Antibacterial activity of nonantibiotics is orthogonal to standard antibiotics

Numerous nonantibiotic drugs have potent antibacterial activity and can adversely affect the human microbiome. The mechanistic underpinning of this toxicity remains largely unknown. We investigated the antibacterial activity of 200 drugs using genetic screens with thousands of barcoded Escherichia coli knockouts. We analyzed 2 million gene-drug interactions underlying drug-specific toxicity. Network-based analysis of drug-drug similarities revealed that antibiotics clustered into modules that are consistent with the mode of action of their established classes, whereas nonantibiotics remained unconnected. Half of the nonantibiotics clustered into separate modules, potentially revealing shared and unexploited targets for new antimicrobials. Analysis of efflux systems revealed that they widely affect antibiotics and nonantibiotics alike, suggesting that the impact of nonantibiotics on antibiotic cross-resistance should be investigated closely in vivo.

Discovery of a structural class of antibiotics with explainable deep learning

The discovery of novel structural classes of antibiotics is urgently needed to address the ongoing antibiotic resistance crisis1-9. Deep learning approaches have aided in exploring chemical spaces1,10-15; these typically use black box models and do not provide chemical insights. Here we reasoned that the chemical substructures associated with antibiotic activity learned by neural network models can be identified and used to predict structural classes of antibiotics. We tested this hypothesis by developing an explainable, substructure-based approach for the efficient, deep learning-guided exploration of chemical spaces. We determined the antibiotic activities and human cell cytotoxicity profiles of 39,312 compounds and applied ensembles of graph neural networks to predict antibiotic activity and cytotoxicity for 12,076,365 compounds. Using explainable graph algorithms, we identified substructure-based rationales for compounds with high predicted antibiotic activity and low predicted cytotoxicity. We empirically tested 283 compounds and found that compounds exhibiting antibiotic activity against Staphylococcus aureus were enriched in putative structural classes arising from rationales. Of these structural classes of compounds, one is selective against methicillin-resistant S. aureus (MRSA) and vancomycin-resistant enterococci, evades substantial resistance, and reduces bacterial titres in mouse models of MRSA skin and systemic thigh infection. Our approach enables the deep learning-guided discovery of structural classes of antibiotics and demonstrates that machine learning models in drug discovery can be explainable, providing insights into the chemical substructures that underlie selective antibiotic activity.

A novel antibiotic class targeting the lipopolysaccharide transporter

Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a major global pathogen with limited treatment options1. No new antibiotic chemical class with activity against A. baumannii has reached patients in over 50 years1. Here we report the identification and optimization of tethered macrocyclic peptide (MCP) antibiotics with potent antibacterial activity against CRAB. The mechanism of action of this molecule class involves blocking the transport of bacterial lipopolysaccharide from the inner membrane to its destination on the outer membrane, through inhibition of the LptB2FGC complex. A clinical candidate derived from the MCP class, zosurabalpin (RG6006), effectively treats highly drug-resistant contemporary isolates of CRAB both in vitro and in mouse models of infection, overcoming existing antibiotic resistance mechanisms. This chemical class represents a promising treatment paradigm for patients with invasive infections due to CRAB, for whom current treatment options are inadequate, and additionally identifies LptB2FGC as a tractable target for antimicrobial drug development.

Impact of Anaerobic Antibacterial Spectrum on Cystic Fibrosis Airway Microbiome Diversity and Pulmonary Function

BACKGROUND

The role of anaerobic organisms in the cystic fibrosis (CF) lung microbiome is unclear. Our objectives were to investigate the effect of broad (BS) versus narrow (NS) spectrum antianaerobic antibiotic activity on lung microbiome diversity and pulmonary function, hypothesizing that BS antibiotics would cause greater change in microbiome diversity without a significant improvement in lung function.

METHODS

Pulmonary function tests and respiratory samples were collected prospectively in persons with CF before and after treatment for pulmonary exacerbations. Treatment antibiotics were classified as BS or NS. Gene sequencing data from 16S rRNA were used for diversity analysis and bacterial genera classification. We compared the effects of BS versus NS on diversity indices, lung function and anaerobic/aerobic ratios. Statistical significance was determined by multilevel mixed-effects generalized linear models and mixed-effects regression models.

RESULTS

Twenty patients, 6-20 years of age, experienced 30 exacerbations. BS therapy had a greater effect on beta diversity than NS therapy when comparing time points before antibiotics to after and at recovery. After antibiotics, the NS therapy group had a greater return toward baseline forced expiratory volume at 1 second and forced expiratory flow 25%-75% values than the BS group. The ratio of anaerobic/aerobic organisms showed a predominance of anaerobes in the NS group with aerobes dominating in the BS group.

CONCLUSIONS

BS antianaerobic therapy had a greater and possibly longer lasting effect on the lung microbiome of persons with CF, without achieving the recovery of pulmonary function seen with the NS therapy. Specific antibiotic therapies may affect disease progression by changing the airway microbiome.

Intrapartum group B Streptococcal prophylaxis and childhood weight gain

OBJECTIVE

To determine the difference in rate of weight gain from birth to 5 years based on exposure to maternal group B streptococcal (GBS) intrapartum antibiotic prophylaxis (IAP).

DESIGN

Retrospective cohort study of 13 804 infants.

SETTING

Two perinatal centres and a primary paediatric care network in Philadelphia.

PARTICIPANTS

Term infants born 2007-2012, followed longitudinally from birth to 5 years of age.

EXPOSURES

GBS IAP defined as penicillin, ampicillin, cefazolin, clindamycin or vancomycin administered ≥4 hours prior to delivery to the mother. Reference infants were defined as born to mothers without (vaginal delivery) or with other (caesarean delivery) intrapartum antibiotic exposure.

OUTCOMES

Difference in rate of weight change from birth to 5 years was assessed using longitudinal rate regression. Analysis was a priori stratified by delivery mode and adjusted for relevant covariates.

RESULTS

GBS IAP was administered to mothers of 2444/13 804 (17.7%) children. GBS IAP-exposed children had a significantly elevated rate of weight gain in the first 5 years among vaginally-born (adjusted rate difference 1.44% (95% CI 0.3% to 2.6%)) and caesarean-born (3.52% (95% CI 1.9% to 5.2%)) children. At 5 years, the rate differences equated to an additional 0.24 kg among vaginally-born children and 0.60 kg among caesarean-born children.

CONCLUSION

GBS-specific IAP was associated with a modest increase in rate of early childhood weight gain. GBS IAP is an effective intervention to prevent perinatal GBS disease-associated morbidity and mortality. However, these findings highlight the need to better understand effects of intrapartum antibiotic exposure on childhood growth and support efforts to develop alternate prevention strategies.

Unravelling the collateral damage of antibiotics on gut bacteria

Antibiotics are used to fight pathogens but also target commensal bacteria, disturbing the composition of gut microbiota and causing dysbiosis and disease1. Despite this well-known collateral damage, the activity spectrum of different antibiotic classes on gut bacteria remains poorly characterized. Here we characterize further 144 antibiotics from a previous screen of more than 1,000 drugs on 38 representative human gut microbiome species2. Antibiotic classes exhibited distinct inhibition spectra, including generation dependence for quinolones and phylogeny independence for β-lactams. Macrolides and tetracyclines, both prototypic bacteriostatic protein synthesis inhibitors, inhibited nearly all commensals tested but also killed several species. Killed bacteria were more readily eliminated from in vitro communities than those inhibited. This species-specific killing activity challenges the long-standing distinction between bactericidal and bacteriostatic antibiotic classes and provides a possible explanation for the strong effect of macrolides on animal3-5 and human6,7 gut microbiomes. To mitigate this collateral damage of macrolides and tetracyclines, we screened for drugs that specifically antagonized the antibiotic activity against abundant Bacteroides species but not against relevant pathogens. Such antidotes selectively protected Bacteroides species from erythromycin treatment in human-stool-derived communities and gnotobiotic mice. These findings illluminate the activity spectra of antibiotics in commensal bacteria and suggest strategies to circumvent their adverse effects on the gut microbiota.

A synthetic antibiotic class overcoming bacterial multidrug resistance

The dearth of new medicines effective against antibiotic-resistant bacteria presents a growing global public health concern1. For more than five decades, the search for new antibiotics has relied heavily on the chemical modification of natural products (semisynthesis), a method ill-equipped to combat rapidly evolving resistance threats. Semisynthetic modifications are typically of limited scope within polyfunctional antibiotics, usually increase molecular weight, and seldom permit modifications of the underlying scaffold. When properly designed, fully synthetic routes can easily address these shortcomings2. Here we report the structure-guided design and component-based synthesis of a rigid oxepanoproline scaffold which, when linked to the aminooctose residue of clindamycin, produces an antibiotic of exceptional potency and spectrum of activity, which we name iboxamycin. Iboxamycin is effective against ESKAPE pathogens including strains expressing Erm and Cfr ribosomal RNA methyltransferase enzymes, products of genes that confer resistance to all clinically relevant antibiotics targeting the large ribosomal subunit, namely macrolides, lincosamides, phenicols, oxazolidinones, pleuromutilins and streptogramins. X-ray crystallographic studies of iboxamycin in complex with the native bacterial ribosome, as well as with the Erm-methylated ribosome, uncover the structural basis for this enhanced activity, including a displacement of the [Formula: see text] nucleotide upon antibiotic binding. Iboxamycin is orally bioavailable, safe and effective in treating both Gram-positive and Gram-negative bacterial infections in mice, attesting to the capacity for chemical synthesis to provide new antibiotics in an era of increasing resistance.

Antimicrobial Selection for Transurethral Procedures Across the United States: A State-by-State Antibiogram Evaluation

OBJECTIVE

To evaluate optimal regimens for perioperative antimicrobial prophylaxis in transurethral procedures by examining antimicrobial susceptibility patterns in the United States.

MATERIALS AND METHODS

Through several methods, we attempted to attain an antibiogram for each state. We focused on microbes known to cause infections after transurethral surgeries and antibiotics referred to in current or prior recommendations and compared susceptibility rates across states using Kruskal Walis tests and the Dwass, Steel, Critchlow-Fligner tests. We also examined susceptibility to (non-ceftazidime) third generation cephalosporins.

RESULTS

Data is included from 40 states. For each microbe studied, there was significant variability in sensitivity to antibiotics studied. Current first line recommendations for antimicrobial prophylaxis include first generation cephalosporins with 82%, 80%, and 87% mean coverage for E coli, Proteus, and Klebsiella respectively and trimethoprim-sulfamethoxazole with 74%, 80%, and 93% coverage, respectively. Susceptibility to aminoglycosides is 91%, 92%, and 96%, respectively and to third generation cephalosporin, it is 92%, 99%, and 94%.

CONCLUSION

Current first line recommended antimicrobials for prophylaxis in transurethral procedures provide overall poor predicted coverage based on our database of antibiograms. Alternatives exist that have higher predicted susceptibility, though clinical significance of this and risk of resultant antimicrobial resistance is unknown. Urologists should consider local patterns when selecting antimicrobial prophylaxis for their patients.

Rapid resistance development to three antistaphylococcal therapies in antibiotic-tolerant staphylococcus aureus bacteremia

Understating how antibiotic tolerance impacts subsequent resistance development in the clinical setting is important to identifying effective therapeutic interventions and prevention measures. This study describes a patient case of methicillin-resistant Staphylococcus aureus (MRSA) bacteremia which rapidly developed resistance to three primary MRSA therapies and identifies genetic and metabolic changes selected in vivo that are associated with rapid resistance evolution. Index blood cultures displayed susceptibility to all (non-beta-lactam) antibiotics with the exception of trimethoprim/ sulfamethoxazole. One month after initial presentation, during the same encounter, blood cultures were again positive for MRSA, now displaying intermediate resistance to vancomycin and ceftaroline and resistance to daptomycin. Two weeks later, blood cultures were positive for a third time, still intermediate resistant to vancomycin and ceftaroline and resistant to daptomycin. Mutations in mprF and vraT were common to all multidrug resistant isolates whereas mutations in tagH, agrB and saeR and secondary mprF mutation emerged sequentially and transiently resulting in distinct in vitro phenotypes. The baseline mutation rate of the patient isolates was unremarkable ruling out the hypermutator phenotype as a contributor to the rapid emergence of resistance. However, the index isolate demonstrated pronounced tolerance to the antibiotic daptomycin, a phenotype that facilitates the subsequent development of resistance during antibiotic exposure. This study exemplifies the capacity of antibiotic-tolerant pathogens to rapidly develop both stable and transient genetic and phenotypic changes, over the course of a single patient encounter.

Classifying cephalosporins: from generation to cross-reactivity

PURPOSE OF REVIEW

To review the most recent literature studying the classifications, immunochemistry, and crossreactivity of allergy reactions to cephalosporins.

RECENT FINDINGS

Over the last five years, research interest has focused on three areas related to cephalosporin allergy: cross-reactivity among cephalosporins and with other beta-lactams; the incidence of adverse reactions in penicillin allergy patients or in reported penicillin allergy labels; and new cephalosporins structures involved in the immunological recognition.

SUMMARY

Meta-analysis of a substantial number of studies shows that cephalosporins are safer than previously thought. Evidence supports two main conclusions in that regard. First, there is a relatively low percentage of cross-reactivity between cephalosporins and other beta-lactams with penicillins in penicillin allergy patients. Second, there is a very low incidence of allergy reactions in nonselected as well as in selected penicillin allergy patients when cephalosporins are used prior to surgical intervention.On the other hand, few structures have been discovered related to the immune mechanism of cephalosporin allergy reactions, and these are far from being ready to use in clinical practice.

Retrospective study of the efficacy of vascularized tissue transfer for treating antibiotic-resistant bacteria-infected wound: Comparison with clean and antibiotic-sensitive bacteria-infected wound

If wounds are infected with bacteria resistant to an empirical antibiotic regimen, effective wound treatment will be delayed. This can delay wound healing and lengthen hospital stays, increasing the costs to patients. Long-term antibiotic use can also result in minor and major complications, such as diarrhea, antibiotic resistance, or life-threatening leukopenia. Multidrug-resistant (MDR) bacteria make wound treatment even more difficult. Traditionally, surgeons thought that adequate infection control should be established before soft tissue coverage. However, wounds infected by MDR do not heal well with this traditional method and there are no optimal treatment guidelines for MDR bacteria-contaminated wounds.We reviewed 203 patients who underwent vascularized flap surgery from 2012 to 2019 to cover wounds. Class IV and I wounds were compared according to the Centers for Disease Control and Prevention classification. Class IV was further classified as antibiotic-resistant (ARB) and antibiotic-sensitive (ASB) bacteria. Wound size, mode, location, pathogens, healing time, and basic demographics were evaluated. Data were compared using Cramer's V and one-way ANOVA or independent t tests.The average healing time was longer in the ARB (19.7 [range 7-44] days) and ASB (17.9 [range 2-36] days) groups than in the Clean group (16.5 [range 7-28] days). Healing time differed in the 3 groups (P = .036). It was longer in the class IV group than in the class I group (P = .01). However, it was not statistically different between the ARB and ASB groups (P = .164).In our study the difference in healing time was small when vascularized tissue transfer was done in ARB-infected wound compared with ASB-infected and clean wound. It is necessary to perform surgery using vascularized tissue for the infected wound of antibiotic-resistant bacteria.

The effect of generic market entry on antibiotic prescriptions in the United States

When patented, brand-name antibiotics lose market exclusivity, generics typically enter the market at lower prices, which may increase consumption of the drug. To examine the effect of generic market entry on antibiotic consumption in the United States, we conducted an interrupted time series analysis of the change in the number of prescriptions per month for antibiotics for which at least one generic entered the US market between 2000 and 2012. Data were acquired from the IQVIA Xponent database. Thirteen antibiotics were analyzed. Here, we show that one year after generic entry, the number of prescriptions increased for five antibiotics (5 to 406%)-aztreonam, cefpodoxime, ciprofloxacin, levofloxacin, ofloxacin-and decreased for one drug: cefdinir. These changes were sustained two years after. Cefprozil, cefuroxime axetil and clarithromycin had significant increases in trend, but no significant level changes. No consistent pattern for antibiotic use following generic entry in the United States was observed.

Urethritis: Rapid Evidence Review

Urethritis refers to inflammation of the urethra and is classified as gonococcal (caused by Neisseria gonorrhoeae) or nongonococcal in origin (most commonly caused by Chlamydia trachomatis, Mycoplasma genitalium, or Trichomonas vaginalis). The most common signs and symptoms include dysuria, mucopurulent urethral discharge, urethral discomfort, and erythema. Diagnostic criteria include typical signs, symptoms, or history of exposure in addition to mucopurulent discharge, Gram stain of urethral secretions showing at least two white blood cells per oil immersion field, first-void urinalysis showing at least 10 white blood cells per high-power field, or a positive leukocyte esterase result with first-void urine. First-line empiric treatment consists of ceftriaxone and doxycycline; however, the antibiotic regimen may be targeted to the isolated organism. Repeat testing is not recommended less than three weeks after treatment because false-positive results are possible during this time. Patients treated for a sexually transmitted infection should have repeat screening in three months, with shared decision-making about future screening intervals. Patients treated for urethritis should abstain from sex for seven days after the start of treatment, until their partners have been adequately treated, and until their symptoms have fully resolved.

Different classes of antibiotics given to women routinely for preventing infection at caesarean section

BACKGROUND

Caesarean section increases the risk of postpartum infection for women and prophylactic antibiotics have been shown to reduce the incidence; however, there are adverse effects. It is important to identify the most effective class of antibiotics to use and those with the least adverse effects.  OBJECTIVES: To determine, from the best available evidence, the balance of benefits and harms between different classes of antibiotic given prophylactically to women undergoing caesarean section, considering their effectiveness in reducing infectious complications for women and adverse effects on both mother and infant.

SEARCH METHODS

For this 2020 update, we searched Cochrane Pregnancy and Childbirth's Trials Register, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform (ICTRP) (2 December 2019), and reference lists of retrieved studies.

SELECTION CRITERIA

We included randomised controlled trials (RCTs) comparing different classes of prophylactic antibiotics given to women undergoing caesarean section.  RCTs published in abstract form were also included. We excluded trials that compared drugs with placebo or drugs within a specific class; these are assessed in other Cochrane Reviews. We excluded quasi-RCTs and cross-over trials. Cluster-RCTs were eligible for inclusion but none were identified.

DATA COLLECTION AND ANALYSIS

Two review authors independently assessed the studies for inclusion, assessed risk of bias and carried out data extraction. We assessed the certainty of the evidence using the GRADE approach.

MAIN RESULTS

We included 39 studies, with 33 providing data (8073 women). Thirty-two studies (7690 women) contributing data administered antibiotics systemically, while one study (383 women) used lavage and was analysed separately. We identified three main comparisons that addressed clinically important questions on antibiotics at caesarean section (all systemic administration), but we only found studies for one comparison, 'antistaphylococcal cephalosporins (1st and 2nd generation) versus broad spectrum penicillins plus betalactamase inhibitors'.   We found no studies for the following comparisons: 'antistaphylococcal cephalosporins (1st and 2nd generation) versus lincosamides' and 'antistaphylococcal cephalosporins (1st and 2nd generation) versus lincosamides plus aminoglycosides'. Twenty-seven studies (22 provided data) included comparisons of cephalosporins (only) versus penicillins (only). However for this update, we only pooled data relating to different sub-classes of penicillins and cephalosporins where they are known to have similar spectra of action against agents likely to cause infection at caesarean section. Eight trials, providing data on 1540 women, reported on our main comparison, 'antistaphylococcal cephalosporins (1st and 2nd generation) versus broad spectrum penicillins plus betalactamase inhibitors'. We found data on four other comparisons of cephalosporins (only) versus penicillins (only) using systemic administration: antistaphylococcal cephalosporins (1st and 2nd generation) versus non-antistaphylococcal penicillins (natural and broad spectrum) (9 studies, 3093 women); minimally antistaphylococcal cephalosporins (3rd generation) versus non-antistaphylococcal penicillins (natural and broad spectrum) (4 studies, 854 women); minimally antistaphylococcal cephalosporins (3rd generation) versus broad spectrum penicillins plus betalactamase inhibitors (2 studies, 865 women); and minimally antistaphylococcal cephalosporins (3rd generation) versus broad spectrum and antistaphylococcal penicillins (1 study, 200 women). For other comparisons of different classes of antibiotics, only a small number of trials provided data for each comparison, and in all but one case data were not pooled. For all comparisons, there was a lack of good quality data and important outcomes often included few women. Three of the studies that contributed data were undertaken with drug company funding, one was funded by the hospital, and for all other studies the funding source was not reported. Most of the studies were at unclear risk of selection bias, reporting bias and other biases, partly due to the inclusion of many older trials where trial reports did not provide sufficient methodological information. We undertook GRADE assessment on the only main comparison reported by the included studies, antistaphylococcal cephalosporins (1st and 2nd generation) versus broad spectrum penicillins plus betalactamase inhibitors, and the certainty ranged from low to very low, mostly due to concerns about risk of bias, wide confidence intervals (CI), and few events. In terms of the primary outcomes for our main comparison of 'antistaphylococcal cephalosporins (1st and 2nd generation) versus broad spectrum penicillins plus betalactamase inhibitors': only one small study reported sepsis, and there were too few events to identify clear differences between the drugs (risk ratio (RR) 2.37, 95% CI 0.10 to 56.41, 1 study, 75 women, very low-certainty evidence). There may be little or no difference between these antibiotics in preventing endometritis (RR 1.10; 95% CI 0.76 to 1.60, 7 studies, 1161 women; low-certainty evidence). None of the included studies reported on infant sepsis or infant oral thrush. For our secondary outcomes, we found there may be little or no difference between interventions for maternal fever (RR 1.07, 95% CI 0.65 to 1.75, 3 studies, 678 women; low-certainty evidence). We are uncertain of the effects on maternal: wound infection (RR 0.78, 95% CI 0.32 to 1.90, 4 studies, 543 women), urinary tract infection (average RR 0.64, 95% CI 0.11 to 3.73, 4 studies, 496 women), composite adverse effects (RR 0.96, 95% CI 0.09 to 10.50, 2 studies, 468 women), and skin rash (RR 1.08, 95% CI 0.28 to 4.1, 3 studies, 591 women) (all very low certainty evidence). Although maternal allergic reactions were reported by two studies, there were no events. There were no infant outcomes reported in the included studies. For the other comparisons, the results for most outcomes had wide CIs, few studies and few women included. None of the included trials reported on longer-term maternal outcomes, or on any infant outcomes.

AUTHORS' CONCLUSIONS

Based on the best currently available evidence, 'antistaphylococcal cephalosporins' and 'broad spectrum penicillins plus betalactamase inhibitors' may have similar efficacy at caesarean section when considering immediate postoperative infection, although we did not have clear evidence for several important outcomes. Most trials administered antibiotics at or after cord clamping, or post-operatively, so results may have limited applicability to current practice which generally favours administration prior to skin incision. We have no data on any infant outcomes, nor on late infections (up to 30 days) in the mother; these are important gaps in the evidence that warrant further research. Antimicrobial resistance is very important but more appropriately investigated by other trial designs.

Rapid Spread and Control of Multidrug-Resistant Gram-Negative Bacteria in COVID-19 Patient Care Units

We describe rapid spread of multidrug-resistant gram-negative bacteria among patients in dedicated coronavirus disease care units in a hospital in Maryland, USA, during May–June 2020. Critical illness, high antibiotic use, double occupancy of single rooms, and modified infection prevention practices were key contributing factors. Surveillance culturing aided in outbreak recognition and control.

European Registry on Helicobacter pylori management (Hp-EuReg): First-line Therapy in Israel

BACKGROUND

The antibiotic resistance profile of Helicobacter pylori (H. pylori) is constantly changing. Up-to-date and reliable data for the effectiveness of first-line H. pylori treatment protocols are necessary to provide evidence-based best-practice guidelines.

OBJECTIVES

To determine the effectiveness, compliance and safety of first-line treatment for H. pylori in Israel.

METHODS

An observational, prospective, multicenter study was conducted in tertiary referral centers in Israel, as part of the European registry on H. pylori management (Hp-EuReg). H. pylori-infected patients were included from 2013 to March 2020. Data collected included demographics, clinical data, diagnostic tests, previous eradication attempts, current treatment, compliance, adverse events, and treatment outcome result.

RESULTS

In total, 242 patients were registered, including 121 (50%) who received first-line therapy, 41% of these individuals received clarithromycin based triple therapy and 58.9% received a four-drug regimen. The overall effectiveness of first-line therapy was 85% and 86% by modified intention-to-treat and per protocol analyses, respectively. The effectiveness of both sequential and concomitant therapies was 100% while clarithromycin-based triple therapy achieved an eradication rate of 79%. Treatment eradication was higher among patients who received high dose proton pump inhibitor (PPI) compared to those treated with low dose PPI (100% vs. 81.5% respectively, P < 0.01). No difference in treatment effectiveness was found between 7-, 10-, and 14-day treatment.

CONCLUSIONS

The effectiveness of clarithromycin-based triple therapy is suboptimal. First-line treatment of H. pylori infection should consist of four drugs, including high dose PPI, according to international guidelines.

Antibiotic prescribing practices of dentists for endodontic infections; a cross-sectional study

Objective

The indiscriminate prescription of antibiotics has led to the emergence of resistance microbes worldwide. This study aimed to investigate the antibiotic prescribing practices amongst general dental practitioners and specialists in managing endodontic infections in the United Arab Emirates (UAE).

Design

General dental practitioners and specialists in the UAE were invited to participate in an online questionnaire survey which included questions on socio-demographics, practitioner’s antibiotic prescribing preferences for various pulpal and periapical diseases, and their choice, in terms of the type, dose and duration of the antibiotic. The link to the survey questionnaire was sent to 250 invited dentists. Data were analyzed by descriptive statistics and chi-square tests for independence and level of significance was set at 0.05.

Results

A total of 174 respondents participated in the survey (response rate = 70%). The respondents who prescribed antibiotics at least once a month were 38.5% while 17.2% did so, more than three times a week; amoxicillin 500 mg was the antibiotic of choice for patients not allergic to penicillin (43.7%), and in cases of penicillin allergies, erythromycin 500 mg (21.3%). There was a significant difference in the antibiotic prescribing practices of GDPs compared to endodontists and other specialties especially in clinical cases such as acute apical abscesses with swelling and moderate to severe pre-operative symptoms and retreatment of endodontic cases (p<0.05). Approximately, three quarters of the respondents (78.7%) did not prescribe a loading dose when prescribing antibiotics. About 15% respondents prescribed antibiotics to their patients if they were not accessible to patients due to a holiday/weekend.

Conclusions

In general, the antibiotic prescribing practices of UAE dentists are congruent with the international norms. However, there were occasions of inappropriate prescriptions such as in patients with irreversible pulpitis, necrotic pulps with no systemic involvement and/or with sinus tracts.

Characterization, modes of action, and application of a novel broad-spectrum bacteriocin BM1300 produced by Lactobacillus crustorum MN047

Bacteriocins are ribosomally synthesized peptides with antibacterial activity against food-borne pathogenic bacteria that cause spoilage, possessing important potential for use as a natural preservative in the food industry. The novel bacteriocin BM1300 produced by Lactobacillus crustorum MN047 was identified after purification in this study. It displayed broad-spectrum antibacterial activity against some selected Gram-positive and Gram-negative bacteria. The minimum inhibitory concentration (MIC) values of BM1300 against Staphylococcus aureus ATCC 25923 and Escherichia coli ATCC 25922 were 13.4 μg/mL and 6.7 μg/mL, respectively. Moreover, BM1300 showed excellent thermal (between 60 and 120 °C), pH (2-11), and chemical (Tween-40, Tween-80, Triton X-100, and EDTA) stabilities. Time-kill curves revealed that BM1300 exhibited bactericidal activity against S. aureus and E. coli. The scanning and transmission electron microscopy indicated that BM1300 acted by disrupting the cell membrane integrity and increasing cell membrane permeabilization of indicator bacteria. The disruption of cell membrane integrity caused by BM1300 was further demonstrated by the uptake of propidium iodide (PI) and the release of intracellular lactate dehydrogenase (LDH) and nucleic acid and proteins. Moreover, BM1300 affected cell cycle distribution to exert antibacterial activity collaboratively. Meanwhile, BM1300 inhibited the growth of S. aureus and E. coli of beef meat and improved the microbiological quality of beef meat. These findings place BM1300 as a potential biopreservative in the food industry.

Antibiotics Approved for Marketing in Populations Specifically Excluded From Premarketing Trials, 1999-2018

Approval by the US Food and Drug Administration (FDA) of a drug for a given indication is thought to reassure clinicians, other health care providers, and patients that substantial evidence of effectiveness exists for specific indicated populations (patients and diseases). This study examines whether FDA approval of certain antibiotics should be so reassuring for all patient populations identified in the FDA-approved labels. Specifically, this study compared patient populations covered by FDA-approved labels for 21 novel antibiotics approved between 1999 and 2018 to the patient exclusion and inclusion criteria of pivotal trials that supported those approvals. We found that every FDA-approved label for these antibiotics included at least one identifiable patient population that was explicitly excluded from enrolling in the supporting pivotal trials. Two antibiotics, bedaquiline and ceftazidime-avibactam, were approved for use in populations that were fully excluded from enrolling in registration trials.

Antimicrobial use in wean to market pigs in the United States assessed via voluntary sharing of proprietary data

Data on antimicrobial use were collected for the 2016 and 2017 calendar years from swine producers in the United States. Nine large systems, collectively producing over 20 million market pigs annually, voluntarily provided data to advance understanding of antimicrobial use in the industry and to support antimicrobial stewardship initiatives. The scope of the study was limited to growing pigs, and the granularity of data varied across the systems. Data were summarized both qualitatively and quantitatively by antimicrobial class, active ingredient and route of administration (injection, water and feed). Data on the purpose of administration, doses and durations of administration were not available, but some information was provided by the responsible veterinarians. Aggregate data were similar both qualitatively and quantitatively in 2016 and 2017, although marked changes between years were evident within systems for some antimicrobials. Antimicrobial use (by weight) was dominated by the tetracycline class (approximately 60% of total use). Antimicrobials in classes categorized as critically important constituted 4.5% and 5.3% of total use in 2016 and 2017, respectively. In both years, fluoroquinolone (0.23%, 0.46%) and 3rd generation cephalosporin (0.15%, 0.11%) use collectively accounted for <1% of total use. Administration was predominantly oral in feed and water, and injection comprised approximately 2% of use overall, but around 12% for critically important antimicrobials. There was considerable variability among systems in patterns of antimicrobial use. This pilot project demonstrates the feasibility of acquiring antimicrobial use data via voluntary sharing. It is currently being expanded among larger swine production systems, and further efforts to enable confidential data sharing and benchmarking for smaller producers are being pursued by the swine industry. Recognized biases in the data caution against over-interpretation of these data as an index of national use.

Association of class number, cumulative exposure, and earlier initiation of antibiotics during the first two-years of life with subsequent childhood obesity

BACKGROUND

Despite the possible association between antibiotic overuse and childhood obesity, studies on this association are lacking in Asia. This study aimed to determine whether there is an association between the number, duration of antibiotic exposure, timing of antibiotics initiation and childhood obesity.

METHODS

In this retrospective cohort study, Korean children born between January 1, 2008 and December 31, 2012, who underwent government-provided health examinations at age 4-6 and 30-36 months, were included. The main outcome was obesity (body mass index in 95th percentile) at 30-36 months. The exposure variable was antibiotic prescription during the first 24 months of life. The number, prevalence, and odds ratio (OR) of obese children based on antibiotic exposure were analyzed using logistic regression.

RESULTS

Of 31,733 children, 31,457 (99.1%) children used antibiotics and 2843 (9%) were obese at 30-36 months. There was a clear dose-response relationship between obesity and number of antibiotic classes, cumulative days, and earlier antibiotic initiation. Children who used five or more antibiotic classes had higher odds of obesity than those who used only one class (OR 1.42, 95% CI 1.12-1.8). Children with >180 days of antibiotic exposure had higher risk of obesity than those with 1-30 exposure days (OR 1.40, 95% CI 1.19-1.64). Children with earlier initiation of antibiotics had higher risk of obesity (OR 1.15 per 6 months, 95% CI 1.08-1.22).

CONCLUSION

Increased number of antibiotic classes, longer duration of antibiotic prescription and earlier antibiotic initiation before 24 months was associated with childhood obesity at 30-36 months. This South Korean retrospective study supports judicious use of antibiotics in the first 24 months of life to avoid the potential risk of childhood obesity. Future studies need to be performed to confirm or refute the results presented herein.

Needs assessment for novel Gram-negative antibiotics in US hospitals: a retrospective cohort study

BACKGROUND

Evidence-based needs assessments for novel antibiotics against highly-resistant Gram-negative infections (GNIs) are scarce. We aimed to use real-world data from an electronic health record repository to identify treatment opportunities in US hospitals for GNIs resistant to all first-line drugs.

METHODS

For this retrospective cohort study, population estimates with an unmet need for novel Gram-negative antibiotics were quantified using the Cerner Health Facts database (2009-15), aggregating episodes of infection in US hospitals with pathogens displaying difficult-to-treat resistance (DTR; resistance to carbapenems, other β-lactams, and fluoroquinolones) and episodes involving empirical coverage with reserve drugs (colistin or polymyxin B and aminoglycosides). Episodes displaying extended-spectrum cephalosporin resistance (ECR) were also estimated. Episodes were multiplied by site-specific and fixed 14-day treatment durations for conservative and liberal days-of-therapy (DOT) estimates and stratified by site and taxon. Hospital type-specific DOT rates were reliability adjusted to account for random variation; cluster analyses quantified contribution from outbreaks.

FINDINGS

Across 2 996 271 inpatient encounters and 134 hospitals, there were 1352 DTR-GNI episodes, 1765 episodes involving empirical therapy with colistin or polymyxin B, and 16 632 episodes involving aminoglycosides. Collectively, these yielded 39·0 (conservative estimate) to 138·2 (liberal estimate) DOT per 10 000 encounters for a novel DTR-GNI-targeted drug, whereas greater treatment opportunities were identified for ECR (six times greater) and β-lactam susceptible GNIs (70 times greater). The most common DTR-GNI site and pathogen was lower respiratory (14·3 [43·3%] of 33 DOT per 10 000 encounters) and Pseudomonas aeruginosa (522 [38·1%] of 1371 episodes), whereas Enterobacteriaceae urinary-tract infections dominated the ECR or carbapenem-sparing niche (59·0% [5589 of 9535 episodes]) equating to 210·7 DOT per 10 000 encounters. DTR Stenotrophomonas maltophilia, Burkholderia spp, and Achromobacter spp represented less than 1 DOT per 10 000 encounters each. The estimated need for DTR-GNI-targeted antibiotics saw minor contributions by outbreaks and varied from 0·5 to 73·1 DOT per 10 000 encounters by hospital type.

INTERPRETATION

Suspected or documented GNIs with no or suboptimal treatment options are relatively infrequent. Non-revenue-based strategies and innovative trial designs are probably essential to the development of antibiotics with improved effectiveness for these GNIs.

FUNDING

Center for Drug Evaluation and Research, US Food and Drug Administration; Intramural Research Program, National Institutes of Health Clinical Center and the National Institute of Allergy and Infectious Diseases and the National Cancer Institute.

Antimicrobial resistance patterns of Pseudomonas aeruginosa isolated from canine clinical cases at a veterinary academic hospital in South Africa

Although Pseudomonas aeruginosa (P. aeruginosa) can infect both animals and humans, there is a paucity of veterinary studies on antimicrobial resistance of P. aeruginosa in South Africa. Secondary data of canine clinical cases presented at the hospital from January 2007 to December 2013 was used. The following information was recorded: type of sample, the date of sampling and the antimicrobial susceptibility results. Frequencies, proportions and their 95% confidence intervals were calculated for all the categorical variables. In total, 155 P. aeruginosa isolates were identified and included in this study. All the isolates were resistant to at least one antimicrobial (AMR), while 92% were multi-drug resistant (MDR). Most isolates were resistant to lincomycin (98%), penicillin-G (96%), orbifloxacin (90%), trimethoprim-sulfamethoxazole (90%) and doxycycline (87%). A low proportion of isolates was resistant to imipenem (6%), tobramycin (12%), amikacin (16%) and gentamicin (18%). A high proportion of MDR-P. aeruginosa isolates was resistant to amoxycillin-clavulanic acid (99%), tylosin (99%), chloramphenicol (97%) and doxycycline (96%). Few (6%) of MDR-P. aeruginosa isolates were resistant to imipenem. Pseudomonas aeruginosa was associated with infections of various organ systems in this study. All P. aeruginosa isolates of P. aeruginosa exhibited resistance to β-lactams, fluoroquinolones and lincosamides. Clinicians at the hospital in question should consider these findings when treating infections associated with P. aeruginosa.

Molecular Topology for the Discovery of New Broad-Spectrum Antibacterial Drugs

In this study, molecular topology was used to develop several discriminant equations capable of classifying compounds according to their antibacterial activity. Topological indices were used as structural descriptors and their relation to antibacterial activity was determined by applying linear discriminant analysis (LDA) on a group of quinolones and quinolone-like compounds. Four equations were constructed, named DF1, DF2, DF3, and DF4, all with good statistical parameters such as Fisher-Snedecor's F (over 25 in all cases), Wilk's lambda (below 0.36 in all cases) and percentage of correct classification (over 80% in all cases), which allows a reliable extrapolation prediction of antibacterial activity in any organic compound. From the four discriminant functions, it can be extracted that the presence of sp3 carbons, ramifications, and secondary amine groups in a molecule enhance antibacterial activity, whereas the presence of 5-member rings, sp2 carbons, and sp2 oxygens hinder it. The results obtained clearly reveal the high efficiency of combining molecular topology with LDA for the prediction of antibacterial activity.

Development of Antibiotic Classification for Measuring Antibiotic Usage in Korean Hospitals Using a Modified Delphi Method

In 2019, a project designed to develop a system for measuring and comparing antibiotic usage in hospitals was launched in Korea. As part of this project, we developed a means to classify antibiotic usage in Korean hospitals using a modified Delphi method. In results, the following categories of antibiotic classification were accepted for use in Korean hospitals: 1) broad-spectrum antibacterial agents predominantly used for hospital-onset infections in adults, 2) broad-spectrum antibacterial agents predominantly used for community-acquired infections in adults, 3) antibacterial agents predominantly used for resistant gram-positive infections in adults, 4) narrow-spectrum beta-lactam agents in adults, 5) antibacterial agents predominantly used for extensive antibiotic resistant gram-negative bacteria in adults, and 6) total antibacterial agents.

Indirect comparison of efficacy between different antibiotic prophylaxis against the intracranial infection after craniotomy

BACKGROUND

Many studies had shown that prophylactic use of antibiotics could significantly reduce the intracranial infection (ICI) rate of craniotomy. However, there has been no comparison of these antibiotics.

METHODS

An electronic database search was performed, from inception to June 102,020. Randomized controlled trials (RCT) using different intravenous antibiotics (IVA) against the ICIs after craniotomy were considered. The primary outcome was the incidence rates of ICIs. An indirect treatment comparison (ITC) was conducted to compare the protective effect among the diverse antibiotic prophylaxis to prevent ICIs after craniotomy. Risk of potential bias was assessed.

RESULTS

A total of 3214 patients after craniotomy in 11 studies were included, 159 patients experienced postoperative ICI, including 33 patients in the antibacterial group and 126 in the control group. The calculate results of meta-analysis showed that except fusidic acid, preoperative intravenous injection of cephalosporin, clindamycin, vancomycin, and penicillin can significantly reduce the incidence of ICI after craniotomy, and ITC showed there was no statistically significance difference in the rates of post craniotomy ICI between the various antibiotics.

CONCLUSION

The current evidence shows that low-grade antibacterial drugs can be selected to prevent ICI after craniotomy, but this may be due to the limited number of studies per antibiotic. It still needs more high-quality, large sample RCT to confirm.

SYSTEMIC REVIEW REGISTRATION

PROSPERO CRD42019133369.

Application of antibiotics in treatment of coronavirus disease 2019 in a designated hospital

OBJECTIVES

To explore the prescribing habits of doctors, and to provide basis for rational use of antibiotics in clinical practice via investigating and analyzing the applications of antibiotics in treatment of coronavirus disease 2019 (COVID-19) in the designated hospital.

METHODS

Specification, quantity, amount, defined daily dose system (DDDs), defined daily dose consumption (DDDc), antibiotics use density (AUD), composition, frequency of use, combined use of antibacterial drugs used in the hospital were analyzed between Feb. 2020 and Mar. 2020.

RESULTS

A total of 25 antibiotic drugs in 12 categories were used. The total cost for antibiotic drugs was 1 million 238 thousand yuan, in which quinolone accounts for 48%, the third generation cephalosporin/lactamase inhibitors accounts for 15.86%, antifungals accounts for 14.17%, oxazolidone accounts for 13.46%, and carbapenms account for 12.73%. The top three drugs of DDDs and AUD were moxifloxacin hydrochloride tablets, moxifloxacin hydrochloride and sodium chloride injection, cefoperazone sodium and sulbactam sodium for injection. The proportion of patients who had been used more than two kinds of antibiotics was 22.36%.

CONCLUSIONS

Broad-spectrum, high-potency antibiotics are used at the beginning of COVID-19 treatment. The varieties of antibiotics meet the requirements of the management of antibiotics, and the utilization rate of antibiotics and the cost proportion of antibiotics in COVID-19 patients are within a reasonable range.In the future, for the treatment of COVID-19, we should continue to summarize the experience, improve the strategies, and rationally apply antibiotics on the basis of guidelines.

Antimicrobial use and resistance in food-producing animals and the environment: an African perspective

BACKGROUND

The overuse of antimicrobials in food animals and the subsequent contamination of the environment have been associated with development and spread of antimicrobial resistance. This review presents information on antimicrobial use, resistance and status of surveillance systems in food animals and the environment in Africa.

METHODS

Information was searched through PubMed, Google Scholar, Web of Science, and African Journal Online databases. Full-length original research and review articles on antimicrobial use, prevalence of AMR from Africa covering a period from 2005 to 2018 were examined. The articles were scrutinized to extract information on the antimicrobial use, resistance and surveillance systems.

RESULTS

A total of 200 articles were recovered. Of these, 176 studies were included in the review while 24 articles were excluded because they were not relevant to antimicrobial use and/or resistance in food animals and the environment. The percentage of farms using antimicrobials in animal production ranged from 77.6% in Nigeria to 100% in Tanzania, Cameroon, Zambia, Ghana and Egypt. The most antibiotics used were tetracycline, aminoglycoside and penicillin groups. The percentage of multi drug resistant isolates ranged from 20% in Nigeria to 100% in South Africa, Zimbabwe and Tunisia. In the environment, percentage of multi drug resistant isolates ranged from 33.3% in South Africa to 100% in Algeria. None of the countries documented national antimicrobial use and resistance surveillance system in animals.

CONCLUSION

There is high level of antimicrobial use, especially tetracycline, aminoglycoside and penicillin in animal production systems in Africa. This is likely to escalate the already high prevalence of antimicrobial resistance and multi drug resistance in the continent. This, coupled with weak antimicrobial resistance surveillance systems in the region is a great concern to the animals, environment and humans as well.

Antimicrobial usage at a large teaching hospital in Lusaka, Zambia

Antimicrobial resistance is a growing global health concern. Antimicrobial stewardship (AMS) curbs resistance rates by encouraging rational antimicrobial use. However, data on antimicrobial stewardship in developing countries is scarce. The objective of this study was to characterize antimicrobial use at the University Teaching Hospital (UTH) in Lusaka, Zambia as a guiding step in the development of an AMS program. This was a cross-sectional, observational study evaluating antimicrobial appropriateness and consumption in non-critically ill adult medicine patients admitted to UTH. Appropriateness was defined as a composite measure based upon daily chart review. Sixty percent (88/146) of all adult patients admitted to the general wards had at least one antimicrobial ordered and were included in this study. The most commonly treated infectious diseases were tuberculosis, pneumonia, and septicemia. Treatment of drug sensitive tuberculosis is standardized in a four-drug combination pill of rifampicin, isoniazid, pyrazinamide and ethambutol, therefore appropriateness of therapy was not further evaluated. The most common antimicrobials ordered were cefotaxime (n = 45), ceftriaxone (n = 28), and metronidazole (n = 14). Overall, 67% of antimicrobial orders were inappropriately prescribed to some extent, largely driven by incorrect dose or frequency in patients with renal dysfunction. Antimicrobial prescribing among hospitalized patients at UTH is common and there is room for optimization of a majority of antimicrobial orders. Availability of certain antimicrobials must be taken into consideration during AMS program development.

Prevalence of E. Coli in Urinary Tract Infection of Children Aged 1-15 Years in A Medical College of Eastern Nepal

Introduction: Urinary tract infection is one of the commonest causes of childhood morbidity. Earlydiagnosis and appropriate choice of antimicrobials is essential. Hence, this study aims to identify theprevalence of Escherichia coli in childhood urinary tract infections. Methods: This was a hospital based descriptive cross-sectional study conducted in Nobel MedicalCollege, Biratnagar over a period of one year. A total of 163 cases aged 1-15 years were included andclinical profile, laboratory reports including bacterial isolates in urine cultures and their sensitivitypatterns were documented. Results: The prevalence of Escherichia coli is 45 (53.57%) C.I. Escherichia coli was the most commonorganism isolated in bacterial cultures followed by Klebsiella 12 (14.29%), Enterococcus 10 (11.90%).Urinary tract infection was common among females with male: female ratio of 1:2.3. Fever 152(93.2%) and abdominal pain 113 (69.3%) were the most common presenting symptoms. Escherichiacoli was found most sensitive to Nitrofurantoin 43 (95.5%) followed by Ciprofloxacin 41 (91.1%) andAmikacin 40 (88.8%). Conclusions: Urinary tract infections in childhood require prompt attention and treatment to preventsignificant morbidity and mortality. From this study it can be concluded that Escherichia coli is oneof the most common isolates in urine culture and Aminoglycosides and Fluoroquinolones can beaccepted as empirical treatment regimens for childhood Urinary tract infections.

Bacteriology of Sputum Samples: A Descriptive Cross-sectional Study in a Tertiary Care Hospital

Introduction:

Lower respiratory tract infection is a common infection and accounts for a greater burden of disease worldwide. It is a great challenge to the clinician and still more, with increasing antimicrobial resistance. Its empirical treatment may vary according to the type of causative organisms. The objective of this study is to identify the pathogenic microorganisms and their antimicrobial susceptibility pattern from sputum sample.

Methods:

This descriptive cross-sectional study was conducted in KIST Medical College and Teaching Hospital from February 2015 to January 2016. Ethical approval was taken from institutional review committee prior to the study with reference no. 0051/2014/15. Data on culture and sensitivity of isolates from sputum samples were collected from the records of the hospital. Sample collection, processing, identification of microorganisms and antimicrobial susceptibility tests were performed according to the Clinical and Laboratory Standards Institute guidelines. All the data were tabulated in an Excel sheet and analyzed using SPSS version 20.

Results:

Out of 2318 samples, 694 (29.93%) sputum samples at 95% confidence interval (737.21650.79) were reported as culture positive. Klebsiella was the most common isolate followed by Pseudomonas, Escherichia coli, Acinetobacter, Staphylococcus aureus, Candida albicans, Streptococcus pneumoniae, Streptococcus pyogenes, and others. Imipenem and vancomycin showed the most sensitivity towards gram-negative and gram-positive bacteria respectively.

Conclusions:

Proper diagnosis, identification of causative agents and their antimicrobial susceptibility pattern are important steps to limit the irrational use of antimicrobials. Prescribing antimicrobials empirically in the case of suspected lower respiratory tract infection is difficult.

[Myiasis by Cochliomyia hominivorax in Argentina]

Miasis is the infestation of man and animals by larvae of flies belonging to the order Diptera, suborder Cyclorrapha. Eighty percent of miasis in Argentina is caused by Cochliomyia hominivorax, a species that induces pronounced tissue invasion and destruction, and results in severe clinical forms. Because of the aggressiveness of its larvae, it is important to reach a specific etiological diagnosis. We present four cases of miasis by C. hominivorax in two patients living in the city of Buenos Aires but working in a rural area and two patients living in the Greater Buenos Aires.

Structured surveillance of Achromobacter, Pandoraea and Ralstonia species from patients in England with cystic fibrosis

A structured survey of the cystic fibrosis pathogens Achromobacter, Pandoraea and Ralstonia species from thirteen sentinel hospitals throughout England was undertaken by Public Health England. One isolate per patient of these genera collected from CF patients during the seven-month survey period in 2015 was requested from participating hospitals. Species-level identification was performed using nrdA/gyrB sequence cluster analysis, and genotyping by pulsed-field gel electrophoresis. In total, 176 isolates were included in the survey; 138 Achromobacter spp. (78.4%), 29 Pandoraea spp. (16.5%) and 9 Ralstonia spp. (5.1%). Novel Achromobacter and Pandoraea clusters were identified. High levels of antimicrobial resistance were found, particularly among Pandoraea isolates. Genotyping analysis revealed considerable diversity, however one geographically-widespread cluster of A. xylosoxidans isolates from six hospitals was found, in addition to two other clusters, both comprising isolates from two hospitals, either derived from the same region (A. xylosoxidans), or from hospitals within the same city (P. apista).

Pathogen Analysis of Central Nervous System Infections in a Chinese Teaching Hospital from 2012-2018: A Laboratory-based Retrospective Study

Central nervous system (CNS) infections are associated with high mortality rates. The clinical presentation of many CNS infections by different pathogens is difficult to distinguish, but the definite diagnosis of the etiology is critical for effective therapy and prognosis. The aim of this study was to explore the etiology of CNS infections with definite diagnoses based on data from a clinical microbiology laboratory in Tongji Hospital, a teaching hospital in China, obtained over a six-year period. We conducted a retrospective study on all cerebrospinal fluid (CSF) specimens submitted to our clinical microbiology laboratory from September, 2012 to December, 2018. The etiology of CNS infections caused by Cryptococcus neoformans, Mycobacterium tuberculosis and common bacteria was analyzed. Antimicrobial susceptibility testing was conducted on all isolates. The results showed that 1972 cases of CNS infections were identified from 18 300 CSF specimens. Common bacterial meningitis (BM), cryptococcal meningitis (CM) and tuberculous meningitis (TM) accounted for 86.3% (677/785), 9.4% (74/785) and 4.3% (34/785) respectively of cases over the six-year period. BM was the most common among the different age groups, followed by CM. Of the TM cases, 44.1% (15/34) were distributed within the age group of 15-34 years, whereas for CM cases, 52.7% (39/74) occurred within the 35-54-year age group, and the age distribution of BM cases was fairly even. Among the bacterial pathogens isolated, Staphylococcus epidermidis was the most common, accounting for 12.5% (98/785), followed by Acinetobacter baumannii (ABA) and Staphylococcus aureus (SAU), accounting for 11.8% (93/785) and 7.6% (60/785) respectively. The resistance rates to antibiotics were >75%, with the exception of the resistance rate of ABA to tegafycline, which was <3%. More than 60% of SAU strains displayed resistance to penicillin, oxacillin, ampicillin/sulbactam, cefazolin, cefuroxime, gentamycin, tobramycin, erythromycin and levofloxacin, whereas more than 90% of SAU strains showed susceptibility to trimethoprim/sulfamethoxazole, tegafycline, vancomycin, teicoplanin and linezolid. For C. neoformans, the susceptibility rates to amphotericin B, 5-fluorocytosine, fluconazol and voriconazole were >95%. Analysis of samples from patients with CNS infection in a clinical microbiology laboratory at a teaching hospital in China over a six-year period indicated that the most common etiological agents were the bacteria ABA and SAU. The antibiotic resistance levels of ABA were found to be high and of concern, whereas isolates of C. neoformans were found to be sensitive to antifungal antibiotics.

Study of 109 Achromobacter spp. isolates from 9 French CF centres reveals the circulation of a multiresistant clone of A. xylosoxidans belonging to ST 137

We previously reported the distribution of Achromobacter spp. (species and Sequence Types (ST)) in our French Cystic Fibrosis (CF) centre. In the present study we collected 109 Achromobacter isolates (1/patient) from 9 other French CF Centres for species identification, antimicrobial susceptibility testings and Multilocus-Sequence-Typing (MLST) analysis. Ten species were detected, A. xylosoxidans being the most predominant one (73.4% of the isolates). Piperacillin-tazobactam, ceftazidime, imipenem, meropenem and ciprofloxacin were respectively active against 88, 70, 79, 72 and 23% of the isolates. Among the 79 A. xylosoxidans isolates, 46 STs were detected. Interestingly, ST 137, recovered in 4 centres (5 patients), was previously detected in our centre (2 patients). The strains from the 7 patients belonged to the same pulsotype (pulsed-field-gel-electrophoresis analysis) and harboured acquired resistance to meropenem, ceftazidime, ciprofloxacin, and except for 2 isolates, to imipenem and piperacillin-tazobactam. This is the first description in France of a circulating multiresistant A. xylosoxidans strain.

Systematic review of randomized controlled trials on antibiotic treatment for osteomyelitis in diabetes

AIM

To evaluate the efficacy of antibiotic therapy in osteomyelitis treatment among people with diabetes.

METHODS

A systematic search of PubMed, EMBASE, AMED, Web of Science, the WHO trial registry, Cochrane library databases, and ClinicalTrials.gov, in addition to hand-searching, was undertaken in July 2018. Two reviewers independently extracted data. The studies' methodological quality was assessed using the modified Jadad scale. Descriptive analysis was performed.

RESULTS

Seven randomized controlled trials, with 393 participants in total, were included. The antibiotic regimens, treatments and follow-up durations varied among the trials. The total scores showed that the overall methodological quality of the seven studies was high, despite two studies showing some flaws in double-blinding and withdrawals/drop-outs. Of four studies comparing different antibiotic regimens, three implied a similar remission effect, while one implied that ertapenem ± vancomycin treatment showed a higher remission rate than tigecycline treatment; this conclusion was not robust because of low power and small sample size. In the other three studies, which included two different doses of ciprofloxacin, an antibiotics group and a conservative surgical group, and two durations of the same antibiotic strategy, no significant differences in remission were reported between the groups. No difference was observed in the analyses of microbiological outcomes, superinfections and relapse, except adverse events.

CONCLUSIONS

There is no definitive evidence supporting the superiority of any particular antibiotic agent, dose, or administration duration in the treatment of osteomyelitis in diabetes. As the included studies had some flaws and limitations, further research is necessary.

Flow Cytometry Analysis of Antibacterial Effects of Universal Dentin Bonding Agents on Streptococcus mutans

There is no consensus on the antibacterial activity of dentin bonding systems (DBS). Many study models have been used to evaluate the antimicrobial activity of dental materials. In this study, a novel detection method, flow cytometry, was introduced. It allows for evaluation of the antibacterial activity of DBS, based on assessment of the disruption of the bacterial physical membrane induced by DBS. The aim of the study was to evaluate the antibacterial properties of selected dentin bonding systems against Streptococcus mutans. The highest antibacterial activity against S. mutans was observed for Adhese Universal (99.68% dead cells) and was comparable to that of Prime&Bond Universal, OptiBond Universal, or Clearfil Universal Bond Quick (p > 0.05). The lowest activity of all tested systems was displayed by the multi-mode adhesive, Universal Bond (12.68% dead bacteria cells), followed by the self-etch adhesive, OptiBond FL (15.58% dead bacteria cells). The present study showed that in the case of two-component DBS, the primer exhibited higher antimicrobial activity than the adhesive (or bond) itself.

Evaluating Antibiotic Sensitivity Patterns of Pseudomonas in Relation to Specimen Type in Jordanian Hospital

OBJECTIVE

To evaluate the sensitivity patterns of different antibiotics of pseudomonas in relation to specimen types.

METHODS

The quantitative retrospective study was conducted at Princess Iman Research and Laboratory Sciences Centre of Royal Medical Services, Amman, Jordan. The specimens of USS, urine, cerebral spinal fluid, and blood were collected from patients, who visited the hospital from January to September 2015. Drugs analysed included ampicillin, ceftazidime, ciprofloxacin, cefotaxime, cefoxitin, nitrofurantoin and gentamicin.

RESULTS

There were 358 samples collected. Ampicillin was found effective (p=0.002). There was a weaker correlation between amikacin and amoxicillin/clavulanic acid (r=-0.001). Similarly, nitrofurantoin was also effective (p=0.001), and the association between amikacin and ceftazidime was positive (r=0.998).

CONCLUSIONS

The selected antibiotics were only examined, concerning the sensitivity patterns as data collected from the patients was insufficient for other drugs.

Antibiotic Susceptibility and Virulence Factors in Escherichia coli from Sympatric Wildlife of the Apuan Alps Regional Park (Tuscany, Italy)

Today a growing number of studies are focusing on antibiotic resistance in wildlife. This is due to the potential role of wild animals as reservoirs and spreaders of pathogenic and resistant bacteria. This study focused on isolating and identifying Escherichia coli from the feces of wild animals living in the Apuan Alps Regional Park (Tuscany, Italy) and evaluating some of their antibiotic resistance and pathogenicity traits. Eighty-five fecal samples from different species were studied. Seventy-one E. coli were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry analysis, subjected to antibiograms and polymerase chain reaction for the detection of antibiotic resistance genes and pathogenicity factors. The highest resistance rates were found against cephalothin (39.4%) and ampicillin (33.8%), followed by amoxicillin/clavulanic acid (15.5%), streptomycin (12.7%), and tetracycline (5.6%). Regarding resistance genes, 39.4% of the isolates were negative for all tested genes. The remaining isolates were positive for bla_CMY-2, sul2, strA-strB and aadA1, tet(B), and tet(A), encoding resistance to beta-lactams, trimethoprim/sulfamethoxazole, streptomycin, and tetracycline, respectively. With regard to virulence factors, 63.4% of the isolates were negative for all genes; 21.1% carried astA alone, which is associated with different pathotypes, 9.9% carried both escV and eaeA (aEPEC); single isolates (1.4%) harbored escV (aEPEC), escV associated with astA and eaeA (aEPEC), astA with stx2 and hlyA (EHEC) or astA and stx1, stx2, and hlyA (EHEC). These results show that wildlife from nonanthropized environments can be a reservoir for antibiotic-resistant microorganisms and suggest the need for a deeper knowledge on their origin and diffusion mechanisms through different ecological niches.

The distribution of antibiotic use and its association with antibiotic resistance

Antibiotic use is a primary driver of antibiotic resistance. However, antibiotic use can be distributed in different ways in a population, and the association between the distribution of use and antibiotic resistance has not been explored. Here, we tested the hypothesis that repeated use of antibiotics has a stronger association with population-wide antibiotic resistance than broadly-distributed, low-intensity use. First, we characterized the distribution of outpatient antibiotic use across US states, finding that antibiotic use is uneven and that repeated use of antibiotics makes up a minority of antibiotic use. Second, we compared antibiotic use with resistance for 72 pathogen-antibiotic combinations across states. Finally, having partitioned total use into extensive and intensive margins, we found that intense use had a weaker association with resistance than extensive use. If the use-resistance relationship is causal, these results suggest that reducing total use and selection intensity will require reducing broadly distributed, low-intensity use.

Prescription and non-prescription antibiotic dispensing practices in part I and part II pharmacies in Moshi Municipality, Kilimanjaro Region in Tanzania: A simulated clients approach

Antibiotic dispensing without a prescription poses a threat to public health as it leads to excessive antibiotic consumption. Inappropriate antibiotic availability to the community has been documented to be amongst drivers of antimicrobial resistance emergence. Community pharmacies are a source of antibiotics in low and middle-income countries (LMICs). We aimed at assessing antibiotic dispensing practices by community pharmacy retailers in Moshi urban, Kilimanjaro, Tanzania and recommend interventions to improve practice. Using a Simulated Client (SC) Method, an observational cross-sectional survey of antibiotic dispensing practices was conducted from 10th June to 10th July 2017. Data analysis was done using Stata 13 (StataCorp, College Station, TX, USA). A total of 82 pharmacies were visited. Part I pharmacies were 26 (31.71%) and 56 (68.29%) were part II. Overall 92.3% (95% CI 77.8-97.6) of retailers dispensed antibiotics without prescriptions. The antibiotics most commonly dispensed without a prescription were ampiclox for cough (3 encounters) and azithromycin for painful urination (3 encounters). An oral third generation cephalosporin (cefixime) was dispensed once for painful urination without prescription by a part I pharmacy retailer. Out of 21, 15(71.43%) prescriptions with incomplete doses were accepted and had antibiotics dispensed. Out of 68, 4(5.9%) retailers gave instructions for medicine use voluntarily. None of the retailers voluntarily explained drug side-effects. In Moshi pharmacies, a high proportion of antibiotics are sold and dispensed without prescriptions. Instructions for medicine use are rarely given and none of the retailers explain side effects. These findings support the need for a legislative enforcement of prescription-only antibiotic dispensing rules and regulations. Initiation of clinician and community antibiotic stewardship and educational programs on proper antibiotic use to both pharmacists and public by the regulatory bodies are highly needed.

Genome sequence analysis of an extensively drug-resistant Acinetobacter baumannii indigo-pigmented strain depicts evidence of increase genome plasticity

Acinetobacter baumannii is a multidrug resistant nosocomial pathogen that shows an outstanding ability to undergo genetic exchange, thereby acquiring different traits that contribute to its success. In this work, we identified genetic features of an indigo-pigmented A. baumannii strain (Ab33405) that belongs to the clonal complex CC113B/CC79P. Ab33405 possesses a high number of genes coding for antibiotic resistance and virulence factors that may contribute to its survival, not only in the human host, but also in the hospital environment. Thirteen genes conferring resistance to different antibiotic families (trimethoprim, florfenicol, β-lactams, aminoglycosides and sulfonamide) as well as the adeIJK genes and the capsule locus (KL) and outer core locus (OCL) were identified. Ab33405 includes 250 unique genes and a significant number of elements associated with Horizontal Gene Transfer, such as insertion sequences and transposons, genomic islands and prophage sequences. Also, the indigo-pigmented uncommon phenotype that could be associated with the monooxygenase or dioxygenase enzyme coded for by the iacA gene within the iac cluster was probably conferred by insertion of a 18-kb DNA fragment into the iacG gene belonging to this cluster. The Ab33405 genome includes all type VI secretion system genes and killing assays showed the ability of Ab33045 to kill Escherichia coli. In addition, Ab33405 can modulate susceptibility antibiotics when exposed to blue light.

Community level antibiotic utilization in India and its comparison vis-à-vis European countries: Evidence from pharmaceutical sales data

India was the largest consumer of antibiotics in 2010 in the world. Evidence suggests that countries with high per-capita antibiotic consumption have higher rates of antibiotic resistance. To control antibiotic resistance, not only reduction in antibiotic consumption is required, socio-economic factors like access to clean water and sanitation, regulation of private healthcare sector and better governance are equally important. The key objective of this research was to investigate the five year trends in consumption of major antibiotic classes in India and compare them with European Surveillance of Antimicrobial Consumption Network (ESAC-Net) countries. We used Intercontinental Marketing Statistics (IMS) Health (now IQVIA) medicine sales audit data of antibiotic sales in the retail private sector (excluding the hospitals sector) in India. We then standardized dosage trends and assigned defined daily dose (DDD) to all formulations based on the ATC/DDD index. We expressed our data in standardized matrices of DDD per 1000 inhabitants’ per day (DID) to compare antibiotic use in India with ESAC-Net countries. The antibiotic use was plotted and reported by year and antibiotic class. Our main findings are—per capita antibiotic consumption in the retail sector in India has increased from 13.1 DID in 2008 to 16.0 DID in 2012—an increase of ~22%; use of newer class of antibiotics like carbapenems (J01DH), lincosamides (J01FF), glycopeptides (J01XA), 3^rd generation cephalosporins (J01DD) and penicillin’s with beta-lactamase inhibitors has risen; and antibiotic consumption rates in India are still low as compared to ESAC-Net countries (16.0 DID vs. 21.54 DID). To conclude our study has provided the first reliable estimates of antibiotic use in the retail sector in India vis-à-vis ESAC-Net countries. In addition, our study could provide a reference point to measure the impact of interventions directed towards reducing antibiotic use.

Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics

Thiopeptides are members of the ribosomally synthesized and post-translationally modified peptide family of natural products. Most characterized thiopeptides display nanomolar potency toward Gram-positive bacteria by blocking protein translation with several being produced at the industrial scale for veterinary and livestock applications. Employing our custom bioinformatics program, RODEO, we expand the thiopeptide family of natural products by a factor of four. This effort revealed many new thiopeptide biosynthetic gene clusters with products predicted to be distinct from characterized thiopeptides and identified gene clusters for previously characterized molecules of unknown biosynthetic origin. To further validate our data set of predicted thiopeptide biosynthetic gene clusters, we isolated and characterized a structurally unique thiopeptide featuring a central piperidine and rare thioamide moiety. Termed saalfelduracin, this thiopeptide displayed potent antibiotic activity toward several drug-resistant Gram-positive pathogens. A combination of whole-genome sequencing, comparative genomics, and heterologous expression experiments confirmed that the thioamide moiety of saalfelduracin is installed post-translationally by the joint action of two proteins, TfuA and YcaO. These results reconcile the previously unknown origin of the thioamide in two long-known thiopeptides, thiopeptin and Sch 18640. Armed with these new insights into thiopeptide chemical-genomic space, we provide a roadmap for the discovery of additional members of this natural product family.

A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance

Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA ('poisoning') in an analogous fashion to fluoroquinolones, but without the requirement for the water-metal-ion bridge. Biochemical experiments and structural studies of cleavage complexes of IPYs compared with an uncleaved gyrase-DNA complex, reveal conformational transitions coupled to DNA cleavage at the DNA gate. These involve movement at the GyrA interface and tilting of the TOPRIM domains toward the scissile phosphate coupled to capture of the catalytic metal ion. Our experiments show that these structural transitions are involved generally in poisoning of gyrase by therapeutic compounds and resemble those undergone by the enzyme during its adenosine triphosphate-coupled strand-passage cycle. In addition to resistance mutations affecting residues that directly interact with the compounds, we characterized a mutant (D82N) that inhibits formation of the cleavage complex by the unpoisoned enzyme. The D82N mutant appears to act by stabilizing the binary conformation of DNA gyrase with uncleaved DNA without direct interaction with the compounds. This provides general insight into the resistance mechanisms to antibiotics targeting bacterial type II topoisomerases.

Congenital Bilateral Eyelid Eversion and Chemosis: A Case Study

This case reports the findings and management of a late preterm female infant born with congenital bilateral eyelid eversion with chemosis. The pathogenic process remains unknown but typically presents at birth, predominantly affecting the upper eyelid of both eyes. Black males, patients with trisomy 21, and collodion infants have a higher incidence of eyelid eversion. Treatment modalities range from conservative therapy including eye patching with antibiotic and lubricating ointment to invasive surgical eyelid suturing. In this case report, successful resolution of chemosis and eyelid inversion occurred with conservative management.

Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations

The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin-antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress.