The nature and epidemiology of OqxAB, a multidrug efflux pump

Biocides as drivers of antibiotic resistance: A critical review of environmental implications and public health risks

The widespread and indiscriminate use of biocides poses significant threats to global health, socioeconomic development, and environmental sustainability by accelerating antibiotic resistance. Bacterial resistance development is highly complex and influenced significantly by environmental factors. Increased biocide usage in households, agriculture, livestock farming, industrial settings, and hospitals produces persistent chemical residues that pollute soil and aquatic environments. Such contaminants contribute to the selection and proliferation of resistant bacteria and antimicrobial resistance genes (ARGs), facilitating their dissemination among humans, animals, and ecosystems. In this review, we conduct a critical assessment of four significant issues pertaining to this topic. Specifically, (i) the role of biocides in exerting selective pressure within the environmental resistome, thereby promoting the proliferation of resistant microbial populations and contributing to the global spread of antimicrobial resistance genes (ARGs); (ii) the role of biocides in triggering transient phenotypic adaptations in bacteria, including efflux pump overexpression, membrane alterations, and reduced porin expression, which often result in cross-resistance to multiple antibiotics; (iii) the capacity of biocides to disrupt bacteria and make the genetic content accessible, releasing DNA into the environment that remains intact under certain conditions, facilitating horizontal gene transfer and the spread of resistance determinants; (iv) the capacity of biocides to disrupt bacterial cells, releasing intact DNA into the environment and enhancing horizontal gene transfer of resistance determinants; and (iv) the selective interactions between biocides and bacterial biofilms in the environment, strengthening biofilm cohesion, inducing resistance mechanisms, and creating reservoirs for resistant microorganisms and ARG dissemination. Collectively, this review highlights the critical environmental and public health implications of biocide use, emphasizing an urgent need for strategic interventions to mitigate their role in antibiotic resistance proliferation.

The investigation of molecular epidemiological characteristics and resistance mechanism of tigecycline resistant Klebsiella pneumoniae from a large teaching hospital in southwest China, Chongqing

Background

Klebsiella pneumoniae is one of the main pathogens of nosocomial infection, among which carbapenems can be used for multidrug-resistant Klebsiella pneumoniae. However, in the past decade, the resistance rate of carbapenem-resistant Klebsiella pneumoniae has increased yearly. Tigecycline has good antibacterial activity in treating severe bacterial infections, but the reports of tigecycline resistance are increasing. This study aimed to investigate the mechanism of drug resistance and epidemiological characteristics of tigecycline-resistant Klebsiella pneumoniae (TRKP) in a large teaching hospital in southwest China, Chongqing.

Methods

We isolated 30 TRKP strains from this hospital between August 2021 and December 2023. By PCR and sequencing, we examined the presence and mutation rates of genes associated with tigecycline resistance, including acrR, oqxR, ramR, tmexC, tet(x), tet(A), tet(L), and rpsj, and performed efflux pump inhibition experiments to verify efflux pump activity. At the same time, real-time RT-PCR was used to detect the expression levels of efflux pump genes (acrB and oqxB) and ramA. To investigate the prevalence trend of TRKP in our hospital, we performed multi-site sequence typing (MLST) analysis.

Results

The mutation rates of ramR (73.3%) and tet(A) (63.3%) were significant. In efflux pump inhibition experiments, PaβN could reverse the resistance of 29 TRKP strains (96.7%) to tigecycline. Real-time RT-PCR results showed that acrB and ramA genes were up-regulated in 22 strains, while oqxB genes were overexpressed in only 4 strains. MLST analysis showed that these strains could be divided into 25 different ST subtypes, indicating that no outbreak of TRKP occurred in our hospital. In addition, two tmexCD-torpj positive strains, ST661 and ST1561, were identified for the first time.

Conclusion

The efflux pump acrB and tet(A) mutations are the primary mechanisms of resistance to tigecycline-resistant Klebsiella pneumoniae at our hospital. The ramR mutation can mediate efflux pump activity of acrB by up-regulating ramA overexpression.

Systematic review and meta-analysis of colistin heteroresistance in Klebsiella pneumoniae isolates

BACKGROUND

Antibiotic heteroresistance is a common phenotype observed in a variety of pathogenic bacteria such as K. pneumonia: A subpopulation of cells with a higher MIC than the dominant population is defined as heteroresistance. Several studies have demonstrated colistin heteroresistance in K. pneumonia leading to treatment failures. Therefore, we performed a systematic meta-analysis to summarize the current evidence on the prevalence of colistin heteroresistance in K. pneumonia isolates.

METHODS

Multiple databases were searched to find relevant literature from 2008 to 2024, including PubMed, Scopus, Embase, and Web of Science.

RESULTS

The meta-analysis included eighteen articles. According to the random effects model, the pooled proportion of heteroresistant K. pneumoniae was 0.315 (95% CI: 0.179-0.492). The heterogeneity was substantial, with Q [17] = 335.020, I² = 94.93%, and p < 0.001, suggesting that heteroresistance rates varied widely across the 18 included studies.

CONCLUSION

In conclusion, our findings revealed that a prevalence of colistin heteroresistant detected in approximately 31.5%, of K. pneumonia. These findings are obtained and highlighted in this meta-analysis as a new guidance document for diagnosing and treating K. pneumonia infections is needed to raise the awareness of infectious disease specialists, gastroenterologists, and microbiologists to the heteroresistance to colistin in patients with a K. pneumonia infection.

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics

Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determine, as isolates could not have been tested for resistance before an antibiotic was discovered. Historical collections, like the British National Collection of Type Cultures (NCTC), stretching back to 1885, provide a window into this history. Here we match 1,817 sequenced high-quality genomes from the NCTC collection to their respective year of isolation to study resistance genes before and concurrent with the age of antibiotics. Concordant with previous work, we find resistance genes in both pathogens and environmental samples before the age of antibiotics. While generally rare before the introduction of an antibiotic, we find an associated increase in frequency with antibiotic introduction. Finally, we observe a trend of resistance elements becoming both increasingly mobile and nested within multiple mobile elements as time goes on. More broadly, our findings suggest that likely-functional antibiotic resistance genes were circulating in clinically relevant isolates before the age of antibiotics, but human usage is associated with increasing both their overall prevalence and mobility.

Phenotypic Profiling of Tigecycline-resistant Klebsiella pneumoniae Strains Induced In vitro

Tigecycline is one of the last-resort treatment options for infections caused by carbapenem-resistant Klebsiella pneumoniae (KP). Unfortunately, tigecycline resistance is increasingly reported and causes an unprecedented public health crisis worldwide. Although studies on tigecycline resistance are expanding, the underlying mechanisms are not fully understood. The goal of this study is to investigate resistance-associated phenotypic changes in descendant tigecycline-resistant KP strains induced in vitro. Compared with the parental KP strains, descendant tigecycline-resistant strains grew slowly and reversed the susceptibility of carbapenems and aminoglycosides from resistance to sensitivity. The efflux pump inhibitor phenylalanyl-arginyl-β-naphthylamine (PAβN) could significantly decrease the MIC values of tigecycline in descendant strains, but the efflux pump inhibitor carbonyl cyanide-m-chlorophenylhydrazine (CCCP), verapamil, and reserpine could not. Although the descendant strains showed inconsistent (increased or decreased) biofilm formation and ethidium bromide uptake, they showed consistently decreased ethidium bromide efflux. As for the expression of efflux pumps and regulators determined by quantitative reverse transcript polymerase chain reaction (qRT-PCR), higher level of efflux pump acrAB-TolC and lower level of regulator ramA were observed in these descendant strains, while the efflux pump oqxAB and the other 6 regulators (acrR, rarA, marA, soxS, bpeT, and Rob) showed inconsistent (higher or lower) expression level. Thus, a global regulatory network driven by regulators (acrR, ramA, rarA, marA, soxS, bpeT, rob, etc.) alone or synergistically might play important roles in conferring tigecycline resistance in KP by regulation of efflux pumps (especially increasing acrAB-TolC) or other pathways.

The mobilome landscape of biocide-resistance in Brazilian ESKAPE isolates

The increasing frequency of antibiotic-resistant bacteria is a constant threat to global human health. Therefore, the pathogens of the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter spp.) are among the most relevant causes of hospital infections responsible for millions of deaths every year. However, little has been explored about the danger of microorganisms resistant to biocides such as antiseptics and disinfectants. Widely used in domestic, industrial, and hospital environments, these substances reach the environment and can cause selective pressure for resistance genes and induce cross-resistance to antibiotics, further aggravating the problem. Therefore, it is necessary to use innovative and efficient strategies to monitor the spread of genes related to resistance to biocides. Whole genome sequencing and bioinformatics analysis aiming to search for sequences encoding resistance mechanisms are essential to help monitor and combat these pathogens. Thus, this work describes the construction of a bioinformatics tool that integrates different databases to identify gene sequences that may confer some resistance advantage about biocides. Furthermore, the tool analyzed all the genomes of Brazilian ESKAPE isolates deposited at NCBI and found a series of different genes related to resistance to benzalkonium chloride, chlorhexidine, and triclosan, which were the focus of this work. As a result, the presence of resistance genes was identified in different types of biological samples, environments, and hosts. Regarding mobile genetic elements (MGEs), around 52% of isolates containing genes related to resistance to these compounds had their genes identified in plasmids, and 48.7% in prophages. These data show that resistance to biocides can be a silent, underestimated danger spreading across different environments and, therefore, requires greater attention.

Insights into durability against resistance from the antibiotic nitrofurantoin

Nitrofurantoin has shown exceptional durability against resistance over 70 years of use. This longevity stems from factors such as rapid achievement of therapeutic concentrations, multiple physiological targets against bacteria, low risk of horizontal gene transfer, and the need to acquire multiple mutations to achieve resistance. These combined features limit resistance emergence and spread of nitrofurantoin resistance. We propose nitrofurantoin as an exemplar for developing other durable treatments.

Occurrence of Plasmid-Mediated Quinolone Resistance and Carbapenemase-Encoding Genes in Pseudomonas aeruginosa Isolates from Nosocomial Patients in Aguascalientes, Mexico

Pseudomonas aeruginosa is a leading cause of healthcare-associated infections, which are related to substantial morbidity and mortality. The incidence of Plasmid-Mediated Quinolone Resistance (PMQR) determinants has been previously reported in this bacterium. However, there is limited information regarding the presence of PMQR and carbapenemase-encoding genes simultaneously. This study aims to analyze the prevalence of these determinants on P. aeruginosa strain isolated from clinical patients in the State of Aguascalientes, Mexico. Fifty-two P. aeruginosa isolates from nosocomial patients were collected from Centenario Hospital Miguel Hidalgo. This is a retrospective observational study conducted at a single center. Antibiotic susceptibility was tested using the Vitek-2 system. Only carbapenem-resistant isolates were included in this study. Carbapenemase-encoding genes and PMQR determinants were screened by polymerase chain reaction (PCR). Resistance rates of 100% were found on tigecycline and ceftriaxone. Of the 52 isolates, 34.6% were positive for the qnr genes, 46.2% for the oqxA gene, and 25% for the aac-(6')-lb gene. The most frequent carbapenemase genes found in the samples were blaOXA-51 (42.3%), blaOXA-1 (15.4%), and blaVIM (15.4%). blaOXA-51 co-carrying oqxA was detected in 21.1% of the isolates, blaOXA-51 co-carrying aac-(6')-lb in 11.5%, blaVIM co-carrying aac-(6')-lb in 3.8%, and blaKPC co-carrying oqxA in 5.8%. Systematic surveillance to detect carbapenemase-encoding genes and PMQR determinants, and rational prescription using the last-line drugs could help in preventing the dissemination of multidrug-resistant determinants.

Genome sequences of Enterobacter asburiae mcr-9 harboring and Enterobacter roggenkampii mcr-10 harboring isolated from a wastewater treatment plant in Japan

Severe infections caused by multi-drug-resistant Gram-negative rods pose a clinical threat due to their high mortality risk. The global spread of plasmid-mediated colistin-resistance genes has become a serious problem. In this study, we identified Enterobacter spp. harboring mcr-9 and mcr-10 from a wastewater treatment plant in Japan.

Metagenome mining divulges virulent and multidrug resistant Pseudomonas aeruginosa ST242 and Klebsiella michiganensis ST∗1b23 coinfecting an 8-month-old meningitis infant under ICU in Kampala, Uganda, East Africa

Pediatric meningitis is a global health problem, with insufficiently known pathogens and antibiotic resistance (AMR) especially in low-resource settings. Here, we sought to uncover the virulence and AMR of pathogens associated with infant meningitis, treated with ceftriaxone, in Kampala, Uganda. In a bid to isolate Klebsiella oxytoca, we coincidentally recovered a co-culture and challenged it with antibiotic susceptibility testing (AST) on a panel of 14 antibiotics. We then combined metagenome binning with antiSMASH/PRISM genome mining to unveil the pathogens, their virulence and molecular targets in relation to meningitis. From AST, the co-culture exhibited resistance to multiple aminoglycosides, fluroquinolones, and β-lactams, including ceftriaxone, the inherently used drug. From metagenome annotation, the first bin was identified as Pseudomonas aeruginosa ST242 and the second as Klebsiella michiganensis ST∗1b23. Among others, P. aeruginosa ST242 virulence factors include type 3 and type 6 secretion systems, biofilm, and nonribosomal peptides (NRPs) of the pyoverdine synthase operon, targeting claudin-5, a component of the tight junctions of the blood-brain barrier (BBB). The P. aeruginosa ST242 genome portrays intrinsic resistance to beta-lactamases (blaOXA-50 and blaPAO), aminoglycosides [aph(3')-IIb)], fluoroquinolones (crpP), tetracycline (tmexD2) and fosfomycin (fosA), among others. From K. michiganensis ST∗1b23 genome mining we elucidated a yersiniabactin-related metabolite, targeting the ligand-binding domain of the human polymeric immunoglobulin receptor (pIgR) and other components of the BBB. The K. michiganensis ST∗1b23 chromosome encodes the genes blaOXY-1 and OqxA/B, conferring resistance to β-lactams, fluoroquinolones, and trimethoprim respectively. Notably, we found one frameshift and nine substitution mutations conferring carbapenem and cephalosporin resistance mechanisms. Overall, our findings strongly suggest coinfection and a mechanistic crosstalk between P. aeruginosa ST242 and K. michiganensis ST∗1b23 in the pathogenesis of meningitis in this case. Importantly, ceftriaxone could be an inappropriate treatment choice for these pathogens. Hence, serious surveillance and experimental studies will improve the management of pediatric meningitis.

Whole genome sequencing reveals antibiotic resistance pattern and virulence factors in Klebsiella quasipneumoniae subsp. Similipneumoniae from Hospital wastewater in South-West, Nigeria

Klebsiella quasipneumoniae is a distinct species from K. pneumoniae, even though it is sometimes mistaken phenotypically for the latter in clinical situations. K. quasipneumoniae is a pathogen and this study aims at understanding the genomic antibiotic resistance and virulence characteristics of Klebsiella quasipneumoniae subsp. similipneumoniae (B105 strain) isolated from tertiary hospital wastewater and the potential risks associated with its environmental spread. The Illumina platform was used for whole-genome sequencing (WGS), the generated raw reads (de novo) was assembled using RAPT NCBI, while other standardized bioinformatics tools were utilized to validate and examine the landscape of the genome's antibiotic resistance and virulence factors. The K. quasipneumoniae subsp. similipneumoniae (B105 strain), belonged to sequence type 1422 and was resistant to ampicillin, amoxicillin-clavulanic acid, ceftazidime, cefepime, meropenem, tetracycline, but susceptible to gentamicin. The annotated genome acknowledged the presence of blaOKP-B-2, ompK 36, fosA5, oqxAB, virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (iutA), salmochelins (iroE, iroN), enterobactin siderophore, efllux pump (acrA, acrB) adherence, (mrkC, mrkD, and fimD) and two plasmids replicon IncFIB(K) and IncR. The study resonates the inadequacy of conventional microbiological identification methods to distinguish K. pneumoniae and K. quasipneumoniae and at the same time heightens the importance of using a genomic platform to extol the identity of K. quasipneumoniae subsp. similipneumoniae strain. Furthermore, the peculiarities of the acquired antimicrobial resistance and virulence genes, in this strain, are a potential risk to the environment.

In vitro evaluation of tigecycline synergy testing with nine antimicrobial agents against Enterobacter cloacae clinical strains

Enterobacterales (especially carbapenem-resistant) are considered an urgent threat to public health. The available antibiotic therapy is limited due to the increase of multidrug-resistant (MDR) strains. Tigecycline, a minocycline derivative, has emerged as a potential key agent in the treatment of MDR isolates. The aim of the study was to evaluate the synergistic effect of tigecycline in combination with nine antimicrobial agents-ceftazidime/avibactam, colistin, ertapenem, gentamicin, imipenem, levofloxacin, meropenem/vaborbactam, polymyxin B, and rifampicin. Eighty clinical Enterobacter cloacae strains were obtained from patients of two University Hospitals in Bialystok, Poland. The E-test method was used to determine synergistic interactions. Among all combinations, synergy was reported in 61% of cases, addition in 32%, and indifference in 7%. The highest synergy rates were observed in tigecycline combinations with: ceftazidime/avibactam (60/80; 75%), imipenem (60/80; 75%), polymyxin B (55/80; 68.75%) and rifampicin (55/80; 68.75%), while the lowest synergy rate was noted in tigecycline-levofloxacin (26/80; 32.5%). The tigecycline-gentamicin showed the highest rate of indifference; antagonism, was not observed in any combination. In conclusion, tigecycline appears more suitable for use in combination therapy rather than as monotherapy and can be effectively paired with various antimicrobial agents against MDR E. cloacae. Further research will be necessary to confirm these results.

Molecular epidemiological analysis of blaNDM-5-producing Klebsiella pneumoniae ST2407-K25 causing infection outbreaks in pediatric patients based on whole genome sequencing

BACKGROUND

Pediatric patients are vulnerable to the threat of carbapenem-resistant Klebsiella pneumoniae (CRKP) due to their limited immunity and few available antibiotics. Especially when these pathogens exhibit hypervirulent phenotypes, they are often associated with poor clinical outcomes.

METHODS

In this study, we investigated a CRKP outbreak in pediatric patients from 2019 to 2021 in a teaching hospital in China based on whole genome sequencing. We sequenced twenty-nine CRKP isolates isolated from unduplicated pediatric patients to understand their genetic relationships, virulence factors, resistance mechanisms, and transmission trajectories. Conjugation experiments were performed to evaluate the horizontal transfer ability of carbapenem resistance determinants in twenty-nine CRKP isolates. We then characterized these isolates for biofilm formation ability and serum resistance. Genetic relatedness, comparison of plasmids, and chromosomal locus variation of CRKP isolates were analyzed by bioinformatics.

RESULTS

All the isolates were carbapenemase-producers harbouring blaNDM-5. Among them, twenty-eight isolates belonged to the ST2407 group, with the consistent capsular serotype K25. The virulence-related factors: ureA, fim, ybtA, irp1/irp2, and mrkA were prevalent in these isolates. Additionally, most CRKP isolates showed moderately adherent biofilm formation. Although the ST2407 clonal group did not exhibit serum resistance, the heterogeneous level of serum resistance was related to the disruption of oqxR. Conjugation and WGS revealed that the blaNDM-5 carried by the twenty-eight CRKP ST2407 isolates was located on nonconjugative IncX3 plasmids associated with deleting the T4SS-encoding genes. Clonal transmission of CRKP ST2407 in pediatric patients was suggested by the phylogenetic tree.

CONCLUSIONS

Our study provides evidence of the clonal spread of blaNDM-5-producing K. pneumoniae in pediatric patients and the necessity for the T4SS system for horizontal transfer of the IncX3 plasmid carrying blaNDM-5. Additionally, the disruption of oqxR may have affected the serum resistance of CRKP. The results of this study emphasize the importance of continuously monitoring for CRKP infection in pediatric patients to prevent recurrent infections.

Discovery of clinical isolation of drug-resistant Klebsiella pneumoniae with overexpression of OqxB efflux pump as the decisive drug resistance factor

Background emergence of multidrug-resistant (MDR) bacterial strains is a public health concern that threatens global and regional security. Efflux pump-overexpressing MDR strains from clinical isolates are the best subjects for studying the mechanisms of MDR caused by bacterial efflux pumps. A Klebsiella pneumoniae strain overexpressing the OqxB-only efflux pump was screened from a clinical strain library to explore reverse OqxB-mediated bacterial resistance strategies. We identified non-repetitive clinical isolated K. pneumoniae strains using a matrix-assisted laser desorption/ionization time-of-flight (TOF) mass spectrometry clinical TOF-II (Clin-TOF-II) and susceptibility test screening against levofloxacin and ciprofloxacin. And the polymorphism analysis was conducted using pulsed-field gel electrophoresis. Efflux pump function of resistant strains is obtained by combined drug sensitivity test of phenylalanine-arginine beta-naphthylamide (PaβN, an efflux pump inhibitor) and detection with ethidium bromide as an indicator. The quantitative reverse transcription PCR was performed to assess whether the oqxB gene was overexpressed in K. pneumoniae isolates. Additional analyses assessed whether the oqxB gene was overexpressed in K. pneumoniae isolates and gene knockout and complementation strains were constructed. The binding mode of PaβN with OqxB was determined using molecular docking modeling. Among the clinical quinolone-resistant K. pneumoniae strains, one mediates resistance almost exclusively through the overexpression of the resistance-nodulation-division efflux pump, OqxB. Crystal structure of OqxB has been reported recently by N. Bharatham, P. Bhowmik, M. Aoki, U. Okada et al. (Nat Commun 12:5400, 2021, https://doi.org/10.1038/s41467-021-25679-0). The discovery of this strain will contribute to a better understanding of the role of the OqxB transporter in K. pneumoniae and builds on the foundation for addressing the threat posed by quinolone resistance.IMPORTANCEThe emergence of antimicrobial resistance is a growing and significant health concern, particularly in the context of K. pneumoniae infections. The upregulation of efflux pump systems is a key factor that contributes to this resistance. Our results indicated that the K. pneumoniae strain GN 172867 exhibited a higher oqxB gene expression compared to the reference strain ATCC 43816. Deletion of oqxB led a decrease in the minimum inhibitory concentration of levofloxacin. Complementation with oqxB rescued antibiotic resistance in the oqxB mutant strain. We demonstrated that the overexpression of the OqxB efflux pump plays an important role in quinolone resistance. The discovery of strain GN 172867 will contribute to a better understanding of the role of the OqxB transporter in K. pneumoniae and promotes further study of antimicrobial resistance.

Prevalence of plasmid-mediated quinolone resistance genes in extended-spectrum beta-lactamase producing Klebsiella pneumoniae isolates in northern Iran

Plasmid-mediated quinolone resistance (PMQR) in extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae (K. pneumoniae) contributes to treatment failures, extended hospital stays, and increased mortality percentages. We aimed to determine the prevalence of PMQR genes in ESBL-producing K. pneumoniae isolates from clinical samples in Babol, North of Iran region. This is the first study in this region to investigate this specific association. A total of 95 K. pneumoniae isolates were obtained from hospitalized patients with various clinical infections during March 2022 to February 2023. Disk diffusion and Combination disk method were performed to identification of antimicrobial resistance profiles and ESBL-producing strains. The presence of ESBL and PMQR genes among K. pneumoniae isolates was assessed using polymerase chain reaction (PCR) method. Of the isolates, 68 (71.57 %) were considered as ESBL-producers. The bla TEM, bla SHV and bla CTX-M genes were detected in 74.73 %, 57.89 %, and 41.05 % of K. pneumoniae isolates, respectively. Among the PMQR encoding genes, the highest and lowest frequency was associated to qepA (67.3 %) and qnrA (4.2 %), respectively. The frequency of qnrA, qnrB, qnrS, acc (6')-Ib-cr, qepA, oqxA, and oqxB genes in 26 MDR-Kp isolates was 11.53 % (n; 3), 69.23 % (n; 18), 65.38 % (n; 17), 73.07 % (n; 19), 80.76 % (n; 21), 84.61 % (n; 22), and 76.92 % (n; 20), respectively. Our result revealed of the 68 ESBL gene-positive isolates, 60 (88.23 %) were positive for the PMQR gene. The co-occurrence of these genes within resistant isolates suggests potential linkage on mobile genetic elements such as plasmids. These findings highlight the significant burden of PMQR determinants in ESBL-producing K. pneumoniae and underscore the urgent need for effective control measures. Implementing robust antimicrobial stewardship programs and strengthening drug-resistance surveillance and control protocols are crucial to prevent the spread of resistant isolates.

Molecular epidemiology of extended-spectrum beta-lactamase-producing-Klebsiella species in East Tennessee dairy cattle farms

Introduction

The rising prevalence of Extended-Spectrum Beta-Lactamase (ESBL)-producing Klebsiella species (spp.) poses a significant threat to human and animal health and environmental safety. To address this pressing issue, a comprehensive study was undertaken to elucidate the burden and dissemination mechanisms of ESBL-Klebsiella spp. in dairy cattle farms.

Methods

Fifty-seven Klebsiella species were isolated on CHROMagar™ ESBL plates and confirmed with MADLI-TOF MS and whole genome sequenced from 14 dairy farms.

Results and discussion

Six families of beta-lactamase (bla) (bla CTX-M, bla SHV, bla TEM, bla OXY, bla OXA, and bla SED) were detected in ESBL-Klebsiella spp. genomes. Most (73%) of isolates had the first three types of beta-lactamase genes, with bla SHV being the most frequent, followed by bla CTX-M. Most (93%) isolates harbored two or more bla genes. The isolates were genotypically MDR, with 26 distinct types of antibiotic resistance genes (ARGs) and point mutations in gyrA, gyrB, and parC genes. The genomes also harbored 22 different plasmid replicon types, including three novel IncFII. The IncFII and Col440I plasmids were the most frequent and were associated with bla CTXM-27 and qnrB19 genes, respectively. Eighteen distinct sequence types (STs), including eight isolates with novel STs of K. pneumoniae, were detected. The most frequently occurring STs were ST353 (n = 8), ST469 (n = 6), and the novel ST7501 (n = 6). Clusters of ESBL-Klebsiella strains with identical STs, plasmids, and ARGs were detected in multiple farms, suggesting possible clonal expansion. The same ESBL variant was linked to identical plasmids in different Klebsiella STs in some farms, suggesting horizontal spread of the resistance gene. The high burden and dual spread mechanism of ESBL genes in Klebsiella species, combined with the emergence of novel sequence types, could swiftly increase the prevalence of ESBL-Klebsiella spp., posing significant risks to human, animal, and environmental health. Immediate action is needed to implement rigorous surveillance and control measures to mitigate this risk.

Mutations in the efflux regulator gene oqxR provide a simple genetic switch for antimicrobial resistance in Klebsiella pneumoniae

Klebsiella pneumoniae is a pathogen of major concern in the global rise of antimicrobial resistance and has been implicated as a reservoir for the transfer of resistance genes between species. The upregulation of efflux pumps is a particularly concerning mechanism of resistance acquisition as, in many instances, a single point mutation can simultaneously provide resistance to a range of antimicrobials and biocides. The current study investigated mutations in oqxR, which encodes a negative regulator of the RND-family efflux pump genes, oqxAB, natively found in the chromosome of K. pneumoniae. Resistant mutants in four K. pneumoniae strains (KP6870155, NTUH-K2044, SGH10, and ATCC43816) were selected from single exposures to 30 µg/mL chloramphenicol and 12 mutants were selected for whole genome sequencing to identify mutations associated with resistance. Resistant mutants generated by single exposures to chloramphenicol, tetracycline, or ciprofloxacin at ≥4 X MIC were replica plated onto all three antibiotics to observe simultaneous cross-resistance to all compounds, indicative of a multidrug resistance phenotype. A variety of novel mutations, including single point mutations, deletions, and insertions, were found to disrupt oqxR leading to significant and simultaneous increases in resistance to chloramphenicol, tetracycline, and ciprofloxacin. The oqxAB-oqxR locus has been mobilized and dispersed on plasmids in many Enterobacteriaceae species and the diversity of these loci was examined to evaluate the evolutionary pressures acting on these genes. Comparison of the promoter regions of oqxR in plasmid-borne copies of the oqxR-oqxAB operon indicated that some constructs may produce truncated versions of the oqxR transcript, which may impact on oqxAB regulation and expression. In some instances, co-carriage of chromosomal and plasmid encoded oqxAB-oqxR was found in K. pneumoniae, implying that there is selective pressure to maintain and expand the efflux pump. Given that OqxR is a repressor of oqxAB, any mutation affecting its expression or function can lead to multidrug resistance. This is in contrast to antibiotic target site mutations that must occur in limited sequence space to be effective and not impact the fitness of the cell. Therefore, oqxR may act as a simple genetic switch to facilitate resistance via OqxAB mediated efflux.

Q48K mutation in the type IB nitroreductase NrmA is responsible for nitrofurantoin resistance in Enterococcus faecium

OBJECTIVES

Nitrofurantoin is recommended as first-line therapy for the optimal treatment of uncomplicated urinary tract infections (UTIs) caused by enterococci and Escherichia coli. However, the mechanisms of nitrofurantoin resistance in enterococci have not been elucidated. This study aimed to investigate the mechanisms of nitrofurantoin resistance in E. faecium, focusing on the role of the nitroreductase NrmA.

METHODS

Enterococcus strains isolated from the urinary tract samples were collected and were tested for nitrofurantoin susceptibility. Potential genes associated with nitrofurantoin resistance were screened in the NCBI nucleotide database and by polymerase chain reaction (PCR). Complementation assays and enzyme kinetic tests were performed to assess the impact of the Q48K mutation in NrmA on nitrofurantoin resistance.

RESULTS

Of the 128 E. faecium isolates tested, 59 (46.1%) were resistant to nitrofurantoin. Analysis revealed the presence of a type IB nitroreductase, designated NrmA, in all E. faecium strains studied, shared 18.7% sequence identity with nitroreductase NfsB in E. coli. Different from NrmA in nitrofurantoin-susceptible E. faecium, nitrofurantoin-resistant strains had a single amino acid substitution, i.e., a lysine instead of a glutamine at position 48 (Q48K mutation). Complementation assays of nitrofurantoin-resistant E. faecium HS17-112 showed that the nitrofurantoin minimal inhibitory concentration of the complemented strain HS17-112: pIB166-nrmA (wild type [WT]) decreased from 128 mg/L to 4 mg/L. Compared with NrmA (WT), NrmA (Q48K) showed significantly reduced catalytic efficiency, with a kcat/Km value decreasing from 0.122 µM-1 s-1 to 0.000042 µM-1 s-1.

CONCLUSION

The Q48K mutation in nitroreductase NrmA is responsible for nitrofurantoin resistance in E. faecium.

Occurrence, antimicrobial resistance and genomic features of Klebsiella pneumoniae from broiler chicken in Faisalabad, Pakistan

Introduction

The dissemination of antimicrobial resistance (AMR) in critical priority pathogens is a significant threat. Non-clinical reservoirs of AMR, such as agriculture and food production facilities, may contribute to the transmission of clinically relevant pathogens such as multidrug-resistant (MDR) Klebsiella pneumoniae. There is currently very limited knowledge regarding the population structure and genomic diversity of K. pneumoniae in poultry production in Pakistan.

Methods

We explored healthy broilers in a commercial farm from Faisalabad, Pakistan, and identified six K. pneumoniae strains from 100 broiler birds. We characterized the strains, determining clonality, virulence and antimicrobial resistance genes using next generation sequencing.

Results

The evaluation of antimicrobial susceptibility revealed that all the strains were MDR. Genomic analysis showed that 3/6 strains belonged to ST152, harbouring acquired resistance aminoglycosides [aadA2, aph(4')-Ia], β-lactams (blaSHV-187 , blaLAP2 ), fosfomycin (fosA6), tetracycline (tetA), trimethoprim (dfrA12), quinolone (qnrS1), sulphonamides (sul2) and phenicol (floR). All the strains harboured the efflux pump genes oqxA, oqxB, emrR, kpnG, kpnH, kpnF, baeR, mtdB and mtdC. All six strains encoded identical virulence profiles possessing six genes, i.e., ureA, iutA, entB, allS, fimH and mrkD. Phylogenomic analysis of the dominant sequence type (ST152) present in our dataset with publicly available genomes showed that the isolates clustered to strains mainly from human sources and could pose a potential threat to food safety and public health.

Discussion

The combination of these findings with antimicrobial use data would allow a better understanding of the selective pressures that may be driving the spread of AMR. This is the first report of MDR K. pneumoniae isolated from broiler hens in Pakistan, and the finding suggests that routine surveillance of WHO critical priority pathogens in such settings would be beneficial to the development of effective control strategies to reduce AMR.

Metagenomic analysis of the bacterial microbiome, resistome and virulome distinguishes Portuguese Serra da Estrela PDO cheeses from similar non-PDO cheeses: An exploratory approach

This study aimed to evaluate the microbiome, resistome and virulome of two types of Portuguese cheese using high throughput sequencing (HTS). Culture-dependent chromogenic methods were also used for certain groups/microorganisms. Eight samples of raw ewe's milk cheese were obtained from four producers: two producers with cheeses with a PDO (Protected Designation of Origin) label and the other two producers with cheeses without a PDO label. Agar-based culture methods were used to quantify total mesophiles, Enterobacteriaceae, Escherichia coli, Staphylococcus, Enterococcus and lactic acid bacteria. The presence of Listeria monocytogenes and Salmonella was also investigated. The selected isolates were identified by 16S rRNA gene sequencing and evaluated to determine antibiotic resistance and the presence of virulence genes. The eight cheese samples analyzed broadly complied with EC regulations in terms of the microbiological safety criteria. The HTS results demonstrated that Leuconostoc mesenteroides, Lactococcus lactis, Lactobacillus plantarum, Lacticaseibacillus rhamnosus, Enterococcus durans and Lactobacillus coryniformis were the most prevalent bacterial species in cheeses. The composition of the bacterial community varied, not only between PDO and non-PDO cheeses, but also between producers, particularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bacterial diversity than non-PDO cheeses, demonstrating that the diversity of spontaneously fermented foods is significantly higher in cheeses produced without the addition of food preservatives and dairy ferments. Despite complying with microbiological regulations, both PDO and non-PDO cheeses harbored potential virulence genes as well as antibiotic resistance genes. However, PDO cheeses exhibited fewer of these virulence and antibiotic resistance genes compared to non-PDO cheeses. Therefore, the combination of conventional microbiological methods and the metagenomic approach could contribute to improving the attribution of the PDO label to this type of cheese.

Effect of Mentha longifolia essential oil on oqxA efflux pump gene expression and biofilm formation in ciprofloxacin-resistant Klebsiella pneumoniae strains

Background and Objectives

Today, medicinal plants and their derivatives are considered to reduce the prevalence of antibiotic resistance. The aim of this study was to investigate the effect of Mentha longifolia essential oil on oqxA efflux pump gene expression and biofilm formation in ciprofloxacin-resistant Klebsiella pneumoniae strains.

Materials and Methods

A total of 50 clinical strains of K. pneumoniae resistant to ciprofloxacin were studied. The minimum inhibitory concentration (MIC) of M. longifolia essential oil and its synergistic effect with ciprofloxacin were determined using the microbroth dilution method and the fractional inhibitory concentration (FIC) method. Minimum biofilm inhibition concentration (MBIC) of M. longifolia essential oil was detected. The effect of essential oils on the expression level of the oqxA gene was detected by Real-time PCR.

Results

M. longifolia essential oil showed inhibitory activity against ciprofloxacin-resistant strains of K. pneumoniae. When M. longifolia essential oil was combined with ciprofloxacin, the MIC was reduced 2-4 times. In 28% of the strains, M. longifolia with ciprofloxacin showed a synergistic effect. M. longifolia essential oil reduces the strength of biofilm formation and alters the biofilm phenotype. A significant decrease in oqxA gene expression was observed in all isolates after treatment with M. longifolia essential oil.

Conclusion

Based on the results of this study, it was observed that supplementing M. longifolia essential oil can help reduce ciprofloxacin resistance and inhibit biofilm formation in fluoroquinolone-resistant K. pneumoniae strains.

Long-term antibiotic exposure landscapes and resistant Escherichia coli colonization in a densely populated setting

Antibiotic exposure is associated with resistant bacterial colonization, but this relationship can be obscured in community settings owing to horizontal bacterial transmission and broad distributions. Locality-level exposure estimates considering inhabitants' length of stay, exposure history, and exposure conditions of areas nearby could clarify these relationships. We used prescription data filled during 2010-2015 for 23 antibiotic types for members of georeferenced households in a population-based infectious disease surveillance platform. For each antibiotic and locality, we generated exposure estimates, expressed in defined daily doses (DDD) per 1000 inhabitant days of observation (IDO). We also estimated relevant environmental parameters, such as the distance of each locality to water, sanitation, and other amenities. We used data on ampicillin, ceftazidime, and trimethoprim-and-sulfamethoxazole resistant Escherichia coli colonization from stool cultures of asymptomatic individuals in randomly selected households. We tested exposure-colonization associations using permutation analysis of variance and logistic generalized linear mixed-effect models. Overall, exposure was highest for trimethoprim-sulfamethoxazole (1.8 DDD per 1000 IDO), followed by amoxicillin (0.7 DDD per 1000 IDO). Of 1,386 unique household samples from 195 locations tested between September 2015 and January 2016, 90%, 85% and 4% were colonized with E. coli resistant to trimethoprim and sulfamethoxazole, ampicillin, and ceftazidime, respectively. Ceftazidime-resistant E. coli colonization was common in areas with increased trimethoprim-sulfamethoxazole, cloxacillin, and erythromycin exposure. No association with any of the physical environmental variables was observed. We did not detect relationships between distribution patterns of ampicillin or trimethoprim-and-sulfamethoxazole resistant E. coli colonization and the risk factors assessed. Appropriate temporal and spatial scaling of raw antibiotic exposure data to account for evolution and ecological contexts of antibiotic resistance could clarify exposure-colonization relationships in community settings and inform community stewardship program.

Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana

OBJECTIVES

Comprehensive data on the genomic epidemiology of hospital-associated Klebsiella pneumoniae in Ghana are scarce. This study investigated the genomic diversity, antimicrobial resistance patterns, and clonal relationships of 103 clinical K. pneumoniae isolates from five tertiary hospitals in Southern Ghana-predominantly from paediatric patients aged under 5 years (67/103; 65%), with the majority collected from urine (32/103; 31%) and blood (25/103; 24%) cultures.

METHODS

We generated hybrid Nanopore-Illumina assemblies and employed Pathogenwatch for genotyping via Kaptive [capsular (K) locus and lipopolysaccharide (O) antigens] and Kleborate (antimicrobial resistance and hypervirulence) and determined clonal relationships using core-genome MLST (cgMLST).

RESULTS

Of 44 distinct STs detected, ST133 was the most common, comprising 23% of isolates (n = 23/103). KL116 (28/103; 27%) and O1 (66/103; 64%) were the most prevalent K-locus and O-antigen types. Single-linkage clustering highlighted the global spread of MDR clones such as ST15, ST307, ST17, ST11, ST101 and ST48, with minimal allele differences (1-5) from publicly available genomes worldwide. Conversely, 17 isolates constituted novel clonal groups and lacked close relatives among publicly available genomes, displaying unique genetic diversity within our study population. A significant proportion of isolates (88/103; 85%) carried resistance genes for ≥3 antibiotic classes, with the blaCTX-M-15 gene present in 78% (n = 80/103). Carbapenem resistance, predominantly due to blaOXA-181 and blaNDM-1 genes, was found in 10% (n = 10/103) of the isolates.

CONCLUSIONS

Our findings reveal a complex genomic landscape of K. pneumoniae in Southern Ghana, underscoring the critical need for ongoing genomic surveillance to manage the substantial burden of antimicrobial resistance.

Current insights into the effects of cationic biocides exposure on Enterococcus spp

Cationic biocides (CBs), such as quaternary ammonium compounds and biguanides, are critical for controlling the spread of bacterial pathogens like Enterococcus spp., a leading cause of multidrug-resistant healthcare-associated infections. The widespread use of CBs in recent decades has prompted concerns about the potential emergence of Enterococcus spp. populations exhibiting resistance to both biocides and antibiotics. Such concerns arise from their frequent exposure to subinhibitory concentrations of CBs in clinical, food chain and diverse environmental settings. This comprehensive narrative review aimed to explore the complexity of the Enterococcus' response to CBs and of their possible evolution toward resistance. To that end, CBs' activity against diverse Enterococcus spp. collections, the prevalence and roles of genes associated with decreased susceptibility to CBs, and the potential for co- and cross-resistance between CBs and antibiotics are reviewed. Significant methodological and knowledge gaps are identified, highlighting areas that future studies should address to enhance our comprehension of the impact of exposure to CBs on Enterococcus spp. populations' epidemiology. This knowledge is essential for developing effective One Health strategies that ensure the continued efficacy of these critical agents in safeguarding Public Health.

Whole-Genome Sequencing of Human and Porcine Escherichia coli Isolates on a Commercial Pig Farm in South Africa

Escherichia coli is an indicator micro-organism in One Health antibiotic resistance surveillance programs. The purpose of the study was to describe and compare E. coli isolates obtained from pigs and human contacts from a commercial farm in South Africa using conventional methods and whole-genome sequencing (WGS). Porcine E. coli isolates were proportionally more resistant phenotypically and harbored a richer diversity of antibiotic resistance genes as compared to human E. coli isolates. Different pathovars, namely ExPEC (12.43%, 21/169), ETEC (4.14%, 7/169), EPEC (2.96%, 5/169), EAEC (2.96%, 5/169) and STEC (1.18%, 2/169), were detected at low frequencies. Sequence type complex (STc) 10 was the most prevalent (85.51%, 59/169) among human and porcine isolates. Six STcs (STc10, STc86, STc168, STc206, STc278 and STc469) were shared at the human-livestock interface according to multilocus sequence typing (MLST). Core-genome MLST and hierarchical clustering (HC) showed that human and porcine isolates were overall genetically diverse, but some clustering at HC2-HC200 was observed. In conclusion, even though the isolates shared a spatiotemporal relationship, there were still differences in the virulence potential, antibiotic resistance profiles and cgMLST and HC according to the source of isolation.

Could traces of fluoroquinolones in food induce ciprofloxacin resistance in Escherichia coli and Klebsiella pneumoniae? An in vivo study in Galleria mellonella with important implications for maximum residue limits in food

We hypothesized that the residual concentrations of fluoroquinolones allowed in food (acceptable daily intake-ADIs) could select for ciprofloxacin resistance in our resident microbiota. We developed models of chronic Escherichia coli and Klebsiella pneumoniae infection in Galleria mellonella larvae and exposed them to ADI doses of ciprofloxacin via single dosing and daily dosing regimens. The emergence of ciprofloxacin resistance was assessed via isolation of the target bacteria in selective agar plates. Exposure to as low as one-tenth of the ADI dose of the single and daily dosing regimens of ciprofloxacin resulted in the selection of ciprofloxacin resistance in K. pneumoniae but not E. coli. This resistance was associated with cross-resistance to doxycycline and ceftriaxone. Whole genome sequencing revealed inactivating mutations in the transcription repressors, ramR and rrf2, as well as mutations in gyrA and gyrB. We found that ciprofloxacin doses 10-fold lower than those classified as acceptable for daily intake could induce resistance to ciprofloxacin in K. pneumoniae. These results suggest that it would be prudent to include the induction of antimicrobial resistance as a significant criterion for determining ADIs and the associated maximum residue limits in food.IMPORTANCEThis study found that the concentrations of ciprofloxacin/enrofloxacin allowed in food can induce de novo ciprofloxacin resistance in Klebsiella pneumoniae. This suggests that it would be prudent to reconsider the criteria used to determine "safe" upper concentration limits in food.

Antibiotic prescribing practice using WHO Access, Watch and Reserve classification and its determinants among outpatient prescriptions dispensed to elderly population in six community chain pharmacies in Asmara, Eritrea: a cross-sectional study

OBJECTIVE

To assess antibiotic prescribing practice and its determinants among outpatient prescriptions dispensed to the elderly population.

DESIGN

A prescription-based, cross-sectional study.

SETTING

Six community chain pharmacies in Asmara, Eritrea.

PARTICIPANTS

All outpatient prescriptions dispensed to the elderly population (aged 65 and above) in the six community chain pharmacies in Asmara, Eritrea.

DATA COLLECTION AND ANALYSIS

Data were collected retrospectively, between 16 June 2023 and 16 July 2023. Antibiotic prescribing practice was assessed using the 2023 World Health Organization (WHO) Access, Watch and Reserve (AWaRe) classification system. Descriptive statistics and logistic regression were performed using IBM SPSS (V.26.0). P values less than 0.05 were considered as significant.

RESULTS

Of the 2680 outpatient prescriptions dispensed to elderly population, 35.8% (95% CI: 34.0, 37.6) contained at least one antibiotic. Moreover, a total of 1061 antibiotics were prescribed to the elderly population. The most commonly prescribed antibiotics were ciprofloxacin (n=322, 30.3%) and amoxicillin/clavulanic acid (n=145, 13.7%). The Access category accounted for the majority of antibiotics (53.7%) with 32.1% from the Watch category. Prescriber qualification (Adjusted Odds Ratio (AOR)= 0.60, 95% CI: 0.44, 0.81) and polypharmacy (AOR= 2.32, 95% CI: 1.26, 4.27) were significant determinants of antibiotic prescribing in the elderly population. Besides, sex (AOR=0.74, 95% CI: 0.56, 0.98), prescriber qualification (AOR=0.49, 95% CI: 0.30 to0.81) and level of health facility (AOR 0.52, 95% CI 0.34 to 0.81) were significant determinants of a Watch antibiotic prescription.

CONCLUSION

Antibiotics were prescribed to a considerable number of the elderly population, with more than half of them falling into the Access category. Further efforts by policy-makers are needed to promote the use of Access antibiotics while reducing the use of Watch antibiotics to mitigate risks associated with antimicrobial resistance.

Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies

OBJECTIVES

Antibiotic-resistant Klebsiella pneumoniae is a human pathogen of major global concern due to its ability to cause multiple severe diseases that are often difficult to treat therapeutically. This study aimed to investigate the resistome of local clinical K. pneumoniae isolates.

METHODS

Herein, we used a whole genome sequencing approach and bioinformatics tools to reconstruct the resistome of 10 clinical K. pneumoniae isolates and one clinical isolate of the closely related Klebsiella quasipneumoniae obtained from patients from three major hospitals in Trinidad, West Indies.

RESULTS

The results of the study revealed the presence of a complex antibiotic-resistant armoury among the local isolates with multiple resistance mechanisms involving (i) inactivation of antibiotics, (ii) efflux pumps, (iii) antibiotic target alteration, protection, and replacement against antibiotics, and (iv) altered porin protein that reduced the permeability to antibiotics. Several resistance genes such as blaCTX-M-15, blaTEM-1B, blaSHV-28, blaKPC-2, oqxA, sul1, tetD, aac(6')-Ib-cr5, aph(6)-Id, and fosA6, which are known to confer resistance to antibiotics used to treat K. pneumoniae infections. In most cases, the resistance genes were flanked by mobile elements, including insertion sequences and transposons, which facilitate the spread of these genetic features among related organisms.

CONCLUSION

This is the first comprehensive study to thoroughly investigate the resistome of clinical K. pneumoniae isolates and K. quasipneumoniae from Trinidad, West Indies. These findings suggest that monitoring K. pneumoniae and its genome-wide antibiotic resistance features in clinical strains would be of critical importance for guiding antibiotic stewardship programs and improving regional disease management systems for this pathogen.

Biocide resistance in Klebsiella pneumoniae: a narrative review

Klebsiella pneumoniae is among the World Health Organization's list of priority pathogens, notorious for its role in causing healthcare-associated infections and neonatal sepsis globally. Containment of K. pneumoniae transmission depends on the continued effectiveness of antimicrobials and of biocides used for topical antisepsis and surface disinfection. Klebsiella pneumoniae is known to disseminate antimicrobial resistance (AMR) through a large auxiliary genome made up of plasmids, transposons and integrons, enabling it to evade antimicrobial killing through the use of efflux systems and biofilm development. Because AMR mechanisms are also known to impart tolerance to biocides, AMR is frequently linked with biocide resistance (BR). However, despite extensive research on AMR, there is a gap in knowledge about BR and the extent to which AMR and BR mechanisms overlap remains debatable. The aim of this paper is to review and summarise the current knowledge on the determinants of BR in K. pneumoniae and highlight content areas that require further inquiry.

Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs

Introduction

Carbapenem and colistin-resistant Enterobacteriaceae, including Klebsiella pneumoniae, have become a growing global concern, posing a significant threat to public health. Currently, there is limited information about the genetic background of carbapenem and colistin-resistant K. pneumoniae isolates infecting humans and dogs in Thailand. This study aimed to characterize carbapenem and colistin-resistant genes in six resistant K. pneumoniae clinical isolates (three from humans and three from dogs) which differed in their pulse field gel electrophoresis profiles.

Methods

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), antimicrobial susceptibility testing, and whole-genome sequencing were employed to identify and analyze the isolates.

Results and discussion

All six isolates were carbapenemase-producing K. pneumoniae isolates with chromosomally carried blaSHV, fosA, oqxA and oqxB genes, as well as nine to 21 virulence genes. The isolates belonged to five multilocus sequence types (STs): one isolate from a human and one from a dog belonged to ST16, with the other two human isolates being from ST340 and ST1269 and the other two dog isolates were ST147 and ST15. One human isolate and two dog isolates harbored the same blaOXA-232 gene on the ColKP3 plasmid, and one dog isolate carried the blaOXA-48 gene on the IncFII plasmid. Notably, one human isolate exhibited resistance to colistin mediated by the mcr-3.5 gene carried on the IncFII plasmid, which co-existed with resistance determinants to other antibiotics, including aminoglycosides and quinolones. In conclusion, this study provides a comprehensive characterization of both chromosome- and plasmid-mediated carbapenem and colistin resistance in a set of K. pneumoniae clinical isolates from unrelated humans and dogs in Thailand. The similarities and differences found contribute to our understanding of the potential widescale dissemination of these important resistance genes among clinical isolates from humans and animals, which in turn may contribute to outbreaks of emerging resistant clones in hospital settings.

Draft genome of the Klebsiella pneumoniae 24Kpn33 and complete sequence of its pCOL-1, a plasmid related to the blaKPC-2 acquisition in Pseudomonas aeruginosa

We report the draft genome of a clinical multi-resistant Klebsiella pneumoniae (24Kpn33) isolate, whose genome (5.7 Mbp) harbored 17 antibiotic resistance genes, including blaKPC-2. Notably, this gene was mobilized within the IncP-6 pCOL-1 plasmid, the first genetic platform related to the acquisition and dissemination of the blaKPC-2 in Pseudomonas aeruginosa.

Molecular mechanisms of tigecycline-resistance among Enterobacterales

The global emergence of antimicrobial resistance to multiple antibiotics has recently become a significant concern. Gram-negative bacteria, known for their ability to acquire mobile genetic elements such as plasmids, represent one of the most hazardous microorganisms. This phenomenon poses a serious threat to public health. Notably, the significance of tigecycline, a member of the antibiotic group glycylcyclines and derivative of tetracyclines has increased. Tigecycline is one of the last-resort antimicrobial drugs used to treat complicated infections caused by multidrug-resistant (MDR) bacteria, extensively drug-resistant (XDR) bacteria or even pan-drug-resistant (PDR) bacteria. The primary mechanisms of tigecycline resistance include efflux pumps' overexpression, tet genes and outer membrane porins. Efflux pumps are crucial in conferring multi-drug resistance by expelling antibiotics (such as tigecycline by direct expelling) and decreasing their concentration to sub-toxic levels. This review discusses the problem of tigecycline resistance, and provides important information for understanding the existing molecular mechanisms of tigecycline resistance in Enterobacterales. The emergence and spread of pathogens resistant to last-resort therapeutic options stands as a major global healthcare concern, especially when microorganisms are already resistant to carbapenems and/or colistin.

Mechanisms of Antibiotic Resistance and Developments in Therapeutic Strategies to Combat Klebsiella pneumoniae Infection

Infections with drug-resistant bacteria have become one of the greatest public health challenges, and K. pneumoniae is among the top six drug-resistant bacteria. K. pneumoniae often causes nosocomial infections, leading to illnesses such as pneumonia, liver abscesses, soft tissue infections, urinary tract infections, bacteremia, and in some cases death. As the pathogen continues to evolve and its multidrug resistance increases, K. pneumoniae poses a direct threat to humans. Drug resistance in K. pneumoniae may occur due to the formation of biofilms, efflux pumps, and the production of β-lactamases. In many cases, resistance is further enhanced by enzymatic modification and loss of porins. Drug resistance to K. pneumoniae has led to a decline in the effectiveness of conventional therapies against this pathogen. Therefore, there is an urgent need to accelerate the development of new antibiotics and explore new therapeutic approaches such as antimicrobial peptides, phages, traditional Chinese medicine, immunotherapy, Antimicrobial nanoparticle technology, antisense oligonucleotides and gene editing technologies. In this review, we discuss the mechanisms of drug resistance in K. pneumoniae and compare several new potential therapeutic strategies to overcome drug resistance in the treatment of K. pneumoniae infections.

A Study of Resistome in Mexican Chili Powder as a Public Health Risk Factor

Chili powder is an important condiment around the world. However, according to various reports, the presence of pathogenic microorganisms could present a public health risk factor during its consumption. Therefore, microbiological quality assessment is required to understand key microbial functional traits, such as antibiotic resistance genes (ARGs). In this study, metagenomic next-generation sequencing (mNGS) and bioinformatics analysis were used to characterize the comprehensive profiles of the bacterial community and antibiotic resistance genes (ARGs) in 15 chili powder samples from different regions of Mexico. The initial bacterial load showed aerobic mesophilic bacteria (AMB) ranging between 6 × 103 and 7 × 108 CFU/g, sporulated mesophilic bacteria (SMB) from 4.3 × 103 to 2 × 109 CFU/g, and enterobacteria (En) from <100 to 2.3 × 106 CFU/g. The most representative families in the samples were Bacillaceae and Enterobacteriaceae, in which 18 potential pathogen-associated species were detected. In total, the resistome profile in the chili powder contained 68 unique genes, which conferred antibiotic resistance distributed in 13 different classes. Among the main classes of antibiotic resistance genes with a high abundance in almost all the samples were those related to multidrug, tetracycline, beta-lactam, aminoglycoside, and phenicol resistance. Our findings reveal the utility of mNGS in elucidating microbiological quality in chili powder to reduce the public health risks and the spread of potential pathogens with antibiotic resistance mechanisms.

Identification of the Major Facilitator Superfamily Efflux Pump KpsrMFS in Klebsiella pneumoniae That Is Down-Regulated in the Presence of Multi-Stress Factors

Efflux pumps play important roles in bacterial detoxification and some of them are stress-response elements that are up-regulated when the host is treated with antibiotics. However, efflux pumps that are down-regulated by stimulations are rarely discovered. Herein, we analyzed multiple transcriptome data and discovered a special (Major Facilitator Superfamily) MFS efflux pump, KpsrMFS, from Klebsiella pneumoniae, which was down-regulated when treated with antibiotics or extra carbon sources. Interestingly, overexpression of kpsrmfs resulted in halted cell growth in normal conditions, while the viable cells were rarely affected. The function of KpsrMFS was further analyzed and this efflux pump was determined to be a proton-driven transporter that can reduce the intracellular tetracycline concentration. In normal conditions, the expression of kpsrmfs was at a low level, while artificial overexpression of it led to increased endogenous reactive oxygen species (ROS) production. Moreover, by comparing the functions of adjacent genes of kpsrmfs, we further discovered another four genes that can confer similar phenotypes, indicating a special regulon that regulates cell growth. Our work provides new insights into the roles of efflux pumps and suggests a possible regulon that may regulate cell growth and endogenous ROS levels.

High-level nitrofurantoin resistance in a clinical isolate of Klebsiella pneumoniae: a comparative genomics and metabolomics analysis

Nitrofurantoin is a commonly used chemotherapeutic agent in the treatment of uncomplicated urinary tract infections caused by the problematic multidrug resistant Gram-negative pathogen Klebsiella pneumoniae. The present study aims to elucidate the mechanism of nitrofurantoin action and high-level resistance in K. pneumoniae using whole-genome sequencing (WGS), qPCR analysis, mutation structural modeling and untargeted metabolomic analysis. WGS profiling of evolved highly resistant mutants (nitrofurantoin minimum inhibitory concentrations > 256 mg/L) revealed modified expression of several genes related to membrane transport (porin ompK36 and efflux pump regulator oqxR) and nitroreductase activity (ribC and nfsB, involved in nitrofurantoin reduction). Untargeted metabolomics analysis of total metabolites extracted at 1 and 4 h post-nitrofurantoin treatment revealed that exposure to the drug caused a delayed effect on the metabolome which was most pronounced after 4 h. Pathway enrichment analysis illustrated that several complex interrelated metabolic pathways related to nitrofurantoin bacterial killing (aminoacyl-tRNA biosynthesis, purine metabolism, central carbohydrate metabolism, and pantothenate and CoA biosynthesis) and the development of nitrofurantoin resistance (riboflavin metabolism) were significantly perturbed. This study highlights for the first time the key role of efflux pump regulator oqxR in nitrofurantoin resistance and reveals global metabolome perturbations in response to nitrofurantoin, in K. pneumoniae.IMPORTANCEA quest for novel antibiotics and revitalizing older ones (such as nitrofurantoin) for treatment of difficult-to-treat Gram-negative bacterial infections has become increasingly popular. The precise antibacterial activity of nitrofurantoin is still not fully understood. Furthermore, although the prevalence of nitrofurantoin resistance remains low currently, the drug's fast-growing consumption worldwide highlights the need to comprehend the emerging resistance mechanisms. Here, we used multidisciplinary techniques to discern the exact mechanism of nitrofurantoin action and high-level resistance in Klebsiella pneumoniae, a common cause of urinary tract infections for which nitrofurantoin is the recommended treatment. We found that the expression of multiple genes related to membrane transport (including active efflux and passive diffusion of drug molecules) and nitroreductase activity was modified in nitrofurantoin-resistant strains, including oqxR, the transcriptional regulator of the oqxAB efflux pump. Furthermore, complex interconnected metabolic pathways that potentially govern the nitrofurantoin-killing mechanisms (e.g., aminoacyl-tRNA biosynthesis) and nitrofurantoin resistance (riboflavin metabolism) were significantly inhibited following nitrofurantoin treatment. Our study could help inform the improvement of nitrofuran derivatives, the development of new pharmacophores, or drug combinations to support the resurgence of nitrofurantoin in the management of multidrug resistant K. pneumouniae infection.

A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life

Antibiotic resistance genes (ARGs) are prevalent in the infant gut microbiota and make up the intestinal resistome, representing a community ARG reservoir. This study focuses on the dynamics and persistence of ARGs in the early gut microbiota, and the effect of early exposures therein. We leveraged 2,328 stool metagenomes from 475 children in the HELMi cohort and the available parental samples to study the diversity, dynamics, and intra-familial sharing of the resistome during the first two years of life. We found higher within-family similarity of the gut resistome composition and ARG load in infant-mother pairs, and between spouses, but not in father-infant pairs. Early gut microbiota composition and development correlated with the ARG load; Bacteroides correlated positively and Bifidobacterium negatively with the load, reflecting the typical resistance levels in these taxa. Caesarean delivered infants harbored lower ARG loads, partly reflecting the scarcity of Bacteroides compared to vaginally delivered. Exposure to intrapartum or post-natal antibiotics showed only modest associations with the ARG load and composition, mainly before 12 months. Our results indicate that the resistome is strongly driven by the normal development of the microbiota in early life, and suggest importance of longer evolution of ARGs over effects of recent antibiotic exposure.

Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients

Despite recognition of the immediate impact of infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-Klebsiella pneumoniae species complex and ESBL-Escherichia coli in individual patients over time, we performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-K. pneumoniae species complex and 284 ESBL-E. coli isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-K. pneumoniae species complex, and 83.6% of patients colonized with ESBL-E. coli. We frequently observed isolates of the same strain recovered from different body sites associated with either colonization or infection. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at prolonged risk of recurrent infection with colonizing strains.

Longitudinal monitoring reveals the emergence and spread of blaGES-5-harboring carbapenem-resistant Klebsiella quasipneumoniae in a Hong Kong hospital wastewater discharge line

Testing hospital wastewater (HWW) is potentially an effective, long-term approach for monitoring trends in antimicrobial resistance (AMR) patterns in health care institutions. Over a year, we collected wastewater samples from the clinical and non-clinical sites of a tertiary hospital and from a downstream wastewater treatment plant (WWTP). We focused on the extent of carbapenem resistance among Enterobacteriaceae isolates given their clinical importance. Escherichia coli and Klebsiella spp. were the most frequently isolated Enterobacteriaceae species at all sampling sites. Additionally, a small number of isolates belonging to ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), except K. pneumoniae, were detected. Of the 232 Klebsiella spp. isolates, 100 (43.1 %) were multi-drug resistant (MDR), with 46 being carbapenem-resistant. Most of these carbapenem-resistant isolates were K. quasipneumoniae (CRKQ) (n = 44). All CRKQ isolates were isolated from the wastewater of a clinical site that includes intensive care units, which also yielded significantly more multi-drug resistant isolates compared to all other sampling sites. Among the CRKQ isolates, blaGES-5 genes (n = 42) were the primary genetic determinant of carbapenem resistance. Notably, three different CRKQ isolates, collected within the same month in HWW and the influent and effluent flow of the WWTP, shared >99 % sequence similarity between their blaGES-5 genes and between their flanking regions and upstream integron-integrase region. The influent isolate was phylogenetically close to K. quasipnuemoniae isolates from wastewater collected in Japan. Its blaGES-5 gene and surrounding sequences were > 99 % identical to blaGES-24 genes found in the Japanese isolates. Our results suggest that testing samples from sites located closer to hospitals could support antibiotic stewardship programs compared to samples collected further downstream. Moreover, testing samples collected regularly from WWTPs may reflect the local and global spread of pathogens and their resistances.

Nitrofurantoin resistance as an indicator for multidrug resistance: an assessment of Escherichia coli urinary tract specimens in England, 2015-19

Objectives

To determine whether MDR occurs more frequently in nitrofurantoin-resistant Escherichia coli urinary isolates in England, compared with nitrofurantoin-susceptible isolates.

Methods

Using routine E. coli urine isolate antibiotic susceptibility laboratory surveillance data for England, 2015-19 inclusive, the percentage of MDR or XDR phenotype was estimated for nitrofurantoin-susceptible and nitrofurantoin-resistant laboratory-reported urinary tract samples by region, patient sex and age group.

Results

Resistance to nitrofurantoin among E. coli urinary samples decreased slightly year on year from 2.9% in 2015 to 2.3% in 2019. Among E. coli UTIs tested for nitrofurantoin susceptibility and  ≥3 additional antibiotics, the percentage that were MDR was consistently 15%-20% percentage points higher for nitrofurantoin-resistant isolates compared with nitrofurantoin-susceptible isolates. Similarly, the percentage of isolates with an XDR phenotype was higher among nitrofurantoin-resistant versus -susceptible isolates (8.7% versus 1.4%, respectively, in 2019); this disparity was greater in male patients, although variation was seen by age group in both sexes. Regional variation was also noted, with the highest MDR percentage amongst nitrofurantoin-resistant E. coli urinary samples in the London region (36.7% in 2019); the lowest was in the North East (2019: 16.9%).

Conclusions

MDR and XDR phenotypes occur more frequently in nitrofurantoin-resistant E. coli urinary isolates in England, compared with nitrofurantoin-susceptible isolates. However, nitrofurantoin resistance is low (<3%) overall. This latest study provides important insights into trends in nitrofurantoin resistance and MDR, which is of particular concern for patients ≥75 years old and those who are male. It also emphasises geographical heterogeneities within England in nitrofurantoin resistance and MDR.

Pathotypes and Phenotypic Resistance to Antimicrobials of Escherichia coli Isolates from One-Day-Old Chickens

The aim of this work was to describe the pathotypes of Escherichia coli strains isolated from one-day-old chickens, as well as the occurrence of resistance and multidrug resistance (MDR) in these strains. A total of 429 mixed swabs from 4290 one-day-old chicks were examined between August 2021 and July 2023 (24 months) during routine point-of-destination inspections at 12 poultry farms in the Czech Republic. All samples were processed via cultivation methods using meat-peptone blood agar and Mc Conkey agar under aerobic conditions at 37 ± 1 °C for 18-24 h. The identification of the strains was performed using MALDI-TOF mass spectrometry. All confirmed strains of E. coli were screened via single or multiplex PCRs for the presence of genes encoding the virulence-associated factors iroN, cvaC, iss, felA, iutA, frz and tsh. Antimicrobial susceptibility tests were performed using the minimal inhibitory concentration (MIC) method, focusing on ampicillin, cefotaxime, tetracycline, doxycycline, enrofloxacin, florfenicol, amoxicillin with clavulanic acid and trimethoprim with sulfamethoxazole. A total of 321 E. coli strains (prevalence of 74.8%) were isolated, and 300 isolates were defined as avian pathogenic strains of E. coli (APEC) via multiplex PCR. Based on the defined virulence genes, the isolates were classified into 31 pathotypes. A total of 15.9% of the tested isolates were susceptible to all the tested antimicrobials. On the other hand, 20.5% of the isolates were identified as multidrug-resistant (8.7% of isolates were resistant to three antimicrobials, 7.3% to four antimicrobials, 3.6% to five antimicrobials and 0.9% to six antimicrobials). Monitoring pathogenic strains of E. coli in different animals and in the environment makes it possible to understand their spread in animal and human populations and, at the same time, reveal the sources of virulence and resistance genes.

Molecular epidemiology and pathogenomics of extended-spectrum beta-lactamase producing- Escherichia coli and - Klebsiella pneumoniae isolates from bulk tank milk in Tennessee, USA

Introduction

The rise in extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in dairy cattle farms poses a risk to human health as they can spread to humans through the food chain, including raw milk. This study was designed to determine the status, antimicrobial resistance, and pathogenic potential of ESBL-producing -E. coli and -Klebsiella spp. isolates from bulk tank milk (BTM).

Methods

Thirty-three BTM samples were collected from 17 dairy farms and screened for ESBL-E. coli and -Klebsiella spp. on CHROMagar ESBL plates. All isolates were confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and subjected to antimicrobial susceptibility testing and whole genome sequencing (WGS).

Results

Ten presumptive ESBL-producing bacteria, eight E. coli, and two K. pneumoniae were isolated. The prevalence of ESBL-E. coli and -K. pneumoniae in BTM was 21.2% and 6.1%, respectively. ESBL-E. coli were detected in 41.2% of the study farms. Seven of the ESBL-E. coli isolates were multidrug resistant (MDR). The two ESBL-producing K. pneumoniae isolates were resistant to ceftriaxone. Seven ESBL-E. coli strains carry the blaCTX-M gene, and five of them co-harbored blaTEM-1. ESBL-E. coli co-harbored blaCTX-M with other resistance genes, including qnrB19, tet(A), aadA1, aph(3'')-Ib, aph(6)-Id), floR, sul2, and chromosomal mutations (gyrA, gyrB, parC, parE, and pmrB). Most E. coli resistance genes were associated with mobile genetic elements, mainly plasmids. Six sequence types (STs) of E. coli were detected. All ESBL-E. coli were predicted to be pathogenic to humans. Four STs (three ST10 and ST69) were high-risk clones of E. coli. Up to 40 virulence markers were detected in all E. coli isolates. One of the K. pneumoniae was ST867; the other was novel strain. K. pneumoniae isolates carried three types of beta-lactamase genes (blaCTX-M, blaTEM-1 and blaSHV). The novel K. pneumoniae ST also carried a novel IncFII(K) plasmid ST.

Conclusion

Detection of high-risk clones of MDR ESBL-E. coli and ESBL-K. pneumoniae in BTM indicates that raw milk could be a reservoir of potentially zoonotic ESBL-E. coli and -K. pneumoniae.

Evaluation of Antibiotic Resistance Mechanisms in Gram-Negative Bacteria

Multidrug-resistant Gram-negative bacterial infections are exponentially increasing, posing one of the most urgent global healthcare and economic threats. Due to the lack of new therapies, the World Health Organization classified these bacterial species as priority pathogens in 2017, known as ESKAPE pathogens. This classification emphasizes the need for urgent research and development of novel targeted therapies. The majority of these priority pathogens are Gram-negative species, which possess a structurally dynamic cell envelope enabling them to resist multiple antibiotics, thereby leading to increased mortality rates. Despite 6 years having passed since the WHO classification, the progress in generating new treatment ideas has not been sufficient, and antimicrobial resistance continues to escalate, acting as a global ticking time bomb. Numerous efforts and strategies have been employed to combat the rising levels of antibiotic resistance by targeting specific resistance mechanisms. These mechanisms include antibiotic inactivating/modifying enzymes, outer membrane porin remodelling, enhanced efflux pump action, and alteration of antibiotic target sites. Some strategies have demonstrated clinical promise, such as the utilization of beta-lactamase inhibitors as antibiotic adjuvants, as well as recent advancements in machine-based learning employing artificial intelligence to facilitate the production of novel narrow-spectrum antibiotics. However, further research into an enhanced understanding of the precise mechanisms by which antibiotic resistance occurs, specifically tailored to each bacterial species, could pave the way for exploring narrow-spectrum targeted therapies. This review aims to introduce the key features of Gram-negative bacteria and their current treatment approaches, summarizing the major antibiotic resistance mechanisms with a focus on Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Additionally, potential directions for alternative therapies will be discussed, along with their relative modes of action, providing a future perspective and insight into the discipline of antimicrobial resistance.

Whole genome structure and resistance genes in carbapenemase-producing multidrug resistant ST378 Klebsiella pneumoniae

BACKGROUND

Carbapenemase-producing Klebsiella pneumoniae (CPKP) is one of the most dangerous multidrug-resistant (MDR) pathogens in human health due to its widespread circulation in the nosocomial environment. CPKP carried by companion dogs, which are close to human beings, should be considered a common threat to public health. However, CPKP dissemination through companion animals is still under consideration of major diagnosis and surveillance systems.

METHODS

Two CPKP isolates which were genotyped to harbor bla NDM-5-encoding IncX3 plasmids, were subjected to the whole-genome study. Whole bacterial DNA was isolated, sequenced, and assembled with Oxford Nanopore long reads and corrected with short reads from the Illumina NovaSeq 6000 platform. The whole-genome structure and positions of antimicrobial resistance (AMR) genes were identified and visualized using CGView. Worldwide datasets were downloaded from the NCBI GenBank database for whole-genome comparative analysis. The whole-genome phylogenetic analysis was constructed using the identified whole-chromosome SNP sites from K. pneumoniae HS11286.

RESULTS

As a result of the whole-genome identification, 4 heterogenous plasmids and a single chromosome were identified, each carrying various AMR genes. Multiple novel structures were identified from the AMR genes, coupled with mobile gene elements (MGE). The comparative whole-genome epidemiology revealed that ST378 K. pneumoniae is a novel type of CPKP, carrying a higher prevalence of AMR genes.

CONCLUSIONS

The characterized whole-genome analysis of this study shows the emergence of a novel type of CPKP strain carrying various AMR genes with variated genomic structures. The presented data in this study show the necessity to develop additional surveillance programs and control measures for a novel type of CPKP strain.

Virulence, antimicrobial resistance, and molecular characteristics of carbapenem-resistant Klebsiella pneumoniae in a hospital in Shijiazhuang City from China

Carbapenem-resistant Klebsiella pneumoniae (CRKP), as one of the most common drug-resistant bacteria threatening human health, is hyper-resistant to multiple antimicrobial drugs and carbapenems, which can be dealt with only limited clinical treatment options. This study described the epidemiological characteristics of CRKP in this tertiary care hospital from 2016 to 2020. Specimen sources included blood, sputum, alveolar lavage fluid, puncture fluid, secretions from a burn wound, and urine. Among the 87 carbapenem-resistant strains, ST11 was the predominant isolate, followed by ST15, ST273, ST340, and ST626. These STs were in broad agreement with the STs defined by pulsed-field gel electrophoresis clustering analysis in discriminating clusters of related strains. Most CRKP isolates contained the blaKPC-2 gene, some isolates carried the blaOXA-1, blaNDM-1, and blaNDM-5 genes, and the isolates carrying carbapenem resistance genes were more resistant to the antimicrobials of β-lactams, carbapenems, macrolides, and fluoroquinolone. The OmpK35 and OmpK37 genes were detected in all CRKP strains, and the Ompk36 gene was detected in some CRKP strains. All detected OmpK37 had 4 mutant sites, and OmpK36 had 11 mutant sites, while no mutant sites were found in OmpK35. More than half of the CRKP strains contained the OqxA and OqxB efflux pump genes. The virulence genes were most commonly combined with urea-wabG-fimH-entB-ybtS-uge-ycf. Only one CRKP isolate was detected with the K54 podoconjugate serotype. This study elucidated the clinical epidemiological features and molecular typing of CRKP, and grasped the distribution of drug-resistant genotypes, podocyte serotypes, and virulence genes of CRKP, providing some guidance for the subsequent treatment of CRKP infection.

Virulence, antimicrobial resistance, and molecular characteristics of carbapenem-resistant Klebsiella pneumoniae in a hospital in Shijiazhuang City from China

Carbapenem-resistant Klebsiella pneumoniae (CRKP), as one of the most common drug-resistant bacteria threatening human health, is hyper-resistant to multiple antimicrobial drugs and carbapenems, which can be dealt with only limited clinical treatment options. This study described the epidemiological characteristics of CRKP in this tertiary care hospital from 2016 to 2020. Specimen sources included blood, sputum, alveolar lavage fluid, puncture fluid, secretions from a burn wound, and urine. Among the 87 carbapenem-resistant strains, ST11 was the predominant isolate, followed by ST15, ST273, ST340, and ST626. These STs were in broad agreement with the STs defined by pulsed-field gel electrophoresis clustering analysis in discriminating clusters of related strains. Most CRKP isolates contained the blaKPC-2 gene, some isolates carried the blaOXA-1, blaNDM-1, and blaNDM-5 genes, and the isolates carrying carbapenem resistance genes were more resistant to the antimicrobials of β-lactams, carbapenems, macrolides, and fluoroquinolone. The OmpK35 and OmpK37 genes were detected in all CRKP strains, and the Ompk36 gene was detected in some CRKP strains. All detected OmpK37 had 4 mutant sites, and OmpK36 had 11 mutant sites, while no mutant sites were found in OmpK35. More than half of the CRKP strains contained the OqxA and OqxB efflux pump genes. The virulence genes were most commonly combined with urea-wabG-fimH-entB-ybtS-uge-ycf. Only one CRKP isolate was detected with the K54 podoconjugate serotype. This study elucidated the clinical epidemiological features and molecular typing of CRKP, and grasped the distribution of drug-resistant genotypes, podocyte serotypes, and virulence genes of CRKP, providing some guidance for the subsequent treatment of CRKP infection.

Comparative Genomics Reveals Novel Species and Insights into the Biotechnological Potential, Virulence, and Resistance of Alcaligenes

Alcaligenes is a cosmopolitan bacterial genus that exhibits diverse properties which are beneficial to plants. However, the genomic versatility of Alcaligenes has also been associated with the ability to cause opportunistic infections in humans, raising concerns about the safety of these microorganisms in biotechnological applications. Here, we report an in-depth comparative analysis of Alcaligenes species using all publicly available genomes to investigate genes associated with species, biotechnological potential, virulence, and resistance to multiple antibiotics. Phylogenomic analysis revealed that Alcaligenes consists of at least seven species, including three novel species. Pan-GWAS analysis uncovered 389 species-associated genes, including cold shock proteins (e.g., cspA) and aquaporins (e.g., aqpZ) found exclusively in the water-isolated species, Alcaligenes aquatilis. Functional annotation of plant-growth-promoting traits revealed enrichment of genes for auxin biosynthesis, siderophores, and organic acids. Genes involved in xenobiotic degradation and toxic metal tolerance were also identified. Virulome and resistome profiles provide insights into selective pressures exerted in clinical settings. Taken together, the results presented here provide the grounds for more detailed clinical and ecological studies of the genus Alcaligenes.

Uropathogenic Escherichia coli (UPEC)-Associated Urinary Tract Infections: The Molecular Basis for Challenges to Effective Treatment

Urinary tract infections (UTIs) are among the most common bacterial infections, especially among women and older adults, leading to a significant global healthcare cost burden. Uropathogenic Escherichia coli (UPEC) are the most common cause and accounts for the majority of community-acquired UTIs. Infection by UPEC can cause discomfort, polyuria, and fever. More serious clinical consequences can result in urosepsis, kidney damage, and death. UPEC is a highly adaptive pathogen which presents significant treatment challenges rooted in a complex interplay of molecular factors that allow UPEC to evade host defences, persist within the urinary tract, and resist antibiotic therapy. This review discusses these factors, which include the key genes responsible for adhesion, toxin production, and iron acquisition. Additionally, it addresses antibiotic resistance mechanisms, including chromosomal gene mutations, antibiotic deactivating enzymes, drug efflux, and the role of mobile genetic elements in their dissemination. Furthermore, we provide a forward-looking analysis of emerging alternative therapies, such as phage therapy, nano-formulations, and interventions based on nanomaterials, as well as vaccines and strategies for immunomodulation. This review underscores the continued need for research into the molecular basis of pathogenesis and antimicrobial resistance in the treatment of UPEC, as well as the need for clinically guided treatment of UTIs, particularly in light of the rapid spread of multidrug resistance.

Prevalence and mechanisms of ciprofloxacin resistance in Escherichia coli isolated from hospitalized patients, healthy carriers, and wastewaters in Iran

BACKGROUND

This study was aimed to evaluate the prevalence and molecular characteristics of ciprofloxacin resistance among 346 Escherichia coli isolates collected from clinical specimens (n = 82), healthy children (n = 176), municipal wastewater (n = 34), hospital wastewater (n = 33), poultry slaughterhouse wastewater (n = 12) and livestock (n = 9) slaughterhouse wastewater in Iran.

METHODS

Ciprofloxacin minimum inhibitory concentration (MIC) was determined by agar dilution assay. Phylogroups and plasmid-mediated quinolone resistance (PMQR) genes were identified using PCR. Mutations in gyrA, gyrB, parC, and parE genes and amino acid alterations were screened through sequencing assay. The effect of efflux pump inhibitor (PAβN) on ciprofloxacin MICs in ciprofloxacin-resistant isolates was investigated using the microdilution method.

RESULTS

In total, 28.03% of E. coli isolates were phenotypically resistant to ciprofloxacin. Based on sources of isolation, 64.63%, 51.51%, 33.33%, 14.70%, 10.22% and 8.33% of isolates from clinical specimens, hospital wastewater, livestock wastewater, municipal wastewater, healthy children and poultry wastewater were ciprofloxacin-resistant, respectively. Eighty-one point eighty-one percent (Ser-83 → Leu + Asp-87 → Asn; 78.78% and Ser-83 → Leu only; 3.03% (of ciprofloxacin-resistant E. coli isolates showed missense mutation in GyrA subunit of DNA gyrase, while no amino-acid substitution was noted in the GyrB subunit. DNA sequence analyses of the ParC and ParE subunits of topoisomerase IV exhibited amino-acid changes in 30.30% (Ser-80 → Ile + Glu-84 → Val; 18.18%, Ser-80 → Ile only; 9.10% and Glu-84 → Val only; 3.03%0 (and 15.38% (Ser-458 → Ala) of ciprofloxacin-resistant E. coli isolates, respectively. The PMQR genes, aac(6')-Ib-cr, qnrS, qnrB, oqxA, oqxB, and qepA were detected in 43.29%, 74.22%, 9.27%, 14.43%, 30.92% and 1.03% of ciprofloxacin-resistant isolates, respectively. No isolate was found to be positive for qnrA and qnrD genes. In isolates harboring the OqxA/B efflux pump, the MIC of ciprofloxacin was reduced twofold in the presence of PAβN, as an efflux pump inhibitor. The phylogroups B2 (48.45%) and A (20.65%) were the most predominant groups identified in ciprofloxacin-resistant isolates.

CONCLUSIONS

This study proved the high incidence of ciprofloxacin-resistant E. coli isolates in both clinical and non-clinical settings in Iran. Chromosomal gene mutations and PMQR genes were identified in ciprofloxacin resistance among E. coli population.