Association of Proton Pump Inhibitor Use With Risk of Acquiring Drug-Resistant Enterobacterales.

Importance: Proton-pump inhibitors (PPIs) have been associated with the risk of colonization with drug-resistant bacteria; however, possible confounding by lifestyle-associated factors and disease severity casts doubt on this association, and whether the risk is dose dependent is not known. Objectives: To assess the association between PPI use and the risk of acquiring drug-resistant Enterobacterales and to examine interactions with possible microbiome-altering agents. Design, Setting, and Participants: This nested case-control study involved 2239 hospitalized adult (aged ≥18 years) patients identified from the microbiology laboratory database of Amsterdam University Medical Centers between December 31, 2018, and January 6, 2021. Patients in the case group had newly detected extended-spectrum ß-lactamase (ESBL)- or carbapenemase-producing Enterobacterales (identified by clinical specimens). Risk-set sampling was used to assign patients with negative results for ESBL- and carbapenemase-producing Enterobacterales to the control group, who were then matched on a 5:1 ratio with patients in the case group by age and culture date. A second validation case-control study included matched pairs (1:1 ratio; 94 in each group) of patients who were prospectively enrolled. Exposures: Proton pump inhibitor use and clinical data at 30 days (primary exposure) and 90 days (secondary exposure) before the date of culture. Main Outcomes and Measures: Adjusted incidence rate ratios (aIRRs) of ESBL- or carbapenemase-producing Enterobacterales acquisition by PPI dose and time risk windows (30 days for the primary outcome and 90 days for the secondary outcome) were estimated using conditional logistic regression models. Results: Among 2239 hospitalized patients (51.1% male; mean [SD] age, 60.9 [16.7] years), 374 were in the case group (51.6% male; mean [SD] age, 61.1 [16.5] years) and 1865 were in the matched control group (51.0% male; mean [SD] age, 60.9 [16.7] years). The aIRR for PPI use overall was 1.48 (95% CI, 1.15-1.91) at 30 days. Sensitivity analyses and the analysis of the pair-matched study with prospectively enrolled patients (aIRR, 2.96, 95% CI, 1.14-7.74) yielded similar results; findings were consistent in subgroups and corroborated by a negative-control exposure analysis. No association with microbiome-disturbing agents was found; laxatives and antibiotics were independently associated with a more than 2-fold increase in the risk of acquisition (antibiotics: aIRR, 2.78 [95% CI, 2.14-3.59]; laxatives: aIRR, 2.26 [95% CI. 1.73-2.94]). Conclusions and Relevance: In this study, after careful control for confounding and sensitivity analyses, PPI use was associated with increases in the risk of acquiring ESBL- or carbapenemase-producing Enterobacterales among adult hospitalized patients. These findings emphasize the need for judicious use of PPIs.

Detecting inappropriate total duration of antimicrobial therapy using semi-automated surveillance.

OBJECTIVES: Evaluation of the appropriateness of the duration of antimicrobial treatment is a cornerstone of antibiotic stewardship programs, but it is time-consuming. Furthermore, it is often restricted to antibiotics prescribed during hospital admission. This study aimed to determine whether mandatory prescription-indication registration at the moment of prescribing antibiotics enables reliable automated assessment of the duration of antibiotic therapy, including post-discharge duration, limiting the need for manual chart review to data validation. METHODS: Antibiotic prescription and admission data, from 1-6-2020 to 31-12-2021, were electronically extracted from the Electronic Medical Record of two hospitals using mandatory indication registration. All consecutively prescribed antibiotics of adult patients who received empiric therapy in the first 24 h of admission were merged to calculate the total length of therapy (LOT) per patient, broken down per registered indication. Endpoints were the accuracy of the data, evaluated by comparing the extracted LOT and registered indication with the clinical notes in 400 randomly selected records, and guideline adherence of treatment duration. Data were analysed using a reproducible syntax, allowing semi-automated surveillance. RESULTS: A total of 3,466 antibiotic courses were analysed. LOT was accurately retrieved in 96% of the 400 evaluated antibiotic courses. The registered indication did not match chart review in 17% of antibiotic courses, of which only half affected the assessment of guideline adherence. On average, in 44% of patients treatment was continued post-discharge, accounting for 60% (± 19%) of their total LOT. Guideline adherence ranged from 26 to 75% across indications. CONCLUSIONS: Mandatory prescription-indication registration data can be used to reliably assess total treatment course duration, including post-discharge antibiotic duration, allowing semi-automated surveillance.

Reducing the dosing frequency of selective digestive tract decontamination to three times daily provides effective decontamination of Gram-negative bacteria.

This study evaluated the effectiveness of selective digestive tract decontamination (SDD) application three times daily (t.i.d.) compared to the standard four times daily (q.i.d.). Retrospective equivalence (combined non-inferiority and non-superiority design) study with a before-and-after design on a tertiary ICU in which the SDD frequency was reduced from q.i.d. to t.i.d. All patients with ICU admissions ≥72h and with ≥2 surveillance cultures collected on different dates were included in this study. We compared successful decontamination of Gram-negative bacteria (GNB). Furthermore, time to decontamination, ICU-acquired GNB bacteraemia and 28-day mortality were compared between the two groups. In total 1958 ICU admissions (1236 q.i.d., 722 t.i.d). Decontamination was achieved during the first week of admission in 77% and 76% of patients receiving SDD q.i.d and t.i.d., respectively. Successful decontamination within 14 days (without consecutive acquisition of Gram-negative bacteria) was achieved in 69.3% of the admissions with q.i.d. versus 66.8% in t.i.d. SDD (p-value = 0.2519). The proportions of successful decontamination of GNB were equivalent in both groups (-0.025, 98% CI: -0.087; 0.037). There was no significant difference in time to decontamination between the two regimens (log-rank test p-value = 0.55). Incidence (episodes/1000 days) of ICU-acquired GNB bacteraemia was 0.9 in both groups, and OR for death at day 28 in the t.i.d. group compared to the q.i.d. group was 0.99 (95% confidence interval, 0.80-1.21). This study shows that a t.i.d. application regimen achieves similar outcomes to the standard q.i.d. regime, for both microbiological and clinical outcome measures.

Next-generation biological control: the need for integrating genetics and genomics.

Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.

Maternal effect determines drought resistance of eggs in the predatory mite Phytoseiulus persimilis.

The ability of an organism to adapt to short-term environmental changes within its lifetime is of fundamental importance. This adaptation may occur through phenotypic plasticity. Insects and mites, in particular, are sensitive to changes in temperature and humidity, especially during the juvenile stages. We studied the role of phenotypic plasticity in the adaptation of eggs to different relative humidity conditions, in the predatory mite Phytoseiulus persimilis, used worldwide as a biological control agent of the spider mite Tetranychus urticae. The biocontrol efficacy of P. persimilis decreases under dry conditions, partly because P. persimilis eggs are sensitive to drought. We exposed P. persimilis adult females from two different strains to constant and variable humidity regimes and evaluated the hatching rate of their eggs in dry conditions, as well as the survival and oviposition rates of these females. Whereas the eggs laid by P. persimilis females exposed to constant high humidity did not survive in dry conditions, females exposed to constant low humidity started laying drought-resistant eggs after 24 h of exposure. Survival and oviposition rates of the females were affected by humidity: females laid fewer eggs under constant low humidity and had a shorter lifespan under constant high and constant low humidity. The humidity regimes tested had similar effects across the two P. persimilis strains. Our results demonstrate that transgenerational phenotypic plasticity, called maternal effect, allows P. persimilis females to prepare their offspring for dry conditions.

Proximate mechanisms of drought resistance in Phytoseiulus persimilis eggs.

Under drought stress, Phytoseiulus persimilis females are able to lay drought-resistant eggs through an adaptive maternal effect. The mechanisms making these eggs drought resistant still remain to be investigated. For this purpose, we studied the physiological differences between drought-resistant and drought-sensitive eggs. We compared the volume and the surface-area-to-volume ratio (SA:V) of the eggs, their sex ratio, their chemical composition (by gas chromatography-mass spectrometry), their internal and external structure [by scanning electron microscope (SEM) and transmission electron microscope (TEM) images], and their developmental time. Our results show that drought-resistant and drought-sensitive eggs have a different chemical composition: drought-resistant eggs contain more compatible solutes (free amino acids and sugar alcohols) and saturated hydrocarbons than drought-sensitive eggs. This difference may contribute to reducing water loss in drought-resistant eggs. Moreover, drought-resistant eggs are on average 8.4% larger in volume, and have a 2.4% smaller SA:V than drought-sensitive eggs. This larger volume and smaller SA:V, probably the result of a higher water content, may make drought-resistant eggs less vulnerable to water loss. We did not find any difference in sex ratio, internal or external structure nor developmental time between drought-resistant and drought-sensitive eggs. These results mark the first step in the understanding of the strategies and the energetic costs involved in the production of drought-resistant eggs in P. persimilis females.

In situ observation of the Cardinium symbionts of Brevipalpus (Acari: Tenuipalpidae) by electron microscopy.

Brevipalpus (Acari: Tenuipalpidae) mites are important pests on a variety of host plant species. The mites damage their hosts directly by feeding and some species also serve as vectors of plant viruses. Among more than 200 described Brevipalpus species, three are recognized as vectors of plant viruses: B. phoenicis, B. californicus and B. obovatus. These species occur worldwide in subtropical and tropical regions. Brevipalpus mites reproduce mostly by thelytokous parthenogenesis and this condition was attributed to a bacterial endosymbiont, recently characterized as a member of the genus Cardinium. The same symbiont infects many other arthropods and is capable of manipulating their host reproduction in various ways. Generally the presence of Cardinium is determined by molecular, PCR based, techniques. In the current work we present visual evidence for the presence of these bacteria by transmission electron microscopy as a complement of previous detection by PCR. Cardinium is easily identified by the presence of a unique array of microtubule-like structures (ML) in the cell. Symbionts have been observed in several organs and eggs from different populations of all three Brevipalpus species known as vector of plant viruses. Cardinium cells were always immersed directly within the cytoplasm of infected cells. Bacteria were observed in all females of all instars, but were absent from all males examined. Females from some Brevipalpus populations were observed to be uninfected by Cardinium. This observation confirmed previous PCR-based results that these populations were aposymbiotic. The observed distribution of the bacteria suggests that these bacteria could have other functions in the mite biology beside feminization.

Cardinium symbionts induce haploid thelytoky in most clones of three closely related Brevipalpus species.

Bacterial symbionts that manipulate the reproduction of their host to increase their own transmission are widespread. Most of these bacteria are Wolbachia, but recently a new bacterium, named Cardinium, was discovered that is capable of the same manipulations. In the host species Brevipalpus phoenicis (Acari: Tenuipalpidae) this bacterium induces thelytoky by feminizing unfertilized haploid eggs. The related species B. obovatus and B. californicus are thelytokous too, suggesting that they reproduce in the same remarkable way as B. phoenicis. Here we investigated the mode of thelytokous reproduction in these three species. Isofemale lines were created of all three species and 19 lines were selected based on variation in mitochondrial COI sequences. All B. phoenicis and B. californicus lines (10 and 4 lines, respectively) produced males under laboratory conditions up to 6.7%. In contrast, males were absent from all B. obovatus lines (5 lines). Additional experiments with two B. phoenicis isofemale lines showed that males can be produced by very young females only, while older females produce daughters exclusively. For most lines it was shown that they are indeed feminized by a bacterium as treatment with antibiotics resulted in increased numbers of males up to 13.5%. Amplification and identification of specific gyrB sequences confirmed that those lines were infected with Cardinium. Three out of the five B. obovatus lines did not produce males after treatments with antibiotics, nor did they contain Cardinium or any other bacterium that might induce thelytoky. In these lines thelytoky is probably a genetic property of the mite itself. Despite the different causes of thelytoky, flow cytometry revealed that all 19 lines were haploid. Finally, the taxonomic inferences based on the mitochondrial COI sequences were incongruent with the classical taxonomy based on morphology, suggesting that a taxonomic revision of this group is necessary.

Adaptation in the asexual false spider mite Brevipalpus phoenicis: evidence for frozen niche variation.

Because asexual species lack recombination, they have little opportunity to produce genetically variable offspring and cannot adapt to changes in their environment. However, a number of asexual species are very successful and appear to contradict this general view. One such species is the phytophagous mite Brevipalpus phoenicis (Geijskes), a species that is found in a wide range of environments. There are two general explanations for this pattern, the General Purpose Genotype (GPG) and Frozen Niche Variation (FNV). According to the GPG model, an asexual species consists of clones that can all survive and reproduce in all the different niches. Alternatively, the FNV model postulates that different clones are specialized to different niches. We have performed a test to distinguish between these models in B. phoenicis. Mites from three populations from three different host plant species (citrus, hibiscus and acerola) were transplanted to their own and the two alternative host plants and mite survival and egg production were measured. Additionally, the mite populations were genotyped using microsatellites. Fitness was seriously reduced when mites were transplanted to the alternative host plant species, except when the alternative host was acerola. We concluded that B. phoenicis clones are specialized to different niches and thus the FNV best describes the broad ecological niche of this species but that there is also some evidence for host plant generalization. This conclusion was strengthened by the observations that on each host plant species the native mite population performed better than the introduced ones, and that three microsatellite markers showed that the mite populations are genetically distinct.