Ecological impact of ciprofloxacin on commensal enterococci in healthy volunteers

Comparative study of virulence factor genes, β-hemolysis and biofilm production in invasive and colonizing enterococci

Objectives: In humans, enterococci are among the most important opportunistic pathogens. This study aims to compare invasive isolates obtained from blood cultures of patients with sepsis and endocarditis with colonizing isolates obtained from healthy donors’ stool samples.

Methods: A case-by-case assessment was conducted on invasive infection cases to determine whether enterococci were involved in their pathogenesis. They were tested for the presence of virulence factor genes, β-hemolysis on agars supplemented with human and sheep blood, and biofilm forming capacity.

Results: Three species of enterococci were identified among invasive isolates: Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans. All endocarditis isolates were biofilm producers. Genes esp, gelE, asa1, ace, hyl, cylB, and cylA were present in 7 (41.2%), 11 (64.7%), 11 (64.7%), 13 (76.5%), 0, 3 (17.6%), and 1 (5.9%) invasive isolate, but none of them could be linked to a particular infection (sepsis or endocarditis). Colonizing isolates proved to have had more virulence factor genes, but the differences were not statistically significant. Members of that group produced a greater amount of biofilm when the ace gene was absent ( p = 0.047). The production of β-hemolysis by noninvasive strains was detected more frequently when agar was supplemented with human blood ( p = 0.021). In general, the presence of either cyl gene on that specific agar was in direct connection with the production of β-hemolysis: cylA ( p = 0.047) or cylB ( p = 0.020).

Conclusion: We have been unable to establish any correlation between invasive isolates and any virulence gene carriage and biofilm formation. β-hemolysis was produced significantly more often by colonizing strains when agar had been supplemented with human blood.

Short treatment duration for community-acquired pneumonia

PURPOSE OF REVIEW

Lower respiratory tract infections are one of the most common indications for antibiotic use in community and hospital settings. Usual guidelines for adults with community-acquired pneumonia (CAP) recommend 5-7 days of antibiotic treatment. In daily practice, physicians often prescribe 9-10 days of antibiotic treatment. Among available strategies to decrease antibiotic use, possibly preventing the emergence of bacterial resistance, reducing treatment durations is the safest and the most acceptable to clinicians. We aim to review data evaluating the efficacy of short antibiotic duration in adult CAP and which criteria can help clinicians to reduce antibiotic treatment.

RECENT FINDINGS

Several studies and meta-analyses demonstrated that the treatment duration of 7 days or less was sufficient for CAP. Two trials found that 3-day treatments were effective, even in hospitalized CAP.To customize and shorten duration, clinical and biological criteria have been studied and reflect patient's response. Indeed, stability criteria were recently shown to be effective to discontinue antibiotic treatment. Procalcitonin was also studied but never compared with clinical criteria.

SUMMARY

Treatment duration for CAP is still under debate, but several studies support short durations. Clinical criteria could be possibly used to discontinue antibiotic treatment.

Antimicrobial resistance among canine enterococci in the northeastern United States, 2007-2020

Introduction

Antimicrobial resistance (AMR) is a growing and complex One Health concern worldwide, threatening the practice of human and veterinary medicine. Although dogs are a potential reservoir of multidrug-resistant bacteria, there are very few surveillance studies on AMR from the canine population in the United States. Here, we assessed the antimicrobial susceptibility patterns, identified temporal resistance and minimum inhibitory concentration trends, and described associations between resistance phenotypes among canine clinical enterococci in the northeastern United States.

Methods

Through a large-scale retrospective study design, we collected species identification, minimum inhibitory concentration, and clinical data from 3,659 canine enterococci isolated at the Cornell University Animal Health Diagnostic Center between 2007 and 2020. We used the Mann-Kendall test, Sen's slope, multivariable logistic regression, and survival analysis models to detect the presence of a significant trend in resistance over the study period.

Results

Enterococcus faecalis was the most prevalent species (67.1% of isolates), followed by Enterococcus faecium (20.4%). We found high levels of AMR among enterococci to almost all the tested antimicrobials, particularly E. faecium. The lowest percentage of resistance was to vancomycin and chloramphenicol. Multidrug resistance was common (80% of E. faecium and 33% of E. faecalis) and 31 isolates were extensively drug resistant. Multidrug resistance among E. faecium increased over time, but not in E. faecalis. Resistance to penicillins, enrofloxacin, and rifampin increased during the study period, but resistance to tetracyclines is on a downward trajectory compared to AMR data from the last decade. Emerging vancomycin-resistant E. faecalis (0.3%) and E. faecium (0.8%) infections in the canine population are of great concern to both human and animal health. One E. faecium isolate with acquired vancomycin resistance was identified in 2017 and four vancomycin-resistant enterococci isolates were identified in 2020.

Conclusion

There is a crucial need to make rational prescribing decisions on the prudent use of antimicrobials and improve the quality of care for patients, especially when empirical antimicrobial treatment for enterococcal infection is common.

Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults

Antibiotics are deployed against bacterial pathogens, but their targeting of conserved microbial processes means they also collaterally perturb the commensal microbiome. To understand acute and persistent effects of antibiotics on the gut microbiota of healthy adult volunteers, we quantify microbiome dynamics before, during, and 6 months after exposure to 4 commonly used antibiotic regimens. We observe an acute decrease in species richness and culturable bacteria after antibiotics, with most healthy adult microbiomes returning to pre-treatment species richness after 2 months, but with an altered taxonomy, resistome, and metabolic output, as well as an increased antibiotic resistance burden. Azithromycin delays the recovery of species richness, resulting in greater compositional distance. A subset of volunteers experience a persistent reduction in microbiome diversity after antibiotics and share compositional similarities with patients hospitalized in intensive care units. These results improve our quantitative understanding of the impact of antibiotics on commensal microbiome dynamics, resilience, and recovery.

The effect of nickel ions on the susceptibility of bacteria to ciprofloxacin and ampicillin

To explore the interaction effects of ciprofloxacin and ampicillin with nickel on the growth of bacteria, Staphylococcus aureus strain ATCC 29213, Enterococcus faecalis ATCC 29212 and Escherichia coli ATCC 25922 were used. Minimum inhibitory concentrations (MICs) were determined for nickel, ciprofloxacin and ampicillin, and the checkerboard method was used to assess their cumulative effects on bacterial growth. The interactions between the metal and antibiotics were assessed by the fractional inhibitory concentration (FIC). The MICs for ciprofloxacin and ampicillin were 0.31 and 1 mg/L for E. faecalis, 0.62 and 1 mg/L for S. aureus and 0.005 and 2.5 for E. coli, respectively. The MIC for nickel was 1000 mg/L for all bacteria. The FIC results for ciprofloxacin and nickel demonstrated an antagonistic effect of the two agents on the growth of E. coli and E. faecalis and an additive effect on S. aureus. The FICs for ampicillin and nickel demonstrated a synergistic effect on the growth of E. faecalis and E. coli. Different interactions of metals and antibiotics were observed depending on the bacteria and the type of antibiotic.

Completing the Picture-Capturing the Resistome in Antibiotic Clinical Trials

Despite the accepted dogma that antibiotic use is the largest contributor to antimicrobial resistance (AMR) and human microbiome disruption, our knowledge of specific antibiotic-microbiome effects remains basic. Detection of associations between new or old antimicrobials and specific AMR burden is patchy and heterogeneous. Various microbiome analysis tools are available to determine antibiotic effects on microbial communities in vivo. Microbiome analysis of treatment groups in antibiotic clinical trials, powered to measure clinically meaningful endpoints would greatly assist the antibiotic development pipeline and clinician antibiotic decision making.

Linezolid-resistant (Tn6246::fexB-poxtA) Enterococcus faecium strains colonizing humans and bovines on different continents: similarity without epidemiological link

OBJECTIVES

poxtA is the most recently described gene conferring acquired resistance to linezolid, a relevant antibiotic for treating enterococcal infections. We retrospectively screened for poxtA in diverse enterococci and aimed to characterize its genetic/genomic contexts.

METHODS

poxtA was screened by PCR in 812 enterococci from 458 samples (hospitals/healthy humans/wastewater/animals/retail food) obtained in Portugal/Angola/Tunisia (1996-2019). Antimicrobial susceptibility testing was performed for 13 antibiotics (EUCAST/CLSI). poxtA stability (∼500 generations), transfer (filter mating), clonality (SmaI-PFGE) and location (S1-PFGE/hybridization) were tested. WGS (Illumina-HiSeq) was performed for clonal representatives.

RESULTS

poxtA was detected in Enterococcus faecium from six samples (1.3%): a healthy human (rectal swab) in Porto, Portugal (ST32/2001); four farm cows (milk) in Mateur, Tunisia (ST1058/2015); and a hospitalized patient (faeces) in Matosinhos, Portugal (ST1058/2015). All expressed resistance to linezolid (MIC = 8 mg/L), chloramphenicol, tetracycline and erythromycin, with variable resistance to ciprofloxacin and streptomycin. ST1058-poxtA-carrying isolates from Tunisia and Portugal differed by two SNPs and had similar plasmid content. poxtA, located in an IS1216-flanked Tn6246-like element, co-hybridized with fexB on one or more plasmids per isolate (one to three plasmids of 30-100 kb), was stable after several generations and transferred only from ST1058. ST1058 strains carried resistance/virulence genes (Efmqnr/acm) possibly induced under selective quinolone treatment.

CONCLUSIONS

poxtA has been circulating in Portugal since at least 2001, corresponding to the oldest description worldwide to date. We also extend the reservoir of poxtA to bovines. The similar linezolid-resistant poxtA-carrying strains colonizing humans and livestock on different continents, and without a noticeable relationship, suggests a recent transmission event or convergent evolution of E. faecium populations in different hosts and geographic regions.

Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944)

BACKGROUND

With increasing concerns about the impact of frequent antibiotic usage on the human microbiome, it is important to characterize the potential for such effects in early antibiotic drug development clinical trials. In a randomised Phase 2a clinical trial study that evaluated the pharmacokinetics of repeated oral doses of gepotidacin, a first-in-chemical-class triazaacenaphthylene antibiotic with a distinct mechanism of action, in adult females with uncomplicated urinary tract infections for gepotidacin (GSK2140944) we evaluated the potential changes in microbiome composition across multiple time points and body-sites ( ClinicalTrials.gov : NCT03568942).

RESULTS

Samples of gastrointestinal tract (GIT), pharyngeal cavity and vaginal microbiota were collected with consent from 22 patients at three time points relative to the gepotidacin dosing regimen; Day 1 (pre-dose), Day 5 (end of dosing) and Follow-up (Day 28 ± 3 days). Microbiota composition was determined by DNA sequencing of 16S rRNA gene variable region 4 amplicons. By Day 5, significant changes were observed in the microbiome diversity relative to pre-dose across the tested body-sites. However, by the Follow-up visit, microbiome diversity changes were reverted to compositions comparable to Day 1. The greatest range of microbiome changes by body-site were GIT followed by the pharyngeal cavity then vagina. In Follow-up visit samples we found no statistically significant occurrences of pathogenic taxa.

CONCLUSION

Our findings suggest that gepotidacin alteration of the human microbiome after 5 days of dosing is temporary and rebound to pre-dosing states is evident within the first month post-treatment. We recommend that future antibiotic drug trials include similar exploratory investigations into the duration and context of microbiome modification and recovery.

TRIAL REGISTRATION

NCT03568942 . Registered 26 June 2018.

Lytic Bacteriophage EFA1 Modulates HCT116 Colon Cancer Cell Growth and Upregulates ROS Production in an Enterococcus faecalis Co-culture System

Enterococcus faecalis is an opportunistic pathogen in the gut microbiota that’s associated with a range of difficult to treat nosocomial infections. It is also known to be associated with some colorectal cancers. Its resistance to a range of antibiotics and capacity to form biofilms increase its virulence. Unlike antibiotics, bacteriophages are capable of disrupting biofilms which are key in the pathogenesis of diseases such as UTIs and some cancers. In this study, bacteriophage EFA1, lytic against E. faecalis, was isolated and its genome fully sequenced and analyzed in silico. Electron microscopy images revealed EFA1 to be a Siphovirus. The bacteriophage was functionally assessed and shown to disrupt E. faecalis biofilms as well as modulate the growth stimulatory effects of E. faecalis in a HCT116 colon cancer cell co-culture system, possibly via the effects of ROS. The potential exists for further testing of bacteriophage EFA1 in these systems as well as in vivo models.

Antibiotic selection based on microbiology and resistance profiles of bile from gallbladder of patients with acute cholecystitis

With the progression of acute cholecystitis, antimicrobial therapy becomes important for infection control. Current antibiotic recommendations were mostly based on reports of patients with acute cholangitis whose bile specimens were sampled from the biliary tract. However, as most infections of acute cholecystitis are limited to the gallbladder, direct sampling from the site increases the probability of identifying the causative pathogen. We investigated 321 positive bile cultures from 931 patients with acute cholecystitis who underwent laparoscopic cholecystectomy between January 2003 and December 2017. The frequency of enterococci declined (P = 0.041), whereas that of Enterobacteriales (P = 0.005), particularly Escherichia (P = 0.008), increased over time. The incidence of ciprofloxacin-resistant Enterobacteriales showed a significant increasing trend (P = 0.031). Vancomycin-resistant E.faecium, carbapenem-resistant Enterobacteriales, and extended-spectrum beta-lactamase-producing Enterobacteriales were recently observed. In grade I and II acute cholecystitis, there were no significant differences in perioperative outcomes in patients with and without early appropriate antimicrobial therapy. In conclusion, the changing incidence of frequently isolated microorganisms and their antibiotic resistance over time would be considered before selecting antibiotics for the treatment of acute cholecystitis. Surgery might be a crucial component of infection control in grade I and II acute cholecystitis.

Oral fosfomycin for the treatment of lower urinary tract infections among kidney transplant recipients-Results of a Spanish multicenter cohort

Oral fosfomycin may constitute an alternative for the treatment of lower urinary tract infections (UTIs) in kidney transplant recipients (KTRs), particularly in view of recent safety concerns with fluroquinolones. Specific data on the efficacy and safety of fosfomycin in KTR are scarce. We performed a retrospective study in 14 Spanish hospitals including KTRs treated with oral fosfomycin (calcium and trometamol salts) for posttransplant cystitis between January 2005 and December 2017. A total of 133 KTRs developed 143 episodes of cystitis. Most episodes (131 [91.6%]) were produced by gram-negative bacilli (GNB), and 78 (54.5%) were categorized as multidrug resistant (including extended-spectrum β-lactamase-producing Enterobacteriaceae [14%] or carbapenem-resistant GNB [3.5%]). A median daily dose of 1.5 g of fosfomycin (interquartile range [IQR]: 1.5-2) was administered for a median of 7 days (IQR: 3-10). Clinical cure (remission of UTI-attributable symptoms at the end of therapy) was achieved in 83.9% (120/143) episodes. Among those episodes with follow-up urine culture, microbiological cure at month 1 was achieved in 70.2% (59/84) episodes. Percutaneous nephrostomy was associated with a lower probability of clinical cure (adjusted odds ratio: 10.50; 95% confidence interval: 0.98-112.29; P = 0.052). In conclusion, fosfomycin is an effective orally available alternative for treating cystitis among KTRs.

The effect of antibiotics on the composition of the intestinal microbiota - a systematic review

OBJECTIVE

Antibiotics change the composition of the intestinal microbiota. The magnitude of the effect of antibiotics on the microbiota and whether the effects are short-term or persist long-term remain uncertain. In this review, we summarise studies that have investigated the effect of antibiotics on the composition of the human intestinal microbiota.

METHODS

A systematic search was done to identify original studies that have investigated the effect of systemic antibiotics on the intestinal microbiota in humans.

RESULTS

We identified 129 studies investigating 2076 participants and 301 controls. Many studies reported a decrease in bacterial diversity with antibiotic treatment. Penicillin only had minor effects on the intestinal microbiota. Amoxicillin, amoxcillin/clavulanate, cephalosporins, lipopolyglycopeptides, macrolides, ketolides, clindamycin, tigecycline, quinolones and fosfomycin all increased abundance of Enterobacteriaea other than E. coli (mainly Citrobacter spp., Enterobacter spp. and Klebsiella spp.). Amoxcillin, cephalosporins, macrolides, clindamycin, quinolones and sulphonamides decreased abundance of E. coli, while amoxcillin/clavulante, in contrast to other penicillins, increased abundance of E. coli. Amoxicllin, piperacillin and ticarcillin, cephalosporins (except fifth generation cephalosporins), carbapenems and lipoglycopeptides were associated with increased abundance of Enterococcus spp., while macrolides and doxycycline decreased its abundance. Piperacillin and ticarcillin, carbapenems, macrolides, clindamycin and quinolones strongly decreased the abundance of anaerobic bacteria. In the studies that investigated persistence, the longest duration of changes was reported after treatment with ciprofloxacin (one year), clindamycin (two years) and clarithromycin plus metronidazole (four years). Many antibiotics were associated with a decrease in butyrate or butryrate-producing bacteria.

CONCLUSION

Antibiotics have profound and sometimes persisting effects on the intestinal microbiota, characterised by diminished abundance of beneficial commensals and increased abundance of potentially detrimental microorganisms. Understanding these effects will help tailor antibiotic treatment and the use of probiotics to minimise this 'collateral damage'.

Chloramphenicol Resurrected: A Journey from Antibiotic Resistance in Eye Infections to Biofilm and Ocular Microbiota

The advent of multidrug resistance among pathogenic bacteria is devastating the worth of antibiotics and changing the way of their administration, as well as the approach to use new or old drugs. The crisis of antimicrobial resistance is also due to the unavailability of newer drugs, attributable to exigent regulatory requirements and reduced financial inducements. The emerging resistance to antibiotics worldwide has led to renewed interest in old drugs that have fallen into disuse because of toxic side effects. Thus, comprehensive efforts are needed to minimize the pace of resistance by studying emergent microorganisms and optimize the use of old antimicrobial agents able to maintain their profile of susceptibility. Chloramphenicol is experiencing its renaissance because it is widely used in the treatment and prevention of superficial eye infections due to its broad spectrum of activity and other useful antimicrobial peculiarities, such as the antibiofilm properties. Concerns have been raised in the past for the risk of aplastic anemia when chloramphenicol is given intravenously. Chloramphenicol seems suitable to be used as topical eye formulation for the limited rate of resistance compared to fluoroquinolones, for its scarce induction of bacterial resistance and antibiofilm activity, and for the hypothetical low impact on ocular microbiota disturbance. Further in-vitro and in vivo studies on pharmacodynamics properties of ocular formulation of chloramphenicol, as well as its real impact against biofilm and the ocular microbiota, need to be better addressed in the near future.

The Enterococcus: a Model of Adaptability to Its Environment

The genus Enterococcus comprises a ubiquitous group of Gram-positive bacteria that are of great relevance to human health for their role as major causative agents of health care-associated infections. The enterococci are resilient and versatile species able to survive under harsh conditions, making them well adapted to the health care environment. Two species cause the majority of enterococcal infections: Enterococcus faecalis and Enterococcus faecium Both species demonstrate intrinsic resistance to common antibiotics, such as virtually all cephalosporins, aminoglycosides, clindamycin, and trimethoprim-sulfamethoxazole. Additionally, a remarkably plastic genome allows these two species to readily acquire resistance to further antibiotics, such as high-level aminoglycoside resistance, high-level ampicillin resistance, and vancomycin resistance, either through mutation or by horizontal transfer of genetic elements conferring resistance determinants.

Double-Serine Fluoroquinolone Resistance Mutations Advance Major International Clones and Lineages of Various Multi-Drug Resistant Bacteria

The major international sequence types/lineages of methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae and ESBL-producing E. coli were demonstrated to have been advanced by favorable fitness balance associated with high-level resistance to fluoroquinolones. The paper shows that favorable fitness in the major STs/lineages of these pathogens was principally attained by the capacity of evolving mutations in the fluoroquinolone-binding serine residues of both the DNA gyrase and topoisomerase IV enzymes. The available information on fitness balance incurred by individual and various combinations of mutations in the enzymes is reviewed in multiple species. Moreover, strong circumstantial evidence is presented that major STs/lineages of other multi-drug resistant bacteria, primarily vancomycin-resistant Enterococcus faecium (VRE), emerged by a similar mechanism. The reason(s) why the major ST/lineage strains of various pathogens proved more adept at evolving favorable mutations than most isolates of the same species remains to be elucidated.

Impact of an antimicrobial stewardship programme to optimize antimicrobial use for outpatients at an emergency department

BACKGROUND

Antimicrobial stewardship programmes (ASPs) have been effective in optimizing antibiotic use for inpatients. However, an emergency department's fast-paced clinical setting can be challenging for a successful ASP.

AIM

In April 2015, an ASP was implemented in our emergency department and we aimed to determine its impact on antimicrobial use for outpatients.

METHODS

This was a single-centre study comparing the quality of antibiotic prescriptions between a one-year period before ASP implementation (November 2012 to October 2013) and a one-year period after its implementation (June 2015 to May 2016). For each period, antimicrobial prescriptions for all adult outpatients (hospitalized for <24h) were evaluated by an infectious disease specialist and an emergency department physician to assess compliance with local prescribing guidelines. Inappropriate prescriptions were then classified.

FINDINGS

Before and after ASP, 34,671 and 35,925 consultations were registered at our emergency department, of which 25,470 and 26,208 were outpatients. Antimicrobials were prescribed in 769 (3.0%) and 580 (2.2%) consultations, respectively (P < 0.0001). There were 484 (62.9%) and 271 (46.7%) (P < 0.0001) instances of non-compliance with guidelines before and after ASP implementation. Non-compliance included unnecessary antimicrobial prescriptions, 197 (25.6%) vs 101 (17.4%) (P<0.0005); inappropriate spectrum, 108 (14.0%) vs 54 (9.3%) (P=0.008); excessive treatment duration, 87 (11.3%) vs 53 (9.1%) (P>0.05); and inappropriate choices, 11 (1.4%) vs 15 (2.6%) (P>0.05).

CONCLUSION

The implementation of an ASP markedly decreased the number of unnecessary antimicrobial prescriptions, but had little impact on most other aspects of inappropriate prescribing.