The Emergence of Quinolone Resistant Shigella sonnei, Pondicherry, India

Prevalence of plasmid-mediated quinolone resistance genes and biofilm formation in different species of quinolone-resistant clinical Shigella isolates: a cross-sectional study

BACKGROUND

The purpose of this study was to look into the presence of plasmid-mediated quinolone resistance (PMQR) genes and biofilm formation in several species of clinical Shigella isolates that were resistant to quinolones.

METHODS

The stool samples of 150 patients (younger than 10 years) with diarrhea were collected in this cross-sectional study (November 2020 to December 2021). After cultivation of samples on Hektoen Enteric agar and xylose lysine deoxycholate agar, standard microbiology tests, VITEK 2 system, and polymerase chain reaction (PCR) were utilized to identify Shigella isolates. The broth microdilution method was used to determine antibiotic susceptibility. PMQR genes including qnrA, qnrB, qnrC, qnrD, qnrE, qnrS, qnrVC, qepA, oqxAB, aac(6')-Ib-cr, and crpP and biofilm formation were investigated in quinolone-resistant isolates by PCR and microtiter plate method, respectively. An enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) technique was used to determine the clonal relatedness of quinolone-resistant isolates.

RESULTS

A total of 95 Shigella isolates including S. sonnei (53, 55.8%), S. flexneri (39, 41.1%), and S. boydii (3, 3.2%) were identified. The highest resistance rates of the isolates were against ampicillin (92.6%, n = 88/95). Overall, 42 of 95 (44.2%) isolates were simultaneously resistant against two or more quinolones including 26 (61.9%) S. sonnei and 16 (38.1%) S. flexneri. All isolates were multidrug-resistant (resistance to more than 3 antibiotics). The occurrence of PMQR genes was as follows: qnrS (52.4%), qnrA and aac(6')-Ib-cr (33.3%), and qnrB (19.0%). The prevalence in species was as follows: 61.5% and 37.5% (qnrS), 19.2% and 56.3% (qnrA), 38.5% and 25.0 (aac(6')-Ib-cr), and 19.2% and 18.8% (qnrB) for S. sonnei and S. flexneri, respectively. The other PMQR genes were not detected. In total, 52.8% (28/53) of quinolone-susceptible and 64.3% (27/42) of quinolone-resistant isolates were biofilm producers. Biofilm formation was not significantly different between quinolone-resistant and quinolone-susceptible isolates (P-value = 0.299). Quinolone-resistant isolates showed a high genetic diversity according to the ERIC-PCR.

CONCLUSION

It seems that qnrS, qnrA, and aac(6')-Ib-cr play a significant role in the quinolone resistance among Shigella isolates in our region. Also the quinolone-resistant S. flexneri and S. sonnei isolates had a high genetic diversity. Hence, antibiotic therapy needs to be routinely revised based on the surveillance findings.

Prevalence and changing antimicrobial resistance profiles of Shigella spp. isolated from diarrheal patients in Kolkata during 2011-2019

BACKGROUND

The primary aim of this study was to investigate the occurrence, characteristics, and antimicrobial resistance patterns of various Shigella serogroups isolated from patients with acute diarrhea of the Infectious Diseases Hospital in Kolkata from 2011-2019.

PRINCIPAL FINDINGS

During the study period, Shigella isolates were tested for their serogroups, antibiotic resistance pattern and virulence gene profiles. A total of 5.8% of Shigella spp. were isolated, among which S. flexneri (76.1%) was the highest, followed by S. sonnei (18.7%), S. boydii (3.4%), and S. dysenteriae (1.8%). Antimicrobial resistance against nalidixic acid was higher in almost all the Shigella isolates, while the resistance to β-lactamases, fluoroquinolones, tetracycline, and chloramphenicol diverged. The occurrence of multidrug resistance was found to be linked with various genes encoding drug-resistance, multiple mutations in the topoisomerase genes, and mobile genetic elements. All the isolates were positive for the invasion plasmid antigen H gene (ipaH). Dendrogram analysis of the plasmid and pulsed-field electrophoresis (PFGE) profiles revealed 70-80% clonal similarity among each Shigella serotype.

CONCLUSION

This comprehensive long-term surveillance report highlights the clonal diversity of clinical Shigella strains circulating in Kolkata, India, and shows alarming resistance trends towards recommended antibiotics. The elucidation of this study's outcome is helpful not only in identifying emerging antimicrobial resistance patterns of Shigella spp. but also in developing treatment guidelines appropriate for this region.

Molecular Characterization of Multidrug-Resistant Shigella flexneri

Due to their propensity for causing diarrheal illnesses and their rising susceptibility to antimicrobials, Shigella infections constitute a serious threat to global public health. This extensive study explores the frequency, antibiotic resistance, genetic evolution, and effects of Shigella infections on vulnerable groups. The research covers a wide range of geographical areas and sheds information on how the prevalence of Shigella species is evolving. Shigella strain antimicrobial resistance patterns are thoroughly examined. Multidrug resistance (MDR) has been found to often occur in investigations, especially when older antimicrobials are used. The improper use of antibiotics in China is blamed for the quick emergence of resistance, and variations in resistance rates have been seen across different geographical areas. Shigella strains' genetic makeup can be used to identify emerging trends and horizontal gene transfer's acquisition of resistance genes. Notably, S. sonnei exhibits the capacity to obtain resistance genes from nearby bacteria, increasing its capacity for infection. The study also emphasizes the difficulties in accurately serotyping Shigella strains due to inconsistencies between molecular and conventional serology. These results highlight the necessity of reliable diagnostic methods for monitoring Shigella infections. In conclusion, this study emphasizes how dynamic Shigella infections are, with varying patterns of occurrence, changing resistance landscapes, and genetic adaptability. In addition to tackling the rising problem of antibiotic resistance in Shigella infections, these findings are essential for guiding efforts for disease surveillance, prevention, and treatment.

Pathogenicity and virulence of Shigella sonnei: A highly drug-resistant pathogen of increasing prevalence

Shigella spp. are the causative agent of shigellosis (or bacillary dysentery), a diarrhoeal disease characterized for the bacterial invasion of gut epithelial cells. Among the 4 species included in the genus, Shigella flexneri is principally responsible for the disease in the developing world while Shigella sonnei is the main causative agent in high-income countries. Remarkably, as more countries improve their socioeconomic conditions, we observe an increase in the relative prevalence of S. sonnei. To date, the reasons behind this change in aetiology depending on economic growth are not understood. S. flexneri has been widely used as a model to study the pathogenesis of the genus, but as more research data are collected, important discrepancies with S. sonnei have come to light. In comparison to S. flexneri, S. sonnei can be differentiated in numerous aspects; it presents a characteristic O-antigen identical to that of one serogroup of the environmental bacterium Plesiomonas shigelloides, a group 4 capsule, antibacterial mechanisms to outcompete and displace gut commensal bacteria, and a poorer adaptation to an intracellular lifestyle. In addition, the World Health Organization (WHO) have recognized the significant threat posed by antibiotic-resistant strains of S. sonnei, demanding new approaches. This review gathers knowledge on what is known about S. sonnei within the context of other Shigella spp. and aims to open the door for future research on understanding the increasing spread of this pathogen.

Burden of Shigella in South Asia: a systematic review and meta-analysis

BACKGROUND

Shigella remains one of the most common causes of diarrhoea in South Asia. Current estimates of the prevalence of Shigella are critical for guiding control measures. We estimated the prevalence of Shigella species and serogroups in South Asia.

METHODS

We performed a systematic review using PubMed, EMBASE, Google Scholar and Web of Science for peer-reviewed studies published between 2000 and 19 June 2022. We also manually searched the reference lists of the reviewed studies to identify additional studies. We included studies that detected the presence of Shigella in stool by culture or polymerase chain reaction (PCR). Studies associated with outbreaks were excluded. Two investigators independently reviewed the studies, extracted the data and performed quality assessment. A random-effects meta-analysis was performed to determine the pooled prevalence of Shigella.

RESULTS

Our search yielded 5707 studies, of which 91 studies from five South Asian countries were included in the systematic review, 79 in the meta-analysis of Shigella prevalence and 63 in the meta-analysis of Shigella serogroups prevalence. The pooled prevalence of Shigella was 7% [95% confidence interval (CI): 6-7%], with heterogeneity (I2 = 98.7; P < 0.01). The prevalence of Shigella was higher in children aged <5 years (10%; 95% CI: 8-11%), in rural areas (12%; 95% CI: 10-14%) and in studies using PCR (15%; 95% CI: 11-19%). Shigella flexneri (58%) was the most abundant serogroup, followed by Shigella sonnei (19%), Shigella boydii (10%) and Shigella dysenteriae (9%). Shigella flexneri 2a was the most frequently isolated serotype (36%), followed by serotype 3a (12%), serotype 6 (12%) and serotype 1b (6%). The prevalence of non-typeable Shigella was 10.0%.

CONCLUSIONS

Although the prevalence of Shigella in South Asia remains generally high, it varies by age group and geographical area, with data lacking in some countries. Effective Shigella vaccines would be advantageous for both endemic communities and travellers.

Prevalence of Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Producing Shigella Species in Asia: A Systematic Review and Meta-Analysis

Shigellosis remains one of the leading causes of morbidity and mortality worldwide and is the second leading cause of diarrheal mortality among all age groups. However, the global emergence of antimicrobial-resistant Shigella strains, limiting the choice of effective drugs for shigellosis, has become the major challenge in the treatment of Shigella infections. The aim of this systematic review and meta-analysis was to provide an updated picture of the prevalence of antimicrobial-resistant Shigella species in Asia. A comprehensive and systematic search was performed on three electronic databases (PubMed, ScienceDirect and Scopus), in which 63 eligible studies published between 2010 and 2022 were identified. From our meta-analysis of proportions using a random-effects model, the overall prevalence of Shigella spp. in Asian patients was estimated to be 8.0% (95% CI: 5.5–10.5). The pooled prevalence rates of multidrug-resistant (MDR) and extended-spectrum beta-lactamase (ESBL)-producing Shigella strains were 68.7% (95% CI: 59.9–77.5) and 23.9% (95% CI: 12.9–34.8), respectively. Concerning recommended antimicrobial drugs for Shigella, the prevalence of resistance was highest for ciprofloxacin (29.8%) and azithromycin (29.2%), followed by ceftriaxone (23.8%), in spite of their importance as first- and second-line treatments for shigellosis. In contrast, resistance to carbapenems, such as ertapenem (0.0%), imipenem (0.1%) and meropenem (0.0%), was almost non-existent among the 49 tested antibiotics. The significantly high prevalence estimation suggests that the multidrug-resistant Shigella is a pressing threat to public health worthy of careful and justified interventions. Effective antibiotic treatment strategies, which may lead to better outcomes for the control and treatment of shigellosis in Asia, are essential.

Antimicrobial resistant Shigella in North India since the turn of the 21st century

PURPOSE

The ubiquitous presence and rampant spread of antibiotic resistant strains of Shigella spp is a major public health concern. Therefore, monitoring the trends of antimicrobial resistance in them is essential.

METHODS

A total of 15440 stool samples were inoculated on MacConkey agar, lysine deoxycholate agar and Selenite F enrichment broth from 2001 to 2015.Out of 491 shigellae isolated, 250 isolates were recovered from our culture collection. Antimicrobial susceptibility was performed by Kirby Bauer disc diffusion method, E-test and phenotypic resistance screening for ESBL and AmpC production was performed. For the detection of beta-lactamase genes, PCR for blaTEM, blaSHV, blaOXA, blaCTX-M-15, CMY-2 and mphA PCR in isolates with decreased susceptibility to azithromycin(DSA) was performed.

RESULTS

S. flexneri (n ​= ​173) was most common, followed by S.dysenteriae (n ​= ​24), S.sonnei (n ​= ​23), S.boydii (n ​= ​10) and Non agglutinating Shigella (NAG, n ​= ​20). A see-saw pattern in the prevalence of S. flexneri and S. dysenteriae and rising prevalence of S. sonnei and NAG was seen. Majority (77%) of the isolates had MICs >4 ​mg/L for ciprofloxacin and >50% had high MIC₉₀ (12 ​mg/L) for ceftriaxone and cefepime (8 ​mg/L). Nearly 20% of S.flexneri were resistant to third generation cephalosporin by disc diffusion and 33.7% had MIC ≥1 ​μg/mL. Among the ceftriaxone resistant isolates (n ​= ​29) the blaTEM beta-lactamase resistance gene was seen in all, blaCTX-M-15 in 37%, blaCMY-2 in 45.6% and blaOXA in 52%. The first report of DSA at our institute was in 2001 (n ​= ​1, 2.5%) which increased to 35.1% (n ​= ​40) in 2011-15. The isolates with DSA included S. flexneri (n ​= ​40), S. boydii (n ​= ​4) and S. sonnei (n ​= ​1) and plasmid mediated resistance to azithromycin by mphA gene was detected in 19 out of 40 isolates of S. flexneri.

CONCLUSION

Global emergence of resistance Shigella is a matter of concern and calls for systematic monitoring and periodic updates of countrywide and local antibiogram.

Virulence factors and molecular characteristics of Shigella flexneri isolated from calves with diarrhea

Background

The natural hosts of Shigella are typically humans and other primates, but it has been shown that the host range of Shigella has expanded to many animals. Although Shigella is becoming a major threat to animals, there is limited information on the genetic background of local strains. The purpose of this study was to assess the presence of virulence factors and the molecular characteristics of S. flexneri isolated from calves with diarrhea.

Results

Fifty-four S. flexneri isolates from Gansun, Shanxi, Qinghai, Xinjiang and Tibet obtained during 2014 to 2016 possessed four typical biochemical characteristics of Shigella. The prevalences of ipaH, virA, ipaBCD, ial, sen, set1A, set1B and stx were 100 %, 100 %, 77.78 %, 79.63 %, 48.15 %, 48.15 and 0 %, respectively. Multilocus variable number tandem repeat analysis (MLVA) based on 8 variable number of tandem repeat (VNTR) loci discriminated the isolates into 39 different MLVA types (MTs), pulsed field gel electrophoresis (PFGE) based on NotI digestion divided the 54 isolates into 31 PFGE types (PTs), and multilocus sequence typing (MLST) based on 15 housekeeping genes differentiated the isolates into 7 MLST sequence types (STs).

Conclusions

The findings from this study enrich our knowledge of the molecular characteristics of S. flexneri collected from calves with diarrhea, which will be important for addressing clinical and epidemiological issues regarding shigellosis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02277-0.

Epidemic and molecular characterization of fluoroquinolone-resistant Shigella dysenteriae 1 isolates from calves with diarrhea

Background

The widespread distribution of antimicrobial-resistant Shigella has become a recurrent challenge in many parts of the developing world. Previous studies indicate that the host of Shigella has expanded from humans to animals. This study aimed to investigate the prevalence of fluoroquinolone resistance and associated molecular characterization of S. dysenteriae 1 isolated from calves.

Results

All 38 unduplicated S. dysenteriae 1 isolates were collected from calves in Gansu Province from October 2014 to December 2016. According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. The most common STs identified were ST228 (34.21%, 13/38) and ST229 (39.47%, 15/38), which were first found in the present study. All isolates harbored virulence genes, and the incidence of the seven virulence genes were ipaH (100%), ipaBCD (92.11%), stx (73.68%), ial (57.89%), sen (28.95%), set1A and set1B (0%). According to the results of antimicrobial susceptibilities, 76.32% (29/38) were resistant to fluoroquinolone and showed multidrug resistance. In a study on the polymorphism of quinolone resistance–determining region (QRDR) of gyrA/B and parC/E genes, we identified two mutations in gyrA (Ser83 → Leu and Asp87 → Asn) and parC (Ser80 → Ile and Ser83 → Leu), respectively. Among them, 55.17% (16/29) of resistant strains had the gyrA point mutations (Ser83 → Leu) and parC point mutation (Ser83 → Leu). Moreover, 41.38% (12/29) of isolates had all five point mutations of gyrA and parC. In addition, the prevalence of the plasmid-mediated quinolone resistance (PMQR) determinant genes was also investigated. All 29 fluoroquinolone-resistant isolates were positive for the aac (6′)-Ib-cr gene but negative for qepA, except for SD001. In addition, only 6 (20.69%, 6/29) isolates harbored the qnr gene, including two with qnrB (6.90%, 2/29) and four with qnrS (13.79%, 4/29).

Conclusion

Given the increased common emergence of multidrug resistant isolates, uninterrupted surveillance will be necessary to understand the actual epidemic burden and control this infection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-020-02050-9.

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. 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.

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.

Spectrum of enteropathogens in cases of traveler's diarrhea that were detected using the FilmArray GI panel: New epidemiology in Japan

INTRODUCTION

Traveler's diarrhea (TD) is the most common illness among people traveling from resource-rich regions to resource-limited regions, although the precise microbial etiology is unclear in many cases.

METHODS

Stool specimens were prospectively collected from 106 consecutive patients with TD and 16 healthy controls without TD, and were tested using both the FilmArray gastrointestinal panel (BioFire Diagnostics) and conventional stool cultures.

RESULTS

The 106 patients had traveled to Southeast Asia (55 cases), South Asia (22 cases), Africa (11 cases), and East Asia (7 cases). Among the 106 specimens, 95 specimens (89.6%) were positive for pathogens during the FilmArray testing. The FilmArray testing also identified multiple pathogens in 75.8% of the specimens from positive cases. Conventional stool cultures only detected pathogens in 23.6% of the specimens.

CONCLUSION

The FilmArray gastrointestinal panel significantly improved the detection of enteropathogens and allowed for a rapid assessment of the TD's etiology. In addition, conventional stool cultures are likely to underestimate co-infections with multiple infectious pathogens.

Development of quinolone resistance and prevalence of different virulence genes among Shigella flexneri and Shigella dysenteriae in environmental water samples

The purpose of this study was to find out the mechanism of quinolone resistance in Shigella sp. isolated from environmental water samples from various parts of Kolkata, India. Out of 196 Shigella sp. isolated from 2014 to 2017, we selected 32 Shigella isolates for antimicrobial susceptibility tests. The minimum inhibitory concentrations (MIC) for quinolones ranged from 30 to 50 μg ml^-1 for ofloxacin, 5-20 μg ml^-1 for ciprofloxacin and 20-30 μg ml^-1 for norfloxacin. A few amino acid changes were found in quinolone resistance determining region (QRDR) of gyrA. Mutations in gyrA lead to a higher increment of MIC of quinolones. Among the plasmid-mediated (PMQR) quinolone resistance genes investigated, qnrB and aac(6')-lb-cr genes were found in all isolates. qnrA and qnrS were found in 25% and 62% of the isolates, respectively. ipaH gene was found in all of the isolates followed by the presence of other virulence genes ial, sen and stx1. Almost all the isolates having high MICs showed efflux pump activity in drug accumulation assay. All the mechanisms may or may not be present in a single strain. Several types of efflux pumps, presence of PMQR genes and mutations in drug target site of QRDR region may play the crucial role for resistance in our isolates.

Antimicrobial susceptibility profile & resistance mechanisms of Global Antimicrobial Resistance Surveillance System (GLASS) priority pathogens from India

Antimicrobial resistance is a major concern globally. Infections due to drug-resistant pathogens are becoming difficult and a challenge to treat. As treatment choices are limited due to the high-drug resistance rates, there is an increase in the health care cost, duration of hospital stay, morbidity and mortality rates. Understanding the true burden of antimicrobial resistance for a geographical location is important to guide effective empirical therapy. To have a national data, it is imperative to have a systemic data capturing across the country through surveillance studies. Very few surveillance studies have been conducted in India to generate national data on antimicrobial resistance. This review aims to report the cumulative antibiogram and the resistance mechanisms of Global Antimicrobial Resistance Surveillance System (GLASS) priority pathogens from India.

Molecular characterization of quinolone resistant Shigella spp. isolates from patients in Ardabil, Iran

BACKGROUND AND OBJECTIVES

Shigella is an etiological agent of shigellosis. Antibiotic therapy has a critical role in decreasing serious complications of shigellosis. The present study aimed to determine the multi-drug resistance strains and to detect fluoroquinolone related mutations.

MATERIALS AND METHODS

In this descriptive, cross sectional study, a total of 113 Shigella isolates were collected from 1280 patients admitted to Bu-Ali hospital in Ardabil province during 2015-17. Antibiotic resistance pattern of isolates was evaluated using Kirby Bauer method and finally, the MICs of ciprofloxacin were determined. In order to determine any mutations in QRDR region, parC and gyrA genes of resistant strains were amplified and sequenced.

RESULTS

Shigella spp. isolates were identified using ipaH amplification and rfc and wbgz genes were used for molecular detection of S. flexneri and S. soneii, respectively. Our results showed that the predominant species in Ardabil province was S. sonnei (69.91%). Most of isolates (82%) were resistant to trimethoprim/sulfamethoxazole (TMP/SMX); 51% were nalidixic acid resistant and 4.4% were floroquinolones resistant. All examined isolates were susceptible to imipenem (100%). Mutation in gyrA and parC genes were detected in all fluoroquinolone resistant isolates (5 isolates). Although, in this study the rate of resistance to ciprofloxacin was low, but in the lack of preventive strategy it will be a major challenge of public health in future.

CONCLUSION

This study provided information on the prevalence and antimicrobial susceptibility patterns of Shigella isolates in Ardabil province, Iran. Also this study showed a high-level of resistance to commonly used antibiotics among Shigella isolates.

Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei

Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent fluoroquinolone-resistant S. sonnei. We reaffirm that extant resistant organisms belong to a single clonal expansion event. Our results indicate that sequential accumulation of defining mutations (gyrA-S83L, parC-S80I, and gyrA-D87G) led to the emergence of the fluoroquinolone-resistant S. sonnei population around 2007 in South Asia. This clone was then transmitted globally, resulting in establishments in Southeast Asia and Europe. Mutation analysis suggests that the clone became dominant through enhanced adaptation to oxidative stress. Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance to the antimicrobial while the susceptible counterpart fails to attain complete resistance.

Shigella sonnei is one of the main species causing shigellosis worldwide. Here the authors analyse nearly 400 S. sonnei genome sequences and carry out experimental evolution experiments to shed light into the evolutionary processes underlying the recent emergence of fluoroquinolone resistance in this pathogen.

Shigella: Antibiotic-Resistance Mechanisms And New Horizons For Treatment

Shigella spp. are a common cause of diarrheal disease and have remained an important pathogen responsible for increased rates of morbidity and mortality caused by dysentery each year around the globe. Antibiotic treatment of Shigella infections plays an essential role in reducing prevalence and death rates of the disease. However, treatment of these infections remains a challenge, due to the global rise in broad-spectrum resistance to many antibiotics. Drug resistance in Shigella spp. can result from many mechanisms, such as decrease in cellular permeability, extrusion of drugs by active efflux pumps, and overexpression of drug-modifying and -inactivating enzymes or target modification by mutation. Therefore, there is an increasing need for identification and evolution of alternative therapeutic strategies presenting innovative avenues against Shigella infections, as well as paying further attention to this infection. The current review focuses on various antibiotic-resistance mechanisms of Shigella spp. with a particular emphasis on epidemiology and new mechanisms of resistance and their acquisition, and also discusses the status of novel strategies for treatment of Shigella infection and vaccine candidates currently under evaluation in preclinical or clinical phases.

Transferable Mechanisms of Quinolone Resistance from 1998 Onward

While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.

Extensive inter-strain diversity among clinical isolates of Shigella flexneri with reference to its serotype, virulence traits and plasmid incompatibility types, a study from south India over a 6-year period

Background

Shigella has evolved as a result of acquiring extragenetic material through horizontal gene exchange. These aid in the rapid emergence of bacterial inter-strain diversity in virulence factors and serotype variants through O-antigenic switching. Plasmid incompatibility typing of isolates is insightful in understanding local expansion of virulence plasmids, as whether virulence dissemination involves diverse plasmids or one dominant ‘epidemic’ type. The broad question underlying this study was that of how inter-strain genetic, serotype and plasmid incompatibility type variations can help understand the emergence of Shigella as a highly virulent pathogen.

Results

A total of 101 confirmed isolates of S. flexneri were included in this study. The distribution of the subtypes were variable, type 2a (48/101, 47.5%), type 6 (15/101, 14.9%), type 1b (8/101, 7.9%), type 1 variant (7/101, 6.9%), type 3b (12/101, 11.9% 0, type 4 (6/101, 6.0%), variant Y (2/101, 1.9%) and variant X (1/101, 1%). All had the ipaH gene (101/101, 100%) followed by ompA (92/101, 91.1%), ial (84/101, 83.4%), sen (82/101, 81.2%), virF (84/101, 83.2%), set1A and set1B (59/101, 58.4%). Out of the total of 49 isolates that showed all the virulence related genes studied here the IncIγ plasmid was detected in all isolates studied followed by FII (33/49, 67.3%), FIIS (20/49, 40.8%). Inc K was positive in two isolates (2/49, 4%) studied. The inc groups IncI1-α, Inc T were detected in 1 isolate each and Inc L and Inc P formed part of the multireplicon in the same isolate.

Conclusions

In order to estimate the burden of the disease caused by the new serotypes, it is important to have knowledge of the locally prevalent serotype. This will prove helpful in developing strategies for prevention of same especially since, the immunity in such diseases is serotype specific. Thus, the emergence of non-typable atypical serotypes of S. flexneri from natural infections needs to be investigated further. This study highlights the emergence of genetic variants exhibiting resistance to many antibiotics which needs to be studied for understanding the ever-changing landscape of this pathogen.

Electronic supplementary material

The online version of this article (10.1186/s13099-019-0314-9) contains supplementary material, which is available to authorized users.

Molecular characterization of fluoroquinolone and/or cephalosporin resistance in Shigella sonnei isolates from yaks

Background

Members of the genus Shigella are intestinal pathogens and a major cause of seasonal outbreaks of bacterial diarrhea worldwide. Although humans are the conventional hosts of Shigella species, expansion of the Shigella host range to certain animals was recently reported. To investigate the prevalence of Shigella sonnei (S. sonnei) in yaks and perform molecular characterization, we analyzed 1132 fresh yak diarrheal stool samples and collected a total of 44 S. sonnei isolates.

Results

We performed multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) with XbaI-digested DNA to study genetic relatedness among the 44 isolates, which were differentiated into 4 sequence types (STs) and 32 PFGE types (PTs). All isolates harbored virulence genes, and 87.36% tested positive for invasion plasmid antigen H (ipaH), invasion associated locus (ial) and the Shigella enterotoxin gene sen. According to the results of antimicrobial susceptibility tests, 45.45% (20/44) were resistant to fluoroquinolones and/or cephalosporin. By sequencing the quinolone resistance determining region (QRDR) genes, we identified double mutations in gyrA (Ser83-Leu and Asp87-Asn) and a single mutation in parC (Ser80-Ile). All 12 fluoroquinolone-resistant S. sonnei isolates tested positive for the aac(6′)-Ib-cr gene but negative for qepA. Three isolates harbored qnr genes, including two with qnrS and one with qnrB. In addition, three types of β-lactamase genes, bla_TEM-1, bla_OXA-1 and bla_CTX-M-14/79, were detected in cephalosporin-resistant isolates.

Conclusions

The findings of this study have enriched our knowledge of fluoroquinolone- and/or cephalosporin-resistant S. sonnei isolates from yaks, which has important public health significance.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1500-6) contains supplementary material, which is available to authorized users.

Out of Asia: the independent rise and global spread of fluoroquinolone-resistant Shigella

Shigella are ranked among the most prevalent aetiologies of diarrhoeal disease worldwide, disproportionately affecting young children in developing countries and high-risk communities in developed settings. Antimicrobial treatment, most commonly with fluoroquinolones, is currently recommended for Shigella infections to alleviate symptoms and control disease transmission. Resistance to fluoroquinolones has emerged in differing Shigella species (S. dysenteriae, flexneri and sonnei) since the turn of the 21st century, originating in endemic areas, and latterly spreading into non-endemic regions. Despite occurring independently, the emergence of fluoroquinolone resistance in these different Shigella species shares striking similarities regarding their epidemiology and resistance mechanisms. Here, we review and discuss the current epidemiology of fluoroquinolone-resistant Shigella species, particularly in the light of recent genomic insights.

Genotypic Diversity of Multidrug Resistant Shigella species from Iran

BACKGROUND

In many developing countries, shigellosis is endemic and also occurs in epidemics and treatment of multidrug-resistant (MDR) isolates are important. The aims of this study were to determine the antimicrobial susceptibility, prevalence of class 1 and 2 integrons and the clonal relatedness of isolates.

MATERIALS AND METHODS

Antimicrobial susceptibility tests were performed by disc diffusion method. Polymerase chain reaction (PCR)-sequencing technique was employed for detection and characterization of integrons. The genetic relatedness was evaluated by using enterobacterial repetitive intergenic consensus (ERIC) PCR.

RESULTS

There was a high percentage of resistance to trimethoprim-sulfamethoxazole (TMP/SMX) (93.7%), ampicillin (AMP) (87.3%), streptomycin (STR) (84.5%) and tetracycline (TET) (78.9%). Multidrug resistant phenotype was seen in 95.1% of total isolates. Most common MDR profile was TMP/SMX/STR/AMP resistant pattern. Among the 142 Shigella spp. analyzed in this study, 28 isolates were positive for class 1 integron with two types of gene cassette arrays (dfrA17/aadA5 = 31.7% and dfrA7 = 3.8%). The class 2 integron was more frequently detected among the isolates (94.7%) with dfrA1/sat1/aadA1 (69.4%) and dfrA1/sat1 (30.6%) gene cassettes. ERIC-PCR results showed 6, 5, 4 and 3 main genotypes among S. flexneri, S. sonnei, S. boydii and S. dysenteriae isolates, respectively.

CONCLUSIONS

Our findings revealed that multidrug resistant Shigella species with high prevalence of class 2 integron were very common in Iran. In addition, ERIC-PCR patterns showed limited variety of clones are responsible for shigellosis in the region of the study.

Frequency of Mutations in Quinolone Resistance-Determining Regions and Plasmid-Mediated Quinolone Resistance in Shigella Isolates Recovered from Pediatric Patients in Tehran, Iran: An Overlooked Problem

Fluoroquinolone (FQ) resistance in clinical isolates of Shigella species has been increasing reported in recent years. This study was carried out to find the mutations within the quinolone resistance-determining regions (QRDRs) and the prevalence of plasmid-mediated quinolone resistance (PMQR) determinants among the clinical isolates of Shigella sp. in Tehran, Iran. A total of 50 Shigella isolates were collected from five teaching therapeutic centers in Tehran, Iran and analyzed for antibiotic susceptibility over a period of 20 months from July 2015 to January 2017. The PCR and direct nucleotide sequencing were used for genetic alterations in the QRDRs. The PMQR genes were detected using PCR. The results revealed four types of mutations in the QRDR of gyrA: 20 (40%) had a S83L mutation, 1 (2%) had a S83A mutation, 2 (4%) had a D87G mutation, and 1 (2%) isolate had a D87Y mutation. Mutations were also found at codon N57D, D200N, and E210K in three isolates. Seven hospitalized children had qnrS determinants, and one isolates had the mutation S83A, while two isolates had double mutations at S83L and/or D87G (Ser83Leu and Asp-87Gly). The PMQR gene-positive isolates had the single replacement of serine with leucine. In hospitalized children, two isolates had two types of PMQR determinants (qnrS and qnrA) and (qnrS and qnrB) at once. The results of this study indicate that the emergence of strains with mutations in the QRDR regions and the capture of PMQR determinants in strains may lead to failure in therapy with FQ and the widespread emergence of strains with high-level FQ resistance.

Molecular characterization of antimicrobial resistance in clinical Shigella isolates during 2014 and 2015: trends in South India

BACKGROUND

Shigella species are an important cause of acute diarrheal disease worldwide. This study describes the prevalence of Shigella spp. serotypes and their resistance profile in Vellore, South India from 2014 to 2015.

METHODS

From 2014 to 2015, 338 Shigella strains were isolated from stool samples at Christian Medical College, Vellore, India. Identification and serotyping was carried out using standard protocols. Antimicrobial susceptibility testing was done against commonly used antibiotics. Multidrug resistance was detected in 157 isolates. A subset of 73 isolates was randomly characterized further for acquired antimicrobial resistance genes in this study.

RESULTS

The resistance profile of the study isolates varied by species and year. S. sonnei isolates were 100% resistant to all tested antibiotics in 2014, whereas in 2015, resistance was found for AMP-NAL-TAX-SXT-FIX. The resistance phenotypes among S. flexneri isolates for the year 2014 and 2015 were AMP-SXT-NAL-NOR-FIX-TAX and AMP-NAL-SXT-TAX-NOR-FIX respectively. Screening for antimicrobial resistance genes in S. flexneri found dhfr1A, sulII, bla_OXA, bla_TEM, bla_CTX-M-1,qnrB, qnrS and AmpC genes while S. sonnei were found to have only dhfr1A, sulII, bla_CTX-M-1 and qnrS genes respectively. Antimicrobial resistance genes were predominantly seen in AMP-SXT-NAL and AMP-SXT-NAL-NOR resistance phenotypes.

CONCLUSION

Shigella prevalence of 4.8% to 4.6% was documented between the years 2014 to 2015 in this study. We show evidence that resistance to commonly used antibiotics continues to increase among Shigella spp. in South India. The presence of qnrS and bla_CTX-M-15 in the study isolates further indicates the threat of spreading resistance to quinolones and third-generation cephalosporins.