Fluoroquinolone resistance in complicated urinary tract infections: association with the increased occurrence and diversity of Escherichia coli of clonal complex 131, together with ST1193.

Introduction: Urinary tract infections (UTIs) are one of the leading causes of multidrug-resistance (MDR) spread and infection-related deaths. Escherichia coli is by far the main causative agent. We conducted a prospective study on complicated urinary tract infections (cUTIs) i) to monitor the high-risk clones that could be compromising the therapeutic management and ii) to compare the cUTI etiology with uncomplicated infections (uUTIs) occurring in the same period and health area. Methods: 154 non-duplicated E. coli recovered from cUTIs in 2020 at the Hospital Universitario Central de Asturias (Spain) constituted the study collection. Results: Most cUTI isolates belonged to phylogroup B2 (72.1%) and met the uropathogenic (UPEC) status (69.5%) (≥3 of chuA, fyuA, vat, and yfcV genes). MDR was exhibited by 35.7% of the isolates, similarly to data observed in the uUTI collection. A significant difference observed in cUTI was the higher level of fluoroquinolone resistance (FQR) (47.4%), where the pandemic clonal groups B2-CC131 and B2-ST1193 (CH14-64) comprised 28% of the 154 E. coli, representing 52.1% of the FQR isolates. Other prevalent FQR clones were D-ST69 (CH35-27), D-ST405 (CH37-27), and B2-ST429 (CH40-20) (three isolates each). We uncovered an increased genetic and genomic diversity of the CC131: 10 different virotypes, 8 clonotypes (CH), and 2 STs. The presence of bla CTX-M-15 was determined in 12 (7.8%) isolates (all CC131), which showed 10 different core genome (cg)STs and 2 fimH types (fimH30 and fimH602) but the same set of chromosomal mutations conferring FQR (gyrA p.S83L, gyrA p.D87N, parC p.S80I, parC p.E84V, and parE p.I529L). In addition, the plasmidome analysis revealed 10 different IncF formulae in CC131 genomes. Conclusion: We proved here that non-lactose fermenting screening, together with the detection of O25b (rfbO25b), H4 (fliCH4), and H5 (fliCH5) genes, and phylogroup and clonotyping assignation, is a reasonable approach that can be easily implemented for the surveillance of emerging high-risk clones associated with FQR spread in cUTIs, such as the uncommonly reported O25b:H4-B2-ST9126-CC131 (CH1267-30). Since E. coli CC131 and ST1193 are also involved in the community uUTIs of this health area, interventions to eradicate these MDR clones, along with surveillance for other emerging ones, are essential for antibiotic use optimization programs.

Trends in DTR, CR, ECR, and FQR in Four Common Gram-Negative Bacteria: A Retrospective Study from 2013 to 2021.

Purpose: The purpose of this study was to examine the prevalence of four important drug-resistance phenotypes: difficult-to-treat resistance (DTR), fluoroquinolone resistance (FQR), carbapenem resistance (CR), and extended-spectrum cephalosporin resistance (ECR). Methods: DTR was defined as insensitivity to all the ß-lactams and fluoroquinolones tested. We retrospectively analyzed the distribution characteristics of specific drug-resistant phenotypes of the main Gram-negative bacteria causing bloodstream infections (BSIs) in Tongji Hospital (Wuhan, China) between 2013 and 2021: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Results: FQR was the main antimicrobial resistance phenotype of E. coli, accounting for 59.45% (1117/1879, 95% confidence interval, 57.21%-61.65%); the detection rates for CR and DTR were low, accounting for 1.86% (35/1879, 1.34%-2.58%), and 1.81% (34/1879, 1.30%-2.52%), respectively. However, the detection rates for CR and DTR in K. pneumoniae were 38.83% (497/1280, 36.20%-41.53%) and 35.94% (460/1280, 33.35%-38.60%), respectively. In P. aeruginosa, the detection rates of the four drug-resistant phenotypes (DTR, CR, FQR, and ECR) were all < 30%, but conversely, for A. baumannii, the detection rates were all > 80%. The changes in the data from 2013 to 2021 showed upward trends (z > 0) for CR-E. coli, DTR-E. coli, FQR-E. coli, CR-K. pneumoniae, DTR-K. pneumoniae, FQR-K. pneumoniae, and ECR-K. pneumoniae, but downward trends (z < 0) for ECR-E. coli, CR-A. baumannii, DTR-A. baumannii, FQR-A. baumannii, ECR-A. baumannii, CR-P. aeruginosa, DTR-P. aeruginosa, FQR-P. aeruginosa, and ECR-P. aeruginosa. Conclusion: DTR warrants further attention, especially in in BSI-associated K. pneumoniae and A. baumannii, in which the detection rates were very high. Between 2013 and 2021 in this region, DTR-E. coli and CR-E. coli showed obvious upward trends, whereas DTR-P. aeruginosa and ECR-P. aeruginosa showed obvious downward trends.

Occurrence and Genomic Characterization of Clone ST1193 Clonotype 14-64 in Uncomplicated Urinary Tract Infections Caused by Escherichia coli in Spain.

We conducted a prospective, multicenter, specific pilot study on uncomplicated urinary tract infections (uUTI). One-hundred non-duplicated uropathogenic Escherichia coli (UPEC) from uUTI occurred in 2020 in women attending 15 primary care centers of a single health region of northern Spain were characterized using a clonal diagnosis approach. Among the high genetic diversity showed by 59 different phylogroup-clonotype combinations, 11 clones accounted for 46% of the isolates: B2-ST73 (CH24-30); B2-ST73 (CH24-103); B2-ST131 (CH40-30); B2-ST141 (CH52-5); B2-ST372 (CH103-9); B2-ST404 (CH14-27); B2-ST404 (CH14-807); B2-ST1193 (CH14-64); D-ST69 (CH35-27); D-ST349 (CH36-54), and F-ST59 (CH32-41). The screening of the UPEC status found that 69% of isolates carried ≥ 3 of chuA, fyuA, vat, and yfcV genes. Multidrug resistance to at least one antibiotic of ≥ 3 antimicrobial categories were exhibited by 30% of the isolates, with the highest rates of resistance against ampicillin/amoxicillin (48%), trimethoprim (35%), norfloxacin (28%), amoxicillin-clavulanic acid (26%), and trimethoprim-sulfamethoxazole (24%). None extended-spectrum beta-lactamase/carbapenemase producer was recovered. According to our results, fosfomycin and nitrofurantoin should be considered as empirical treatment of choice for uUTI by E. coli (resistance rates 4% and 2%, respectively). We uncover the high prevalence of the pandemic fluoroquinolone-resistant ST1193 clone (6%) in uUTI, which represents the first report in Spain in this pathology. The genomic analysis showed similar key traits than those ST1193 clones disseminated worldwide. Through the SNP comparison based on the core genome, the Spanish ST1193 clustered with isolates retrieved from the Enterobase, showing high genomic similarity than the global ST1193 described in the United States, Canada and Australia. IMPORTANCE Analyzing the clonal structure and antimicrobial resistance of E. coli isolates implicated in uncomplicated urinary tract infections, one of the most frequent visits managed in primary health care, is of interest for clinicians to detect changes in the dynamics of emerging uropathogenic clones associated with the spread of fluoroquinolone resistance. It can also provide consensus concerning optimal control and antibiotic prescribing.

Whole genome sequence analysis of Shigella from Malawi identifies fluoroquinolone resistance.

Increasing antimicrobial resistance and limited alternative treatments have led to fluoroquinolone-resistant Shigella strain inclusion on the WHO global priority pathogens list. In this study we characterized multiple Shigella isolates from Malawi with whole genome sequence analysis, identifying the acquirable fluoroquinolone resistance determinant qnrS1.

PGRL1 overexpression in Phaeodactylum tricornutum inhibits growth and reduces apparent PSII activity.

Proton gradient regulation 5-like photosynthetic phenotype 1 (PGRL1)-dependent cyclic electron transport around photosystem I (PSI) plays important roles in the response to different stresses, including high light. Although the function of PGRL1 in higher plants and green algae has been thoroughly investigated, little information is available on the molecular mechanism of PGRL1 in diatoms. We created PGRL1 overexpression and knockdown transformants of Phaeodactylum tricornutum, the diatom model species, and investigated the impact on growth and photosynthesis under constant and fluctuating light conditions. PGRL1 over-accumulation resulted in significant decreases in growth rate and apparent photosystem II (PSII) activity and led to an opposing change of apparent PSII activity when turning to high light, demonstrating a similar influence on photosynthesis as a PSII inhibitor. Our results suggested that PGRL1 overexpression can reduce the apparent efficiency of PSII and inhibit growth in P. tricornutum. These findings provide physiological evidence that the accumulation of PGRL1 mainly functions around PSII instead of PSI.

Response of Chloroplast NAD(P)H Dehydrogenase-Mediated Cyclic Electron Flow to a Shortage or Lack in Ferredoxin-Quinone Oxidoreductase-Dependent Pathway in Rice Following Short-Term Heat Stress.

Cyclic electron flow (CEF) around photosystem I (PSI) can protect photosynthetic electron carriers under conditions of stromal over-reduction. The goal of the research reported in this paper was to investigate the responses of both PSI and photosystem II (PSII) to a short-term heat stress in two rice lines with different capacities of cyclic electron transfer, i.e., Q4149 with a high capacity (hcef) and C4023 with a low capacity (lcef). The absorbance change at 820 nm (ΔA820) was used here to assess the charge separation in the PSI reaction center (P700). The results obtained show that short-term heat stress abolishes the ferredoxin-quinone oxidoreductase (FQR)-dependent CEF in rice and accelerates the initial rate of P700 (+) re-reduction. The P700 (+) amplitude was slightly increased at a moderate heat-stress (35°C) because of a partial restriction of FQR but it was decreased following high heat-stress (42°C). Assessment of PSI and PSII activities shows that PSI is more susceptible to heat stress than PSII. Under high temperature, FQR-dependent CEF was completely removed and NDH-dependent CEF was up-regulated and strengthened to a higher extent in C4023 than in Q4149. Specifically, under normal growth temperature, hcef (Q4149) was characterized by higher FQR- and chloroplast NAD(P)H dehydrogenase (NDH)-dependent CEF rates than lcef (C4023). Following thermal stress, the activation of NDH-pathway was 130 and 10% for C4023 and Q4149, respectively. Thus, the NDH-dependent CEF may constitute the second layer of plant protection and defense against heat stress after the main route, i.e., FQR-dependent CEF, reaches its capacity. We discuss the possibility that under high heat stress, the NDH pathway serves as a safety valve to dissipate excess energy by cyclic photophosphorylation and overcome the stroma over-reduction following inhibition of CO2 assimilation and any shortage or lack in the FQR pathway. The potential role of the NDH-dependent pathway during the evolution of C4 photosynthesis is briefly discussed.

The antimycin A-sensitive pathway of cyclic electron flow: from 1963 to 2015.

Cyclic electron flow has puzzled and divided the field of photosynthesis researchers for decades. This mainly concerns the proportion of its overall contribution to photosynthesis, as well as its components and molecular mechanism. Yet, it is irrefutable that the absence of cyclic electron flow has severe effects on plant growth. One of the two pathways mediating cyclic electron flow can be inhibited by antimycin A, a chemical that has also widely been used to characterize the mitochondrial respiratory chain. For the characterization of cyclic electron flow, antimycin A has been used since 1963, when ferredoxin was found to be the electron donor of the pathway. In 2013, antimycin A was used to identify the PGRL1/PGR5 complex as the ferredoxin:plastoquinone reductase completing the last puzzle piece of this pathway. The controversy has not ended, and here, we review the history of research on this process using the perspective of antimycin A as a crucial chemical for its characterization.

A single amino acid alteration in PGR5 confers resistance to antimycin A in cyclic electron transport around PSI.

In Arabidopsis thaliana, the main route of cyclic electron transport around PSI is sensitive to antimycin A, but the site of inhibition has not been clarified. We discovered that ferredoxin-dependent plastoquinone reduction in ruptured chloroplasts was less sensitive to antimycin A in Arabidopsis that overaccumulated PGR5 (PROTON GRADIENT REGULATION 5) originating from Pinus taeda (PtPGR5) than that in the wild type. Consistent with this in vitro observation, infiltration of antimycin A reduced PSII yields and the non-photochemical quenching (NPQ) of Chl fluorescence in wild-type leaves but not in leaves accumulating PtPGR5. There are eight amino acid differences between PGR5 of Arabidopsis (AtPGR5) and PtPGR5 in their mature forms. To determine the site conferring antimycin A resistance, a series of AtPGR5 and PtPGR5 variants was introduced into the Arabidopsis pgr5 mutant. We determined that the presence of lysine rather than valine at the third amino acid position was necessary and sufficient for resistance to antimycin A. High levels of resistance to antimycin A required overaccumulation of PtPGR5 in ruptured chloroplasts, suggesting that PtPGR5 is partly resistant to antimycin A. In contrast, PSII yield was almost fully resistant to antimycin A in leaves accumulating endogenous levels of PtPGR5 or AtPGR5 V3K that had lysine instead of valine at the third position. NPQ was also dramatically recovered in leaves of these lines. These results imply that partial recovery of PSI cyclic electron transport is sufficient for maintaining redox homeostasis in photosynthesis. Our discovery suggests that antimycin A inhibits the function of PGR5 or proteins localized close to PGR5.

How does iron deficiency disrupt the electron flow in photosystem I of lettuce leaves?

The changes observed photosystem I activity of lettuce plants exposed to iron deficiency were investigated. Photooxidation/reduction kinetics of P700 monitored as ΔA820 in the presence and absence of electron transport inhibitors and acceptors demonstrated that deprivation in iron decreased the population of active photo-oxidizable P700. In the complete absence of iron, the addition of plant inhibitors (DCMU and MV) could not recover the full PSI activity owing to the abolition of a part of P700 centers. In leaves with total iron deprivation (0µM Fe), only 15% of photo-oxidizable P700 remained. In addition, iron deficiency appeared to affect the pool size of NADP(+) as shown by the decline in the magnitude of the first phase of the photooxidation kinetics of P700 by FR-light. Concomitantly, chlorophyll content gradually declined with the iron concentration added to culture medium. In addition, pronounced changes were found in chlorophyll fluorescence spectra. Also, the global fluorescence intensity was affected. The above changes led to an increased rate of cyclic electron transport around PSI mainly supported by stromal reductants.

Comparative analysis of the chloroplast proteomes of a wheat (Triticum aestivum L.) single seed descent line and its parents.

To understand the photosynthetic basis in a single seed descent line 10 (SSDL10) of wheat contained high ATP in leaves, the chloroplast proteome was compared to SSDL10 and its parents using a combination of 2-DE and MALDI-TOF MS and MS/MS. More than 300 protein spots could be reproducibly detected in the 2D gel. 18 spots were differentially expressed between SSDL10 and the parents, 16 of which were identified by MS with the localization in chloroplasts. These proteins are grouped into diverse functional categories, including Calvin cycle and electron transport in photosynthesis, redox homeostasis, metabolism, and regulation. In addition to Rubisco large subunit, the content of photosynthetic electron transfers such as chlorophyll a-b binding protein, ATP synthase δ subunit, ferredoxin-NADP⁺ oxidoreductase (FNR) was higher in SSDL10 than in its parents. Furthermore, cyclic electron transfer around photosystem I (CET) was faster in SSDL10 than in the parents. Analysis of NADPH-NBT oxidoreductase activity combined with immuno-detection further revealed that, the activity of two high molecular mass protein complexes containing FNR probably involved, the CET appeared higher in SSDL10 than in the parents. The possible mechanism for the regulative role of CET in photosynthesis in SSDL10 is discussed.