalent species globally and commonly isolated from developing countries. However, it is being replaced by Shigella sonnei that is currently the main causative agent for dysentery pandemic in many emerging industrialized countries such as Asia and the Middle East. For a better understanding of S. sonnei virulence and antibiotic resistance, we sequenced 12 clinical S. sonnei strains with varied antibiotic-resistance profiles collected from four cities in Jiangsu Province, China. Phylogenomic analysis clustered antibiotic-sensitive and resistant S. sonnei into two distinct groups while pan-genome analysis reveals the presence and absence of unique genes in each group. Screening of 31 classes of virulence factors found out that type 2 secretion system is doubled in resistant strains. Further principle component analysis based on the interactions between virulence and resistance indicated that abundant virulence factors are associated with higher levels of antibiotic resistance. The result present here is based on statistical analysis of a small sample size and serves basically as a guidance for further experimental and theoretical studies.

An in-vitro study on a novel six-phage cocktail against multi-drug resistant-ESBL Shigella in aquatic environment.

Shigella spp. are water-borne pathogens responsible for mild to severe cases bacilli dysentery all around the world known as Shigellosis. The progressively increasing of antibiotic resistance among Shigella calls for developing and establishing novel alternative therapeutic methods. The present study aimed to evaluate a novel phage cocktail of lytic phages against extended spectrum beta lactamase isolates of Shigella species in an aquatic environment. The phage cocktail containing six novel Shigella specific phages showed a broad host spectrum. The cocktail was very stable in aquatic environment. The cocktail resulted in about 99% decrease in the bacterial counts in the contaminated water by several species and strains of Shigella such as Shigella sonnei, Shigella flexneri and Shigella dysenteriae. Achieving such a high efficiency in this in-vitro study demonstrates a high potential for in-vivo and in-situ application of this phage cocktail as a bio-controlling agent against Shigella spp. contamination and infections.

Phylogenetic and Evolutionary Analysis Reveals the Recent Dominance of Ciprofloxacin-Resistant Shigella sonnei and Local Persistence of S. flexneri Clones in India.

Shigella is the second leading cause of bacterial diarrhea worldwide. Recently, Shigella sonnei seems to be replacing Shigella flexneri in low- and middle-income countries undergoing economic development. Despite this, studies focusing on these species at the genomic level remain largely unexplored. Here, we compared the genome sequences of S. flexneri and S. sonnei isolates from India with the publicly available genomes of global strains. Our analysis provides evidence for the long-term persistence of all phylogenetic groups (PGs) of S. flexneri and the recent dominance of the ciprofloxacin-resistant S. sonnei lineage in India. Within S. flexneri PGs, the majority of the study isolates belonged to PG3 within the predominance of serotype 2. For S. sonnei, the current pandemic involves globally distributed multidrug-resistant (MDR) clones that belong to Central Asia lineage III. The presence of such epidemiologically dominant lineages in association with stable antimicrobial resistance (AMR) determinants results in successful survival in the community.IMPORTANCEShigella is the second leading cause of bacterial diarrhea worldwide. This has been categorized as a priority pathogen among enteric bacteria by the Global Antimicrobial Resistance Surveillance System (GLASS) of the World Health Organization (WHO). Recently, S. sonnei seems to be replacing S. flexneri in low- and middle-income countries undergoing economic development. Antimicrobial resistance in S. flexneri and S. sonnei is a growing international concern, specifically with the international dominance of the multidrug-resistant (MDR) lineage. Genomic studies focusing on S. flexneri and S. sonnei in India remain largely unexplored. This study provides information on the introduction and expansion of drug-resistant Shigella strains in India for the first time by comparing the genome sequences of S. flexneri and S. sonnei isolates from India with the publicly available genomes of global strains. The study discusses the key differences between the two dominant species of Shigella at the genomic level to understand the evolutionary trends and genome dynamics of emerging and existing resistance clones. The present work demonstrates evidence for the long-term persistence of all PGs of S. flexneri and the recent dominance of a ciprofloxacin-resistant S. sonnei lineage in India.

Screening of the Dichloromethane: Methanolic Extract of Centella asiatica for Antibacterial Activities against Salmonella typhi, Escherichia coli, Shigella sonnei, Bacillus subtilis, and Staphylococcus aureus.

Bacterial infections are responsible for a large number of deaths every year worldwide. On average, 80% of the African population cannot afford conventional drugs. Moreover, many synthetic antibiotics are associated with side effects and progressive increase in antimicrobial resistance. Currently, there is growing interest in discovering new antibacterial agents from ethnomedicinal plants. About 60% of the population living in developing countries depends on herbal drugs for healthcare needs. This study involved the screening of Centella asiatica commonly used by herbal medicine practitioners in Kisii County to treat symptoms related to bacterial infections. Standard bioassay methods were applied throughout the study. They included preliminary screening of dichloromethane: methanolic extract of Centella asiatica against human pathogenic bacteria including Salmonella typhi ATCC 19430, Escherichia coli ATCC 25922, Shigella sonnei ATCC 25931, Bacillus subtilis ATCC 21332, and Staphylococcus aureus ATCC 25923 using agar disc diffusion, broth microdilution method, and time-kill kinetics with tetracycline as a positive control. Phytochemical screening was carried out to determine the different classes of compounds in the crude extracts. Data were analyzed using one way ANOVA and means separated by Tukey's test. Dichloromethane: methanolic extract of Centella asiatica was screened against the selected bacterial strains. Time-kill kinetic studies of the extracts showed dose- and time-dependent kinetics of antibacterial properties. Phytochemical screening of the DCM-MeOH extract revealed the presence of alkaloids, flavonoids, phenolics, terpenoids, cardiac glycosides, saponins, steroids, and tannins. The present study indicates that the tested plant can be an important source of antibacterial agents and recommends that the active phytoconstituents be isolated, identified, and screened individually for activities and also subjected further for in vivo and toxicological studies.

A New Phage Cocktail Against Multidrug, ESBL-Producer Isolates of Shigella sonnei and Shigella flexneri with Highly Efficient Bacteriolytic Activity.

The globally increasing incidence of antibiotic resistance in pathogenic microorganisms such as Shigella, a cause of human acute gastrointestinal infections, calls for developing effective alternatives. In this study, the antibiotic resistance pattern, extended-spectrum ß-lactamase (ESBL)-production, and molecular characteristics of 70 multidrug-resistant isolates belong to the two most frequent species of Shigella genus, that is, Shigella sonnei (44 isolates) and Shigella flexneri (26 isolates) were investigated. These isolates were used to evaluate both specificity and activity of Shigella-specific bacteriophages, vB_SflS-ISF001, vB_SsoS-ISF002, and a cocktail of both. Twelve out of the 21 tested resistance genes were detected in the isolates. About 59% of S. sonnei and 46% of S. flexneri isolates were identified as ESBL producers. The bacteriophages showed a high efficiency of plating (EOP ≥0.5) in about 75% of the isolates. Moreover, the growth of >85% of the isolates was inhibited by the phage cocktail of vB_SflS-ISF001 and vB_SsoS-ISF002. The phage cocktail was effective against a wide range of ESBL-positive and -negative isolates of S. sonnei and S. flexneri. Therefore, this phage cocktail has the potential to inhibit or significantly decrease the spread of drug-resistant Shigella in humans, food chains, and water/wastewater sanitation systems.

Commensal Escherichia coli are a reservoir for the transfer of XDR plasmids into epidemic fluoroquinolone-resistant Shigella sonnei.

Despite the sporadic detection of fluoroquinolone-resistant Shigella in Asia in the early 2000s and the subsequent global spread of ciprofloxacin-resistant (cipR) Shigella sonnei from 2010, fluoroquinolones remain the recommended therapy for shigellosis1-7. The potential for cipR S. sonnei to develop resistance to alternative second-line drugs may further limit future treatment options8. Here, we aim to understand the evolution of novel antimicrobial resistant (AMR) S. sonnei variants after introduction into Vietnam. We found that cipR S. sonnei displaced the resident ciprofloxacin-susceptible (cipS) lineage while rapidly acquiring additional resistance to multiple alternative antimicrobial classes. We identified several independent acquisitions of extensively drug-resistant/multidrug-resistant-inducing plasmids, probably facilitated by horizontal transfer from commensals in the human gut. By characterizing commensal Escherichia coli from Shigella-infected and healthy children, we identified an extensive array of AMR genes and plasmids, including an identical multidrug-resistant plasmid isolated from both S. sonnei and E. coli in the gut of a single child. We additionally found that antimicrobial usage may impact plasmid transfer between commensal E. coli and S. sonnei. These results suggest that, in a setting with high antimicrobial use and a high prevalence of AMR commensals, cipR S. sonnei may be propelled towards pan-resistance by adherence to outdated international treatment guidelines.

Isolation of ß-glucan from Eleusine coracana and its antibiofilm, antidiabetic, antioxidant, and biocompatible activities.

Eleusine coracana (Finger millet) has high nutritional value with numerous health benefits and is of low cost. Isolation of beta-glucan (ßG) from E. coracana (Ec-ßG) has gained increasing research attention. UV-vis spectroscopy used to measure the surface plasmon resonance at 361 nm to confirm the presence of polysaccharides (glucan molecules) in Ec-ßG. X-ray diffraction analysis of Ec-ßG displayed a crystalline nature and confirmed the presence of the ßG molecule. Further, the bioactive compounds of Ec-ßG were screened using gas chromatography-mass spectrometry. The antibacterial activity of Ec-ßG against both Gram-positive (Lysinibacillus fusiformis, Enterococcus faecalis) and Gram-negative (Proteus vulgaris, Shigella sonnei) bacteria were assessed through minimum inhibitory concentrations <70 µg/ml of Ec-ßG. In addition, the antibiofilm activity and bacterial viability of Ec-ßG at 100 µg/ml was confirmed by light and confocal laser scanning microscopy. Furthermore, Ec-ßG inhibits α-amylase and α-glucosidase at an IC50 -value of 1.23 and 1.42 µg/ml, respectively. Superoxide anion scavenging activity at IC50-1.4 µg/ml and DPPH radical scavenging activity at IC50-1.2 µg/ml showed that Ec-ßG had potential antioxidant property. The in vitro hemolysis assay for biocompatibility of Ec-ßG at 200 µg/ml showed 0.06 ± 0.09%. Therefore, Ec-ßG has the potential to act as a suggestive agent for antibacterial, antidiabetic, and antioxidant activity.

[Epidemiological and pathogenic features of a bacillary dysentery outbreak in a boarding school caused by Shigella sonneri].

Objective: To investigate the etiologic and epidemiologic features of an infectious diarrhea outbreak in a boarding school in Fuyang city, Anhui province. Methods: Traceability hypothesis of this study was tested according to the epidemiological characteristics of the cases. Feces, anal swabs, water samples and food residues related to the patients and chefs were collected for pathogen isolation and detection. Biochemical identification, virulence gene detection, drug susceptibility test, PFGE and multilocus sequence typing were performed. Results: The incidence rate (3.41%) of different dormitory buildings within the water supply area by shallow wells was higher than that (0.98%) of the deep wells, with statistical significance (χ(2)=17.215, P<0.001). Sixteen strains belonged to the Shigella Sonneri family were isolated from the patient's samples, and all carrying the ipaH gene. Seven strains belonged to sen and ial genes. Set1 gene that did not appear in all the 16 strains were highly resistant to ampicillin, tetracycline, compound xinnomine, cefazoline, cefotaxime, gentamicin, naphthidinic acid and streptomycin, including 9 strains to doxycycline. The pulse field pattern of the 16 strains of Shigella sonneri appeared the same, with the ST type as ST152. Conclusion: When combined data from the etiological and epidemiological investigation, it was confirmed that Shigella sonneri was the pathogen of this outbreak, and water from the shallow wells might be responsible for the source of infection.

The role of international travellers in the spread of CTX-M-15-producing Shigella sonnei in the Republic of Korea.

BACKGROUND: Multidrug-resistant Shigella isolates have recently emerged as a serious public health threat worldwide. In particular, overseas travel is a risk factor for acquisition of antimicrobial-resistant Shigella strains. To explore the role of travel in the spread of cefotaxime-resistant Shigella sonnei in Korea, we screened 751 Shigella spp. isolates from 2007 to 2016 through the National Surveillance system, and 28 cephalosporin-resistant S. sonnei isolates were identified. METHODS: For cephalosporin-resistant S. sonnei isolates, epidemiological and molecular analyses (plasmid structure analysis, pulsed-field gel electrophoresis (PFGE) and high-quality single-nucleotide polymorphisms (hqSNPs) based on whole-genome sequencing (WGS)) were conducted to investigate the source of infection and transmission route. RESULTS: Among the 28 cefotaxime-resistant S. sonnei strains, 18 were isolated from travellers returning from Asia, including Vietnam (n=11). Molecular analysis of 18 blaCTX-M-type isolates revealed that 15 contain CTX-M-15; 50% of isolates from domestic patients contain CTX-M-14. Analysis of the genetic environments of the blaCTX-M-14 and blaCTX-M-15 genes revealed different genetic organization surrounding the blaCTX-M genes. Additionally, PFGE and hqSNP results suggested a large phylogenetic distance between the S. sonnei isolates related to overseas travel and those acquired domestically in Korea. CONCLUSION: Our study data demonstrates that two prevalent blaCTX-M genes, blaCTX-M-14 and blaCTX-M-15, have been circulating in S. sonnei in Korea over the last 10 years. Recently, international travellers are at a high risk for acquisition of CTX-M-15-producing S. sonnei in Korea.

Dissemination of Multidrug-Resistant Shigella flexneri and Shigella sonnei with Class 1, Class 2, and Atypical Class 1 Integrons in China.

Background: Emergence of multidrug-resistant Shigella, a major causative agent of bacterial dysentery, has generated many concerns not only in China but also worldwide. However, the prevalence of Shigella resistance caused by integron in the nonpopular season of diarrhea is not clear. Materials and Methods: Thirty-one Shigella flexneri and 22 Shigella sonnei samples collected in December 2010 from 10 cities of China were characterized for antimicrobial susceptibility, gene cassettes, widespread of integrons, and pulsed-field gel electrophoresis (PFGE) profile. Results: Multidrug resistance (MDR) was detected in 29 (93.5%) S. flexneri and 20 (90.9%) S. sonnei isolates. Class 1 integrons were detected in 25 (80.6%) S. flexneri and in 13 (59.1%) S. sonnei isolates; class 2 integrons were detected in 26 (83.9%) S. flexneri and in 19 (86.4%) S. sonnei isolates. Interestingly, the atypical class 1 integrons were mostly detected in S. flexneri (45.2%) isolates, whereas in only 1 (4.5%) S. sonnei isolate. DNA sequencing revealed two novel cassette arrays, dfrA5 and aacA4-cmlA, of class 1 integrons in S. flexneri, and dfrA17-aadA5 in S. sonnei isolates. The cassette arrays, dfrA1-sat1-aadA1 of class 2 integron and blaoxa-30-aadA1 of atypical class 1 integron, were also identified. PFGE profiles demonstrated A6 subtype of S. flexneri strains prevalent in Shanghai, Changchun, Jinan, and Changsha; and F6 subtype of S. sonnei prevalent in Jinan, Changchun, and Shanghai. Conclusion: The dissemination of MDR Shigella strains with integrons makes it an increasing public health problem in China. Increased surveillance and the development of adequate prevention strategies are warranted.

Use of whole genome sequencing in surveillance for antimicrobial-resistant Shigella sonnei infections acquired from domestic and international sources.

Shigella species are a major cause of gastroenteritis worldwide, and Shigella sonnei is the most common species isolated within the United States. Previous surveillance work in Pennsylvania documented increased antimicrobial resistance (AMR) in S. sonnei associated with reported illnesses. The present study examined a subset of these isolates by whole genome sequencing (WGS) to determine the relationship between domestic and international isolates, to identify genes that may be useful for identifying specific Global Lineages of S. sonnei and to test the accuracy of WGS for predicting AMR phenotype. A collection of 22 antimicrobial-resistant isolates from patients infected within the United States or while travelling internationally between 2009 and 2014 was chosen for WGS. Phylogenetic analysis revealed both international and domestic isolates were one of two previously defined Global Lineages of S. sonnei, designated Lineage II and Lineage III. Twelve of 17 alleles tested distinguish these two lineages. Lastly, genome analysis was used to identify AMR determinants. Genotypic analysis was concordant with phenotypic resistance for six of eight antibiotic classes. For aminoglycosides and trimethoprim, resistance genes were identified in two and three phenotypically sensitive isolates, respectively. This article contains data hosted by Microreact.