Exploring antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in E. coli and K. pneumoniae using proteogenomics

Loss and gain of ceftazidime-avibactam susceptibility in a non-carbapenemase-producing K1-ST23 hypervirulent Klebsiella pneumoniae

OBJECTIVES

This study aimed at revealing the underlying mechanisms of the loss and gain of ceftazidime-avibactam susceptibility in a non-carbapenemase-producing hypervirulent Klebsiella pneumoniae (hvKp).

METHODS

Here we longitudinally recovered 3 non-carbapenemase-producing K1-ST23 hvKp strains at a one-month interval (KP29105, KP29499 and KP30086) from an elderly male. Antimicrobial susceptibility testing, whole genome sequencing, transcriptomic sequencing, gene cloning, plasmid conjugation, quantitative real-time PCR (qRT-PCR), and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) were conducted.

RESULTS

Among the 3 hvKp strains, KP29105 was resistant to the third- and fourth-generation cephalosporins, KP29499 acquired resistance to both ceftazidime-avibactam and carbapenems, while KP30086 restored its susceptibility to ceftazidime-avibactam, imipenem and meropenem but retained low-level resistance to ertapenem. KP29105 and KP29499 carried plasmid-encoded genes blaCTX-M-15 and blaCTX-M-71, respectively, but KP30086 lost both. Cloning of gene blaCTX-M-71 and conjugation experiment of blaCTX-M-71-carrying plasmid showed that the transformant and transconjugant were susceptible to ceftazidime-avibactam but had a more than 8-fold increase in MICs. Supplementation with an outer membrane permeabilizer could reduce the MIC of ceftazidime-avibactam by 32 folds, indicating that porins play a key role in ceftazidime-avibactam resistance. The OmpK35 of the 3 isolates was not expressed, and the OmpK36 of KP29499 and KP30086 had a novel amino acid substitution (L359R). SDS-PAGE and qRT-PCR showed that the expression of porin OmpK36 of KP29499 and KP30086 was significantly down-regulated compared with KP29105.

CONCLUSIONS

In summary, we reported the rare ceftazidime-avibactam resistance in a non-carbapenemase-producing hvKp strain. Resistance plasmid carrying blaCTX-M-71 and mutated OmpK36 had a synergetic effect on the resistance.

Resistance to cephalosporins and quinolones in Escherichia coli isolated from irrigation water from the Rímac river in east Lima, Peru

OBJECTIVES.

To evaluate the presence and sensitivity to antimicrobials of Escherichia coli strains isolated from 24 irrigation water samples from the Rimac river of East Lima, Peru.

MATERIALS AND METHODS.

The E. coli strains were identified by PCR. Antibiotic susceptibility was processed by the disk diffusion method. Genes involved in extended spectrum beta-lactamases (BLEE), quinolones and virulence were determined by PCR.

RESULTS.

All samples exceeded the acceptable limits established in the Environmental Quality Standards for vegetable irrigation. Of the 94 isolates, 72.3% showed resistance to at least one antibiotic, 24.5% were multidrug resistant (MDR) and 2.1% were extremely resistant. The highest percentages of resistance were observed for ampicillin-sulbactam (57.1%), nalidixic acid (50%), trimethoprim-sulfamethoxazole (35.5%) and ciprofloxacin (20.4%). Among the isolates, 3.2% had a BLEE phenotype related to the bla CTX-M-15 gene. qnrB (20.4%) was the most frequent transferable mechanism of resistance to quinolones, and 2.04% had qnrS. It was estimated that 5.3% were diarrheagenic E. coli and of these, 60% were enterotoxigenic E. coli, 20% were enteropathogenic E. coli and 20% were enteroaggregative E. coli.

CONCLUSIONS.

The results show the existence of diarrheogenic pathotypes in the water used for irrigation of fresh produce and highlight the presence of BLEE- and MDR-producing E. coli, demonstrating the role played by irrigation water in the dissemination of resistance genes in Peru.

Motivation for the study. Aquatic systems, including irrigation water, have been identified as reservoirs of antimicrobial resistance, with few studies in Peru on the presence of Escherichia coli and their levels of virulence and antimicrobial resistance. Main findings. Our results show the presence of E. coli above the established standard for vegetable irrigation water, some with very high levels of antimicrobial resistance. Implications. The presence of ESBL-producing strains of extended-spectrum beta-lactamases and multidrug-resistant E. coli in irrigation water could contribute to the dissemination of resistance genes in Peru, posing a significant threat to public health.

Proteomic assay for rapid characterisation of Staphylococcus aureus antimicrobial resistance mechanisms directly from blood cultures

PURPOSE

Staphylococcus aureus is one of the most common pathogens causing bloodstream infection. A rapid characterisation of resistance to methicillin and, occasionally, to aminoglycosides for particular indications, is therefore crucial to quickly adapt the treatment and improve the clinical outcomes of septic patients. Among analytical technologies, targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as a promising tool to detect resistance mechanisms in clinical samples.

METHODS

A rapid proteomic method was developed to detect and quantify the most clinically relevant antimicrobial resistance effectors in S. aureus in the context of sepsis: PBP2a, PBP2c, APH(3')-III, ANT(4')-I, and AAC(6')-APH(2''), directly from positive blood cultures and in less than 70 min including a 30-min cefoxitin-induction step. The method was tested on spiked blood culture bottles inoculated with 124 S.aureus, accounting for the known genomic diversity of SCCmec types and the genetic background of the strains.

RESULTS

This method provided 99% agreement for PBP2a (n = 98/99 strains) detection. Agreement was 100% for PBP2c (n = 5/5), APH(3')-III (n = 16/16), and ANT(4')-I (n = 20/20), and 94% for AAC(6')-APH(2'') (n = 16/17). Across the entire strain collection, 100% negative agreement was reported for each of the 5 resistance proteins. Additionally, relative quantification of ANT(4')-I expression allowed to discriminate kanamycin-susceptible and -resistant strains, in all strains harbouring the ant(4')-Ia gene.

CONCLUSION

The LC-MS/MS method presented herein demonstrates its ability to provide a reliable determination of S. aureus resistance mechanisms, directly from positive blood cultures and in a short turnaround time, as required in clinical laboratories.

Two synonymous single-nucleotide polymorphisms promoting fluoroquinolone resistance of Escherichia coli in the environment

Single-nucleotide polymorphism (SNP) is one of the core mechanisms that respond to antibiotic resistance of Escherichia coli (E. coli), which is a major issue in environmental pollution. A specific type of SNPs, synonymous SNPs, have been generally considered as the "silent" SNPs since they do not change the encoded amino acid. However, the impact of synonymous SNPs on mRNA splicing, nucleo-cytoplasmic export, stability, and translation was gradually discovered in the last decades. Figuring out the mechanism of synonymous SNPs in regulating antibiotic resistance is critical to improve antimicrobial therapy strategies in clinics and biological treatment strategies of antibiotic-resistant E. coli-polluted materials. With our newly designed antibiotic resistant SNPs prediction algorithm, Multilocus Sequence Type based Identification for Phenotype-single nucleotide polymorphism Analysis (MIPHA), and in vivo validation, we identified 2 important synonymous SNPs 522 G>A and 972 C>T, located at hisD gene, which was previously predicted as a fluoroquinolone resistance-related gene without a detailed mechanism in the E. coli samples with environmental backgrounds. We first discovered that hisD causes gyrA mutation via the upregulation of sbmC and its downstream gene umuD. Moreover, those 2 synonymous SNPs of hisD cause its own translational slowdown and further reduce the expression levels of sbmC and its downstream gene umuD, making the fluoroquinolone resistance determining region of gyrA remains unmutated, ultimately causing the bacteria to lose their ability to resist drugs. This study provided valuable insight into the role of synonymous SNPs in mediating antibiotic resistance of bacteria and a new perspective for the treatment of environmental pollution caused by drug-resistant bacteria.

Beyond the identifiable proteome: Delving into the proteomics of polymyxin-resistant and non-resistant Acinetobacter baumannii from Brazilian hospitals

This work discloses a unique, comprehensive proteomic dataset of Acinetobacter baumannii strains, both resistant and non-resistant to polymyxin B, isolated in Brazil generated using Orbitrap Fusion Lumos. From nearly 4 million tandem mass spectra, the software DiagnoMass produced 240,685 quality-filtered mass spectral clusters, of which PatternLab for proteomics identified 44,553 peptides mapping to 3479 proteins. Crucially, DiagnoMass shortlisted 3550 and 1408 unique mass spectral clusters for the resistant and non-resistant strains, respectively, with only about a third with sequences (and PTMs) identified by PatternLab. Further open-search attempts via FragPipe yielded an additional ∼20% identifications, suggesting the remaining unidentified spectra likely arise from complex combinations of post-translational modifications and amino-acid substitutions. This highlights the untapped potential of the dataset for future discoveries, particularly given the importance of PTMs, which remain elusive to nucleotide sequencing approaches but are crucial for understanding biological mechanisms. Our innovative approach extends beyond the identifications that are typically subjected to the bias of a search engine; we discern which spectral clusters are differential and subject them to increased scrutiny, akin to spectral library matching by comparing captured spectra to themselves. Our analysis reveals adaptations in the resistant strain, including enhanced detoxification, altered protein synthesis, and metabolic adjustments. SIGNIFICANCE: We present comprehensive proteomic profiles of non-resistant and resistant Acinetobacter baumannii from Brazilian Hospitals strains, and highlight the presence of discriminative and yet unidentified mass spectral clusters. Our work emphasizes the importance of exploring this overlooked data, as it could hold the key to understanding the complex dynamics of antibiotic resistance. This approach not only informs antimicrobial stewardship efforts but also paves the way for the development of innovative diagnostic tools. Thus, our findings have profound implications for the field, as far as methods for providing a new perspective on diagnosing antibiotic resistance as well as classifying proteomes in general.

Antimicrobial resistance patterns of Acinetobacter baumannii and Klebsiella pneumoniae isolated from dogs presented at a veterinary academic hospital in South Africa

Background

Acinetobacter baumannii and Klebsiella pneumoniae are opportunistic bacterial pathogens responsible for hospital-acquired infections in veterinary medicine. Infection with these bacteria always requires urgent antimicrobial therapy. However, there is no evidence of studies that have investigated the antimicrobial drug resistance profile of these organisms in a veterinary setting in South Africa. This study investigated the antimicrobial resistance (AMR) patterns of A. baumannii and K. pneumoniae from clinical specimens obtained from dogs presented at a veterinary academic hospital. The findings of this study contribute to an improved understanding of the AMR profile of these bacteria in veterinary medicine.

Materials and Methods

Retrospective data of clinical samples from dogs that were positive for A. baumannii and K. pneumoniae between 2007 and 2013 were used in this study. The antimicrobial susceptibility of the isolates was determined using the disk diffusion method following the Clinical and Laboratory Standards Institute guidelines. The A. baumannii isolates were subjected to a panel of 20 antibiotics, while K. pneumoniae isolates were subjected to a panel of 22 antibiotics. Data were analyzed using descriptive statistics and presented using tables and figures.

Results

Twenty (n = 20) A. baumannii isolates were isolated from bronchoalveolar lavage, foreign objects, bone, urine, skin, blood, ear, nasal, and oral cavity. Almost all A. baumannii (95%, 19/20) isolates were resistant to at least one antibiotic, and 60% (12/20) were multidrug-resistant (MDR). Klebsiella pneumoniae (n = 56) was isolated from urine, foreign objects, abscesses, ears, eyes, tracheal aspirations, bronchoalveolar lavages, eyes, abdominal aspirates, anal glands, bones, and intestinal and lung biopsies. All K. pneumoniae (100%, 56/56) isolates were resistant to at least one antibiotic, and 98% (55/56) were MDR.

Conclusion

Both A. baumannii and K. pneumoniae were isolated in various clinical tissue samples and exhibited a high prevalence of resistance to multiple antibiotics. In addition, these bacteria exhibited a high prevalence of resistance to β-lactam compared to other classes of antibiotics, which is likely to impact treatment options and patient prognosis.

Food wastes as a potential hotspot of antibiotic resistance: synergistic expression of multidrug resistance and ESBL genes confer antibiotic resistance to microbial communities

This study investigated antibiotic resistance (ABR) and extended-spectrum ß-lactamases (ESBL) patterns in bacterial isolates collected from the dairy, hotel, meat, and canteen food waste samples. A total of 144 bacterial strains were collected and screened for resistance against 9 standard antibiotics belonging to three generations and ESBL production. The ABR profile of the bacterial isolates was observed against all four major antibiotic groups (aminoglycosides, β-lactams, quinolone, and others), where resistance against cefotaxime (> 70%) and methicillin (> 50%) was high. Though the ABR pattern of strains from dairy waste (> 50%) was high against first-generation antibiotics, the strains from meat waste (> 50%) showed considerable resistance against second- and third-generation antibiotics. ESBL-producing isolates were screened (> 60%, n = 144) through primary identification tests (combined disk test and double disk synergy tests) and further confirmed through Hexa G-minus 23 and 24 and MIC E-stripe following CLSI guidelines. Genes conferring ESBL resistance bla_CTX-M, bla_SHV, bla_OXA, bla_TEM, bla_KPC genes and multidrug resistance (MDR) mexF gene were detected in the selected isolates with ABR and ESBL traits. Isolates with multidrug ABR and ESBL phenotype were further genotypically identified through 16 s rRNA gene sequencing. The synergy of ABR was detected through the co-expression of ESBL and MDR in isolates with a high occurrence of ABR and ESBL. The results demonstrate the significance of food waste as a natural reservoir of ABR and ESBL-producing pathogens, highlighting the importance of resistance monitoring and its interventions.

Systems Biology: New Insight into Antibiotic Resistance

Over the past few decades, antimicrobial resistance (AMR) has emerged as an important threat to public health, resulting from the global propagation of multidrug-resistant strains of various bacterial species. Knowledge of the intrinsic factors leading to this resistance is necessary to overcome these new strains. This has contributed to the increased use of omics technologies and their extrapolation to the system level. Understanding the mechanisms involved in antimicrobial resistance acquired by microorganisms at the system level is essential to obtain answers and explore options to combat this resistance. Therefore, the use of robust whole-genome sequencing approaches and other omics techniques such as transcriptomics, proteomics, and metabolomics provide fundamental insights into the physiology of antimicrobial resistance. To improve the efficiency of data obtained through omics approaches, and thus gain a predictive understanding of bacterial responses to antibiotics, the integration of mathematical models with genome-scale metabolic models (GEMs) is essential. In this context, here we outline recent efforts that have demonstrated that the use of omics technology and systems biology, as quantitative and robust hypothesis-generating frameworks, can improve the understanding of antibiotic resistance, and it is hoped that this emerging field can provide support for these new efforts.

Using Targeted Liquid Chromatography-Tandem Mass Spectrometry to Rapidly Detect β-Lactam, Aminoglycoside, and Fluoroquinolone Resistance Mechanisms in Blood Cultures Growing E. coli or K. pneumoniae

New and rapid antimicrobial susceptibility/resistance testing methods are required for bacteria from positive blood cultures. In this study, a multiplex-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was developed and validated for the detection of β-lactam, aminoglycoside, and fluoroquinolone resistance mechanisms in blood cultures growing Escherichia coli or Klebsiella pneumoniae complex. Selected targets were the β-lactamases SHV, TEM, OXA-1-like, CTX-M-1-like, CMY-2-like, chromosomal E. coli AmpC (cAmpC), OXA-48-like, NDM, VIM, and KPC; the aminoglycoside-modifying enzymes AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6′)-Ib, ANT(2′′)-I, and APH(3′)-VI; the 16S-RMTases ArmA, RmtB, RmtC, and RmtF; the quinolone resistance mechanisms QnrA, QnrB, AAC(6′)-Ib-cr; the wildtype quinolone resistance determining region of GyrA; and the E. coli porins OmpC and OmpF. The developed assay was evaluated using 100 prospectively collected positive blood cultures, and 148 negative blood culture samples spiked with isolates previously collected from blood cultures or isolates carrying less prevalent resistance mechanisms. The time to result was approximately 3 h. LC-MS/MS results were compared with whole-genome sequencing and antimicrobial susceptibility testing results. Overall, there was a high agreement between LC-MS/MS results and whole-genome sequencing results. In addition, the majority of susceptible and non-susceptible phenotypes were correctly predicted based on LC-MS/MS results. Exceptions were the predictions for ciprofloxacin and amoxicillin/clavulanic acid that matched with the phenotype in 85.9 and 63.7% of the isolates, respectively. Targeted LC-MS/MS based on parallel reaction monitoring can be applied for the rapid and accurate detection of various resistance mechanisms in blood cultures growing E. coli or K. pneumoniae complex.

Liquid Chromatography-Tandem Mass Spectrometry Analysis Demonstrates a Decrease in Porins and Increase in CMY-2 β-Lactamases in Escherichia coli Exposed to Increasing Concentrations of Meropenem

While Extended-Spectrum β-Lactamases (ESBL) and AmpC β-lactamases barely degrade carbapenem antibiotics, they are able to bind carbapenems and prevent them from interacting with penicillin-binding proteins, thereby inhibiting their activity. Further, it has been shown that Enterobacterales can become resistant to carbapenems when high concentrations of ESBL and AmpC β-lactamases are present in the bacterial cell in combination with a decreased influx of antibiotics (due to a decrease in porins and outer-membrane permeability). In this study, a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was developed for the detection of the Escherichia coli porins OmpC and OmpF, its chromosomal AmpC β-lactamase, and the plasmid-mediated CMY-2 β-lactamase. BlaCMY–2–like positive E. coli isolates were cultured in the presence of increasing concentrations of meropenem, and resistant mutants were analyzed using the developed LC-MS/MS assay, Western blotting, and whole genome sequencing. In five strains that became meropenem resistant, a decrease in OmpC and/or OmpF (caused by premature stop codons or gene interruptions) was the first event toward meropenem resistance. In four of these strains, an additional increase in MICs was caused by an increase in CMY-2 production, and in one strain this was most likely caused by an increase in CTX-M-15 production. The LC-MS/MS assay developed proved to be suitable for the (semi-)quantitative analysis of CMY-2-like β-lactamases and porins within 4 h. Targeted LC-MS/MS could have additional clinical value in the early detection of non-carbapenemase-producing carbapenem-resistant E. coli.

Antibiotic Heteroresistance in Klebsiella pneumoniae

Klebsiella pneumoniae is one of the most common pathogens responsible for infections, including pneumonia, urinary tract infections, and bacteremias. The increasing prevalence of multidrug-resistant K. pneumoniae was recognized in 2017 by the World Health Organization as a critical public health threat. Heteroresistance, defined as the presence of a subpopulation of cells with a higher MIC than the dominant population, is a frequent phenotype in many pathogens. Numerous reports on heteroresistant K. pneumoniae isolates have been published in the last few years. Heteroresistance is difficult to detect and study due to its phenotypic and genetic instability. Recent findings provide strong evidence that heteroresistance may be associated with an increased risk of recurrent infections and antibiotic treatment failure. This review focuses on antibiotic heteroresistance mechanisms in K. pneumoniae and potential therapeutic strategies against antibiotic heteroresistant isolates.

The Case against Antibiotics and for Anti-Virulence Therapeutics

Although antibiotics have been indispensable in the advancement of modern medicine, there are downsides to their use. Growing resistance to broad-spectrum antibiotics is leading to an epidemic of infections untreatable by first-line therapies. Resistance is exacerbated by antibiotics used as growth factors in livestock, over-prescribing by doctors, and poor treatment adherence by patients. This generates populations of resistant bacteria that can then spread resistance genes horizontally to other bacterial species, including commensals. Furthermore, even when antibiotics are used appropriately, they harm commensal bacteria leading to increased secondary infection risk. Effective antibiotic treatment can induce bacterial survival tactics, such as toxin release and increasing resistance gene transfer. These problems highlight the need for new approaches to treating bacterial infection. Current solutions include combination therapies, narrow-spectrum therapeutics, and antibiotic stewardship programs. These mediate the issues but do not address their root cause. One emerging solution to these problems is anti-virulence treatment: preventing bacterial pathogenesis instead of using bactericidal agents. In this review, we discuss select examples of potential anti-virulence targets and strategies that could be developed into bacterial infection treatments: the bacterial type III secretion system, quorum sensing, and liposomes.