gyrA Mutations Research Articles

Point Mutations in the Helicobacter pylori gyrA gene in Patients with peptic ulcer disease and suspected gastric cancer

Helicobacter pylori (H. pylori) is a major causative agent of peptic ulcer disease and gastric cancer. Levofloxacin, a fluoroquinolone antibiotic, is commonly used in H. pylori treatment regimens. However, the increasing resistance of H. pylori to levofloxacin in Vietnam has compromised treatment efficacy. This study aimed to determine the prevalence of point mutations in the gyrA gene and investigate their associated factors. A total of 164 H. pylori strains were isolated from patients with peptic ulcer disease or suspected gastric cancer at the 108 Military Central Hospital between 2019 and 2022. The gyrA gene was sequenced using the Sanger method to identify mutations conferring levofloxacin (LVX) resistance. The overall LVX resistance rate was 29.9% (49/164). Eighteen distinct gyrA mutations were identified, including M191I, G208E/K/R, N87K/I, V199A/I, R130K, R140K, D91G/Y/N, A66T, I194T, D161N, V172I, V65I, A88P, D155G, D192G, D210N, T132A, and V150A. Among these, M191I (92.7%) and G208E/K/R (30.5%) were the most prevalent. Etest results showed a significant association between the N87K/I mutation and LVX resistance (p < 0.05). Logistic regression analysis further revealed that the mutation combinations D91G/Y/N+M191I and N87K/ I+M191I were significantly associated with LVX resistance. These novel findings contribute to a deeper understanding of fluoroquinolone resistance mechanisms in H. pylori. Continuous monitoring and the development of more effective diagnostic and treatment strategies are essential for controlling H. pylori infection.

Genomic insights into the spread of methicillin-resistant Staphylococcus aureus involved in ear infections

BackgroundMethicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen causing ear infections. However, genomic epidemiology and determinants influencing transmission of ear infections associated MRSA (EIA-MRSA) in community remain unknown.MethodsIn 2020–2021, 105 EIA-MRSA isolates were collected and sequenced from outpatients across different households in Shanghai, China. Antimicrobial susceptibility testing, core genome MLST, and phylodynamic analyses were conducted to characterize EIA-MRSA dissemination.ResultsQuinolone resistance was identified as a risk factor for EIA-MRSA spread (OR 9, [95% CI 3–31]). The ST764 clone and two subclones of ST22-PT hypervirulent clone have developed an extensive quinolone-resistant (eQR) phenotype, conferring additional resistance to advanced quinolones due to the accumulation of four mutations in gyrA (S84L and either S85P, E88K, or E88G) and parC (S80F and either E84K or E84G). These ST764- and ST22-PT-eQR isolates were highly transmissible and showed increased resistance to other commonly used antimicrobials, posing potential high-risk clones. The eQR phenotype may be inherent to the ST764 lineage, which emerged in the late 1980s, coinciding with the widespread fluoroquinolone usage. The ST22-PT-eQR subclones emerged in around 2017 and are accumulating resistance genes.ConclusionVigilance is crucial for eQR high-risk clones, particularly the convergent ST22-PT-eQR subclones that accumulate resistance and virulence traits, posing risks for ear infections.Clinical trial numberNot applicable.

Identification of genetic determinants of antibiotic resistance in Helicobacter pylori isolates in Vietnam by high-throughput sequencing

The aim of this study was to identify genetic factors responsible for antibiotic resistance in Helicobacter pylori, a bacterium that can cause long-term gastroduodenal disease. The primary resistance of H. pylori to commonly used antibiotics was studied, and high-throughput next-generation sequencing (NGS) was employed to discover genetic determinants of resistance using a reference-based approach. A total of 123 H. pylori strains were cultured and tested for antibiotic susceptibility using an E test. Genotypic analysis was performed using NGS data with ARIBA v2.14.7 and PlasmidSeeker v1.3 for plasmid detection. Statistical correlations between resistant genotypes and phenotypes were evaluated. In addition, a genome-wide association study (GWAS) and linear mixed model were used to identify genetic variants associated with antimicrobial resistance phenotypes while adjusting for covariates such as population structure. Our results showed that 78.2% of the strains were resistant to metronidazole (MTZ), 22.5% to levofloxacin (LVX), 43.5% to clarithromycin (CLR) and 13.7% to amoxicillin (AMX). Resistance to tetracycline was not detected. Multi-drug resistance was detected in 48.8% of the strains. While plasmids were not detected, chromosomal genetic determinants of resistance to CLR, LVX, and AMX were identified, including mutations in 23S rRNA (A2142G and A2143G), gyrA (N87K/Y and D91Y/N/G), and pbp1 A (F366L, S414R, F473V, G595_V596insE, as well as the mutations T558S and T593A/G/P/S). Additionally, missense, frameshift, and nonsense mutations in rdxA were identified as genetic determinants of resistance to MTZ. No genetic determinants associated with tetracycline resistance were detected. A strong correlation was observed between resistance genotypes and phenotypes for CLR, LVX, AMX, and MTZ. In addition, we found that missense, frameshift and nonsense mutations in rdxA were genetic determinants of resistance to MTZ. We did not detect any genetic determinants associated with tetracycline resistance. There was a strong correlation between resistance genotypes and phenotypes for CLR, LVX, AMX, and MTZ. Furthermore, unitig-based GWAS revealed that AMX, LVX, and CLR resistance in H. pylori was mainly caused by chromosomal mutations that affected the targets of these antibiotics (pbp1 A, gyrA, and 23S rRNA, respectively). Our results highlight the need for regular evaluation and alternative therapies in Vietnam, given the high rates of H. pylori resistance to CLR, MTZ, and LVX. Our study also demonstrated the high capacity of NGS to detect genetic resistance determinants and its potential for implementation in local treatment policies.

Differences in antimicrobial resistance between exoU and exoS isolates of Pseudomonas aeruginosa.

This study compared antimicrobial resistance between exoU and exoS Pseudomonas aeruginosa strains isolated from microbial keratitis (MK) and examined their resistance genotypes. The presence of exoU and exoS was determined in 187 MK isolates using PCR. Minimum inhibitory concentrations of ciprofloxacin, levofloxacin, gentamicin, and tobramycin were measured. Whole genome sequencing of 39 isolates was used to identify resistance genes via Resfinder. Mutations in key genes, including DNA gyrase, topoisomerase IV, efflux pumps, and DNA repair systems, were analyzed using Geneious Prime. Functional effects of novel SNPs were predicted using SIFT. Antibiotic resistance was significantly higher in exoU than exoS: 38.2% vs. 20.5% for ciprofloxacin, 29.1% vs. 12.1% for levofloxacin, 40% vs. 23.5% for gentamicin, and 29.1% vs. 14.4% for tobramycin (all p < 0.05). ExoU isolates exclusively had mutations in GyrA (Thr83Ile) and ParC (Ser87Ile), as well as in efflux pump regulators MexZ (Gly89Ser), NalC (Asp79Glu) and MexS (Val73Ala) (p < 0.01). They also more frequently harbored the acquired resistance genes aph(6)-Id (55% vs. 0%) and aph(3'')-Ib (60% vs. 5.3%) and had higher mutation rates in DNA repair genes mutL (70% vs. 15.8%) and mutS (45% vs. 5.3%) (p < 0.01). Mutations in gyrA, parC, efflux pump (mexB, mexD, mexY) and regulator (mexZ, nalC, mexS) genes correlated with fluoroquinolone resistance (R ≥ 0.33; p ≤ 0.04). Possession of aph(3'')-Ib, aph(6)- Id and SNPs in efflux pump regulators mexZ and parR were associated with aminoglycoside resistance. ExoU strains exhibited more resistance genes and mutations, contributing to higher resistance to fluoroquinolones and aminoglycosides.

Efficacy of Doxycycline-Sitafloxacin Sequential Therapy for Urogenital Mycoplasma genitalium Infection in Nanjing, China.

The aim of this study was to evaluate the efficacy of doxycycline-sitafloxacin sequential therapy in the treatment of Mycoplasma genitalium (Mg) urogenital infections in Nanjing, China. Potential subjects were tested initially for Mg infection by nucleic acid amplification testing and again at least 21 days after completion of doxycycline (100 mg twice daily for 7 days)-sitafloxacin (100 mg twice daily for 7 days) sequential therapy. The presence of macrolide and quinolone resistance-associated mutations in 23S rRNA, parC, gyrA, and gyrB genes in Mg was examined at baseline and upon retesting of specimens from subjects that did not clear Mg. A total of 218 patients were screened for Mg, of whom 65 were positive for Mg; 63 Mg-infected patients were enrolled. Twenty-two (35%) Mg-infected subjects (16 heterosexual men, 5 women, and 1 man who had sex with men [MSM]) were successfully evaluated with a test of cure; 20 (91%) cleared Mg infection. In pretreatment specimens, mutations in 23S rRNA, parC (G248T [S83I]), gyrA (G277T [G93C]), and gyrB genes were present in 100% (19 of 19), 61.1% (11 of 18), 6.7% (1 of 15), and 7.1% (1 of 14), respectively. Mg clearance rates were 4 of 4 in infected subjects that possessed both wild-type parC and gyrA genes, and 9 of 10 when a parC G248T mutation and an otherwise wild-type gyrA gene were identified. Two subjects (9%) reported mild adverse events. Doxycycline-sitafloxacin sequential therapy was well tolerated and effective against most urogenital Mg infections in Nanjing and may provide an option for treatment.

Deciphering spread of quinolone resistance in mariculture ponds: Cross-species and cross-environment transmission of resistome.

Deciphering spread of quinolone resistance in mariculture ponds: Cross-species and cross-environment transmission of resistome.

Exploring Non-QRDR Mutations in gyrA and gyrB and Their Impact on Quinolone Resistance in Helicobacter pylori

Exploring Non-QRDR Mutations in gyrA and gyrB and Their Impact on Quinolone Resistance in Helicobacter pylori

Phenotypic and Genomic Assessment of Antimicrobial Resistance and Virulence Factors Determinants in Salmonella Heidelberg Isolated from Broiler Chickens.

Salmonella Heidelberg is frequently found in poultry and poultry products and is associated with antimicrobial resistance strains and infections and mortality in humans. Whole-genome sequencing is used to monitor and understand epidemiological factors related to antimicrobial resistance. This study aimed to characterize the phenotypic resistance and sequence the whole genome of Salmonella Heidelberg strains isolated from poultry products in Brazil. Fourteen Salmonella Heidelberg strains isolated from whole broiler chicken carcasses and portions in Brazil between 2013 and 2019 were used in this study. Genus confirmation was performed by polymerase chain reaction. The disk diffusion test was conducted to assess the phenotypical antimicrobial susceptibility of the strains. Whole-genome sequencing was carried out to investigate the presence of antimicrobial resistance genes, plasmids, multilocus sequence typing, and virulence-associated genes. A high frequency of phenotypic resistance to cephalosporins, tetracyclines, and sulfonamides was detected. All strains had mutations in gyrA and parC and contained the genes tet(A), fosA7, and sul. The presence of genes originating from Yersinia pathogenicity islands was also detected. This study identified a high frequency of antimicrobial resistance in Salmonella Heidelberg strains from broilers slaughtered in different regions of Brazil, all belonging to the same sequence type (ST15) and associated with multiple resistance and virulence genes. The presence of the Yersinia high-pathogenicity island was detected, indicating potential virulence. These findings highlight the importance of continuously monitoring antimicrobial resistance to control and prevent foodborne infections and maintain the efficacy of treatments for human salmonellosis.

Detection of chromosomal and plasmid mediated fluoroquinolone resistance among clinical isolates of &lt;em&gt;Salmonella&lt;/em&gt; species from urban and peri-urban settings of South India

Background: Enteric fever remains a major public health problem. Fluoroquinolones have became the drug of choice for the treatment of multidrug resistant Salmonella species. However, increased use of fluoroquinolone antibiotics leads to the emergence of Salmonella strains with reduced susceptibility to fluoroquinolones. This study was performed to detect chromosomal and plasmid mediated fluoroquinolone resistance among clinical isolates of Salmonella species from urban and periurban settings of South India. Method: A total of 250 blood culture isolates of Salmonella spp. from patients with suspected enteric fever attending tertiary care hospitals in urban and peri-urban settings of South India were included. Antibiotic susceptibility testing was performed using disc diffusion and agar dilution methods. Genes encoding Qnr, QepA and AAC(6′)-Ib-cr proteins and mutations in quinolone resistance determining regions (QRDRs) of genes encoding DNA gyrase (gyrA and gyrB) and toposiomerase IV (parC and parE) were detected using PCR and nucleotide sequencing analysis. Results: Most of the Salmonella isolates were intermediate resistant to ciprofloxacin. The majority of the isolates were sensitive to a third generation fluoroquinolone, levofloxacin. No mutation was detected in Salmonella isolates with ciprofloxacin MIC of 0.032 µg/ml whereas isolates with ciprofloxacin MIC of ≥4 µg/ml had triple mutation in QRDR. All the isolates were negative for plasmid encoded qnr genes, efflux pump (qepA) and fluoroquinolone acetylating aminoglycoside-(6)-N-acetyltransferase (aac(6')-Ib-cr) genes. Conclusion: We have observed Salmonella strains with reduced susceptibility to fluoroquinolone. A lower proportion of MDR Salmonella isolates was detected in this study. Fluoroquinolone resistant isolates were found to have chromosomal mutations in gyrA and parC genes and all the isolates were negative for plasmid encoded fluoroquinolone resistance genes.

Genomic analyses reveal presence of extensively drug-resistant Salmonella enterica serovars isolated from clinical samples in Guizhou province, China, 2019-2023.

The emergence of extensively drug-resistant (XDR) Salmonella in humans poses a significant public health and therapeutic challenge. However, limited data are available on XDR Salmonella isolates from Guizhou province, China. This study aimed to investigate the molecular epidemiology and resistance patterns of XDR Salmonella isolates from clinical samples in this region. A total of 931 Salmonella isolates were screened for XDR isolates through antimicrobial susceptibility testing. These XDR isolates were subjected to whole-genome sequencing (WGS) and bioinformatic analysis to further systematically investigating the molecular epidemiology and resistance patterns of XDR Salmonella isolates. Between 2019 and 2023, 931 Salmonella isolates were collected from clinical samples in Guizhou. Of these isolates, 51 (5.5%) were identified as XDR and classified into 16 serovars. Among the serovars, 15 corresponded to a specific sequence type, except for S. Typhimurium serovars. The predominant serovars, S. 1,4,[5],12:i:-, S. Enteritidis, and S. Kentucky, were divided into ST34, ST11, and ST198, respectively. Genomic analysis showed that all XDR isolates harbored at least eight antimicrobial resistance genes (ARGs) and multidrug efflux pumps. Highly prevalent point mutations in gyrA (D87 and S83) and parC (S80I) were detected, along with eight plasmid-mediated quinolone resistance (PMQR) genes. The qnrS1 gene was the most common (43.1%), followed by oqxA, aac-(6')-lb-cr variant, qnrB4, qnrS2, qnrA1, qepA2, and oqxB. The predominant β-lactamase gene was blaTEM-1 (54.9%), and blaCTX-M-55 (35.3%) was the most prevalent extended-spectrum β-lactamase subtype. Notably, blaNDM-1 gene was identified for the first time in Salmonella from Guizhou, and one S. 1,4,[5],12:i:- isolate contained the mcr-1.1 gene. ARGs profiles varied by serovars, with S. 1,4,[5],12:i:- isolates carrying the highest number. Ten plasmid types were identified, predominantly IncHI2/IncHI2A (47.5%). Key resistance genes such as tetA, PMQR, blaCTX-M , mcr-1.1, and blaNDM-1 were located on IncHI2/IncHI2A plasmids. Notably, 75.0% of the conjugative plasmids belonged to IncHI2/IncHI2A, indicating that horizontal gene transfer through conjugation facilitates ARGs dissemination. Core genome multilocus sequence typing (cgMLST) analysis revealed significant genetic diversity, with 39 core genome sequence types (cgSTs) identified and no evidence of outbreaks. The rising prevalence of XDR Salmonella in Guizhou province is concerning. Initial whole-genome sequencing (WGS) data provide critical insights for understanding and controlling XDR Salmonella infections, aiding public health officials in identifying emerging threats and trends.

Molecular Tracing and Molecular Characteristics of Strains from Campylobacter jejuni Bacteremia in a 23-Day-Old Infant in China.

Campylobacter jejuni (C. jejuni), a common foodborne zoonotic pathogen, usually causes gastroenteritis and rarely causes extraintestinal infections such as bacteremia. This study investigates a rare case of invasive C. jejuni bacteremia in a 23-day-old infant in Nanchang, China. Epidemiological data were collected from the infant's cohabitants (3). The cohabitants' anal swabs (3), milk powder (1), a feeding bottle (1), and kitchen items (3) were collected and screened for C. jejuni. Antimicrobial susceptibility testing was conducted, and whole genome sequencing was performed for genetic analysis, including whole genome multilocus sequence typing (wgMLST), single-nucleotide polymorphism, antimicrobial resistance (AMR) and virulence gene profiling. As a result, three C. jejuni strains were isolated from the infant, the infant's grandmother, and the feeding bottle. The results revealed that the three C. jejuni isolates were clonally related, sharing minimal genetic differences. The infant's grandmother, who had slaughtered a live chicken 4 days before the infant's illness, was identified as the likely source of transmission. AMR profiles showed resistance to fluoroquinolones and cephalosporins. The three isolates were found to carry the blaOXA-184 gene and a chromosomal mutation in gyrA (T86I). Additionally, 69 virulence genes were identified in all isolates, including those associated with adherence (4), glycosylation system (23), motility and export apparatus (38), cytolethal toxin (3), and invasion (1). This case represents the third reported instance of C. jejuni bacteremia in an infant in China. The analysis confirmed a transmission pathway from the grandmother.

Impact of meropenem exposure on fluoroquinolone and carbapenem resistance in Pseudomonas aeruginosa infection in inpatients in a Japanese university hospital: Insights into oprD mutations and efflux pump overexpression.

Impact of meropenem exposure on fluoroquinolone and carbapenem resistance in Pseudomonas aeruginosa infection in inpatients in a Japanese university hospital: Insights into oprD mutations and efflux pump overexpression.

Molecular epidemiology of a multidrug-resistant Shigella sonnei outbreak in Tunisia (2022-2023) using whole-genome sequencing.

Purpose. The prevalence of multidrug-resistant (MDR) Shigella sonnei is increasing globally, raising concerns for public health. In 2022, an outbreak of MDR S. sonnei was observed in Tunisia. We aimed to evaluate the genetic profile of S. sonnei isolates during the outbreak, including their clonal relationship, antimicrobial determinants and connection to international strains.Methods. In this study, we sequenced the whole genome of 24 S. sonnei strains collected from South Tunisia between July 2022 and November 2023. Bioinformatic analysis was conducted to confirm species identification, assign sequence types, determine core genome sequence types, analyse phylogenetic relationships and identify antimicrobial resistance determinants. Phylodynamic and phylogeographic analyses were performed to trace the spatiotemporal spread of the outbreak genotype.Results. Our investigation revealed that 23 out of 24 isolates were grouped into the HC10-20662 genotype within the 3.6.3 subclade. All isolates carried the blaCTX-M-15 gene associated with extended-spectrum beta-lactamase production, as well as the dfrA1 and qnrS1 genes, along with the D87G mutation in gyrA. Additionally, the sul2, tet(A) and mph(A) resistance genes were present in most isolates (96%, 96 and 83, respectively). Phylogeographic analysis suggested that the outbreak genotype likely spread in Europe before being introduced into Tunisia.Conclusion. To the best of our knowledge, this is the first MDR S. sonnei outbreak in the country. The HC10-20662 genotype appears to be responsible for a multi-country outbreak, affecting both Tunisia and Europe. Continued genomic surveillance efforts, both nationally and internationally, are essential for monitoring the dynamic evolution and global spread of MDR S. sonnei.

TtrAgo-mediated nucleic acid detection system and portable device for rapid detection of sexually transmitted diseases.

TtrAgo-mediated nucleic acid detection system and portable device for rapid detection of sexually transmitted diseases.

Genomic analysis of Brucella melitensis isolates recovered from humans in south Tunisia over 35 years between 1988 and 2022

Brucella melitensis is a zoonotic pathogen that poses a worldwide public health challenge. In recent years, whole-genome sequencing has become a widely accepted molecular typing method for the genomic epidemiology of brucellosis. This study reports the genomic characteristics of 24 B. melitensis strains isolated from human infections in southern Tunisia over 35 years (1988–2022). We utilized WGS to analyze the clonal relationships of these strains, their relatedness to international sequences, their antimicrobial resistance determinants, and their virulence factors. Our findings revealed a high genetic stability over three decades. All isolates were identified as B. melitensis biovar 3 and were assigned to the same sequence type, ST11, using the MLST-9 scheme. Using the MLST-21, Tunisian sequences shared 20 out of 21 alleles and were assigned to 2 closely related STs (ST89 and ST114). Phylogenetic analysis indicated that all Tunisian sequences were grouped into a single subcluster within lineage I, the West Mediterranean clade, and were highly related to other strains from the Maghreb region (Morocco and Algeria). Antimicrobial resistance analysis revealed no classical resistance determinants. However, mprF, bepCDEFG genes, and missense mutations in rpoB, gyrA, gyrB, and parC genes were identified. Virulence analysis identified 67 genes, predominantly involved in lipopolysaccharide biosynthesis and the type IV secretion system. To our knowledge, this study represents the first genomic investigation of B. melitensis strains circulating in Tunisia. Our findings underscore the importance of genomic surveillance in understanding the epidemiology and evolution of brucellosis in North Africa.

Mutational alterations in the QRDR regions associated with fluoroquinolone resistance in Pseudomonas aeruginosa of clinical origin from Savar, Dhaka.

Bacterial DNA gyrase and topoisomerase IV are the major targets of quinolone antibiotic, and mutational alterations in quinolone resistance determining regions (QRDR) serve as major mechanism of resistance in most bacterial species, including P. aeruginosa. The present investigation was aimed to study the molecular mechanism of fluoroquinolone resistance among clinical P. aeruginosa isolated from Dhaka, Bangladesh, including alterations in target sites of the antimicrobial action. Laboratory collection of 53 P. aeruginosa were subjected to conventional cultural and biochemical characterization, followed by molecular identification using 16S rDNA sequencing. Susceptibility to ciprofloxacin and levofloxacin was tested by disc diffusion method followed by MIC assay. Resistant isolates were analyzed for mutation in their QRDR regions of gyrA and parC, and subjected to PCR detection of plasmid mediated quinolone resistance (PMQR) genes qnrA, qnrS and qnrB. Among the isolates, 28% were found to be resistant to both fluoroquinolones tested. All of the fluoroquinolone resistant isolates carried a single mutation in gyrA (Thr-83-Ile), while 20% carried a single parC mutation (Ser-87-Leu). Higher level of MIC was observed in isolates carrying alterations at both sites. None of the isolates harbored any PMQR genes investigated, suggesting that chromosomal mutations in QRDR regions to be the major contributing factor for quinolone resistance in P. aeruginosa under investigation.

Genetic characterization and in silico serotyping of 62 Salmonella enterica isolated from Korean poultry operations

BackgroundThe conventional method of antigen-based serotyping for Salmonella poses challenges due to the necessity of utilizing over 150 antisera. More recently, in silico Salmonella serotyping has emerged as a predictive alternative. The purpose of this study was to predict the serovars of 62 Salmonella enterica strains isolated from Korean poultry operations and their genetic characteristics using whole genome sequencing. The analysis employed diverse methods, including ribosomal, and core genome multi-locus sequence typing (MLST), based on Salmonella In Silico Typing Resource (SISTR). Pangenome, clusters of orthologous groups (COG) analysis, and identification of virulence and antibiotic resistance genes were conducted.ResultsSalmonella enterica subspecies enterica serovars were observed and clustered based on the pangenome and phylogenetic tree: 21 Salmonella Albany (Albany), 13 Salmonella Bareilly (Bareilly), and 28 Salmonella Mbandaka (Mbandaka). The most frequently observed sequence types for the three serovars were ST292 in Albany, ST203 in Bareilly, and ST413 in Mbandaka. 18 antibiotic resistance genes showed varying presences based on the serovars, including Albany (qacEdelta1, tet(D), CARB-3 (blaCARB-3), and dfrA1) and Bareilly (aac(6')-ly). Intriguingly, a mutated gyrA (Ser83 → Phe, serine to phenylalanine) was observed in all 21 Albany strains, whereas Bareilly and Mbandaka carried the wild-type gyrA. Among 130 virulence genes analyzed, 107 were present in all 62 Salmonella strains, with Mbandaka strains exhibiting a higher prevalence of virulence genes related to fimbrial adherence compared to those of Albany and Bareilly.ConclusionsThe study identified distinct genetic characteristics among the three Salmonella serovars using whole genome sequencing. Albany carried a unique mutation in gyrA, occurring in the quinolone resistance-determining region. Additionally, the virulence gene profile of Mbandaka differed from the other serovars, particularly in fimbrial adherence genes. These findings demonstrate the effectiveness of in silico approaches in predicting Salmonella serovars and highlight genetic differences that may inform strategies for antibiotic resistance and virulence control, such as developing rapid diagnostic tools to detect the AMR (e.g. tet (D), and gyrA) or targeting serovar-specific virulence factors like fimbrial adherence genes in Mbandaka to mitigate pathogenicity.

Surveying genetic markers of antibiotic resistance and genomic background in Chlamydia trachomatis: insights from a multiplex NGS-based approach in clinical strains from Portugal.

To survey genetic markers of potential antimicrobial resistance (AMR) to macrolides and fluoroquinolones among Chlamydia trachomatis-positive samples from the collection of the Portuguese National Reference Laboratory for Sexually Transmitted Infections (STIs), and explore a multiplex PCR approach coupled with NGS to provide complementary information regarding a strain's genomic backbone. A total of 502 C. trachomatis-positive samples, mostly anorectal exudates, were subjected to PCR and sequencing of five targets, including loci potentially driving AMR (23S rRNA, gyrA and parC) and loci potentially informative about a strain's genomic backbone with emphasis on differentiation of lymphogranuloma venereum (LGV)/non-LGV and L2/L2b (a 9 bp insertion in pmpH, a 74 bp insertion upstream from CT105 and the polymorphic CT442). No samples evidenced 23S rRNA mutations recognizably linked to macrolide resistance. Three samples harboured the Ser83Ile mutation in GyrA putatively driving fluoroquinolone resistance: two recombinant L2-L2b/D-Da (0.4%) and one L2 (0.2%). The screened regions in pmpH, upstream CT105 and CT442 were fully concordant with LGV/non-LGV differentiation. As expected, the pmpH L2b-specific genetic trait locus was detected in all L2b and recombinant L2-L2b/D-Da ompA genotypes, but also in 96.0% of L2 specimens, which also likely possess an L2b genomic backbone. The insertion upstream from CT105 exhibited full LGV specificity, constituting a promising target for the development of rapid LGV diagnostic assays. This study contributes to enhancing the knowledge of C. trachomatis molecular epidemiology, suggesting that the known genetic determinants of AMR are not disseminated in clinical C. trachomatis strains, and presents an exploratory approach that can be suitable for LGV/non-LGV and L2/L2b genomic background differentiation.

Genotypic pattern of fluoroquinolone resistance among extended-spectrum beta-lactamase-producing &lt;em&gt;Escherichia coli&lt;/em&gt;

BACKGROUND Fluoroquinolone (FQ) is one of the therapeutic options for treating extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec) infection, but its use could increase the resistance level of ESBL-Ec. This study aimed to analyze the resistant genes responsible for ESBL production and FQ resistance among the ESBL-Ec isolated from healthy humans and communal wastewater. METHODS This was an observational study using stored isolates and laboratory data. Genome sequencing was done on 43 E. coli DNA isolates before resistance genes, mutations, and high-risk clones were examined through bioinformatic data analysis. RESULTS The analysis of 39 ESBL-Ec isolates showed ESBL genes, including blaCTX-M-55 (56%), blaCTX-M-15 (31%), and blaCTX-M-27 (8%). ESBL-Ec isolates exhibited mutations in gyrA (54%), gyrB (0%), parC (28%), and parE (10%). Plasmid-mediated quinolone resistance genes detected included qnrS1 (54%), qnrS13 (13%), qnrB2 (3%), aac(6’)-Ib-cr5 (3%), qepA (0%), and oqxAB (0%). ESBL and FQ resistance genes were simultaneously detected in 33 ESBL-Ec isolates, with high-risk clones identified as ST155, ST10, ST23, ST38, ST131, and ST69 Cplx. CONCLUSIONS ESBL and FQ resistance genes were simultaneously detected in ESBL-Ec isolated from healthy humans and communal wastewater.

Progression of antibiotic resistance in Neisseria meningitidis.

SUMMARYThe human pathogen Neisseria meningitidis (Nm) is the causative agent of invasive meningococcal disease (IMD), usually presenting as meningitis, bacteremia, or sepsis. Unlike Neisseria gonorrhoeae, antibiotic resistance in Nm has developed slowly. However, in the last two decades and with the reemergence of IMD following the COVID-19 pandemic, antibiotic-resistant Nm isolates, especially to penicillin and fluoroquinolones, have progressively increased. Recent worldwide studies of penicillin intermediate and resistant Nm isolates and the PubMLST global database reveal a notable increase in fully penicillin-resistant isolates since 2016, mediated by mosaic penA alleles or the β-lactamase genes blaROB-1 and blaTEM-1. Fluoroquinolone-resistant isolates, mediated by gyrA mutations, have increased since 2005. Also, while still exceptionally rare, four Nm isolates have been identified with third-generation cephalosporin-resistance since 2011. We review the emergence of antibiotic resistance determinants and lineages in Nm, the resistance to agents previously or currently used in treatment or chemoprophylaxis, and summarize updated treatment and prevention guidelines for IMD. Special populations (e.g., individuals on complement inhibitors) and antibiotic resistance in Nm urethritis isolates are also reviewed. The increasing number of resistant Nm isolates worldwide affects chemoprophylaxis and treatment options for IMD and emphasizes the need for enhanced global surveillance of antibiotic resistance in Nm.