Prevalence, resistance patterns, and characterization of integrons of Shigella flexneri isolated from Jiangsu Province in China, 2001-2011

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.

Outbreak of multi-drug-resistant (MDR) Shigella flexneri in northern Australia due to an endemic regional clone acquiring an IncFII plasmid

Epidemiological surveillance of Shigella spp. in Australia is conducted to inform public health response. Multi-drug resistance has recently emerged as a contributing factor to sustained local transmission of Shigella spp. All data were collected as part of routine public health surveillance, and strains were whole-genome sequenced for further molecular characterisation. 108 patients with an endemic regional Shigella flexneri strain were identified between 2016 and 2019. The S. flexneri phylogroup 3 strain endemic to northern Australia acquired a multi-drug resistance conferring blaDHA plasmid, which has an IncFII plasmid backbone with virulence and resistance elements typically found in IncR plasmids. This is the first report of multi-drug resistance in Shigella sp. in Australia that is not associated with men who have sex with men. This strain caused an outbreak of multi-drug-resistant S. flexneri in northern Australia that disproportionality affects Aboriginal and Torres Strait Islander children. Community controlled public health action is recommended.

Prevalence and characterisation of third-generation cephalosporin-resistant Shigella flexneri isolates from Jiangsu Province, China, 2013-2015

OBJECTIVES

The aim of this study was to assess the prevalence of Shigella flexneri resistance to third-generation cephalosporins (3GCs) and to characterise the underlying resistance mechanisms.

METHODS

A total of 282 S. flexneri strains isolated in 2013-2015 in Jiangsu Province, China, were identified, serotyped and analysed for their susceptibility to 3GCs. The bla_TEM, bla_SHV, bla_OXA-1-like and bla_CTX-M-type extended-spectrum β-lactamase (ESBL) genes were amplified and sequenced by PCR.

RESULTS

Of the 282 S. flexneri strains, 97 (34.4%) were resistant to cefotaxime, from which 68 (24.1%) were also resistant to ceftazidime. ESBL genes were detected in 73/97 isolates (75.3%), of which 66/73 (90.4%) showed resistance to 3GCs. Of the 73 ESBL-positive isolates, 32 (43.8%) were positive for CTX-M-1 group (17 for CTX-M-55, 4 for CTX-M-3, 1 for CTX-M-15, 3 for CTX-M-79 and 7 for CTX-M-123), 31 (42.5%) were positive for CTX-M-9 group (29 for CTX-M-14, 1 for CTX-M-24 and 1 for CTX-M-27), 25 (34.2%) were positive for TEM-types (21 for TEM-1 and 4 for TEM-1b) and 1 (1.4%) was positive for SHV-type (SHV-12); none were positive for CTX-M-2 group, CTX-M-8 group and OXA-type.

CONCLUSION

ESBLs play an important role in Shigella resistance to 3GCs. CTX-M-14 and CTX-M-55 appeared to be the dominant ESBLs in 13 cities of Jiangsu Province. Therefore, it is time to regularly monitor resistance of S. flexneri to 3GCs and to take appropriate measures to manage this problem.

Molecular analysis of multidrug resistance in clinical isolates of Shigella spp. from 2001-2010 in Kolkata, India: role of integrons, plasmids, and topoisomerase mutations

To understand the genetic basis of high drug resistance in Shigella, 95 clinical isolates of Shigella spp. (2001-2010) were obtained from the Infectious Diseases Hospital, Kolkata, India. Ninety-three isolates were resistant to three or more antibiotics. Resistance to nalidixic acid, trimethoprim, streptomycin, and co-trimoxazole was most common in this population. Dendrogram analysis showed that S. sonnei strains were more clonally related when compared to the other Shigella species. The role of mobile genetic elements and chromosome-borne resistance factors was analyzed in detail. Integron analysis indicated the preponderance of class 2 and atypical class 1 integrons in that population. Typical class 1 integron was present in only one S. sonnei isolate and harbored trimethoprim resistance-encoding gene dfrV, while atypical class 1 integrons harbored dfrA1-aadA or bla_OXA-aadA gene cassettes responsible for resistance to trimethoprim, aminoglycosides, and β-lactams. Class 2 integrons harbored either dfrA1-sat-aadA or dfrA1-sat gene cassettes. Most importantly, a novel gene cassette array InsE-InsO-dfrA1-sat was found in class 2 integron of S. sonnei NK4846. Many of the resistance traits for antibiotics such as trimethoprim, co-trimoxazole, kanamycin, ampicillin, and tetracycline were transferred from parent Shigella isolates to recipient Escherichia coli during conjugation, establishing the role of plasmids in horizontal transfer of resistance genes. Multiple mutations such as S₈₀→I, S₈₃→L, and D₈₇→G/N/Y in quinolone resistance determining regions of topoisomerases from the representative quinolone-resistant isolates could explain the spectrum of minimal inhibitory concentration values for various quinolones. To the best of our knowledge, this is the first comprehensive report that describes the contribution of mobile (plasmids, integrons, and quinolone resistance genes named qnr) and innate genetic elements (mutations in topoisomerases) in determining the resistance phenotype of all the four species of Shigella over a span of ten years.

Integrons in Enterobacteriaceae: diversity, distribution and epidemiology

Integrons are versatile gene acquisition systems that allow efficient capturing of exogenous genes and ensure their expression. Various classes of integrons possessing a wide variety of gene cassettes are ubiquitously distributed in enteric bacteria worldwide. The epidemiology of integrons associated multidrug resistance in Enterobacteriaceae is rapidly evolving. In the past two decades, the incidence of integrons in enteric bacteria has increased drastically with evolution of multiple gene cassettes, novel gene arrangements and complex chromosomal integrons such as Salmonella genomic islands. This review focuses on the distribution, versatility, spread and global trends of integrons among important members of the Enterobacteriaceae, including Escherichia coli, Klebsiella, Shigella and Salmonella, which are known to cause infections globally. Such a comprehensive understanding of integron-associated antibiotic resistance, their role in the spread of such resistance traits and their clinical relevance especially with regard to each genus individually is paramount to contain the global spread of antibiotic resistance.

Newest data on fluoroquinolone resistance mechanism of Shigella flexneri isolates in Jiangsu Province of China

Background

To determine the prevalence, antimicrobial susceptibility patterns and related presence of mutations in quinolone resistance-determining region (QRDR) genes and plasmid-mediated quinolone resistance (PMQR) among Shigella flexneri isolates obtained from Jiangsu Province, China.

Methods

A total of 400 Shigella flexneri clinical isolates collected during 2012–2015 were identified by biochemical and serological methods, and the antimicrobial susceptibility pattern was evaluated using the disc-diffusion method. PCR and DNA sequencing were accomplished to identify mutations in gyrA, gyrB, parC and parE, and the presence of qnrA, qnrB, qnrC, qnrD, qnrS, qepA and aac(6′)-Ib-cr genes were also detected.

Results

Of all the Shigella flexneri, 75.8% were resistant to nalidixic acid, and 37.0% were categorized as norfloxacin resistant. Overall, 75.5% of isolates possessed gyrA mutations (Ser83Leu, Asp87Gly/Asn and His211Tyr), while 84.3% had parC mutations (Ser80Ile, Ala81Pho, Gln91His and Ser129Pro). The most prevalent point mutations in gyrA and parC were Ser83Leu (75.5%, 302/400) and Ser80Ile (74.5%, 298/400), relatively. Besides, the Gln517Arg alternation in gyrB was detected in 13 S. flexneri isolates and no mutations were identified in parE. PMQR determinations of qnrB, qnrS and aac(6′)-Ib-cr were detected among 16 strains (4.0%).

Conclusions

The results presented here show that fluoroquinolone resistance in these clinical isolates result from mutations in chromosome, besides, despite the low prevalence of PMQR determinants in Jiangsu, it is essential to continue surveillance PMQR determinants in this area.

A 10-year surveillance of antimicrobial susceptibility patterns in Shigella sonnei isolates circulating in Jiangsu Province, China

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Long-term multicentre surveillance of antimicrobial susceptibility patterns in Shigella sonnei.

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Epidemic clones and integron types and resistance gene cassettes were characterised.

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PFGE indicated large-scale clonal transmission among different cities occurred several times during 10 years.

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Class 1, 2 and atypical class 1 integrons were detected in S. sonnei.

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High prevalence of integrons and gene cassettes was related to the increasing antimicrobial resistance.

Objectives

The rapid emergence of drug-resistant Shigella sonnei is a serious public health problem. This study aimed to characterise the antimicrobial resistance patterns, molecular subtypes, and integron types and resistance gene cassettes in S. sonnei from Jiangsu Province, China.

Methods

In total, 340 S. sonnei were collected in 2002–2011 throughout Jiangsu Province. Antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), PCR amplification of integrons, restriction fragment length polymorphism (RFLP) and DNA sequencing of cassette regions were performed.

Results

Resistance rates to ampicillin (67.7%), nalidixic acid (75.2%), tetracycline (73.7%) and trimethoprim/sulfamethoxazole (68.7%) remained high. Strains from Centre and South Jiangsu showed higher resistance and multiresistance rates compared with the North. PFGE analysis indicated that large-scale clonal transmission among different cities occurred several times during 10 years. Among all strains, 55.9% (190/340) harboured class 1 integrons, 80.3% (273/340) harboured class 2 integrons and 49.4% (168/340) harboured an atypical class 1 integron. Resistance rates to nine antimicrobials in the class 1 integron-positive group were significantly higher than in the negative group (P < 0.05). Seven different gene cassettes were detected in class 1 integrons. The most prevalent type was aacA4–cmlA1 (114/286). Class 2 integrons carried the gene cassette array dfrA1–sat1–aadA1, and the atypical class 1 integron carried bla_OXA-30–aadA1.

Conclusions

The increasing antimicrobial resistance and significant clonal transmission of S. sonnei circulating in Jiangsu were closely related to the high prevalence of integrons and gene cassettes. Long-term cross-regional monitoring of antimicrobial resistance is urgently required for S. sonnei.

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

BACKGROUND

Shigellosis 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 bla_CTX-M-14, which was recovered from the patient with diarrhea, was subjected to whole genome sequencing.

RESULTS

The 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.

CONCLUSIONS

In this study, we report the whole genome sequence of a bla_CTX-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.

An 11-year study of shigellosis and Shigella species in Taiyuan, China: Active surveillance, epidemic characteristics, and molecular serotyping

A hospital-based surveillance of shigellosis was conducted in Taiyuan from 2005 to 2015. A total of 2655 stool cultures were collected from patients with diarrhea, 115 were identified as S. flexneri and 107 were S. sonnei. The highest infection rates were found among children under 5 years of age (34.2 %), and during the summer (61.0 %). ​Six serotypes were identified among S. flexneriisolates:1a, 2a, 2b, Xv, X and Y. Serotype 2a and Xv were the dominant serotypes in two periods, 2012-2015 and 2005-2008, respectively. High shigellosis rates over the past decade highlight shigellosis is still a major public health problem in Taiyuan.