Emergence of resistance to fluoroquinolones and third-generation cephalosporins in Shigella flexneri subserotype 1c isolates from China

Dissemination of Multiple Drug-Resistant Shigella flexneri 2a Isolates Among Pediatric Outpatients in Urumqi, China

Multiple drug-resistant (MDR) Shigella isolates have been reported worldwide. Between May 2017 and September 2018, 55 Shigella flexneri 2a isolates were collected from 3322 stool samples of 0-10-year-old outpatients with diarrhea at the Children's Hospital of Urumqi, China. All isolates were characterized using serotyping, antimicrobial susceptibility testing, and whole-genome sequencing. A total of 54 of 55 (98.2%) isolates exhibited MDR phenotypes and had accumulated multiple resistance determinants, particularly of fluoroquinolones and cephalosporins preferred for shigellosis treatment: point mutations in quinolone resistance-determining regions (QRDRs) of topoisomerases (GyrA (S83L, D87N) and ParC (S80I) [n = 9]; GyrA (S83L) and ParC (S80I) [n = 45]) and acquisition of qnrS1 (n = 3) and bla_CTX-M (n = 8). Over 70% of isolates acquired two point mutations of GyrA (S83L) and ParC (S80I) in QRDRs and 11 highly resistant isolates accumulated three point mutations in QRDRs or acquired qnrS1. Four S. flexneri 2a isolates from three single-nucleotide polymorphism clusters exhibited coresistance to ciprofloxacin, cefotaxime, or azithromycin (AZM), which are used as first- and second-line shigellosis treatment antimicrobials in clinics. Our data indicated that fluoroquinolones should be terminated in shigellosis treatment for outpatients in Urumqi. The transferable antimicrobial resistance determinants have been identified for third-generation cephalosporins and AZM. Novel strategies are urgently required for developing empirical medication to reduce the antimicrobial selective pressure and prevent dissemination of MDR S. flexneri 2a isolates.

Clonal serotype 1c multidrug-resistant Shigella flexneri detected in multiple institutions by sentinel-site sequencing

Shigella flexneri is a major diarrhoeal pathogen, and the emergence of multidrug-resistant S. flexneri is of public health concern. We report the detection of a clonal cluster of multidrug-resistant serotype 1c (7a) S. flexneri in Singapore in April 2022. Long-read whole-genome sequence analysis found five S. flexneri isolates to be clonal and harboring the extended-spectrum β-lactamases bla_CTX−M−15 and bla_TEM−1. The isolates were phenotypically resistant to ceftriaxone and had intermediate susceptibility to ciprofloxacin. The S. flexneri clonal cluster was first detected in a tertiary hospital diagnostic laboratory (sentinel-site), to which the S. flexneri isolates were sent from other hospitals for routine serogrouping. Long-read whole-genome sequence analysis was performed in the sentinel-site near real-time in view of the unusually high number of S. flexneri isolates received within a short time frame. This study demonstrates that near real-time sentinel-site sequence-based surveillance of convenience samples can detect possible clonal outbreak clusters and may provide alerts useful for public health mitigations at the earliest possible opportunity.

Newly Emerged Serotype 1c of Shigella flexneri: Multiple Origins and Changing Drug Resistance Landscape

Bacillary dysentery caused by Shigella flexneri is a major cause of under-five mortality in developing countries, where a novel S. flexneri serotype 1c has become very common since the 1980s. However, the origin and diversification of serotype 1c remain poorly understood. To understand the evolution of serotype 1c and their antimicrobial resistance, we sequenced and analyzed the whole-genome of 85 clinical isolates from the United Kingdom, Egypt, Bangladesh, Vietnam, and Japan belonging to serotype 1c and related serotypes of 1a, 1b and Y/Yv. We identified up to three distinct O-antigen modifying genes in S. flexneri 1c strains, which were acquired from three different bacteriophages. Our analysis shows that S. flexneri 1c strains have originated from serotype 1a and serotype 1b strains after the acquisition of bacteriophage-encoding gtrIc operon. The maximum-likelihood phylogenetic analysis using core genes suggests two distinct S. flexneri 1c lineages, one specific to Bangladesh, which originated from ancestral serotype 1a strains and the other from the United Kingdom, Egypt, and Vietnam originated from ancestral serotype 1b strains. We also identified 63 isolates containing multiple drug-resistant genes in them conferring resistance against streptomycin, sulfonamide, quinolone, trimethoprim, tetracycline, chloramphenicol, and beta-lactamase. Furthermore, antibiotic susceptibility assays showed 83 (97.6%) isolates as either complete or intermediate resistance to the WHO-recommended first- and second-line drugs. This changing drug resistance pattern demonstrates the urgent need for drug resistance surveillance and renewed treatment guidelines.

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.

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.

Single Domain Antibodies as New Biomarker Detectors

Biomarkers are defined as indicators of biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. Biomarkers have been widely used for early detection, prediction of response after treatment, and for monitoring the progression of diseases. Antibodies represent promising tools for recognition of biomarkers, and are widely deployed as analytical tools in clinical settings. For immunodiagnostics, antibodies are now exploited as binders for antigens of interest across a range of platforms. More recently, the discovery of antibody surface display and combinatorial chemistry techniques has allowed the exploration of new binders from a range of animals, for instance variable domains of new antigen receptors (V_NAR) from shark and variable heavy chain domains (V_HH) or nanobodies from camelids. These single domain antibodies (sdAbs) have some advantages over conventional murine immunoglobulin owing to the lack of a light chain, making them the smallest natural biomarker binders thus far identified. In this review, we will discuss several biomarkers used as a means to validate diseases progress. The potential functionality of modern singe domain antigen binders derived from phylogenetically early animals as new biomarker detectors for current diagnostic and research platforms development will be described.

Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis

BACKGROUND

Shigella flexneri is the primary cause of bacillary dysentery in the developing countries. S. flexneri serotype 1c is a novel serotype, which is found to be endemic in many developing countries, but little is known about its genomic architecture and virulence signatures. We have sequenced for the first time, the complete genome of S. flexneri serotype 1c strain Y394, to provide insights into its diversity and evolution.

RESULTS

We generated a high-quality reference genome of S. flexneri serotype 1c using the hybrid methods of long-read single-molecule real-time (SMRT) sequencing technology and short-read MiSeq (Illumina) sequencing technology. The Y394 chromosome is 4.58 Mb in size and shares the basic genomic features with other S. flexneri complete genomes. However, it possesses unique and highly modified O-antigen structure comprising of three distinct O-antigen modifying gene clusters that potentially came from three different bacteriophages. It also possesses a large number of hypothetical unique genes compared to other S. flexneri genomes.

CONCLUSIONS

Despite a high level of structural and functional similarities of Y394 genome with other S. flexneri genomes, there are marked differences in the pathogenic islands. The diversity in the pathogenic islands suggests that these bacterial pathogens are well adapted to respond to the selection pressures during their evolution, which might contribute to the differences in their virulence potential.

Gallic acid conjugated with gold nanoparticles: antibacterial activity and mechanism of action on foodborne pathogens

Foodborne pathogens, including Plesiomonas shigelloides and Shigella flexneri B, are the major cause of diarrheal endemics worldwide. Antibiotic drug resistance is increasing. Therefore, bioactive compounds with antibacterial activity, such as gallic acid (GA), are needed. Gold nanoparticles (AuNPs) are used as drug delivery agents. This study aimed to conjugate and characterize AuNP–GA and to evaluate the antibacterial activity. AuNP was conjugated with GA, and the core–shell structures were characterized by small-angle X-ray scattering and transmission electron microscopy. Antibacterial activity of AuNP–GA against P. shigelloides and S. flexneri B was evaluated by well diffusion method. AuNP–GA bactericidal mechanism was elucidated by Fourier transform infrared microspectroscopic analysis. The results of small-angle X-ray scattering showed that AuNP–GA conjugation was successful. Antibacterial activity of GA against both bacteria was improved by conjugation with AuNP because the minimum inhibitory concentration value of AuNP–GA was significantly decreased (P<0.0001) compared to that of GA. Fourier transform infrared analysis revealed that AuNP–GA resulted in alterations of lipids, proteins, and nucleic acids at the bacterial cell membrane. Our findings show that AuNP–GA has potential for further application in biomedical sciences.

Shift in serotype distribution of Shigella species in China, 2003-2013

We identified 2912 Shigella isolates from diarrhoeal patients in China during 2003-2013. The most common species was Shigella flexneri (55.3%), followed by Shigella sonnei (44.1%); however, S. sonnei is becoming increasingly prevalent. Among the S. flexneri isolates, serotypes 2a and X variant (-:7,8, E1037) were the two most prevalent serotypes, and serologically atypical isolates were also commonly identified. Overall, S. sonnei, S. flexneri 2a and S. flexneri X variant (-:7,8, E1037) accounted for 76.1% of all Shigella isolates, and their prevalence increased from 54.0% during 2003-2004 to 84.1% during 2011-2013. A change was observed in the serotype distribution of Shigella in China during this period, and we propose an ideal strategy to inform the development of a broadly effective Shigella vaccine candidate.

Potential novel antibiotics from HTS targeting the virulence-regulating transcription factor, VirF, from Shigella flexneri

VirF is an AraC-type transcriptional regulator responsible for activating the transcription of virulence genes required for the intracellular invasion and cell-to-cell spread of Shigella flexneri. Gene disruption studies have validated VirF as a potential target for an anti-virulence therapy to treat shigellosis by determining that VirF is necessary for virulence, but not required for bacterial viability. Using a bacteria-based, β-galactosidase reporter assay we completed a high-throughput screening (HTS) campaign monitoring VirF activity in the presence of over 140,000 small molecules. From our screening campaign we identified five lead compounds to pursue in tissue-culture-based invasion and cell-to-cell spread assays and toxicity screens. Our observations of activity in these models for infection have validated our approach of targeting virulence regulation and have allowed us to identify a promising chemical scaffold from our HTS for hit-to-lead development. Interestingly, differential effects on invasion versus cell-to-cell spread suggest that the compounds’ efficacies may depend, in part, on the specific promoter that VirF is recognizing.

Serotype distribution and characteristics of antimicrobial resistance inShigellaisolated from Henan province, China, 2001–2008

The serotype distribution and susceptibility to 14 antimicrobial agents of 526 isolates ofShigellaspp. from four hospitals in Sun county, Henan province, China during 2001–2008, were analysed to identify associations of serotypes with resistance trends.S.flexneriwas the most frequent species (92·4%), the remainder wasS.sonnei. The prevalent serotype ofS.flexneriwas 2a (26·7%). Almost all (>99%) isolates were resistant to tetracycline, nalidixic acid and pipemidic acid; >80% were resistant to chloramphenicol, amoxicillin and co-trimoxazole but less than 5% were resistant to polymyxin B, furazolidone, cefotaxime and gentamicin.S.flexnerishowed statistically significant higher resistance thanS.sonneito amoxicillin, ampicillin, chloramphenicol and ciprofloxacin but resistance to co-trimoxazole was more common inS.sonneithan inS.flexneri. These results emphasize that monitoring of emerging resistance inShigellaisolates is essential for timely and appropriate recommendations for antimicrobial therapy.