Genomic Characterization of Methicillin-Susceptible Staphylococcus aureus Carriage in Patients on Home Parenteral Nutrition and Their Caregivers

In this prospective study, patients on home parenteral nutrition were twice as likely to be colonized with Staphylococcus aureus if their caregivers were carriers. Among S. aureus-positive patients and their caregivers, molecular analysis showed 68% genetically related strains. Despite decolonization, genetically related strains reappeared in 70% of patients.

Clofazimine as a substitute for rifampicin improves efficacy of Mycobacterium avium pulmonary disease treatment in the hollow-fiber model

Mycobacterium avium complex pulmonary disease is treated with an azithromycin, ethambutol, and rifampicin regimen, with limited efficacy. The role of rifampicin is controversial due to inactivity, adverse effects, and drug interactions. Here, we evaluated the efficacy of clofazimine as a substitute for rifampicin in an intracellular hollow-fiber infection model. THP-1 cells, which are monocytes isolated from peripheral blood from an acute monocytic leukemia patient, were infected with M. avium ATCC 700898 and exposed to a regimen of azithromycin and ethambutol with either rifampicin or clofazimine. Intrapulmonary pharmacokinetic profiles of azithromycin, ethambutol, and rifampicin were simulated. For clofazimine, a steady-state average concentration was targeted. Drug concentrations and bacterial densities were monitored over 21 days. Exposures to azithromycin and ethambutol were 20%-40% lower than targeted but within clinically observed ranges. Clofazimine exposures were 1.7 times higher than targeted. Until day 7, both regimens were able to maintain stasis. Thereafter, regrowth was observed for the rifampicin-containing regimen, while the clofazimine-containing regimen yielded a 2 Log10 colony forming unit (CFU) per mL decrease in bacterial load. The clofazimine regimen also successfully suppressed the emergence of macrolide tolerance. In summary, substitution of rifampicin with clofazimine in the hollow-fiber model improved the antimycobacterial activity of the regimen. Clofazimine-containing regimens merit investigation in clinical trials.

The diagnostic accuracy of the GeneXpert ESBL-ampC prototype assay for rapid PCR-based detection of extended-spectrum beta-lactamase genes directly from urine

IMPORTANCE

Early identification of complicated urinary tract infections caused by ESBL-producing Enterobacterales has the potential to limit the use of carbapenems to those patients without alternative antibiotic options and avoid the empirical use of carbapenems in patients without ESBL-producing bacteria. The purpose for such a test will differ by setting and ESBL prevalence rates. Countries with low ESBL rates and cephalosporins as empiric treatment (e.g., The Netherlands) will need a rule-in test to decide to use carbapenems, while countries with high ESBL rates and empiric carbapenem treatment will need a rule-out test for ESBLs to de-escalate therapy early. Anyway, such as a test would-at least theoretically-improve patient care and reduce selective pressure for the emergence of carbapenem resistance.

Decision-making regarding antibiotic therapy duration: An observational study of multidisciplinary meetings in the intensive care unit

PURPOSE

Antibiotic therapy is commonly prescribed longer than recommended in intensive care patients (ICU). We aimed to provide insight into the decision-making process on antibiotic therapy duration in the ICU.

METHODS

A qualitative study was conducted, involving direct observations of antibiotic decision-making during multidisciplinary meetings in four Dutch ICUs. The study used an observation guide, audio recordings, and detailed field notes to gather information about the discussions on antibiotic therapy duration. We described the participants' roles in the decision-making process and focused on arguments contributing to decision-making.

RESULTS

We observed 121 discussions on antibiotic therapy duration in sixty multidisciplinary meetings. 24.8% of discussions led to a decision to stop antibiotics immediately. In 37.2%, a prospective stop date was determined. Arguments for decisions were most often brought forward by intensivists (35.5%) and clinical microbiologists (22.3%). In 28.9% of discussions, multiple healthcare professionals participated equally in the decision. We identified 13 main argument categories. While intensivists mostly used arguments based on clinical status, clinical microbiologists used diagnostic results in the discussion.

CONCLUSIONS

Multidisciplinary decision-making regarding the duration of antibiotic therapy is a complex but valuable process, involving different healthcare professionals, using a variety of argument-types to determine the duration of antibiotic therapy. To optimize the decision-making process, structured discussions, involvement of relevant specialties, and clear communication and documentation of the antibiotic plan are recommended.

Seroprevalence of SARS-CoV-2 antibodies among healthcare workers in Dutch hospitals after the 2020 first wave: a multicentre cross-sectional study with prospective follow-up

BACKGROUND

We aimed to estimate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence and describe its determinants and associated symptoms among unvaccinated healthcare workers (HCWs) after the first wave of the pandemic.

METHODS

HCWs from 13 Dutch hospitals were screened for antibodies against the spike protein of SARS-CoV-2 in June-July 2020 and after three months. Participants completed a retrospective questionnaire on determinants for occupational and community exposure to SARS-CoV-2 and symptoms suggestive of COVID-19 experienced since January 2020. The seroprevalence was calculated per baseline characteristic and symptom at baseline and after follow-up. Adjusted odds ratios (aOR) for seropositivity were determined using logistic regression.

RESULTS

Among 2328 HCWs, 323 (13.9%) were seropositive at enrolment, 49 of whom (15%) reported no previous symptoms suggestive of COVID-19. During follow-up, only 1% of the tested participants seroconverted. Seroprevalence was higher in younger HCWs compared to the mid-age category (aOR 1.53, 95% CI 1.07-2.18). Nurses (aOR 2.21, 95% CI 1.34-3.64) and administrative staff (aOR 1.87, 95% CI 1.02-3.43) had a higher seroprevalence than physicians. The highest seroprevalence was observed in HCWs in the emergency department (ED) (aOR 1.79, 95% CI 1.10-2.91), the lowest in HCWs in the intensive, high, or medium care units (aOR 0.47, 95% CI 0.31-0.71). Chronic respiratory disease, smoking, and having a dog were independently associated with a lower seroprevalence, while HCWs with diabetes mellitus had a higher seroprevalence. In a multivariable model containing all self-reported symptoms since January 2020, altered smell and taste, fever, general malaise/fatigue, and muscle aches were positively associated with developing antibodies, while sore throat and chills were negatively associated.

CONCLUSIONS

The SARS-CoV-2 seroprevalence in unvaccinated HCWs of 13 Dutch hospitals was 14% in June-July 2020 and remained stable after three months. A higher seroprevalence was observed in the ED and among nurses, administrative and young staff, and those with diabetes mellitus, while a lower seroprevalence was found in HCWs in intensive, high, or medium care, and those with self-reported lung disease, smokers, and dog owners. A history of altered smell or taste, fever, muscle aches and fatigue were independently associated with the presence of SARS-CoV-2 antibodies in unvaccinated HCWs.

The role of rifampicin within the treatment of Mycobacterium avium pulmonary disease

Rifampicin is recommended for the treatment of Mycobacterium avium complex pulmonary disease alongside azithromycin and ethambutol. We evaluated the azithromycin-ethambutol backbone with and without rifampicin in an intracellular hollow fiber model and performed RNA sequencing to study the differences in adaptation. In an in vitro hollow fiber experiment, we simulated epithelial lining fluid pharmacokinetic profiles of the recommended 3-drug (rifampicin, ethambutol, and azithromycin) or a 2-drug (ethambutol and azithromycin) treatment. THP-1 cells infected with M. avium ATCC700898 were exposed to these regimens for 21 days. We determined intra- and extra-cellular bacterial load- and THP-1 cell densities on days 0, 3, 7, 14, and 21, alongside RNA sequencing. The emergence of macrolide resistance was studied by inoculating intra- and extra-cellular fractions of azithromycin-containing Middlebrook 7H10 agar plates. Complete pharmacokinetic profiles were determined at days 0 and 21. Both therapies maintained stasis of both intra- and extra-cellular bacterial populations for 3 days, whilst regrowth coinciding with the emergence of a macrolide-resistant subpopulation was seen after 7 days. THP-1 cell density remained static. Similar transcriptional profiles were observed for both therapies that were minimally influenced by exposure duration. Transcriptional response was slightly larger during 2-drug treatment. Rifampicin did not add to the antimycobacterial effect to the 2-drug therapy or suppression of emergence resistance. RNA transcription was not greatly altered by the addition of rifampicin, which may be due to strong transcriptional influence of azithromycin and host cells. This questions the role of rifampicin in the currently recommended therapy. These findings should be confirmed in clinical trials.

The potential role of drug transporters and amikacin modifying enzymes in M. avium

OBJECTIVES

Mycobacterium avium (M. avium) complex bacteria cause opportunistic infections in humans. Treatment yields cure rates of 60% and consists of a macrolide, a rifamycin, and ethambutol, and in severe cases, amikacin. Mechanisms of antibiotic tolerance remain mostly unknown. Therefore, we studied the contribution of efflux and amikacin modification to antibiotic susceptibility.

METHODS

We characterised M. avium ABC transporters and studied their expression together with other transporters following exposure to clarithromycin, amikacin, ethambutol, and rifampicin. We determined the effect of combining the efflux pump inhibitors berberine, verapamil and CCCP (carbonyl cyanide m-chlorophenyl hydrazone), to study the role of efflux on susceptibility. Finally, we studied the modification of amikacin by M. avium using metabolomic analysis.

RESULTS

Clustering shows conservation between M. avium and M. tuberculosis and transporters from most bacterial subfamilies (2-6, 7a/b, 10-12) were found. The largest number of transporter encoding genes was up-regulated after clarithromycin exposure, and the least following amikacin exposure. Only berberine increased the susceptibility to clarithromycin. Finally, because of the limited effect of amikacin on transporter expression, we studied amikacin modification and showed that M. avium, in contrast to M. abscessus, is not able to modify amikacin.

CONCLUSION

We show that M. avium carries ABC transporters from all major families important for antibiotic efflux, including homologues shown to have affinity for drugs included in treatment. Efflux inhibition in M. avium can increase susceptibility, but this effect is efflux pump inhibitor- and antibiotic-specific. Finally, the lack of amikacin modifying activity in M. avium is important for its activity.

Is this pill an antibiotic or a painkiller? Improving the identification of oral antibiotics for better use

In this Viewpoint, we discuss how the identification of oral antibiotics and their distinction from other commonly used medicines can be challenging for consumers, suppliers, and health-care professionals. There is a large variation in the names that people use to refer to antibiotics and these often relate to their physical appearance, although antibiotics come in many different physical presentations. We also reflect on how the physical appearance of medicine influences health care and public health by affecting communication between patients and health-care professionals, dispensing , medicine use, and the public understanding of health campaigns. Furthermore, we report expert and stakeholder consultations on improving the identification of oral antibiotics and discuss next steps towards a new identification system for antibiotics. We propose to use the physical appearance as a tool to support and nudge awareness about antibiotics and their responsible use.

Targeting the 16S rRNA Gene by Reverse Complement PCR Next-Generation Sequencing: Specific and Sensitive Detection and Identification of Microbes Directly in Clinical Samples

The detection and accurate identification of bacterial species in clinical samples are crucial for diagnosis and appropriate antibiotic treatment. To date, sequencing of the 16S rRNA gene has been widely used as a complementary molecular approach when identification by culture fails. The accuracy and sensitivity of this method are highly affected by the selection of the 16S rRNA gene region targeted. In this study, we assessed the clinical utility of 16S rRNA reverse complement PCR (16S RC-PCR), a novel method based on next-generation sequencing (NGS), for the identification of bacterial species. We investigated the performance of 16S RC-PCR on 11 bacterial isolates, 2 polymicrobial community samples, and 59 clinical samples from patients suspected of having a bacterial infection. The results were compared to culture results, if available, and to the results of Sanger sequencing of the 16S rRNA gene (16S Sanger sequencing). By 16S RC-PCR, all bacterial isolates were accurately identified to the species level. Furthermore, in culture-negative clinical samples, the rate of identification increased from 17.1% (7/41) to 46.3% (19/41) when comparing 16S Sanger sequencing to 16S RC-PCR. We conclude that the use of 16S RC-PCR in the clinical setting leads to an increased sensitivity of detection of bacterial pathogens, resulting in a higher number of diagnosed bacterial infections, and thereby can improve patient care. IMPORTANCE The identification of the causative infectious pathogen in patients suspected of having a bacterial infection is essential for diagnosis and the start of appropriate treatment. Over the past 2 decades, molecular diagnostics have improved the ability to detect and identify bacteria. However, novel techniques that can accurately detect and identify bacteria in clinical samples and that can be implemented in clinical diagnostics are needed. Here, we demonstrate the clinical utility of bacterial identification in clinical samples by a novel method called 16S RC-PCR. Using 16S RC-PCR, we reveal a significant increase in the number of clinical samples in which a potentially clinically relevant pathogen is identified compared to the commonly used 16S Sanger method. Moreover, RC-PCR allows automation and is well suited for implementation in a diagnostic laboratory. In conclusion, the implementation of this method as a diagnostic tool is expected to result in an increased number of diagnosed bacterial infections, and in combination with adequate treatment, this could improve clinical outcomes for patients.

MGIT Enriched Shotgun Metagenomics for Routine Identification of Nontuberculous Mycobacteria: a Route to Personalized Health Care

Currently, nontuberculous mycobacteria (NTM) are identified using small genomic regions, and species-level identification is often not possible. We introduce a next-generation sequencing (NGS) workflow that identifies mycobacteria to (sub)species level on the basis of the whole genome extracted from enriched shotgun metagenomic data. This technique is used to study the association between genotypes and clinical manifestations to pave the way to more personalized health care. Two sets of clinical isolates (explorative set [n = 212] and validation set [n = 235]) were included. All data were analyzed using a custom pipeline called MyCodentifier. Sequences were matched against a custom hsp65 database (NGS-hsp65) and whole-genome database (NGS-WG) created based on the phylogeny presented by Tortoli et al. (E. Tortoli, T. Fedrizzi, C. J. Meehan, A. Trovato, et al., Infect Genet Evol 56:19-25, 2017, https://doi.org/10.1016/j.meegid.2017.10.013). Lastly, phylogenetic analysis was performed and correlated with clinical manifestation. In the explorative set, we observed 98.6% agreement between the line probe assay and the NGS-hsp65 database. In the validation set, 99.1% agreement between the NGS-WG and NGS-hsp65 databases was seen on the complex level. We identified a cluster of Mycobacterium marinum isolates not represented by the Tortoli et al. phylogeny. Phylogenetic analysis of M. avium complex isolates confirmed misclassification of M. timonense and M. bouchedurhonense and identified subclusters within M. avium although no correlation with clinical manifestation was observed. We performed routine NGS to identify NTM from MGIT enriched shotgun metagenomic data. Phylogenetic analyses identified subtypes of M. avium, but in our set of isolates no correlation with clinical manifestation was found. However, this NGS workflow paves a way for more personalized health care in the future.

Randomized clinical trial: Long-term Staphylococcus aureus decolonization in patients on home parenteral nutrition

BACKGROUND & AIMS

Staphylococcus aureus decolonization has proven successful in prevention of S. aureus infections and is a key strategy to maintain venous access and avoid hospitalization in patients receiving home parenteral nutrition (HPN). We aimed to determine the most effective and safe long-term S. aureus decolonization regimen.

METHODS

A randomized, open-label, multicenter clinical trial was conducted. Adult intestinal failure patients with HPN support and carrying S. aureus were randomly assigned to a 'continuous suppression' (CS) strategy, a repeated chronic topical antibiotic treatment or a 'search and destroy' (SD) strategy, a short and systemic antibiotic treatment. Primary outcome was the proportion of patients in whom S. aureus was totally eradicated during a 1-year period. Secondary outcomes included risk factors for decolonization failure and S. aureus infections, antimicrobial resistance, adverse events, patient compliance and cost-effectivity.

RESULTS

63 participants were included (CS 31; SD 32). The mean 1-year S. aureus decolonization rate was 61% (95% CI 44, 75) for the CS group and 39% (95% CI 25, 56) for the SD group with an OR of 2.38 (95% CI 0.92, 6.11, P = 0.07). More adverse effects occurred in the SD group (P = 0.01). Predictors for eradication failure were a S. aureus positive caregiver and presence of a (gastro)enterostomy.

CONCLUSION

We did not demonstrate an increased efficacy of a short and systemic S. aureus decolonization strategy over a continuous topical suppression treatment. The latter may be the best option for HPN patients as it achieved a higher long-term decolonization rate and was well-tolerated (NCT03173053).

Assessment of antimicrobial mismatches in empirical treatment in early PJI after aseptic revision arthroplasty

Background

In early periprosthetic joint infection (PJI), 'debridement, antibiotics and implant retention' (DAIR) is a widely accepted form of treatment. Empirical antimicrobial treatment is started while culture results of tissue samples taken during debridement are pending.

Objectives

In this retrospective study we assessed the antimicrobial mismatch rate between empirical treatment and the susceptibility of the causative microorganisms of PJI after aseptic revision arthroplasty. We analysed risk factors for antimicrobial mismatches and the impact of mismatches on the outcome of PJI treatment.

Results

A total of 119 patients were included in the analysis. In 72% (86/119) of the cases there was an antimicrobial mismatch in empirical treatment. Most of the antimicrobial mismatches were caused by multidrug-resistant (MDR) Staphylococcus spp. (77%, 66/86). In multivariable analysis, polymicrobial PJI was significantly associated with antimicrobial mismatch (OR: 6.89; 95% CI: 2.38-19.53; P < 0.001), and antimicrobial mismatch was significantly associated with reduced success rate of PJI treatment (OR: 0.20; 95% CI: 0.05 ± 0.82; P = 0.026). There was no difference in successful outcome between PJI caused by Gram-negative bacilli (61%) and Gram-positive bacteria (69%, P = 0.516).

Conclusions

Mismatching empirical antimicrobial treatment after DAIR following aseptic revision arthroplasty was significantly associated with failure of PJI treatment. Polymicrobial PJI is a risk factor for antimicrobial mismatch of the empirical treatment of PJI. Antimicrobial mismatch and delay in targeted treatment should be integrated in the approach to optimize antibiotic treatment to improve clinical outcomes, while minimizing unintended side effects of antimicrobial use (antimicrobial stewardship).

Aetiology and Potential Animal Exposure in Central Nervous System Infections in Vietnam

An estimated 73% of emerging infections are zoonotic in origin, with animal contact and encroachment on their habitats increasing the risk of spill-over events. In Vietnam, close exposure to a wide range of animals and animal products can lead to acquisition of zoonotic pathogens, a number of which cause central nervous system (CNS) infections. However, studies show the aetiology of CNS infections remains unknown in around half of cases. We used samples and data from hospitalised patients with CNS infections, enrolled into the Vietnam Initiative on Zoonotic Infections multicentre study, to determine the association between aetiology and animal contact including those in whom the cause was unknown. Among 933 patients, a pathogen or an antibody response to it was identified in 291 (31.2%, 95% CI 28.3-34.3%). The most common pathogens were Streptococcus suis (n = 91 (9.8%, 8.0-11.9%)) and Japanese encephalitis virus (JEV) (n = 72 (7.7%, 6.1-9.7%)). Commonly reported animal contact included keeping, raising or handling (n = 364 (39.0%, 35.9-42.2%)) and handling, cooking or consuming raw meat, blood or viscera in the 2 weeks prior to symptom onset (n = 371 (39.8%, 36.6-43.0%)), with the latter most commonly from pigs (n = 343 (36.9%, 33.8-40.1%). There was no association between an unknown aetiology and exposure to animals in a multivariate logistic regression. Further testing for unknown or undetected pathogens may increase diagnostic yield, however, given the high proportion of zoonotic pathogens and the presence of risk factors, increasing public awareness about zoonoses and preventive measures can be considered.

Success rates of MRSA decolonization and factors associated with failure

Background

We evaluated the success rate of MRSA decolonization directly after treatment and after one year in patients who were treated at the outpatient MRSA clinic of a large university medical centre to identify potential contributing factors to treatment success and failure.

Methods

Data from November 1, 2013 to August 1, 2020 were used. Only patients who had undergone complete MRSA decolonization were included. Risk factors for MRSA treatment failure were identified using a multivariable logistic regression model.

Results

In total, 127 MRSA carriers were included: 7 had uncomplicated carriage, 91 had complicated carriage, and 29 patients had complicated carriage in combination with an infection. In complicated carriers and complicated carriers with an infection final treatment was successful in 75.0%. Risk factors for initial treatment failure included having one or more comorbidities and not testing the household members. Risk factors for final treatment failure were living in a refugee centre, being of younger age (0–17 years), and having one or more comorbidities.

Conclusions

The results of this study indicate that patients with a refugee status and children treated at the paediatric clinic have a higher risk of MRSA decolonisation treatment failure. For this reason, it might be useful to revise decolonization strategies for these subgroups and to refer these patients to specialized outpatient clinics in order to achieve higher treatment success rates.

[Carbapenems: take it when needed but leave it if you can]

Surveillance data and literature have shown a worldwide increase in infections with resistant bacteria, which has led to increased prescriptions of carbapenems, which in turn has led to increased carbapenem resistance. There is also an increasing use of carbapenems in the Netherlands, a county usually very conservative in antibiotic use. Carbapenem sparing strategies are essential in an attempt to prevent further rise of infections caused by carbapenem resistant bacteria. This article discusses carbapenem sparing strategies with old forgotten antibiotics and novel antibiotics from a Dutch perspective.

Current Practices and Opportunities for Outpatient Parenteral Antimicrobial Therapy in Hospitals: A National Cross-Sectional Survey

This nationwide study assessed how outpatient parenteral antimicrobial therapy (OPAT) is organised by Dutch acute care hospitals, the barriers experienced, and how an OPAT program affects the way hospitals organised OPAT care. We systematically developed and administered a survey to all 71 Dutch acute care hospitals between November 2021 and February 2022. Analyses were primarily descriptive and included a comparison between hospitals with and without an OPAT program. Sixty of the 71 hospitals (84.5%) responded. Fifty-five (91.7%) performed OPAT, with a median number of 20.8 (interquartile range [IQR] 10.3-29.7) patients per 100 hospital beds per year. Of these 55 hospitals, 31 (56.4%) had selection criteria for OPAT and 34 (61.8%) had a protocol for laboratory follow-up. Sixteen hospitals (29.1%) offered self-administered OPAT (S-OPAT), with a median percentage of 5.0% of patients (IQR: 2.3%-10.0%) actually performing self-administration. Twenty-five hospitals (45.5%) had an OPAT-related outcome registration. The presence of an OPAT program (22 hospitals, 40.0%) was significantly associated with aspects of well-organised OPAT care. The most commonly experienced barriers to OPAT implementation were a lack of financial, administrative, and IT support and insufficient time of healthcare staff. Concluding, hospital-initiated OPAT is widely available in the Netherlands, but various aspects of well-organised OPAT care can be improved. Implementation of a team-based OPAT program can contribute to such improvements. The observed variation provides leads for further scientific research, guidelines, and practical implementation programs.

Endocarditis caused by non-typeable Streptococcus pneumoniae

The Streptococcus pneumoniae capsule is regarded as indispensable in bacteremia. We report an infant with a ventricular septal defect and infective endocarditis caused by nontypeable S. pneumoniae. In-depth investigation confirmed a deficient capsule yet favored pneumococcal fitness for causing infective endocarditis, rather than a host immune disorder, as the cause of infective endocarditis in this case.

Acceptability of innovative culture-based antibiotic prophylaxis strategies: a multi-method study on experiences regarding transrectal prostate biopsy

Background

The acceptability of innovative medical strategies among healthcare providers and patients affects their uptake in daily clinical practice.

Objectives

To explore experiences of healthcare providers and patients with culture-based antibiotic prophylaxis in transrectal prostate biopsy with three swab-screening scenarios: self-sampling at home, self-sampling in the hospital and sampling by a healthcare provider.

Methods

We performed focus group interviews with urologists and medical microbiologists from 11 hospitals and six connected clinical microbiological laboratories. We used Flottorp's comprehensive checklist for identifying determinants of practice to guide data collection and analysis. The experiences of 10 laboratory technicians from five laboratories and 452 patients from nine hospitals were assessed using a questionnaire.

Results

Overall, culture-based prophylaxis strategies were experienced as feasible in daily clinical practice. None of the three swab-screening scenarios performed better. For urologists (n = 5), implementation depended on the effectiveness of the strategy. In addition, it was important to them that the speed of existing oncology care pathways is preserved. Medical microbiologists (n = 5) and laboratory technicians (n = 8) expected the strategy to be fairly easy to implement. Patients (n = 430; response rate 95.1%) were generally satisfied with the screening scenario presented to them. To meet the various patients' needs and preferences, multiple scenarios within a hospital are probably needed.

Conclusions

This multi-method study has increased our understanding of the acceptability of culture-based prophylaxis strategies in prostate biopsy, which can help healthcare providers to offer high-quality patient-centred care. The strategy seems relatively straightforward to implement as overall acceptance appears to be high.

SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis

During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monitoring transmission and rising levels of mutant strains. Here we report a novel WGS technique for SARS-CoV-2, the EasySeq™ RC-PCR SARS-CoV-2 WGS kit. By applying a reverse complement polymerase chain reaction (RC-PCR), an Illumina library preparation is obtained in a single PCR, thereby saving time, resources and facilitating high-throughput screening. Using this WGS technique, we evaluated SARS-CoV-2 diversity and possible transmission within a group of 173 patients and healthcare workers (HCW) of the Radboud university medical center during 2020. Due to the emergence of variants of concern, we screened SARS-CoV-2 positive samples in 2021 for identification of mutations and lineages. With use of EasySeq™ RC-PCR SARS-CoV-2 WGS kit we were able to obtain reliable results to confirm outbreak clusters and additionally identify new previously unassociated links in a considerably easier workaround compared to current methods. Furthermore, various SARS-CoV-2 variants of interest were detected among samples and validated against an Oxford Nanopore sequencing amplicon strategy which illustrates this technique is suitable for surveillance and monitoring current circulating variants.

The drop in reported invasive pneumococcal disease among adults during the first COVID-19 wave in the Netherlands explained

Objectives: Streptococcus pneumoniae is the leading bacterial pathogen causing respiratory infections. Since the COVID-19 pandemic emerged, less invasive pneumococcal disease (IPD) was identified by surveillance systems worldwide. Measures to prevent transmission of SARS-CoV-2 also reduce transmission of pneumococci, but this would gradually lead to lower disease rates. Design: Here, we explore additional factors contributing to the instant drop in pneumococcal disease cases captured in surveillance. Results: Our observations on referral practices and other impediments to diagnostic testing indicate that residual IPD has likely occurred but remained undetected by conventional hospital-based surveillance. Conclusions: Depending on the setting, we discuss alternative monitoring strategies that could improve understanding of pneumococcal disease dynamics.

C-Reactive Protein to rule out complicated pneumococcal disease manifestations; a retrospective cohort study in adults with pneumococcal bacteraemia

OBJECTIVES

To explore the negative predictive value (NPV) of CRP at admission to exclude complicated disease manifestations.

METHODS

A Dutch multicentre retrospective cohort study was conducted between 01-01-2012 and 30-06-2020. Adults with positive blood cultures for S. pneumoniae, whose CRP was measured at admission, and whose infection focus was known, were included. Electronic medical and microbiological records were reviewed.

RESULTS

Of the 832 bacteremic patients enrolled, 30% had complicated manifestations of pneumococcal disease. Most frequent were pleural effusion (8.9%), pleural empyema (5.4%), and meningitis (7.5%). Compared to solitary pneumonia, patients with pleural effusion and empyema presented with higher CRP levels. Although low CRP did not exclude complicated disease in general, a CRP level < 114 mg/L at admission could reliably exclude empyema among adult pneumonia patients with an NPV of 93% and a specificity of 26%. However, in cases where pleural fluid was present, CRP levels were mostly above 114 mg/L, such that suspicion of empyema could only be ruled out in a minority of cases (10%).

CONCLUSIONS

Complicated manifestations are prevalent in adult pneumococcal bacteraemia. Low blood CRP levels can reliably exclude the development of pulmonary empyema. Practical value may be largest in settings without thoracic imaging at hand.

Centre-specific bacterial pathogen typing affects infection-control decision making

Whole-genome sequencing is becoming the de facto standard for bacterial outbreak surveillance and infection prevention. This is accompanied by a variety of bioinformatic tools and needs bioinformatics expertise for implementation. However, little is known about the concordance of reported outbreaks when using different bioinformatic workflows. In this multi-centre proficiency testing among 13 major Dutch healthcare-affiliated centres, bacterial whole-genome outbreak analysis was assessed. Centres who participated obtained two randomized bacterial datasets of Illumina sequences, a Klebsiella pneumoniae and a Vancomycin-resistant Enterococcus faecium, and were asked to apply their bioinformatic workflows. Centres reported back on antimicrobial resistance, multi-locus sequence typing (MLST), and outbreak clusters. The reported clusters were analysed using a method to compare landscapes of phylogenetic trees and calculating Kendall–Colijn distances. Furthermore, fasta files were analysed by state-of-the-art single nucleotide polymorphism (SNP) analysis to mitigate the differences introduced by each centre and determine standardized SNP cut-offs. Thirteen centres participated in this study. The reported outbreak clusters revealed discrepancies between centres, even when almost identical bioinformatic workflows were used. Due to stringent filtering, some centres failed to detect extended-spectrum beta-lactamase genes and MLST loci. Applying a standardized method to determine outbreak clusters on the reported de novo assemblies, did not result in uniformity of outbreak-cluster composition among centres.

Stakeholders' perspectives on training over the counter medicine sellers and Community-based Health Planning and Services facilities to dispense antibiotics in Ghana

Background

Dispensing of antibiotics by over the counter medicine sellers (OTCMS) is a major driver of inappropriate use and resistance in low and middle income countries. Recent studies in Ghana revealed the need to consider training OTCMS and Community-based Health Planning and Services (CHPS)/health posts to dispense some antibiotics. Feasibility of training OTCMS and CHPS to dispense some antibiotics was explored in this study.

Methods

This was an explorative study involving 10 in-depth interviews (IDIs) among staff of Ghana health services (GHS), pharmacy council and the association of OTCMS at the district and regional levels. Next, findings were presented to the Ghana Antimicrobial Resistance (AMR) platform for further discussions at the national level. Five IDIs were also performed among selected members of the AMR platform as a follow-up on emerging issues. Data were thematically analysed and presented as narratives with quotes to support the findings.

Results

Two opposing views were found in our study. Leadership of OTCMS and GHS staff at the district health directorate supported the suggestion that OTCMS and CHPS should be trained to dispense specific antibiotics because they are already dispensing them. The leadership of OTCMS explained that some of their members are experienced and could be trained to improve their practices. In contrast, participants from pharmacy council, GHS in the region and national AMR platform generally alluded that OTCMS and CHPS should not be trained to dispense antibiotics because their level of education is inadequate. GHS personnel from the region further explained that training OTCMS could further compromise inappropriate antibiotic use in the context of already weak regulation enforcement. GHS and pharmacy council in the region rather suggested that OTCMS and CHPS should focus on public health education on disease prevention and appropriate antibiotic use.

Conclusions

There is general lack of consensus among stakeholders on whether OTCMS and CHPS should be trained to dispense specific antibiotics. Further stakeholder engagement is required to carefully consider this suggestion as views on feasibility differ. Ministries of health and healthcare agencies in Ghana and LMIC should improve access to approved health services to improve antibiotic use in rural settings.

The epidemiology of nontuberculous mycobacterial pulmonary disease in the Netherlands

Background

Nontuberculous mycobacteria (NTM) are emerging opportunistic pathogens of humans. Because NTM pulmonary disease (PD) is not a notifiable disease in Europe, the epidemiology of NTM-PD is not well known. However, the prevalence of NTM-PD is thought to be increasing, particularly in countries where tuberculosis rates have decreased. Here we aim to determine the prevalence of NTM-PD in the Netherlands.

Methods

Annual prevalence estimates of NTM-PD in the Netherlands (2012-2019) were derived from four separate databases, including two drug dispensing databases, an ICD-10 code database and a hospitalisation database. Databases covered a fraction of the Dutch population and were extrapolated. In addition, annual NTM-PD prevalence was also estimated by means of a pulmonologist survey.

Results

The estimated annual prevalence of NTM-PD using databases is between 2.3 and 5.9 patients per 100 000 inhabitants. Prevalence estimates derived from the drug dispensing databases, the hospitalisation database and the claims database were 2.3, 5.9, 3.5 and 4.5 per 100 000 inhabitants, respectively. The annual prevalence estimated in the pulmonologist survey was between 6.2 and 9.9 per 100 000 inhabitants. The annual prevalence remained stable over the included period.

Conclusion

The estimated annual prevalence of NTM-PD using databases was between 2.3 and 5.9 patients per 100 000 inhabitants. Due to the possible presence of tuberculosis patients and low coverage in one dispensing database, we believe an annual prevalence of between 2.3 and 4.5 patients per 100 000 inhabitants is more probable, which still renders NTM-PD a serious health threat. This estimate is lower than the estimate from the pulmonologist survey, indicating physicians likely overestimate prevalence.

Is there a role for tedizolid in the treatment of non-tuberculous mycobacterial disease?

Background

Pulmonary infections caused by non-tuberculous mycobacteria (NTM) are hard to treat and have low cure rates despite intensive multidrug therapy.

Objectives

To assess the feasibility of tedizolid, a new oxazolidinone, for the treatment of Mycobacterium avium and Mycobacterium abscessus.

Methods

We determined MICs of tedizolid for 113 isolates of NTM. Synergy with key antimycobacterial drugs was assessed using the chequerboard method and calculation of the FIC index (FICI). We performed time–kill kinetics assays of tedizolid alone and combined with amikacin for M. abscessus and with ethambutol for M. avium. Human macrophages were infected with M. abscessus and M. avium and subsequently treated with tedizolid; intracellular and extracellular cfu were quantified over time.

Results

NTM isolates generally had a lower MIC of tedizolid than of linezolid. FICIs were lowest between tedizolid and amikacin for M. abscessus (FICI = 0.75) and between tedizolid and ethambutol for M. avium (FICI = 0.72). Clarithromycin and tedizolid showed initial synergy, which was abrogated by erm(41)-induced macrolide resistance (FICI = 0.53). Tedizolid had a weak bacteriostatic effect on M. abscessus and combination with amikacin slightly prolonged its effect. Tedizolid had concentration-dependent activity against M. avium and its efficacy was enhanced by ethambutol. Both combinations had a concentration-dependent synergistic effect. Tedizolid could inhibit the intracellular bacterial population of both M. avium and M. abscessus.

Conclusions

Tedizolid should be further investigated in pharmacodynamic studies and clinical trials for M. avium complex pulmonary disease. It is less active against M. abscessus, but still promising.

Inhaled tigecycline is effective against Mycobacterium abscessus in vitro and in vivo

BACKGROUND

Mycobacterium abscessus causes chronic pulmonary infections. Owing to its resistance to most classes of antibiotics, treatment is complex and cure rates are only 45%. Tigecycline is active against M. abscessus, but severe toxicity and the need for IV administration limit its use.

OBJECTIVES

To assess the potential of inhaled tigecycline as a treatment for M. abscessus pulmonary disease, by measuring its efficacy in a mouse model of chronic M. abscessus pulmonary disease, establishing the intracellular activity of tigecycline against M. abscessus in human macrophages and measuring the activity of tigecycline in the sputum of cystic fibrosis patients.

METHODS

We infected GM-CSF knockout mice with M. abscessus by intrapulmonary aerosol. Infected mice were treated with tigecycline in 0.25, 1.25 and 2.5 mg doses, by inhalation, or untreated, for 28 days. Tigecycline was added to human peripheral blood-derived macrophages infected with M. abscessus to assess its intracellular activity. We performed a time-kill kinetics experiment of tigecycline against M. abscessus with and without sputum of cystic fibrosis patients.

RESULTS

Inhaled tigecycline proved highly effective against M. abscessus in GM-CSF knockout mice. The effect was dose dependent. Tigecycline showed potent activity against M. abscessus in macrophages and retained most of its activity in the presence of sputum of cystic fibrosis patients.

CONCLUSIONS

Inhaled tigecycline may represent a viable treatment option for M. abscessus pulmonary disease, where treatment outcomes are currently very poor. A stable and safe formulation is required to proceed to further pharmacodynamic studies and ultimately clinical trials.

Efficacy and safety of selective decontamination of the digestive tract (SDD) to prevent recurrent hepatic cyst infections in polycystic liver disease: a retrospective case series

Background

Hepatic cyst infection is a complication of polycystic liver disease (PLD) that causes substantial morbidity. Repetitive infection is frequent and is increasingly difficult to treat. As translocated gut bacteria are considered the cause, we hypothesize that selective decontamination of the digestive tract (SDD) reduces recurrence of hepatic cyst infection.

Methods

We performed a retrospective, observational study in two referral centres. All patients with PLD treated with SDD for hepatic cyst infection were included. Efficacy was determined by calculating the infection incidence (hepatic cyst infections per month) before and during SDD therapy. Adverse events were scored according to the Common Terminology Criteria for Adverse Events (CTCAE).

Results

We identified eight patients who received SDD (88% female, 88% polycystic kidney disease). The median age was 65 years (IQR: 51–74 years). SDD lowered the median incidence from 0.09 episodes per month (IQR: 0.06–0.25 episodes per month) to 0.01 episodes per month (IQR: 0.00–0.05 episodes per month) (P = 0.12). Discontinuation of SDD led to rapid recurrence of cyst infection (71% within 6 weeks). SDD consisted of polymyxins with/without aminoglycosides. The median SDD treatment duration was 20 months (range: 3–89 months). Six patients (75%) developed adverse events [CTCAE Grade 1 (gastrointestinal: n = 3) or Grade 3 (ototoxicity: n = 1; fungal infection: n = 1)], mostly attributable to aminoglycosides; one patient developed polymyxin E resistance.

Conclusions

SDD prophylaxis provides a novel strategy for limiting recurrent hepatic cyst infection in PLD patients. However, adverse events are frequent and curtail its use. As most were attributable to aminoglycosides, polymyxin E is considered the preferred therapy.

Antimicrobial susceptibility testing results from 13 hospitals in Viet Nam: VINARES 2016-2017

OBJECTIVE

To analyse data from 2016-17 from a hospital-based antimicrobial resistance surveillance with national coverage in a network of hospitals Viet Nam.

METHODS

We analysed data from 13 hospitals, 3 less than the dataset from the 2012-13 period. Identification and antimicrobial susceptibility testing data from the clinical microbiology laboratories from samples sent in for routine diagnostics were used. Clinical and Laboratory Standards Institute 2018 guidelines were used for antimicrobial susceptibility testing interpretation. WHONET was used for data entry, management and analysis.

RESULTS

42,553 deduplicated isolates were included in this analysis; including 30,222 (71%) Gram-negative and 12,331 (29%) Gram-positive bacteria. 8,793 (21%) were from ICUs and 7,439 (18%) isolates were from invasive infections. Escherichia coli and Staphylococcus aureus were the most frequently detected species with 9,092 (21%) and 4,833 isolates (11%), respectively; followed by Klebsiella pneumoniae (3,858 isolates - 9.1%) and Acinetobacter baumannii (3,870 isolates - 9%). Bacteria were mainly isolated from sputum (8,798 isolates - 21%), blood (7,118 isolates - 17%) and urine (5,202 isolates - 12%). Among Gram-positives 3,302/4,515 isolates (73%) of S. aureus were MRSA; 99/290 (34%) of Enterococcus faecium were resistant to vancomycin; and 58% (663/1,136) of Streptococcus pneumoniae proportion were reduced susceptible to penicillin. Among Gram-negatives 59% (4,085/6,953) and 40% (1,186/2,958) of E. coli and K. pneumoniae produced ESBL and 29% (376/1,298) and 11% (961/8,830) were resistant to carbapenems, respectively. 79% (2855/3622) and 45% (1,514/3,376) of Acinetobacter spp. and Pseudomonas aeruginosa were carbapenem resistant, respectively. 88% (804/911) of Haemophilus influenzae were ampicillin resistant and 18/253 (7%) of Salmonella spp. and 7/46 (15%) of Shigella spp. were resistant to fluoroquinolones. The number of isolates from which data were submitted in the 2016-2017 period was twice as high as in 2012-2013. AMR proportions were higher in 2016-2017 for most pathogen-antimicrobial combinations of interest including imipenem-resistant A. baumannii, P. aeruginosa and Enterobacterales.

CONCLUSIONS

The data show alarmingly high and increasing resistant proportions among important organisms in Viet Nam. AMR proportions varied across hospital types and should be interpreted with caution because existing sampling bias and missing information on whether isolates were community or hospital acquired. Affordable and scalable ways to adopt a sample- or case-based approach across the network should be explored and clinical data should be integrated to help provide more accurate inferences of the surveillance data.

Community-based antibiotic access and use in six low-income and middle-income countries: a mixed-method approach

BACKGROUND

Antimicrobial misuse is common in low-income and middle-income countries (LMICs), and this practice is a driver of antibiotic resistance. We compared community-based antibiotic access and use practices across communities in LMICs to identify contextually specific targets for interventions to improve antibiotic use practices.

METHODS

We did quantitative and qualitative assessments of antibiotic access and use in six LMICs across Africa (Mozambique, Ghana, and South Africa) and Asia (Bangladesh, Vietnam, and Thailand) over a 2·5-year study period (July 1, 2016-Dec 31, 2018). We did quantitative assessments of community antibiotic access and use through supplier mapping, customer exit interviews, and household surveys. These quantitative assessments were triangulated with qualitative drug supplier and consumer interviews and discussions.

FINDINGS

Vietnam and Bangladesh had the largest proportions of non-licensed antibiotic dispensing points. For mild illness, drug stores were the most common point of contact when seeking antibiotics in most countries, except South Africa and Mozambique, where public facilities were most common. Self-medication with antibiotics was found to be widespread in Vietnam (55·2% of antibiotics dispensed without prescription), Bangladesh (45·7%), and Ghana (36·1%), but less so in Mozambique (8·0%), South Africa (1·2%), and Thailand (3·9%). Self-medication was considered to be less time consuming, cheaper, and overall, more convenient than accessing them through health-care facilities. Factors determining where treatment was sought often involved relevant policies, trust in the supplier and the drug, disease severity, and whether the antibiotic was intended for a child. Confusion regarding how to identify oral antibiotics was revealed in both Africa and Asia.

INTERPRETATION

Contextual complexities and differences between countries with different incomes, policy frameworks, and cultural norms were revealed. These contextual differences render a single strategy inadequate and instead necessitate context-tailored, integrated intervention packages to improve antibiotic use in LMICs as part of global efforts to combat antibiotic resistance.

FUNDING

Wellcome Trust and Volkswagen Foundation.

Genome-wide analysis in Escherichia coli unravels a high level of genetic homoplasy associated with cefotaxime resistance

Cefotaxime (CTX) is a third-generation cephalosporin (3GC) commonly used to treat infections caused by Escherichia coli. Two genetic mechanisms have been associated with 3GC resistance in E. coli. The first is the conjugative transfer of a plasmid harbouring antibiotic-resistance genes. The second is the introduction of mutations in the promoter region of the ampC β-lactamase gene that cause chromosome-encoded β-lactamase hyperproduction. A wide variety of promoter mutations related to AmpC hyperproduction have been described. However, their link to CTX resistance has not been reported. We recultured 172 cefoxitin-resistant E. coli isolates with known CTX minimum inhibitory concentrations and performed genome-wide analysis of homoplastic mutations associated with CTX resistance by comparing Illumina whole-genome sequencing data of all isolates to a PacBio sequenced reference chromosome. We mapped the mutations on the reference chromosome and determined their occurrence in the phylogeny, revealing extreme homoplasy at the -42 position of the ampC promoter. The 24 occurrences of a T at the -42 position rather than the wild-type C, resulted from 18 independent C>T mutations in five phylogroups. The -42 C>T mutation was only observed in E. coli lacking a plasmid-encoded ampC gene. The association of the -42 C>T mutation with CTX resistance was confirmed to be significant (false discovery rate <0.05). To conclude, genome-wide analysis of homoplasy in combination with CTX resistance identifies the -42 C>T mutation of the ampC promotor as significantly associated with CTX resistance and underlines the role of recurrent mutations in the spread of antibiotic resistance.

Comparative Performance Testing of Respirator versus Surgical Mask Using a Water Droplet Spray Model

BACKGROUND

During the SARS-CoV-2 pandemic, there was shortage of the standard respiratory protective equipment (RPE). The aim of this study was to develop a procedure to test the performance of alternative RPEs used in the care of COVID-19 patients.

METHODS

A laboratory-based test was developed to compare RPEs by total inward leakage (TIL). We used a crossflow nebulizer to produce a jet spray of 1-100 µm water droplets with a fluorescent marker. The RPEs were placed on a dummy head and sprayed at distances of 30 and 60 cm. The outcome was determined as the recovery of the fluorescent marker on a membrane filter placed on the mouth of the dummy head.

RESULTS

At 30 cm, a type IIR surgical mask gave a 17.7% lower TIL compared with an FFP2 respirator. At 60 cm, this difference was similar, with a 21.7% lower TIL for the surgical mask compared to the respirator. When adding a face shield, the TIL at 30 cm was further reduced by 9.5% for the respirator and 16.6% in the case of the surgical mask.

CONCLUSIONS

A safe, fast and very sensitive test method was developed to assess the effectiveness of RPE by comparison under controlled conditions.

Antibiotic use and prescription and its effects on Enterobacteriaceae in the gut in children with mild respiratory infections in Ho Chi Minh City, Vietnam. A prospective observational outpatient study

BACKGROUND AND OBJECTIVES

Treatment guidelines do not recommend antibiotic use for acute respiratory infections (ARI), except for streptococcal pharyngitis/tonsillitis and pneumonia. However, antibiotics are prescribed frequently for children with ARI, often in absence of evidence for bacterial infection. The objectives of this study were 1) to assess the appropriateness of antibiotic prescriptions for mild ARI in paediatric outpatients in relation to available guidelines and detected pathogens, 2) to assess antibiotic use on presentation using questionnaires and detection in urine 3) to assess the carriage rates and proportions of resistant intestinal Enterobacteriaceae before, during and after consultation.

MATERIALS AND METHODS

Patients were prospectively enrolled in Children's Hospital 1, Ho Chi Minh City, Vietnam and diagnoses, prescribed therapy and outcome were recorded on first visit and on follow-up after 7 days. Respiratory bacterial and viral pathogens were detected using molecular assays. Antibiotic use before presentation was assessed using questionnaires and urine HPLC. The impact of antibiotic usage on intestinal Enterobacteriaceae was assessed with semi-quantitative culture on agar with and without antibiotics on presentation and after 7 and 28 days.

RESULTS

A total of 563 patients were enrolled between February 2009 and February 2010. Antibiotics were prescribed for all except 2 of 563 patients. The majority were 2nd and 3rd generation oral cephalosporins and amoxicillin with or without clavulanic acid. Respiratory viruses were detected in respiratory specimens of 72.5% of patients. Antibiotic use was considered inappropriate in 90.1% and 67.5%, based on guidelines and detected pathogens, respectively. On presentation parents reported antibiotic use for 22% of patients, 41% of parents did not know and 37% denied antibiotic use. Among these three groups, six commonly used antibiotics were detected with HPLC in patients' urine in 49%, 40% and 14%, respectively. Temporary selection of 3rd generation cephalosporin resistant intestinal Enterobacteriaceae during antibiotic use was observed, with co-selection of resistance to aminoglycosides and fluoroquinolones.

CONCLUSIONS

We report overuse and overprescription of antibiotics for uncomplicated ARI with selection of resistant intestinal Enterobacteriaceae, posing a risk for community transmission and persistence in a setting of a highly granular healthcare system and unrestricted access to antibiotics through private pharmacies.

REGISTRATION

This study was registered at the International Standard Randomised Controlled Trials Number registry under number ISRCTN32862422: http://www.isrctn.com/ISRCTN32862422.

Development of an algorithm to discriminate between plasmid- and chromosomal-mediated AmpC β-lactamase production in Escherichia coli by elaborate phenotypic and genotypic characterization

OBJECTIVES

AmpC-β-lactamase production is an under-recognized antibiotic resistance mechanism that renders Gram-negative bacteria resistant to common β-lactam antibiotics, similar to the well-known ESBLs. For infection control purposes, it is important to be able to discriminate between plasmid-mediated AmpC (pAmpC) production and chromosomal-mediated AmpC (cAmpC) hyperproduction in Gram-negative bacteria as pAmpC requires isolation precautions to minimize the risk of horizontal gene transmission. Detecting pAmpC in Escherichia coli is challenging, as both pAmpC production and cAmpC hyperproduction may lead to third-generation cephalosporin resistance.

METHODS

We tested a collection of E. coli strains suspected to produce AmpC. Elaborate susceptibility testing for third-generation cephalosporins, WGS and machine learning were used to develop an algorithm to determine ampC genotypes in E. coli. WGS was applied to detect pampC genes, cAmpC hyperproducers and STs.

RESULTS

In total, 172 E. coli strains (n=75 ST) were divided into a training set and two validation sets. Ninety strains were pampC positive, the predominant gene being blaCMY-2 (86.7%), followed by blaDHA-1 (7.8%), and 59 strains were cAmpC hyperproducers. The algorithm used a cefotaxime MIC value above 6 mg/L to identify pampC-positive E. coli and an MIC value of 0.5 mg/L to discriminate between cAmpC-hyperproducing and non-cAmpC-hyperproducing E. coli strains. Accuracy was 0.88 (95% CI=0.79-0.94) on the training set, 0.79 (95% CI=0.64-0.89) on validation set 1 and 0.85 (95% CI=0.71-0.94) on validation set 2.

CONCLUSIONS

This approach resulted in a pragmatic algorithm for differentiating ampC genotypes in E. coli based on phenotypic susceptibility testing.

Community-level consumption of antibiotics according to the AWaRe (Access, Watch, Reserve) classification in rural Vietnam

Objectives

To review community-level consumption of antibiotics in rural Vietnam, according to the WHO Access, Watch, Reserve (AWaRe) classification of 2019, and identify factors associated with the choice of these antibiotics.

Methods

In this cross-sectional study, data on antibiotic purchases were collected through a customer exit survey of 20 community antibiotic suppliers in Ba Vi District, Hanoi, between September 2017 and July 2018. Antibiotic consumption was estimated through the number of antibiotic encounters, the number of DDDs supplied and the number of treatment days (DOTs) with antibiotics, and analysed according to the AWaRe classification. The factors associated with watch-group antibiotic supply were identified through multivariable logistic regression analysis.

Results

In total, there were 1342 antibiotic encounters, with access-group antibiotics supplied in 792 encounters (59.0%), watch-group antibiotics supplied in 527 encounters (39.3%) and not-recommended antibiotics supplied in 23 encounters (1.7%). No reserve-group antibiotics were supplied. In children, the consumption of watch-group antibiotics dominated in all three measures (54.8% of encounters, 53.0% of DOTs and 53.6% of DDDs). Factors associated with a higher likelihood of watch-group antibiotic supply were: private pharmacy (OR, 4.23; 95% CI, 2.8–6.38; P < 0.001), non-prescription antibiotic sale (OR, 2.62; 95% CI, 1.78–3.87; P < 0.001) and children (OR, 2.56; 95% CI, 1.84–3.55; P < 0.001).

Conclusions

High consumption of watch-group antibiotics was observed, especially for use in children. The frequent supply of watch-group antibiotics at private pharmacies reconfirms the need for implementing pharmacy-targeted interventions in Vietnam.

Eradication of Staphylococcus aureus colonization by chronic use of mupirocin in patients on home parenteral nutrition

OBJECTIVES

Although in other groups Staphylococcus aureus eradication has proven to be an effective infection prevention measure, to our knowledge, no such studies have been performed in patients on home parenteral nutrition (HPN). The aim of this study was to investigate the efficacy of chronic nasal mupirocin use on S. aureus eradication and prevention of catheter related infections in patients on HPN.

METHODS

This was a cohort study with data collected from adult patients on HPN who were screened for S. aureus carriage. In case of carriage, the patient was instructed to apply mupirocin nasal ointment monthly. Outcomes were the percentage of successful S. aureus eradication and the effect on the incidence of catheter-related infections and development of mupirocin resistance.

RESULTS

S. aureus nasal carriage was found in 54% of the patients. Eradication was successful in 66% (70 of 106) of patients treated with mupirocin. Overall S. aureus catheter-related infection rates decreased by 50% (P = 0.02). The decrease was mostly due to a drop in central line-associated bloodstream infection (CLABSI) rates (0.26versus 0.1 per 1000 central venous catheter days; P = 0.04). The overall CLABSI rates decreased as well (incidence ratio rate, 0.43; 95% confidence interval. 0.24-0.76; P < 0.01). Low-level mupirocin resistance was observed in four patients.

CONCLUSIONS

Findings from the present study highlighted the potential usefulness of mupirocin ointment prophylaxis to establish S. aureus eradication in patients on HPN. However, awareness for the development of mupirocin resistance is prudent. Further research needs to be carried out to validate these findings.

Minocycline treatment for pulmonary Mycobacterium avium complex disease based on pharmacokinetics/pharmacodynamics and Bayesian framework mathematical models

OBJECTIVES

Our aim was to identify the pharmacokinetic/pharmacodynamic parameters of minocycline in the hollow-fibre system (HFS) model of pulmonary Mycobacterium avium complex (MAC) and to identify the optimal clinical dose.

METHODS

Minocycline MICs for 55 MAC clinical isolates from the Netherlands were determined. We also co-incubated primary isolated macrophages infected with MAC with minocycline. Next, we performed a 28 day HFS-MAC model dose-response study in which we mimicked pulmonary concentration-time profiles achieved in patients. The HFS-MAC model was sampled at intervals to determine the minocycline pharmacokinetics and MAC burden. We identified the AUC0-24/MIC ratios associated with 1.0 log10 cfu/mL kill below day 0 (stasis), defined as a bactericidal effect. We then performed 10000 Monte Carlo experiments to identify the optimal dose for a bactericidal effect in patients.

RESULTS

The MIC for 50% and 90% of cumulative clinical isolates was 8 and 64 mg/L, respectively. Minocycline decreased MAC bacterial burden below stasis in primary isolated macrophages. In the HFS-MAC model, minocycline achieved a microbial kill of 3.6 log10 cfu/mL below stasis. The AUC0-24/MIC exposure associated with a bactericidal effect was 59. Monte Carlo experiments identified a minocycline susceptibility MIC breakpoint of 16 mg/L. At this proposed breakpoint, the clinical dose of 200 mg/day achieved the bactericidal effect exposure target in ∼50% of patients, while 400 mg/day achieved this in 73.6% of patients, in Monte Carlo experiments.

CONCLUSIONS

Minocycline at a dose of 400 mg/day is expected to be bactericidal. We propose a clinical trial for validation.

Every medicine is medicine; exploring inappropriate antibiotic use at the community level in rural Ghana

Background

Inappropriate antibiotic use is an important driver of antibiotic resistance. This study sought to explore inappropriate antibiotic use and confusing antibiotics with other medicines in Ghana using ethnomethodology research approach.

Methods

This was an explorative study involving 15 in-depth interviews among health professionals and private dispensers and eight focus group discussions among 55 community members. Qualitative data were coded using Nvivo 12, thematically analysed and presented as narratives with quotes to support the findings.

Results

Self-medication was common and antibiotics were used to treat specific diseases but respondents were not aware these were ‘antibiotics’. Various antibiotics were used for indications that in principle do not require systemic antibiotics, like stomach ache and sores on the body. Antibiotics, in particular tetracycline and metronidazole, were poured into “akpeteshie” (local gin) to treat hernia and perceived stomach sores (stomach ulcer). These practices were copied/learnt from various sources like over-the-counter medicine sellers, family, friends, radio/television, drug peddlers, pharmacies and doctors. Medicines in capsules were referred to as ‘topaye’ or ‘abombelt’ in Twi (local dialect) and perceived to treat pain associated with diseases. Antibiotics in capsules were described with colours which appeared confusing as some capsules with different drugs in them have similar colours.

Conclusion

Inappropriate antibiotic use were influenced by general lack of knowledge on antibiotics and identification of antibiotics by colours of capsules which leads to confusion and could lead to inappropriate antibiotic use. There is the need for public health education on appropriate antibiotic use and standardization of appearance of antibiotics and other drugs to optimize use.

A bedaquiline/clofazimine combination regimen might add activity to the treatment of clinically relevant non-tuberculous mycobacteria

BACKGROUND

Non-tuberculous mycobacteria (NTM) infections are hard to treat. New antimicrobial drugs and smarter combination regimens are needed.

OBJECTIVES

Our aim was to determine the in vitro activity of bedaquiline against NTM and assess its synergy with established antimycobacterials.

METHODS

We determined MICs of bedaquiline for clinically relevant NTM species and Mycobacterium tuberculosis by broth microdilution for 30 isolates. Synergy testing was performed using the chequerboard method for 22 reference strains and clinical isolates of Mycobacterium abscessus (MAB) and Mycobacterium avium complex (MAC). Time-kill kinetics (TK) assays with resistance monitoring of bedaquiline alone and combined with clofazimine were performed for MAB CIP 104536 and M. avium ATCC 700898; bedaquiline/clarithromycin combinations were evaluated against M. avium ATCC 700898. Interactions were assessed for TK experiments based on Bliss independence.

RESULTS

Bedaquiline had modest activity against tested NTM, with MICs between <0.007 and 1 mg/L. Bedaquiline showed no interaction with tested drugs against MAB or MAC. Lowest mean fractional inhibitory concentration index (FICI) values were 0.79 with clofazimine for MAB and 0.97 with clofazimine and 0.82 with clarithromycin for MAC. In TK assays, bedaquiline showed a bacteriostatic effect. Clofazimine extended the bacteriostatic activity of bedaquiline against MAB and yielded a slight bactericidal effect against M. avium. The bedaquiline/clofazimine combination slowed emergence of bedaquiline resistance for M. avium but promoted it for MAB. Relative to Bliss independence, bedaquiline/clofazimine showed synergistic interaction over time for MAB and no interaction for M. avium and bedaquiline/clarithromycin showed antagonistic interaction for M. avium.

CONCLUSIONS

Following these in vitro data, a bedaquiline/clofazimine combination might add activity to MAB and MAC treatment. The bedaquiline/clarithromycin combination might have lower activity compared with bedaquiline alone for MAC treatment.

Burden of disease and economic impact of human Streptococcus suis infection in Viet Nam

BACKGROUND

Streptococcus suis is a zoonotic disease mainly affecting men of working age and can result in death or long-term sequelae, including severe hearing loss and vestibular dysfunction. We aimed to quantify the burden of disease and economic impact of this infection in Viet Nam.

METHODS

The annual disease incidence for the period 2011-2014 was estimated based on surveillance data using a multiple imputation approach. We calculated disease burden in disability-adjusted life years (DALYs) and economic costs using an incidence-based approach from a patient's perspective and including direct and indirect impacts of S. suis infection and its long-term sequelae.

RESULTS

The estimated annual incidence rate was 0.318, 0.324, 0.255 and 0.249 cases per 100 000 population in 2011, 2012, 2013 and 2014, respectively. The corresponding DALYs lost were 1832, 1866, 1467 and 1437. The mean direct cost per episode was US$1635 (95% confidence interval 1352-1923). The annual direct cost was US$370 000-500 000 and the indirect cost was US$2.27-2.88 million in this time period.

CONCLUSIONS

This study showed a large disease burden and high economic impact of S. suis infection and provides important data for disease monitoring and control.

Evaluation of Prolonged vs Short Courses of Antibiotic Prophylaxis Following Ear, Nose, Throat, and Oral and Maxillofacial Surgery: A Systematic Review and Meta-analysis

Importance

Antibiotic prophylaxis is widely used after surgical procedures operating on the mucosal tissues of the aerodigestive tract, but the optimal duration of these prophylactic therapies is often unclear.

Objective

To compare short-course antibiotic prophylaxis (≤24 hours) vs extended-course antibiotic prophylaxis (≥72 hours) after ear, nose, throat, and oral and maxillofacial surgery.

Data Sources and Study Selection

Literature searches of PubMed were completed in October 2017 and included prospective trials that compared antibiotic prophylaxis courses of 24 hours or less vs 72 hours or more after ear, nose, throat, and oral and maxillofacial surgery. Some studies were also handpicked from reference lists of studies found with the initial search terms. All analysis was performed between September 2017 and October 2018.

Data Extraction and Synthesis

All review stages were conducted in consensus by 2 reviewers. Data extraction and study quality assessment were performed with the Cochrane data extraction form and the Cochrane risk of bias tool. Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were used for reporting. The fixed-effects Mantel-Haenszel method was used for meta-analysis.

Main Outcomes and Measures

Relative risk (RR) of surgical site infections, microbial origins of surgical site infections, adverse events, duration of hospital stay, and treatment costs.

Results

Included in the meta-analysis were 21 articles with a cumulative 1974 patients. In patients receiving 24 hours or shorter vs 72 hours or longer antibiotic prophylaxis regimens, no significant difference was found in the occurrence of postoperative infections in the pooled population (RR, 0.90; 95% CI, 0.67-1.19), or in the ear, nose, throat (RR, 0.89; 95% CI, 0.54-1.45), and oral and maxillofacial populations (RR, 0.88; 95% CI, 0.63-1.21), separately. No heterogeneity was observed overall or in the subgroups. Patients receiving extended-course antibiotic prophylaxis were significantly more likely to develop adverse events unrelated to the surgical site (RR, 2.40; 95% CI, 1.20-3.54).

Conclusions and Relevance

No difference was found in the occurrence of postoperative infections between short-course and extended-course antibiotic prophylaxis after ear, nose, throat, and oral and maxillofacial surgery. Therefore, a short course of antibiotic prophylaxis is recommended unless documented conditions are present that would be best treated with an extended course. Using short-course antibiotics could avoid additional adverse events, antibiotic resistance development, and higher hospital costs. Future research should focus on identifying risk groups that might benefit from prolonged prophylaxis.

Recovery of aerobic gram-negative bacteria from the Copan Eswab transport system after long-term storage

We evaluated the Copan Eswab transport system for the quantitative recovery of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa after 1, 2, 3, 5, and 7 days of storage at room and refrigerator temperatures, and 7 and 30 days of storage at -80 °C and -20 °C using mono- and polymicrobial samples. The study was based on Clinical and Laboratory Standards Institute (CLSI) M40-A2 standard procedures on the quality control of microbiological transport systems. Eswab met the CLSI standards at room and refrigerator temperatures for all (combinations of) bacterial strains tested. At room temperature, after 24 h, bacterial growth was observed. At -80 °C, bacterial viability was maintained in monomicrobial samples; however, in polymicrobial samples, P. aeruginosa recovery was compromised. Storage at -20 °C was unsuitable. We conclude that specimens collected using Eswab should be transported to the laboratory as soon as possible. If transport or processing is delayed, specimens should preferably be stored at refrigerator temperatures.

Aetiology of acute febrile illness in children in a high malaria transmission area in West Africa

OBJECTIVES

Areas with declining malaria transmission in sub-Saharan Africa have recently witnessed important changes in the aetiology of childhood acute febrile illness (AFI). We describe the aetiology of AFI in a high malaria transmission area in rural Burkina Faso.

METHODS

In a prospective hospital-based diagnostic study, children aged 3 months to 15 years with AFI were recruited and assessed using a systematic diagnostic protocol, including blood cultures, whole blood PCR on a selection of bacterial pathogens, malaria diagnostics and a multiplex PCR on nasopharyngeal swabs targeting 21 viral and 4 bacterial respiratory pathogens.

RESULTS

A total of 589 children with AFI were enrolled from whom an infectious disease was considered in 575 cases. Acute respiratory tract infections, malaria and invasive bacterial infections (IBI) accounted for 179 (31.1%), 175 (30.4%) and 75 (13%) of AFI cases respectively; 16 (21.3%) of IBI cases also had malarial parasitaemia. A viral pathogen was demonstrated from the nasopharynx in 157 children (90.7%) with respiratory tract symptoms. Of all children with viral respiratory tract infections, 154 (92.4% received antibiotics, whereas no antibiotic was provided in 13 (17%) of IBI cases.

CONCLUSIONS

Viral respiratory infections are a common cause of childhood AFI in high malaria transmission areas, next to malaria and IBI. These findings highlight the importance of interventions to improve targeted treatment with antimicrobials. Most patients with viral infections received antibiotics unnecessarily, while a considerable number with IBI did not receive antibiotics.

Influenza A(H1N1)pdm09 but not A(H3N2) virus infection induces durable sero-protection: results from the Ha Nam Cohort

Background

The extent to which influenza recurrence depends upon waning immunity from prior infection is undefined. We used antibody titers of Ha-Nam cohort participants to estimate protection curves and decay trajectories.

Methods

Households (270) participated in influenza-like–illness (ILI) surveillance and provided blood at intervals spanning laboratory–confirmed virus transmission. Sera were tested in hemagglutination inhibition assay. Infection was defined as influenza virus-positive ILI and/or seroconversion. Median protective titers were estimated using scaled-logistic regression to model pretransmission titer against infection status in that season, limiting analysis to households with infection(s). Titers were modelled against month since infection using mixed-effects linear regression to estimate decay and when titers fell below protection thresholds.

Results

From December 2008–2012, 295 and 314 participants were infected with H1N1pdm09-like and A/Perth/16/09-like (H3N2Pe09) viruses, respectively. The proportion protected rose more steeply with titer for H1N1pdm09 than for H3N2Pe09, and estimated 50% protection titers were 19.6 and 37.3, respectively. Postinfection titers started higher against H3N2Pe09 but decayed more steeply than against H1N1pdm09. Seroprotection was estimated to be sustained against H1N1pdm09 but to wane by 8-months for H3N2Pe09.

Conclusions

Estimates indicate that infection induces durable seroprotection against H1N1pdm09 but not H3N2Pe09, which could in part account for the younger age of A(H1N1) versus A(H3N2) cases.

Determinants of Inappropriate Antibiotics Use in Rural Central Ghana Using a Mixed Methods Approach

Background: The consequences of antibiotic resistance are projected to be most severe in low and middle income countries with high infectious disease burden. This study examined determinants of inappropriate antibiotic use at the community level in rural Ghana.

Methods: An observational study involving qualitative and quantitative methods was conducted between July, 2016 and September, 2018 in Ghana. Two household surveys were conducted at two time points (2017 and 2018) among 1,100 randomly selected households over 1 year. The surveys focused on antibiotic use episodes in the past month. Four in-depth interviews and two focus group discussions were performed to further explain the survey results. Determinants of inappropriate antibiotic use were assessed using a mixed effect logistic regression analysis (multilevel analysis) to account for the clustered nature of data. We defined inappropriate antibiotic use as either use without prescription, not completing treatment course or non-adherence to instruction for use. Qualitative data were thematically analyzed.

Results: A total of 1,100 households was enrolled in which antibiotics were used in 585 (53.2%) households in the month prior to the surveys. A total of 676 (21.2%) participants out of 3,193 members from the 585 reportedly used antibiotics for 761 episodes of illness. Out of the 761 antibiotic use episodes, 659 (86.6%) were used inappropriately. Paying for healthcare without health insurance (Odds Ratio (OR): 2.10, 95% CI: 1.1–7.4, p-value: 0.026), not seeking healthcare from health centers (OR: 2.4, 95% CI: 1.2–5.0, p-value: 0.018), or pharmacies (OR: 4.6, 95% CI: 1.7–13.0, p-value: 0.003) were significantly associated with inappropriate antibiotic use. Socio-demographic characteristics were not significantly associated with inappropriate antibiotic use. However, the qualitative study described the influence of cost of medicines on inappropriate antibiotic use. It also revealed that antibiotic users with low socioeconomic status purchased antibiotics in installments which, could facilitate inappropriate use.

Conclusion: Inappropriate antibiotic use was high and influenced by out-of-pocket payment for healthcare, seeking healthcare outside health centers, pharmacies, and buying antibiotics in installments due to cost. To improve appropriate antibiotic use, there is the need for ministry of health and healthcare agencies in Ghana to enhance healthcare access and healthcare insurance, and to provide affordable antibiotics.

Prostate biopsy techniques and pre-biopsy prophylactic measures: variation in current practice patterns in the Netherlands

BACKGROUND

The clinical landscape of prostate biopsy (PB) is evolving with changes in procedures and techniques. Moreover, antibiotic resistance is increasing and influences the efficacy of pre-biopsy prophylactic regimens. Therefore, increasing antibiotic resistance may impact on clinical care, which probably results in differences between hospitals. The objective of our study is to determine the (variability in) current practices of PB in the Netherlands and to gain insight into Dutch urologists' perceptions of fluoroquinolone resistance and biopsy related infections.

METHODS

An online questionnaire was prepared using SurveyMonkey® platform and distributed to all 420 members of the Dutch Association of Urology, who work in 81 Dutch hospitals. Information about PB techniques and periprocedural antimicrobial prophylaxis was collected. Urologists' perceptions regarding pre-biopsy antibiotic prophylaxis in an era of antibiotic resistance was assessed. Descriptive statistical analysis was performed.

RESULTS

One hundred sixty-one responses (38.3%) were analyzed representing 65 (80.3%) of all Dutch hospitals performing PB. Transrectal ultrasound guided prostate biopsy (TRUSPB) was performed in 64 (98.5%) hospitals. 43.1% of the hospitals (also) used other image-guided biopsy techniques. Twenty-three different empirical prophylactic regimens were reported among the hospitals. Ciprofloxacin was most commonly prescribed (84.4%). The duration ranged from one pre-biopsy dose (59.4%) to 5 days extended prophylaxis. 25.2% of the urologists experienced ciprofloxacin resistance as a current problem in the prevention of biopsy related infections and 73.6% as a future problem.

CONCLUSIONS

There is a wide variation in practice patterns among Dutch urologists. TRUSPB is the most commonly used biopsy technique, but other image-guided biopsy techniques are increasingly used. Antimicrobial prophylaxis is not standardized and prolonged prophylaxis is common. The wide variation in practice patterns and lack of standardization underlines the need for evidence-based recommendations to guide urologists in choosing appropriate antimicrobial prophylaxis for PB in the context of increasing antibiotic resistance.

Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit

We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly neonatal MSSA carriage surveillance and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. Traditional clustering of MSSA isolates by spa typing and Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections. We investigated whether whole-genome sequencing (WGS) of MSSA surveillance would provide additional evidence for transmission. MSSA isolates from neonatal infections, carriage surveillance, and HCWs were subjected to WGS and bioinformatic analysis for identification and localization of high-quality single nucleotide polymorphisms, and in-depth analysis of subsets of isolates. By measuring the genetic diversity in background surveillance, we defined transmission-level relatedness and identified isolates that had been unjustly assigned to clusters based on MLVA, while spa typing was concordant but of insufficient resolution. Detailing particular subsets of isolates provided evidence that HCWs were involved in multiple outbreaks, yet it alleviated concerns about one particular HCW. The improved resolution and accuracy of genomic outbreak analyses substantially altered the view on outbreaks, along with apposite measures. Therefore, inclusion of the circulating background population has the potential to overcome current issues in genomic outbreak inference.