Novel mutations in quinolone resistance-determining regions of gyrA, gyrB, parC and parE in Shigella flexneri clinical isolates from eastern Chinese populations between 2001 and 2011

Concordance between Genotypic and Phenotypic Drug-Resistant Profiles of Shigella Isolates from Taiyuan City, Shanxi Province, China, 2005 to 2016

Antimicrobial resistance in Shigella spp. is a global public health concern. In this study, the AMR phenotypic profiles of 10 kinds of antibiotics were compared with the genotypic profiles using genomic analysis of 218 Shigella isolates from Taiyuan City, Shanxi Province, China, 2005 to 2016. Core genome Multilocus Sequence Typing (cgMLST) based on the EnteroBase Escherichia/Shigella scheme was used to obtain the genetic relatedness of Shigella isolates. Multiple-drug resistance was observed in 96.79% Shigella spp., and the resistance to antimicrobial agents varied between S. flexneri and S. sonnei. The genotypic results correlated well with the phenotypic profiles with concordance rates of 96.42% and 94.50% in S. flexneri and S. sonnei isolates, respectively, from Taiyuan City, Shanxi Province. The sensitivity and specificity of the genotypic antimicrobial susceptibility testing (AST) were 97.56% and 95.34% for S. flexneri, and 95.65% and 93.31% for S. sonnei isolates, respectively. A discrepancy of genotypic and phenotypic AST results existed in some cephalosporin- and azithromycin-resistant Shigella isolates; there were no clear resistance patterns to predict ciprofloxacin resistance. There were major discrepancies between genotypic and phenotypic AST in the genotypically resistant but phenotypically susceptible isolates. The drug-resistance patterns and essential drug-resistance genes to predict the phenotypic drug-resistant profiles were the discrepancies between S. flexneri and S. sonnei isolates. Phylogenetic analysis showed that isolates of the same cluster but with different antibiotic-resistance gene patterns occurred because of the loss or gain of antibiotic-resistance genes located in the plasmids and multidrug-resistance islands. IMPORTANCE Antimicrobial resistance in Shigella spp. has become a global public health concern. In this study, we identified the antimicrobial susceptibility testing (AST) characteristics based on genomic sequences of 218 Shigella isolates and analyzed the correlation between genotypic and phenotypic antibiotic resistance profiles of Shigella spp., especially for fluoroquinolone, macrolides, and third-generation cephalosporins. Our results show that the genotypic results correlated with the phenotypic profiles with concordance rates of 96.42% and 94.50% in S. flexneri and S. sonnei isolates, respectively. The drug-resistance patterns and essential drug-resistance genes to predict the phenotypic drug-resistant profiles of S. flexneri and S. sonnei isolates in Taiyuan city were distinct. The discrepancy between genotypic and phenotypic AST was considerable in the genotypically resistant but phenotypically susceptible isolates. The information on drug resistance and resistance genes in this study can offer more details on the prevalence of drug resistance of Shigella spp.

Prevalence of fluoroquinolone resistance and mutations in the gyrA, parC and parE genes of Riemerella anatipestifer isolated from ducks in China

BACKGROUND

Riemerella anatipestifer is one of the most serious infectious disease-causing pathogens in the duck industry. Drug administration is an important method for prevention and treatment of infection in duck production, leading to widespread drug resistance in R. anatipestifer.

METHODS

For a total of 162 isolates of R. anatipestifer, the MICs were determined for a quinolone antimicrobial agent, namely, nalidixic acid, and three fluoroquinolones, namely, ciprofloxacin, enrofloxacin and ofloxacin. The gyrA, parC, and parE gene fragments were amplified by PCR to identify the mutation sites in these strains. Site-directed mutants with mutations that were detected at a high frequency in vivo were constructed (hereafter referred to as site-directed in vivo mutants), and the MICs of these four drugs for these strains were determined.

RESULTS

In total, 100, 97.8, 99.3 and 97.8% of the 137 R. anatipestifer strains isolated between 2013 and 2018 showed resistance to nalidixic acid, ciprofloxacin, enrofloxacin, and ofloxacin, respectively. The high-frequency mutation sites were detected in a total of 162 R. anatipestifer strains, such as Ser83Ile and Ser83Arg, which are two types of substitution mutations of amino acid 83 in GyrA; Val799Ala and Ile811Val in ParC; and Val357Ile, His358Tyr, and Arg541Lys in ParE. MIC analysis results for the site-directed in vivo mutants showed that the strains with only the Ser83Ile mutation in GyrA exhibited an 8-16-fold increase in MIC values, and all mutants showed resistance to ampicillin and ceftiofur.

CONCLUSIONS

The resistance of R. anatipestifer to quinolone agents is a serious problem. Amino acid 83 in GyrA is the major target mutation site for the fluoroquinolone resistance mechanism of R. anatipestifer.

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.

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 bla_oxa-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.

In vitro activity of ceftazidime-avibactam, ceftolozane-tazobactam, and other comparable agents against clinically important Gram-negative bacilli: results from the 2017 Surveillance of Multicenter Antimicrobial Resistance in Taiwan (SMART)

Objectives

We investigated the in vitro antimicrobial susceptibilities of clinically important Gram-negative bacteria (GNB) from 16 major teaching hospitals in Taiwan in 2017.

Materials and methods

Escherichia coli (n=686) and Klebsiella pneumoniae bloodstream isolates (n=673), non-typhoid Salmonella (NTS; n=221) from various sources, Shigella species (n=21) from fecal samples, and Neisseria gonorrhoeae (n=129) from the genitourinary tract were collected. Antibiotic minimum inhibitory concentrations (MICs) were determined using the broth microdilution method. Alleles encoding K. pneumoniae carbapenemases (KPCs), New Delhi metallo-β-lactamases (NDMs), Verona integron-encoded metallo-β-lactamase, imipenemase, _OXA-48-like, and mcr-1-5 genes were detected by molecular methods in Enterobacteriaceae isolates.

Results

Five (0.7%) E. coli isolates harbored mcr-1 alleles. Twenty-four (3.6%), seven (1.0%), four (0.6%), and one (0.15%) K. pneumoniae isolates contained bla_KPC, bla_OXA-48-like, mcr-1, and bla_NDM, respectively. Three (1.4%) NTS and no Shigella isolates harbored mcr-1 genes. Seventy-one (10.5%) K. pneumoniae isolates displayed non-susceptibility (NS) to carbapenem agent(s). Phenotypically extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae isolates showed significantly higher rates of ertapenem, tigecycline, and ceftolozane–tazobactam (CLZ– TAZ) NS (40.2%, 16.3%, and 71%–80%, respectively) than E. coli isolates exhibiting ESBL phenotypes (5.4%, 0.7%, and 18%–28%, respectively). All phenotypically ESBL-producing E. coli isolates were ceftazidime–avibactam (CAZ–AVB) susceptible. Two (8.3%) KPC-producing K. pneumoniae isolates showed CAZ–AVB NS. Hospital-acquired K. pneumoniae isolates were significantly less susceptible to ertapenem and CLZ–TAZ than hospital-acquired E. coli isolates.

Conclusion

Third-generation cephalosporins remain the optimal choice for treating NTS, Shigella, and gonococcal infections in Taiwan. Hospital-acquired and phenotypically ESBL-producing K. pneumoniae are a heavy resistance burden in Taiwan.

Fluoroquinolone Resistance Mechanisms in Shigella Isolates in Shanghai, China, Between 2010 and 2015

OBJECTIVES

This study aimed to investigate the antimicrobial susceptibility of Shigella isolated in Shanghai, China and to determine the genetic basis of its resistance to fluoroquinolones.

MATERIALS AND METHODS

A total of 402 strains of Shigella, including 145 Shigella flexneri and 257 Shigella sonnei isolates, were analyzed. The Kirby-Bauer disk diffusion method was used to determine the susceptibility of the strains to 13 antimicrobials. Minimum inhibitory concentration of ciprofloxacin was determined by E-test. Mutations within the quinolone resistance-determining regions (QRDRs) of gyrA and parC and in the plasmid-mediated quinolone resistance (PMQR) genes, including qnrA, qnrB, qnrS, and aac (6')-Ib-cr, were detected by polymerase chain reaction. All the products were then sequenced.

RESULTS

Most of the Shigella isolates were found to be resistant to nalidixic acid (96.4%), streptomycin (96.4%), ampicillin (86.2%), tetracycline (79.8%), and sulfamethoxazole/trimethoprim (80.6%). S. flexneri isolates showed a significantly higher resistance to cefepime (33.6%), ciprofloxacin (54.2%), norfloxacin (34.1%), and levofloxacin (12.1%) compared with that observed for the S. sonnei strains (χ² analysis, p < 0.05). Three mutations (Ser83, Asp87, and His211) in gyrA and one mutation (Ser80) in parC were detected. Of 257 S. sonnei isolates, 11.7% possessed gyrA mutations and 2% had parC mutations. Of 145 S. flexneri isolates, 98.6% possessed gyrA mutations and 97.9% had parC mutations. The plasmid-mediated resistance genes of qnrS and aac (6')-Ib-cr were detected among 17 strains (4.2%).

CONCLUSIONS

The mutation percentage within the QRDR of S. flexneri was as high as 98.6 in gyrA and 97.9 in parC. The significant abundance of mutations within QRDRs conferred high levels of fluoroquinolone resistance. Moreover, the PMQR genes, particularly qnrS, played an important role in the decreased susceptibility of Shigella to fluoroquinolones.

Two novel mutations in parE among Shigella flexneri isolated from Jiangsu Province of China, 2016

Background

The study was conducted to assess the resistance capacity of quinolone against Shigella flexneri, and to investigate the involved quinolone resistance mechanism. The data were collected from Jiangsu Province, China in 2016.

Methods

The number of 81 S. flexneri was obtained from 12 cities in Jiangsu Province of China during 2016. Slide agglutination was taken for serotyping, and susceptibility test was identified by the disc diffusion method. PCR aimed to amplify the quinolone resistance-determining region (QRDR) genes and screen for plasmid-mediated quinolone resistance (PMQR) determinants. Chromosomal mutation was confirmed by sequencing and Blast comparison.

Results

2a was the commonest serotype, accounting for 40.7% (33/81) of the 81 S. flexneri. 70.4% (57/81) isolates expressed resistance against nalidixic acid, and the resistance against ciprofloxacin even reached up to a high proportion of 58.0% (47/81). A total of 8 point mutations were identified, including 2 novel mutations discovered in parE (Ser458Leu and Gly408Asp). The common mutation Ser83Leu in gyrA was still the most prevalent here with a percentage of 70.4% (57/81), followed by the approximate mutation of 69.1% (56/81) in parC (Ser80Ile) and His211Tyr in gyrA. Meanwhile, 35.8% (29/81) isolates were confirmed with mutation of Gln517Arg in gyrB. In addition, qnrS positive isolates occupied a proportion of 7.4% (6/81), but only 1 strain was observed with aac(6')-Ib-cr. All PMQR positive isolates were resistant to nalidixic acid. However, 5 of them didn't stay susceptible to ciprofloxacin any more.

Conclusions

This is the first time that a study researches the occurrence of mutations in parE among S. flexneri, Ser458Leu and Gly408Asp included. The study indicates that the high resistance to fluoroquinolone remains a serious problem in Jiangsu, China. Thus, the prevention and control of current infection urge for a comprehensive and systematic surveillance based on persistent surveys.

Iron-dependent essential genes in Salmonella Typhimurium

Background

The molecular mechanisms underlying bacterial cell death due to stresses or bactericidal antibiotics are complex and remain puzzling. Due to the current crisis of antibiotic resistance, development of effective antibiotics is urgently required. Previously, it has been shown that iron is required for effective killing of bacterial cells by numerous bactericidal antibiotics.

Results

We investigated the death or growth inhibition of S. Typhimurium under iron-restricted conditions, following disruption of essential genes, by transposon mutagenesis using transposon sequencing (Tn-seq). Our high-resolution Tn-seq analysis revealed that transposon mutants of S. Typhimurium with insertions in essential genes escaped immediate killing or growth inhibition under iron-restricted conditions for approximately one-third of all previously known essential genes. Based on this result, we classified all essential genes into two categories, iron-dependent essential genes, for which the insertion mutants can grow slowly if iron is restricted, and iron-independent essential genes, for which the mutants become nonviable regardless of iron concentration. The iron-dependency of the iron-dependent essential genes was further validated by the fact that the relative abundance of these essential gene mutants increased further with more severe iron restrictions. Our unexpected observation can be explained well by the common killing mechanisms of bactericidal antibiotics via production of reactive oxygen species (ROS). In this model, iron restriction would inhibit production of ROS, leading to reduced killing activity following blocking of essential gene functions. Interestingly, the targets of most antibiotics currently in use clinically are iron-dependent essential genes.

Conclusions

Our result suggests that targeting iron-independent essential genes may be a better strategy for future antibiotic development, because blocking their essential gene functions would lead to immediate cell death regardless of the iron concentration. This work expands our knowledge on the role of iron to a broad range of essential functions and pathways, providing novel insights for development of more effective antibiotics.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4986-1) contains supplementary material, which is available to authorized users.

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

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 bla_OXA, bla_TEM, bla_CTX-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.

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.

Low distribution of genes encoding virulence factors in Shigella flexneri serotypes 1b clinical isolates from eastern Chinese populations

Background

The ability of Shigella to invade, colonize, and eventually kill host cells is influenced by many virulence factors. However, there is no analysis of related genes in Jiangsu Province of China so far. Shigella flexneri was collected from 13 cities of Jiangsu Province through the provincial Centers for Disease Control (CDC) for analysis of distribution of major virulence genes (ipaH, ipaBCD, ial, virF, virB, sigA, set1A, sepA, sat, pic, set1B and sen) detected by PCR technology.

Results

A total of 545 isolates received were confirmed as S. flexneri which belongs to 11 serotypes of S. flexneri, among which serotype 2a was the most predominant (n = 223, 40.9%). All isolates were positive for ipaH gene, followed by sat (94.1%), sigA (78.9%), set1B (78.0%), pic (77.6%), set1A (74.5%), virF (64.8%), sepA (63.5%), sen (56.9%), ipaBCD (50.5%), ial (47.0%) and virB (47.0%). The presence of virulence genes in different serotypes was distinct. The existence of virulence genes of serotype 1b was generally lower than other serotype-the positive rate for virulence genes was between 0.0 and 14.1% except for ipaH and sat. In addition, virulence genes also fluctuated in different regions and at different times in Jiangsu province. The result of analysis on the relationship between virulence genes of S. flexneri showed that the existence of virulence genes of Shigella could be well represented by multiplex PCR combination ipaH + ial + set1A, which had a high clinical value.

Conclusions

The present study was designed to explore the prevalence of 12 S. flexneri-associated virulence genes. The data showed high diversity of virulence genes with regard to periods, regions and serotypes in Jiangsu Province of China.

Electronic supplementary material

The online version of this article (10.1186/s13099-017-0222-9) contains supplementary material, which is available to authorized users.

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.

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.

First report of the qnrA determinant in Shigella sonnei isolated from China

We investigated the first presence of qnrA among Shigella sonnei clinical isolates in Jiangsu Province, China. The qnrA-positive isolates coexisted with the mutation in gyrA at codon 83, these isolates were resistant to nalidixic acid and 22·2% (2 of 9) of them were resistant to norfloxacin.