Molecular characterization of extended-spectrum cephalosporin and fluoroquinolone resistance genes in Salmonella and Shigella isolated from clinical specimens in Thailand

Association of fluoroquinolone resistance with rare quinolone resistance-determining region (QRDR) mutations and protein-quinolone binding affinity (PQBA) in multidrug-resistant Escherichia coli isolated from patients with urinary tract infection

BACKGROUND

Urinary tract infections (UTIs) caused by Escherichia coli pose significant public health risks, particularly in developing countries like Bangladesh. This study aimed to elucidate resistance patterns among UTI isolates and comprehensively investigate the mutational spectrum and its impact on drug-microbe interactions.

METHODS

We collected and identified E. coli isolates from hospitalized UTI patients at Dhaka Medical College Hospital and determined their resistance patterns using the disc diffusion method and broth microdilution. Quinolone resistance-determining regions (QRDRs) of the target genes (gyrA, gyrB, parC, and parE) associated with fluoroquinolone resistance were amplified by polymerase chain reaction (PCR) and analyzed through BTSeq™ sequencing for mutations, followed by molecular docking analysis using PyMOL and AutoDock for the protein-quinolone binding affinity (PQBA) study.

RESULTS

All isolates (100 %) displayed multidrug resistance, with chloramphenicol (16 % resistant) and colistin (28 % resistant) demonstrating superior efficacy compared to other antibiotics. The isolates resistant to colistin, as determined by disc diffusion testing, exhibited remarkably high minimum inhibitory concentrations (MICs), with one isolate registering an MIC exceeding 512 µg/mL. Alarming resistance rates were observed for five antibiotic classes, except for polymyxins (28 % resistant) and protein synthesis inhibitors (48 % resistant). Fifty-two percent (52 %) of the isolates exhibited resistance to all five tested quinolones. Sequence analysis revealed a novel L88Q mutation in ParC, affecting PQBA and binding conformation. Additionally, three ParC mutations (S80I, E84V, and E84G) and two ParE mutations (S458A and I529L) were identified, which had not been previously reported in Bangladesh. Among these, S80I appeared in all isolates. Double-mutations (S83L+D87N) in GyrA, L88Q and S80I in ParC, and I529L in ParE were identified as key drivers of fluoroquinolone resistance.

CONCLUSION

Our findings underscore the accumulation of significant mutations within QRDRs of UTI isolates, potentially compromising fluoroquinolone efficacy. The emergence of these novel mutations warrants further investigation to impede their dissemination and combat quinolone resistance.

Antimicrobial resistance, virulence gene profiles, and phylogenetic groups of Escherichia coli isolated from healthy broilers and broilers with colibacillosis in Thailand

BACKGROUND

Multidrug resistance in Escherichia coli has a significant global impact on poultry production. This study aimed to determine the phenotypic and genotypic backgrounds of antimicrobial resistance (AMR) and virulence gene profiles of E. coli strains isolated from diseased and healthy broilers. A total of 211 E. coli isolates were recovered from diseased (n = 110) and healthy broilers (n = 101). All the isolates were subjected to antimicrobial susceptibility testing. A PCR-based technique was applied to screen AMR genes, virulence genes and analyze phylogenetic groups.

RESULTS

Phylogenetic groups B1 and D were the most prevalent for E. coli isolated from diseased and healthy birds. Among virulence genes, the detection rates of cva/cvi, iutA, iucD, iroN, iss and ompT were considerably greater in E.coli strains from diseased birds than in healthy birds. The virulence gene pattern of hlyF-iutA-iucD-iroN-iss-ompT (16.4%) was frequently observed in E.coli isolated from diseased birds, whereas approximately 22.8% of E.coli from healthy birds did not carry any virulence genes. Analysis of AMR profiles revealed that 58.3% of E.coli were resistant to multiple classes of antibiotics, and 96.7% carried at least one antibiotic resistance gene AMR genes.

CONCLUSION

The findings of this study demonstrate the variable distribution of phylogenetic groups and virulence genes. E.coli strains isolated from broilers had multidrug resistance profiles. The study emphasizes the need for continuous monitoring of AMR emergence in E. coli from broilers. This monitoring allows for early detection and implementation of strategies to control the spread of resistant strains.

Antimicrobial susceptibility and virulence gene analysis of Shigella species causing dysentery in Iranian children: Implications for fluroquinolone resistance

Shigella species significantly impact global health due to their role in diarrheal diseases. A 2019-2022 cross-sectional study on 432 stool samples from pediatric patients in Mashhad, Iran, identified Shigella spp. and tested their susceptibility to 12 antimicrobials by the disk diffusion method. The presence of virulence factors, namely ipaH, virA, stx1, and stx2, as well as plasmid-mediated quinolone resistance (PMQR) genes, including qnrA, qnrB, qnrC, qnrD, and qnrS, were ascertained through the utilization of polymerase chain reaction techniques. Sequencing of 15 isolates detected mutations within quinolone resistance-determining regions (QRDRs) at the gyrA and parC genes, indicating fluoroquinolone (FQ) resistance. 19.2 % (83/432) of stool samples contained Shigella, primarily S. sonnei (77.1 %), followed by S. flexneri (21.6 %) and S. boydii (1.2 %). Most isolates were from children under five (55.4 %). All strains had the ipaH gene, lacked stx1 and stx2, and 86.7 % had virA. High resistance was noted for ampicillin and tetracycline (84.3 % each), trimethoprim-sulfamethoxazole (81.9 %), and azithromycin (60.2 %). 87.1 % of isolates were multidrug-resistant (MDR). The most common PMQR genes were qnrA and qnrS (41 % each). The qnrD gene, prevalent in 36.1 % of cases, is reported in Iran for the first time. The most common PMQR profile was qnrADS (15.7 %). Resistance to nalidixic acid and ciprofloxacin was 45.8 % and 12 %, respectively. The Shigella isolates exhibited mutations in the gyrA (at codons 83, 87, and 211) and parC (at codons 80, 84, 93, 126, 128, 129, and 132) genes. The D87Y mutation in the gyrA gene was the most common in Shigella isolates, occurring in 73 % of cases. The F93S and L132T mutations in the parC gene were unique to this study. Empirical FQ therapy in patients infected with MDR Shigella, possessing PMQR determinants and/or mutations in the QRDRs of gyrA and parC, may escalate the risks of secondary diseases, extended treatment duration, therapeutic failure, and resistance spread. Consequently, the necessity for continuous surveillance and genetic testing to detect FQ-resistant Shigella strains is of paramount importance.

An outbreak of acute diarrhoeal disease caused by Shigella sonnei in a village in Dibrugarh district, Assam

Background & objectives Food and waterborne illnesses remain a neglected public health issue in India. Events with large gatherings frequently witness outbreaks of acute diarrheal diseases due to consumption of contaminated food or water or poor food handling practices. In the present study, an outbreak of acute diarrhoeal disease (ADD) occurring among the attendees of a birthday party in rural Dibrugarh district in the northeastern Indian State of Assam was investigated. Methods Sociodemographic information along with details of ADD outbreak that included information about source of foods, food handlers, illness details, etc., were collected using an outbreak investigation form for descriptive and analytical epidemiology. Rectal swabs from affected individuals and food handlers were collected along with bore-well water samples and tested in the laboratory by performing bacterial culture, biochemical analysis and polymerase chain reaction. Due to the delayed report on the outbreak, collecting leftover food for laboratory testing and analysis was impossible. Results A total of 25 cases of ADD had similar signs and symptoms. The mean incubation period for developing acute diarrhoea was 26.36±8.76 (± standard deviation) hours from food consumption. The overall attack rate was 60.04 per cent (25/41); 20 per cent (5/25) required hospitalization. Thirteen rectal swab samples were tested for pathogens and found positive for Shigella sonnei. Antibiotic susceptibility test of isolated S. sonnei showed resistance to nalidixic acid, ciprofloxacin and cefotaxime. Consumption of one of the food items - chicken curry was significantly associated with illness (Odds Ratio=14.8; 95% Confidence Interval: 2.75-85.11); P value<0.05 and Population Attributable Fraction (PAF) was 70.18 per cent. The water samples were found satisfactory for human consumption. Interpretation & conclusions The findings suggested that S. sonnei infection could be implicated in the investigated food-borne diarrhoeal disease outbreak and that there was a potential for human-poultry cross-infection. Additionally, the study revealed concerning levels of S. sonnei resistance to recommended antibiotics and drew attention to their public health relevance.

High levels of multidrug-resistant isolates of genetically similar Salmonella 1,4, [5],12:I:- from Brazil between 1983 and 2020

Introduction. Salmonella 1,4, [5],12:i:- strains with different antimicrobial resistance profiles have been associated with foodborne disease outbreaks in several countries. In Brazil, S. 1,4, [5],12:i:- was identified as one of the most prevalent serovars in São Paulo State during 2004-2020.Gap Statement. However, few studies have characterized this serovar in Brazil.Aim. This study aimed to determine the antimicrobial resistance profiles of S. 1,4, [5],12:i:- strains isolated from different sources in Southeast Brazil and compare their genetic diversity.Methodology. We analysed 113 S. 1,4, [5],12:i:- strains isolated from humans (n=99), animals (n=7), food (n=5) and the environment (n=2) between 1983 and 2020. Susceptibility testing against 13 antimicrobials was performed using the disc diffusion method for all the strains. Plasmid resistance genes and mutations in the quinolone resistance-determining regions were identified in phenotypically fluoroquinolone-resistant strains. Molecular typing was performed using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) for all strains and multilocus sequence typing (MLST) for 40 selected strains.Results. Of the 113 strains, 54.87 % were resistant to at least one antimicrobial. The highest resistance rates were observed against ampicillin (51.33 %), nalidixic acid (39.82 %) and tetracycline (38.05 %). Additionally, 39 (34.51 %) strains were classified as multidrug-resistant (MDR). Nine fluoroquinolone-resistant strains exhibited the gyrA mutation (Ser96→Tyr96) and contained the qnrB gene. The 113 strains were grouped into two clusters using ERIC-PCR, and most of strains were present in one cluster, with a genetic similarity of ≥80 %. Finally, 40 strains were typed as ST19 using MLST.Conclusion. The prevalence of MDR strains is alarming because antimicrobial treatment against these strains may lead to therapeutic failure. Furthermore, the ERIC-PCR and MLST results suggested that most strains belonged to one main cluster. Thus, a prevalent subtype of Salmonella 1,4, [5],12:i:- strains has probably been circulating among different sources in São Paulo, Brazil, over decades.

Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance

In this study, we characterized 54 clinical isolates of Shigella collected in North Lebanon between 2009 and 2017 through phenotypic and genomic analyses. The most prevalent serogroup was S. sonnei, accounting for 46.3 % (25/54) of the isolates, followed by S. flexneri (27.8 %, 15/54), S. boydii (18.5 %, 10/54) and S. dysenteriae (7.4 %, 4/54). Only three isolates were pan-susceptible, and 87 % (47/54) of the isolates had multidrug resistance phenotypes. Notably, 27.8 % (15/54) of the isolates were resistant to third-generation cephalosporins (3GCs) and 77.8 % (42/54) were resistant to nalidixic acid. 3GC resistance was mediated by the extended-spectrum beta-lactamase genes bla CTX-M-15 and bla CTX-M-3, which were present on various plasmids. Quinolone resistance was conferred by single point mutations in the gyrA DNA gyrase gene, leading to GyrA S83L, GyrA D87Y or GyrA S83A amino acid substitutions. This is the first study, to our knowledge, to provide genomic insights into the serotypes of Shigella circulating in Lebanon and the various antimicrobial resistance determinants carried by these strains.