Community factors in the development of antibiotic resistance

Unraveling the determinants of antibiotic resistance evolution in farmland under fertilizations

Organic fertilization is a major driver potentiating soil antibiotic resistance in farmland. However, it remains unclear how bacterial antibiotic resistance evolves in fertilized soils and even spreads to crops. Compared with no fertilizer and commercial fertilizer treatments, organic fertilizers markedly increased the abundance of soil antibiotic resistance genes (ARGs) but the relatively weaker transfer of resistance genes from soil to crops. The introduction of organic fertilizers enriches the soil with nutrients, driving indigenous microorganisms towards a K-strategy. The pH, EC, and nutrients as key drivers influenced the ARGs abundance. The neutral (pH 7.2), low salt (TDS 1.4 %) and mesotrophic (carbon content 3.54 g/L) habitats similar to the soil environment conditioned by organic fertilizers. These environmental conditions clearly prolonged the persistence of resistant plasmids, and facilitated their dissemination to massive conjugators soil microbiome but not to plant endophytes. This suggested that organic fertilizers inhibited the spread of ARGs to crops. Moreover, the composition of conjugators showed differential selection of resistant plasmids by endophytes under these conditions. This study sheds light on the evolution and dissemination of antibiotic resistance in farmlands and can aid in the development of antimicrobial resistance control strategies in agriculture.

Landscape of global urban environmental resistome and its association with local socioeconomic and medical status

Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

Challenges in the distribution of antimicrobial medications in community dispensaries in Accra, Ghana

INTRODUCTION

The dispensation of medicines in some low- and middle-income countries is often carried out by private vendors operating under constrained conditions. The aim of this study was to understand the challenges reported by employees of dispensaries, specifically, chemical and herbal shops and pharmacies in Accra, Ghana. Our objectives were twofold: (1) to assess challenges faced by medicine vendors related to dispensing antimicrobials (antibiotic and antimalarial medications), and (2) to identify opportunities for improving their stewardship of antimicrobials.

METHODS

Data were collected in 79 dispensaries throughout Accra, in 2021, using a survey questionnaire. We used open-ended questions, grounded on an adapted socioecological model of public health, to analyze these data and determine challenges faced by respondents.

RESULTS

We identified multiple, interlocking challenges faced by medicine vendors. Many of these relate to challenges of antimicrobial stewardship (following evidence-based practices when dispensing medicines). Overall, medicine vendors frequently reported challenges at the Customer and Community levels. These included strained interactions with customers and the prohibitive costs of medications. The consequences of these challenges reverberated and manifested through all levels of the socioecological model of public health (Entity, Customer, Community, Global).

DISCUSSION

The safe and effective distribution of medications was truncated by strained interactions, often related to the cost of medicines and gaps in knowledge. While addressing these challenges requires multifaceted approaches, we identified several areas that, if intervened upon, could unlock the great potential of antimicrobal stewardship. The effective and efficient implementation of key interventions could facilitate efforts spearheaded by medicine vendors and leverage the benefits of their role as health educators and service providers.

CONCLUSION

Addressing barriers faced by medicine vendors would provide an opportunity to significantly improve the provision of medications, and ultimately population health. Such efforts will likely expand access to populations who may otherwise be unable to access medications and treatment in formal institutions of care such as hospitals. Our findings also highlight the broad range of care provided by shopkeepers and vendors at dispensaries. These findings suggest that the meaningful engagement of dispensaries as valued conduits of community health is a promising pathway for interventions aiming to improve antimicrobial stewardship.

Antibiotic overuse, poor antimicrobial stewardship, and low specificity of syndromic case management in a cross section of men with urethral discharge syndrome in Kampala, Uganda

OBJECTIVE

High prevalence of sexually transmitted infections (STIs) combined with poor antimicrobial stewardship are drivers of STI antimicrobial resistance (AMR) especially in resource-limited settings where syndromic case management (SCM) is the norm. We characterized patterns of antibiotic use prior to clinic attendance and study enrollment in Ugandan men with urethral discharge syndrome (UDS), evaluated in-clinic prescribing, and the performance characteristics of SCM.

METHODS

Participants were recruited from government clinics participating in an existing gonococcal surveillance program in Kampala, Uganda. Questionnaires including antimicrobial use prior to attendance, prior episodes of UDS, penile swabs, and blood samples were collected. Bivariable and multivariable logistic regression models were used to estimate odds ratios (OR) for preselected factors likely to be associated with antibiotic use. In-clinic antibiotic treatment data were extracted from clinical notes, and the performance of SCM against laboratory-based STI diagnoses was evaluated.

FINDINGS

Between October 2019 and November 2020, 100(40%) of 250 men with UDS reported taking antibiotics in the 14days prior to attending the clinic. Of these 210(84%) had at least one curable STI and 20% had a reactive point-of-care HIV test. Multivariable analysis demonstrated significant associations between recent antimicrobial use and duration of UDS symptoms <6 days (OR 2.98(95%CI 1.07,8.36), p = 0.038), and sex with women only (OR 0.08(95%CI 0.01,0.82),p = 0.038). The sensitivity of SCM ranged from 80.0% to 94.4%; specificity was low between 5.6% and 33.1%. The positive predictive value of SCM ranged from 2.4(95%CI 0.7,6.0) for trichomoniasis to 63.4(95%CI 56.5,69.9) for gonorrhea.

CONCLUSION

Pre-enrollment antibiotic use was common in this population at high risk of STI and HIV. Combined with the poor specificity of SCM for male UDS, extensive antibiotic use is a likely driver of STI-AMR in Ugandan men. Interventions to improve antimicrobial stewardship and deliver affordable diagnostics to augment SCM and decrease overtreatment of STI syndromes are required.

Occurrence and influencing factors of antibiotics and antibiotic resistance genes in sediments of the largest multi-habitat lakes in Northern China

Baiyangdian Lake is a typical and largest multi-habitat lake in the North plain of China. To understand the generation and transmission of antibiotics resistance genes (ARGs) in multi-habitat lakes, the contents of nutrients (TC, TOC, TN, TP and TS), heavy metals (Zn, Cr, Ni, Cu, Pb, As, Cd and Hg), 22 antibiotics, 16S-rRNA(16S), Class I integron (intI1) and 20 ARGs were determined. Samples were taken from the Fuhe river, river estuaries, reed marshes, living area, fish ponds and open water of Baiyangdian Lake. The results showed that quinolones were the main pollutants in six habitats, and the content range was ND-104.94 ng/g. Thereinto, aac (6') -IB, blaTEM-1, ermF, qnrA, qnrD, tetG, sul1, sul2 and tetM were detected in all the analyzed samples. The absolute abundance of sul1 was the highest (5.25 × 10⁵ copies/g-6.21 × 10⁷ copies/g) in most of the samples. In these different habitats, the abundance of antibiotics and ARGs in river estuary was the highest, and that in reed marshes was the lowest. There was a significant positive correlation between the abundance of heavy metals (Cu, Pb, Zn, Ni, Cd, Hg) and the absolute abundance of 11 ARGs (P < 0.01). Redundancy analysis showed that Cu, Zn, intI1, TP and macrolides were the important factors affecting the distribution of ARGs. Our finding provides a more likely driving and influencing factor for the transmission of ARGs in lakes with complex and diverse habitats.

Sustainable γ-cyclodextrin frameworks containing ultra-fine silver nanoparticles with enhanced antimicrobial efficacy

Cyclodextrin metal-organic frameworks (CD-MOF) are a class of biocompatible MOF with a great potential in drug delivery applications. Original CD-MOF crystals are fragile and large (0.2-1 mm), which are less useful in pharmaceutical applications. Cetyltrimethylammonium bromide and long chain poly(ethylene) glycol, used in size modulation to produce nanosized CD-MOF can compromise the biocompatibility, and physiochemical properties of CD-MOF as their complete removal from frameworks is difficult. To avoid the use of above-mentioned modulators, herein, we demonstrate the synthesis of nanosized CD-MOF using triethylamine (TEA) as a modulator to reduce their size to ~254 nm. The MOF characteristics such as crystal and chemical structure remain unaffected and the surface area of CD-MOF synthesised with TEA is measured 1075.5 m²/g, almost 50 % higher than those of synthesised using bulky modulators. The improved CD-MOF architecture utilized for the in-situ synthesis of silver nanoparticles resulted in enhanced antimicrobial efficacy tested against Staphylococcus aureus and Escherichia coli bacteria and Candida albicans fungus. And minimum inhibitory concentration (MIC) is recorded in the range of 31-15 μg/mL. Overall, the structural improvement in CD-MOF supported with thorough comparative investigations and enhanced antimicrobial efficacy could be very helpful in further establishing them in biomedicine field.

Multidrug-Resistant Uropathogens Causing Community Acquired Urinary Tract Infections among Patients Attending Health Facilities in Mwanza and Dar es Salaam, Tanzania

In low-income countries, the empirical treatment of urinary tract infections (UTIs) without laboratory confirmation is very common, especially in primary health facilities. This scenario often leads to unnecessary and ineffective antibiotic prescriptions, prompting the emergence and spread of antimicrobial resistance. We conducted this study to examine the antibiogram of uropathogens causing community-acquired urinary tract infections among outpatients attending selected health facilities in Tanzania.

METHOD

This was a cross-sectional health centre-based survey conducted for a period of five months, from July to November 2021, in the Mwanza and Dar es Salaam regions in Tanzania. We enrolled consecutively a total of 1327 patients aged between 2 and 96 years with a median [IQR] age of 28 [22-39] from Dar es Salaam (n = 649) and Mwanza (n = 678).

RESULTS

Significant bacteriuria was observed in 364 (27.4% [95%CI: 25.0-29.9]) patients, from whom 412 urinary pathogens were isolated. Gram-negative bacteria contributed to 57.8% (238) of the 412 uropathogens isolated, of which 221 were Enterobacterales, and Escherichia coli was the most frequent. Staphylococcus aureus and Staphylococcus haemolyticus were the most frequently isolated among Gram-positive uropathogens (n = 156). Generally, resistance among Escherichia coli ranged from 0.7% (meropenem) to 86.0% (ampicillin) and from 0.0% (meropenem) to 75.6% (ampicillin) in other Enterobacterales. Moreover, about 45.4% (108) of Enterobacterales and 22.4% (35) of Gram-positive bacteria were multidrug resistant (MDR), p = 0.008. We observed 33 MDR patterns among Gram-negative bacteria, predominantly AMP-CIP-TCY (23/108; 21.3%), and 10 MDR patterns among Gram-positive bacteria, most commonly CIP-GEN-TCY (22/35; 62.9%).

CONCLUSION

the presence of a high number of wide-ranging uropathogens that are multidrug resistant to a variety of antibiotics points to the need to strengthen the laboratory diagnostic systems for the regular surveillance of the antimicrobial resistance of uropathogens to guide and update empirical treatment guidelines.

Respiratory microorganisms in acute pharyngitis patients: Identification, antibiotic prescription patterns and appropriateness, and antibiotic resistance in private primary care, central Malaysia

Acute pharyngitis (AP) is a common reason for private primary care consultations, thus providing an avenue for widespread antibiotic intake among the community. However, there is limited data on the antibiotic prescription appropriateness and resistance information in the Malaysian private primary care setting, therefore, this study aimed to investigate the prevalence of isolated viruses and bacteria, antibiotic resistance patterns, antibiotic prescription patterns and appropriateness by general practitioners (GPs) and factors affecting antibiotic resistance and antibiotic prescription patterns. To investigate, a cross-sectional study was conducted among 205 patients presenting with AP symptoms at private primary care clinics in central Malaysia from 3rd January 2016 to 30th November 2016. Throat swabs were collected from 205 AP patients for two purposes: (i) the detection of four common respiratory viruses associated with AP via reverse-transcription real-time PCR (qRT-PCR); and (ii) bacterial identification using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Bacterial isolates were then subjected to antibiotic susceptibility screening and McIsaac scoring was calculated post-prescription based on GP selection of criteria. Generalized estimating equations analysis with multiple logistic regression was conducted to identify factors associated with presence of virus and antibiotic prescription. The results showed that 95.1% (195/205) of patients had at least one of the four viruses, with rhinovirus (88.5%) being the most prevalent, followed by adenovirus (74.9%), influenza A virus (4.6%) and enterovirus (2.1%). A total of 862 non-repetitive colonies were isolated from the culture of throat swabs from 205 patients who were positive for bacteria. From a total of 22 genera, Streptococcus constitutes the most prevalent bacteria genus (40.9%), followed by Neisseria (20%), Rothia (13.0%), Staphylococcus (11%) and Klebsiella (4.9%). Only 5 patients carried group A beta-hemolytic streptococci (GABHS). We also report the presence of vancomycin-resistant S. aureus or VRSA (n = 9, 10.1%) among which one isolate is a multidrug-resistant methicillin-resistant S. aureus (MDR-MRSA), while 54.1% (n = 111) were found to carry at least one antibiotic-resistant bacteria species. Application of the McIsaac scoring system indicated that 87.8% (n = 180) of patients should not be prescribed antibiotics as the majority of AP patients in this study had viral pharyngitis. The antibiotic prescription appropriateness by applying post-prescription McIsaac scoring was able to rule out GABHS pharyngitis in this sample with a GABHS culture-positive sensitivity of 40% (n = 2/5) and specificity of 90% (180/200). In conclusion, antibiotic-resistant throat isolates and over-prescription of antibiotics were observed and McIsaac scoring system is effective in guiding GPs to determine occurrences of viral pharyngitis to reduce unnecessary antibiotic prescription.

Evidence of Community-Wide Spread of Multi-Drug Resistant Escherichia coli in Young Children in Lusaka and Ndola Districts, Zambia

Increased antimicrobial resistance (AMR) has been reported for pathogenic and commensal Escherichia coli (E. coli), hampering the treatment, and increasing the burden of infectious diarrhoeal diseases in children in developing countries. This study focused on exploring the occurrence, patterns, and possible drivers of AMR E. coli isolated from children under-five years in Zambia. A hospital-based cross-sectional study was conducted in the Lusaka and Ndola districts. Rectal swabs were collected from 565 and 455 diarrhoeic and healthy children, respectively, from which 1020 E. coli were cultured and subjected to antibiotic susceptibility testing. Nearly all E. coli (96.9%) were resistant to at least one antimicrobial agent tested. Further, 700 isolates were Multi-Drug Resistant, 136 were possibly Extensively-Drug Resistant and nine were Pan-Drug-Resistant. Forty percent of the isolates were imipenem-resistant, mostly from healthy children. A questionnaire survey documented a complex pattern of associations between and within the subgroups of the levels of MDR and socio-demographic characteristics, antibiotic stewardship, and guardians’ knowledge of AMR. This study has revealed the severity of AMR in children and the need for a community-specific-risk-based approach to implementing measures to curb the problem.

Fate of antibiotic resistant genes in wastewater environments and treatment strategies - A review

Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) have emerged in aquatic environments through the discharge of large amounts of antibiotics into wastewater. Well-designed wastewater treatment plants (WWTPs) with effective treatment processes are essential to prevent the release of ARGs directly into the environment. Although some systematic sequential treatment methods are used to remove ARGs, considerable gaps in removal mechanisms will be discussed. Therefore, deep analysis and discussion of various treatment methods are required to understand the ARGs removal mechanisms. In this manuscript, the role of antibiotics and the resistance mechanism of ARB are discussed in depth. In addition, the fate of ARGs in an aquatic environment and detection methods are compared comprehensively and discussed. In particular, the advantages and disadvantages of various methods are summarized and reviewed critically. Finally, combined technologies, such as advanced oxidation process (AOP) with biochemical systems, membrane separation with electrochemical AOP, ultrafiltration (UF) membrane coupled with photocatalytic treatment, and UF membrane separation coupled with sonication, are introduced. Overall, low-energy anaerobic treatment reactors with any of the above combined treatments might reduce the discharge of large quantities of ARGs into the environment. Finally, this review provides valuable insights for better ARG removal technologies by introducing combined effective treatment strategies used in real WWTPs.

Mobile Colistin Resistance (mcr) Genes in Cats and Dogs and Their Zoonotic Transmission Risks

Background: Pets, especially cats and dogs, represent a great potential for zoonotic transmission, leading to major health problems. The purpose of this systematic review was to present the latest developments concerning colistin resistance through mcr genes in pets. The current study also highlights the health risks of the transmission of colistin resistance between pets and humans. Methods: We conducted a systematic review on mcr-positive bacteria in pets and studies reporting their zoonotic transmission to humans. Bibliographic research queries were performed on the following databases: Google Scholar, PubMed, Scopus, Microsoft Academic, and Web of Science. Articles of interest were selected using the PRISMA guideline principles. Results: The analyzed articles from the investigated databases described the presence of mcr gene variants in pets including mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-8, mcr-9, and mcr-10. Among these articles, four studies reported potential zoonotic transmission of mcr genes between pets and humans. The epidemiological analysis revealed that dogs and cats can be colonized by mcr genes that are beginning to spread in different countries worldwide. Overall, reported articles on this subject highlight the high risk of zoonotic transmission of colistin resistance genes between pets and their owners. Conclusions: This review demonstrated the spread of mcr genes in pets and their transmission to humans, indicating the need for further measures to control this significant threat to public health. Therefore, we suggest here some strategies against this threat such as avoiding zoonotic transmission.

Knowledge of Antimicrobial Resistance and Associated Factors Among Health Professionals at the University of Gondar Specialized Hospital: Institution-Based Cross-Sectional Study

Background

Antimicrobial resistance is one of the many health challenges worldwide, particularly in resource-limited countries like Ethiopia. Increasing knowledge of health professionals can reduce the occurrence of antimicrobial resistance. In this study, we determined the antimicrobial resistance knowledge and examined the associated factors among the University of Gondar Hospital health professionals.

Methods

An institution-based cross-sectional survey was carried out. The samples were randomly recruited. Statistical analysis was performed by using the statistical package for social sciences (SPSS) version 20 after entering the data using Epidemiological information (Epi-Info). To identify associated factors, the authors executed binary logistic regression and multivariate analysis wherein the statistical significance was decided at p < 0.05.

Results

Four hundred and twelve health professionals with ages ranging from 20-60 years and mean age of 29.9 years took part in the study. Fifty-three-point-four percent of participants were males. The majority of the total respondents (84.7%, 95% CI: 80.08–88.30) had good knowledge of antimicrobial resistance. It was found that being male (AOR = 1.94, 95% CI: 1.10, 3.52), a work experience of 6–10 years (AOR = 2.45, 95% CI: 1.28, 4.68), having 30–38working hours per week (AOR = 3.93, 95% CI: 1.38, 5.11), and antibiotic intake (AOR = 3.71, 95% CI: 1.75, 7.87) were significant factors of antimicrobial resistance knowledge.

Conclusion

In the current study, about 84.5% of health professionals had good knowledge of antimicrobial resistance. Reducing working hours per week and increasing the experience of workers are recommended to increase the knowledge on AMR.

Colorectal Cancer: A Review of Carcinogenesis, Global Epidemiology, Current Challenges, Risk Factors, Preventive and Treatment Strategies

Colorectal cancer (CRC) is the second most deadly cancer. Global incidence and mortality are likely to be increased in the coming decades. Although the deaths associated with CRC are very high in high-income countries, the incidence and fatalities related to CRC are growing in developing countries too. CRC detected early is entirely curable by surgery and subsequent medications. However, the recurrence rate is high, and cancer drug resistance increases the treatment failure rate. Access to early diagnosis and treatment of CRC for survival is somewhat possible in developed countries. However, these facilities are rarely available in developing countries. Highlighting the current status of CRC, its development, risk factors, and management is crucial in creating public awareness. Therefore, in this review, we have comprehensively discussed the current global epidemiology, drug resistance, challenges, risk factors, and preventive and treatment strategies of CRC. Additionally, there is a brief discussion on the CRC development pathways and recommendations for preventing and treating CRC.

Detection of Multidrug-Resistant Enterobacterales-From ESBLs to Carbapenemases

Multidrug-resistant Enterobacterales (MDRE) are an emerging threat to global health, leading to rising health care costs, morbidity and mortality. Multidrug-resistance is commonly caused by different β-lactamases (e.g., ESBLs and carbapenemases), sometimes in combination with other resistance mechanisms (e.g., porin loss, efflux). The continuous spread of MDRE among patients in hospital settings and the healthy population require adjustments in healthcare management and routine diagnostics. Rapid and reliable detection of MDRE infections as well as gastrointestinal colonization is key to guide therapy and infection control measures. However, proper implementation of these strategies requires diagnostic methods with short time-to-result, high sensitivity and specificity. Therefore, research on new techniques and improvement of already established protocols is inevitable. In this review, current methods for detection of MDRE are summarized with focus on culture based and molecular techniques, which are useful for the clinical microbiology laboratory.

Multi-country cross-sectional study of colonization with multidrug-resistant organisms: protocol and methods for the Antibiotic Resistance in Communities and Hospitals (ARCH) studies

BACKGROUND

Antimicrobial resistance is a global health emergency. Persons colonized with multidrug-resistant organisms (MDROs) are at risk for developing subsequent multidrug-resistant infections, as colonization represents an important precursor to invasive infection. Despite reports documenting the worldwide dissemination of MDROs, fundamental questions remain regarding the burden of resistance, metrics to measure prevalence, and determinants of spread. We describe a multi-site colonization survey protocol that aims to quantify the population-based prevalence and associated risk factors for colonization with high-threat MDROs among community dwelling participants and patients admitted to hospitals within a defined population-catchment area.

METHODS

Researchers in five countries (Bangladesh, Chile, Guatemala, Kenya, and India) will conduct a cross-sectional, population-based prevalence survey consisting of a risk factor questionnaire and collection of specimens to evaluate colonization with three high-threat MDROs: extended-spectrum cephalosporin-resistant Enterobacteriaceae (ESCrE), carbapenem-resistant Enterobacteriaceae (CRE), and methicillin-resistant Staphylococcus aureus (MRSA). Healthy adults residing in a household within the sampling area will be enrolled in addition to eligible hospitalized adults. Colonizing isolates of these MDROs will be compared by multilocus sequence typing (MLST) to routinely collected invasive clinical isolates, where available, to determine potential pathogenicity. A colonizing MDRO isolate will be categorized as potentially pathogenic if the MLST pattern of the colonizing isolate matches the MLST pattern of an invasive clinical isolate. The outcomes of this study will be estimates of the population-based prevalence of colonization with ESCrE, CRE, and MRSA; determination of the proportion of colonizing ESCrE, CRE, and MRSA with pathogenic characteristics based on MLST; identification of factors independently associated with ESCrE, CRE, and MRSA colonization; and creation an archive of ESCrE, CRE, and MRSA isolates for future study.

DISCUSSION

This is the first study to use a common protocol to evaluate population-based prevalence and risk factors associated with MDRO colonization among community-dwelling and hospitalized adults in multiple countries with diverse epidemiological conditions, including low- and middle-income settings. The results will be used to better describe the global epidemiology of MDROs and guide the development of mitigation strategies in both community and healthcare settings. These standardized baseline surveys can also inform future studies seeking to further characterize MDRO epidemiology globally.

Sortase A (SrtA) inhibitors as an alternative treatment for superbug infections

Virulence factor, sortase A (SrtA), has crucial roles in the pathogenesis of Gram-positive superbugs. SrtA is a bacterial cell membrane enzyme that anchors crucial virulence factors to the cell wall surface of Gram-positive bacteria. SrtA is not necessary for bacterial growth and viability and is conveniently accessible in the cell membrane; therefore, it is an ideal target for antivirulence drug development. In this review, we focus on antimicrobial resistance (AMR)-expressing bacteria and SrtA as a potential target for overcoming AMR. The mechanism of action of SrtA and its inhibition by various types of inhibitors, such as synthetic small molecules, peptides, and natural products, are provided. Future SrtA research perspectives for alternative drug development to antibiotics are also proposed.

Procalcitonin in clinical practice: from diagnosis of sepsis to antibiotic therapy

A diagnostic algorithm that allows for the rapid identification of sepsis and possibly guides the appropriate antimicrobial therapy application is the cornerstone to obtaining effective treatment and better results. The use of emerging surrogate markers could significantly improve clinical practice, but the validity and clinical utility have been proved only for very few of them, and their availability in clinical routine is limited. For this purpose, numerous scientific evidence has indicated procalcitonin as a marker linked to sepsis and its evolution. This review aims to retrace the main evidence relating to the use of procalcitonin in sepsis. We analyzed the primary studies in the literature and the existing meta-analysis evaluating the behavior of procalcitonin as a marker of bacterial sepsis, its prognostic power, and its ability to influence antibiotic therapy. Recent evidence has suggested that procalcitonin could be an efficient marker for diagnosing sepsis and its therapeutic management in many types of patients. The choice of the appropriate timing to initiate and suspend antibiotic therapy, with obvious clinical advantages, the favorable effects could also include reducing health costs, both avoiding the administration of inappropriate antibiotic therapies, and reducing the duration of hospitalization. Moreover, limited studies reported high procalcitonin levels in coronavirus disease 2019 patients with a worse prognosis. Despite the considerable evidence in favor of the potential of procalcitonin as an index for managing septic patients, there are conflicting data that deserve specific and detailed studies.

Discontinuation of Antibiotics in Patients with Neurological Conditions - A Study on the Impact of an Antimicrobial Stewardship Program (ASP) in a Tertiary Institution

BACKGROUND

Up to 50% of antibiotics are prescribed either unnecessarily or inappropriately in most hospitals worldwide. In the largest tertiary hospital in Singapore, patients with neurological conditions were often initiated on antibiotics for change in mental state or isolated fevers. We hypothesize that Antimicrobial Stewardship Program (ASP) interventions to discontinue empirical antibiotics in neurological patients with no clinical evidence of bacterial infection are safe. The aim of this study was to compare clinical impact and safety outcomes of ASP interventions between accepted and rejected groups.

METHODS

A retrospective review of the ASP database was conducted for all patients admitted to the neurology department in Singapore General Hospital between January 2014 and December 2017. Interventions were followed up and patients were classified into two intervention groups, the accepted and rejected groups. Demographic data, age-adjusted Charlson co-morbidity index, duration of antibiotic therapy, length of hospital stay post-ASP intervention (PLOS), infection-related readmissions and mortality were compared between the two groups. Data were expressed as mean ± standard deviation for continuous variables, and unpaired Student's t-test was performed to determine intergroup differences between mean values.

RESULTS

The ASP team recommended 184 interventions, with an overall acceptance rate of 82.6% (152/184). There was no significant difference in demographics and age-adjusted Charlson co-morbidity index between the two groups. The accepted group had a shorter duration of therapy by 1.67 days (4.99±2.50 days vs. 6.66±2.34 days; P<0.01) and a shorter PLOS by 2 days, although this was not statistically significant (22.5±22.2 days vs. 24.5±51.4 days; P=0.83). There were no significant differences between the two groups in 14-day mortality and readmission rates.

CONCLUSION

In neurological patients with no clinical evidence of bacterial infections, ASP interventions to discontinue empirical antibiotics were not associated with increased mortality and readmissions but were associated with significant reduction in duration of therapy.

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.

Characterization of SCCmec, spa types and Multi Drug Resistant of methicillin-resistant Staphylococcus aureus isolates among inpatients and outpatients in a referral hospital in Shiraz, Iran

Objectives

Molecular typing such as spa typing is used to control and prevent Staphylococcus aureus widespread in hospitals and communities. Hence, the aim of this study was to find the most common types of S. aureus strain circulating in Shiraz via spa and SCCmec typing methods.

Results

Total of 159 S. aureus isolates were collected from two tertiary hospitals in Shiraz. Isolates were identified by biochemical tests. Antimicrobial susceptibility tests were performed by standard disk diffusion method and then genetic analysis of bacteria was performed using SCCmec and spa typing. In this study 31.4% of the isolates were methicillin-resistant S. aureus. The majority of isolates were SSCmec type III. Spa type t030 was the most prominent type among MRSA strains. For the first time in Iran, spa003, t386, t1877, t314, t186, t1816, t304, t325, t345 were reported in this study. It was shown that there is a possibility that these spa types are native to this region. Our findings showed that SCCmec II, III and IV disseminate from hospital to community and vice versa. Thus, effective monitoring of MRSA in hospital and community is necessary.

Parental Knowledge and Awareness Linked to Antibiotic Use and Resistance: Comparison of Urban and Rural Population in Croatia

Purpose: To investigate the differences in parental knowledge, attitudes, and practice about antibiotic use and resistance among the urban and rural populations in Croatia. Materials and Methods: A cross-sectional study based on a structured questionnaire was distributed to 1,000 parents of children attending 11 elementary schools of Primorsko-Goranska County in 2017. Results: The overall response rate was 65.1% (651/1,000)-50.6% (253/500) in urban and 79.6% (398/500) in rural population. Urban parents had a higher overall knowledge about antibiotics (p < 0.001), while urban and rural parents held mostly similar knowledge and attitudes related to antibiotic use when split into individual statements (p > 0.05). Age, education, income, work, and family member working in a health-related field were significantly related with the overall knowledge about antibiotics. In the previous year, 28.2% of children and 28.9% of parents reported using an antibiotic. Croatian parents had a high level of trust in doctors' antibiotic-prescribing practices (96.3% reported trusting the doctors' decision not to prescribe antibiotics, 93.5% to prescribe antibiotics) and high awareness of antimicrobial resistance (94.8%). The public's misconception regarding the terms "bacteria" and "virus" was found in 15.5% of parents. The source of information about antimicrobial resistance was television (60.4%), internet (57.1%), newspapers (44.2%), and medical professionals (30.9%). Conclusions: Although the knowledge about antibiotics was higher in urban parents, it was not reflected on the level of antibiotic consumption. There are indications that medical professionals should be more involved in communicating the problems of antibiotic use and resistance to patients.

Discontinuation of antibiotic therapy within 24 hours of treatment initiation for patients with no clinical evidence of bacterial infection: a 5-year safety and outcome study from Singapore General Hospital Antimicrobial Stewardship Program

BACKGROUND

Overprescribing antibiotics for patients with no bacterial infection is of growing global concern. It is important for timely Antimicrobial Stewardship Program (ASP) intervention to discontinue antibiotics for patients whose symptoms can be explained by non-infective causes, and without availability of bacterial cultures and susceptibilities reports. This study aimed to evaluate clinical outcomes and safety of early ASP review in these patients.

METHODS

A retrospective review of the ASP database (January 2010 to December 2014) was conducted to identify patients for whom ASP recommended discontinuation of empiric antibiotics within 24 hours of prescribing. Demographics were collected. Clinical outcomes - duration of therapy, length of hospital stay (LOS), infection-related readmissions, and all-cause mortality - were compared between interventions accepted and rejected groups. Continuous data were analysed via unpaired Student's t-test. Categorical data were analysed using χ² test or Fisher's exact test, as appropriate.

RESULTS

The ASP team recommended 794 interventions (overall acceptance rate of 72.9%, 579 of 794). There were no significant between-group differences in underlying demographics, and Charlson comorbidity index score. However, the interventions acceptance group had significantly shorter duration of therapy by 2.61 days (2.72 ± 3.04 vs. 5.33 ± 2.54 days; P < 0.01) and LOS by 7.41 days (7.98 ± 13.14 vs. 15.39 ± 22.62 days; P < 0.01), with estimated cost savings of SGD10 817 per patient. There were no significant between-group differences in 14-day mortality and readmission rates.

CONCLUSION

Prompt ASP interventions at Singapore General Hospital were associated with significant reductions in duration of therapy and LOS, with cost savings. It was demonstrated that it is safe to discontinue antibiotics within 24 hours of prescribing for patients with no evidence of bacterial infections.

The association between cement type and the subsequent risk of revision surgery in primary total hip replacement

Background and purpose - To further improve the success of joint replacement surgery, attention needs to be paid to variations associated with improved or worsened outcomes. We investigated the association between the type of bone cement used and the risk of revision surgery after primary total hip replacement. Methods - We conducted a prospective study of data from the National Joint Registry for England and Wales between April 1, 2003 and December 31, 2013. 199,205 primary total hip replacements performed for osteoarthritis where bone cement was used were included. A multilevel over-dispersed piecewise Poisson model was used to estimate differences in the rate of revision by bone cement type adjusted for implant type, head size, age, sex, ASA grade, and surgical approach. Results - The rate of revision was higher in DePuy CMW3 medium viscosity with gentamicin (IRR 2.0, 95% CI 1.5-2.7) and DePuy SmartSet high viscosity plain (IRR 2.7, 95% CI 1.1-5.5), and lower in DePuy CMW1 high viscosity plain (IRR 0.44, 95% CI 0.19-0.89) bone cements compared with Heraeus Palacos high viscosity with gentamicin. Revision rates were similar between plain and antibiotic-loaded bone cement. Interpretation - The majority of bone cements performed similarly well, excluding DePuy SmartSet high viscosity and CMW3 high viscosity with gentamicin, which both had higher revision rates. We found no clear differences by viscosity or antibiotic content.

Distribution of Virulence Factors According to Antibiotic Susceptibility among Escherichia coli Isolated from Urinary Tract Infection

Escherichia coli is the major causative pathogen of urinary tract infection (UTI) in humans. Virulence and drug resistance play important roles in the pathogenesis of E. coli infections. The aims were to investigate the presence of uropathogenic virulence genes and to evaluate a relationship between antibiotic resistance and virulence in E. coli from UTI. A total of 132 E. coli were collected between April and June 2015 in two hospitals of Sanandaj, Iran. Isolates were examined for susceptibility to 16 antibiotic disks using the disk diffusion method and for possession of virulence genes by polymerase chain reaction. Associations between antimicrobial resistance and virulence genes were investigated. A P < 0.05 was considered significant. Of the 132 isolates, the most prevalent virulence gene was pap (31.1%), followed by cnf (28.8%), hly (16.7%), and afa (10.6%). Different patterns of virulence genes were identified. A significant association was detected between the simultaneous presence of hly and pap. The most effective antibiotics were nitrofurantoin, cefoxitin, and imipenem and the least effective were ampicillin, trimethoprim-sulfamethoxazole, and cefotaxime. An association was seen between the presence of cnf and susceptibility to the certain antibiotics, whereas strains with a reduced susceptibility to the certain antibiotics were associated with a significantly increased prevalence of afa and hly (P < 0.05). These findings suggest a correlation between the presence of virulence gene and resistance in E. coli strains from UTI. The results indicate that there is a need for surveillance programs to monitor drug resistance in pathogenic E. coli.

Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements

The intensive use of antibiotics results in their continuous release into the environment and the subsequent widespread occurrence of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). This study used Illumina high-throughput sequencing to investigate the broad-spectrum profiles of both ARGs and MGEs in activated sludge and anaerobically digested sludge from a full-scale wastewater treatment plant. A pipeline for identifying antibiotic resistance determinants was developed that consisted of four categories: gene transfer potential, ARG potential, ARGs pathway and ARGs phylogenetic origin. The metagenomic analysis showed that the activated sludge and the digested sludge exhibited different microbial communities and changes in the types and occurrence of ARGs and MGEs. In total, 42 ARGs subtypes were identified in the activated sludge, while 51 ARG subtypes were detected in the digested sludge. Additionally, MGEs including plasmids, transposons, integrons (intI1) and insertion sequences (e.g. ISSsp4, ISMsa21 and ISMba16) were abundant in the two sludge samples. The co-occurrence pattern between ARGs and microbial taxa revealed by network analysis indicated that some environmental bacteria (e.g. Clostridium and Nitrosomonas) might be potential hosts of multiple ARGs. The findings increase our understanding of WWTPs as hotspots of ARGs and MGEs, and contribute towards preventing their release into the downstream environment.

Characterization of SCCmec and spa types of methicillin-resistant Staphylococcus aureus isolates from health-care and community-acquired infections in Kerman, Iran

Spread of methicillin-resistant Staphylococcus aureus (MRSA) isolates is a worldwide problem. Molecular typing is a useful tool to understand MRSA epidemiology. Herein, we determined vancomycin-resistant, SCCmec and spa types among MRSA isolates recovered from healthcare and community-acquired infections in Kerman, Iran. A total of 170 S. aureus isolates were collected from different patients who were admitted to affiliated hospitals of Kerman University of Medical science. MRSA and vancomycin-resistant S. aureus (VRSA) isolates were detected by phenotypic methods. Polymerase chain reaction (PCR) technique was used for detection of mecA, vanA and vanB genes. Staphylococcal cassette chromosomemec (SCCmec) and spa typing were used for molecular typing of among MRSA isolates. Overall, 53% of isolates were considered as MRSA. Two MRSA isolates were resistant to vancomycin and vanA was detected in only one of VRSA isolates. SCCmec type III belonged to spa types t030 and t459 which they were the dominant spa types among community-associated MRSA (CA-MRSA) and healthcare-acquired MRSA (HA-MRSA) isolates. Our findings showed that the SCCmec type I and III spread from hospital settings to community, although the SCCmec type IV spread from community to healthcare systems. We have also reported VRSA isolates from hospitalized patients, therefore, appropriate policies should be enforced in order to prevent the spread of antibiotic resistance isolates in hospitals settings.

Procalcitonin: a promising diagnostic marker for sepsis and antibiotic therapy

BACKGROUND

Sepsis is a global healthcare problem, characterized by whole body inflammation in response to microbial infection, which leads to organ dysfunction. It is becoming a frequent complication in hospitalized patients. Early and differential diagnosis of sepsis is needed critically to avoid unnecessary usage of antimicrobial agents and for proper antibiotic treatments through the screening of biomarkers that sustains with diagnostic significance.

MAIN BODY OF ABSTRACT

Current targeting conventional markers (C-reactive protein, white blood cell, tumour necrosis factor-α, interleukins, etc.) are non-specific for diagnosing sepsis. Procalcitonin (PCT), a member of the calcitonin super family could be a critical tool for the diagnosis of sepsis. But to distinguish between bacterial versus viral infections, procalcitonin alone may not be effective. Rapid elevation in the concentration of procalcitonin and other newly emerging biomarkers during an infection and its correlation with severity of illness makes it an ideal biomarker for bacterial infection. Beside this, the procalcitonin levels can be used for monitoring response to antimicrobial therapy, diagnosis of secondary inflammations, diagnosis of renal involvement in paediatric urinary tract infection, etc. The present article summarizes the relevance of procalcitonin in the diagnosis of sepsis and how it can be useful in determining the therapeutic approaches.

CONCLUSION

Further studies are needed to better understand the application of PCT in the diagnosis of sepsis, differentiating between microbial and non-microbial infection cases and determining the therapeutic approaches for sepsis.

Randomized, Controlled, Crossover trial of Prevention of Clindamycin-Induced Gastrointestinal Signs Using a Synbiotic in Healthy Research Cats

Background

Synbiotics often are prescribed to limit antibiotic‐associated gastrointestinal signs (AAGS) in cats, but data to support this recommendation are lacking.

Objective

To determine whether synbiotic co‐administration mitigates AAGS in healthy research cats treated with clindamycin.

Animals

16 healthy research cats.

Methods

A randomized, double‐blinded, placebo‐controlled, 2‐way, 2‐period, crossover study with a 6‐week washout was performed. Each study period consisted of a 1‐week baseline and a 3‐week treatment period. Cats received 75 mg clindamycin with food once daily for 3 weeks, followed 1 hour later by either 2 capsules of a synbiotic or placebo. Food consumption, vomiting, fecal score, and completion of treatment were compared using repeated measures split plot or crossover designs with covariates, with P < 0.05 considered significant.

Results

Cats that received the synbiotic were more likely to complete treatment in period 1 (100% vs. 50%, P = 0.04). Cats vomited less when receiving the synbiotic but this was not significant, but there were significant period effects (F‐value = 11.4, P < 0.01). Cats had higher food intake while receiving the synbiotic (F‐value = 31.1, P < 0.01) despite period effects (F‐value = 8.6, P < 0.01). There was no significant effect of treatment on fecal scores, which significantly increased over time (F‐value = 17.9, P < 0.01).

Conclusions and Clinical Importance

Administration of a synbiotic 1 hour after clindamycin administration decreased hyporexia and vomiting in healthy cats. Additionally, significant period effects suggest that clinical benefits of synbiotic administration persist for at least 6 weeks after discontinuation, decreasing the severity of AAGS in cats that subsequently received clindamycin with placebo. Unlike in people, synbiotic administration did not decrease antibiotic‐associated diarrhea.

Identification of a Ligand-Binding Site on the Staphylococcus aureus DnaG Primase C-Terminal Domain

The interface between the DnaG primase C-terminal domain (CTD) and the N-terminal domain of DnaB helicase is essential for bacterial DNA replication because it allows coordinated priming of DNA synthesis at the replication fork while the DNA is being unwound. Because these two proteins are conserved in all bacteria and distinct from those in eukaryotes, their interface is an attractive antibiotic target. To learn more about this interface, we determined the solution structure and dynamics of the DnaG primase CTD from Staphylococcus aureus, a medically important bacterial species. Comparison with the known primase CTD structures shows there are two biologically relevant conformations, an open conformation that likely binds to DnaB helicase and a closed conformation that does not. The S. aureus primase CTD is in the closed conformation, but nuclear magnetic resonance (NMR) dynamic studies indicate there is considerable movement in the linker between the two subdomains and that N564 is the most dynamic residue within the linker. A high-throughput NMR ligand affinity screen identified potential binding compounds, among which were acycloguanosine and myricetin. Although the affinity for these compounds and adenosine was in the millimolar range, all three bind to a common pocket that is present only on the closed conformation of the CTD. This binding pocket is at the opposite end of helices 6 and 7 from N564, the key hinge residue. The identification of this binding pocket should allow the development of stronger-binding ligands that can prevent formation of the CTD open conformation that binds to DnaB helicase.

Experimental and In-Silico Investigation of Anti-Microbial Activity of 1-Chloro-2-Isocyanatoethane Derivatives of Thiomorpholine, Piperazine and Morpholine

The Antibiogram properties of 1-chloro-2-isocyanatoethane derivatives of thiomorpholine (CTC), piperazine (CPC) and morpholine (CMC) were evaluated by the approved agar well diffusion, the minimum inhibitory concentration (MIC) and in silico techniques. A total of fourteen microbial cultures consisting of ten bacteria and four yeast strains were used in the biological study while affinity of the compounds for DNA gyrase, a validated antibacterial drug target, was investigated by docking method. Results indicate that both thiomorpholine and piperazine had zero activity against the Gram negative organisms tested. With morpholine, similar result was obtained except that cultures of Escherichia coli (ATCC 15442) and Salmonella typhi (ATCC 6539) presented with weak sensitivity (7-8 mm) as shown by the inhibition zone diameter (IZD) measurement. The Gram positive organisms were more sensitive to morpholine than the other compounds. The highest IZD values of 15-18 mm were achieved except for Streptococcus pneumoniae (ATCC 49619) in which mobility of the compound stopped after 12 mm. S. pneumoniae was resistant to both thiomorpholine and piperazine. The yeast strains were not sensitive to any of the studied compounds investigated. The MIC tests evaluated against a reference antibiotic show that while morpholine was most active at 4 μg.ml-1 against both B. cereus ATCC (14579) and B. subtilis, the least active compound was thiomorpholine which inhibited S. aureus (ATCC 25923) at 64 μg.ml-1. The three compounds demonstrated high affinity for the target protein (DNA gyrase) ranging from -4.63 to -5.64 Kcal/mol and even showed better ligand efficiencies than three known antibiotics; chlorobiocin, ciprofloxacin and tetracycline. This study identified the studied compounds as potential antibiotic leads with acceptable physicochemical properties and gave the molecular basis for the observed interactions between the compounds and the target protein which can be harnessed in structural optimization process.

Polycyclic aromatic hydrocarbons (PAHs) enriching antibiotic resistance genes (ARGs) in the soils

The prevalence of antibiotic resistance genes (ARGs) in modern environment raises an emerging global health concern. In this study, soil samples were collected from three sites in petrochemical plant that represented different pollution levels of polycyclic aromatic hydrocarbons (PAHs). Metagenomic profiling of these soils demonstrated that ARGs in the PAHs-contaminated soils were approximately 15 times more abundant than those in the less-contaminated ones, with Proteobacterial being the preponderant phylum. Resistance profile of ARGs in the PAHs-polluted soils was characterized by the dominance of efflux pump-encoding ARGs associated with aromatic antibiotics (e.g., fluoroquinolones and acriflavine) that accounted for more than 70% of the total ARGs, which was significantly different from representative sources of ARG pollution due to wide use of antibiotics. Most of ARGs enriched in the PAHs-contaminated soils were not carried by plasmids, indicating the low possibilities of them being transferred between bacteria. Significant correlation was observed between the total abundance of ARGs and that of Proteobacteria in the soils. Proteobacteria selected by PAHs led to simultaneously enriching of ARGs carried by them in the soils. Our results suggested that PAHs could serve as one of selective stresses for greatly enriching of ARGs in the human-impacted environment.

Escherichia coli β-Lactamases: What Really Matters

Escherichia coli strains belonging to diverse pathotypes have increasingly been recognized as a major public health concern. The β-lactam antibiotics have been used successfully to treat infections caused by pathogenic E. coli. However, currently, the utility of β-lactams is being challenged severely by a large number of hydrolytic enzymes – the β-lactamases expressed by bacteria. The menace is further compounded by the highly flexible genome of E. coli, and propensity of resistance dissemination through horizontal gene transfer and clonal spread. Successful management of infections caused by such resistant strains requires an understanding of the diversity of β-lactamases, their unambiguous detection, and molecular mechanisms underlying their expression and spread with regard to the most relevant information about individual bacterial species. Thus, this review comprises first such effort in this direction for E. coli, a bacterial species known to be associated with production of diverse classes of β-lactamases. The review also highlights the role of commensal E. coli as a potential but under-estimated reservoir of β-lactamases-encoding genes.

Resistance to Antibiotics and Antifungal Medicinal Products: Can Complementary and Alternative Medicine Help Solve the Problem in Common Infection Diseases? The Introduction of a Dutch Research Consortium

The increase of antibiotic resistance worldwide, rising numbers of deaths and costs associated with this, and the fact that hardly any new antimicrobial drugs have been developed during the last decade have increased the interest in Complementary and Alternative Medicine (CAM) therapeutic interventions, if proven safe and effective. Observational studies on clinical CAM practices demonstrate positive effects of treatment of infections with CAM therapies (clinical effects, patient satisfaction) in combination with small percentages of antibiotics prescription. However, Cochrane reviews and other studies demonstrate that in most instances the quality of clinical trials on CAM treatment of infections is currently too low to provide sufficient evidence. Therefore a Dutch consortium on (in vitro and clinical) scientific research on CAM and antibiotic resistance has been formed. The aim and objective of the consortium is to establish an enduring partnership and to develop expertise to further develop and investigate safe and effective CAM treatments for infectious diseases of humans (and animals). A first ongoing project on the development of safe and effective biobased CAM antimycotics in women with (recurrent) vaginal candidiasis infection is introduced.

Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.

Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach

Antibiotic resistance has become a serious threat to human health. Sewage treatment plant (STP) is one of the major sources of antibiotic resistance genes (ARGs) in natural environment. High-throughput sequencing-based metagenomic approach was applied to investigate the broad-spectrum profiles and fate of ARGs in a full scale STP. Totally, 271 ARGs subtypes belonging to 18 ARGs types were identified by the broad scanning of metagenomic analysis. Influent had the highest ARGs abundance, followed by effluent, anaerobic digestion sludge and activated sludge. 78 ARGs subtypes persisted through the biological wastewater and sludge treatment process. The high removal efficiency of 99.82% for total ARGs in wastewater suggested that sewage treatment process is effective in reducing ARGs. But the removal efficiency of ARGs in sludge treatment was not as good as that in sewage treatment. Furthermore, the composition of microbial communities was examined and the correlation between microbial community and ARGs was investigated using redundancy analysis. Significant correlation between 6 genera and the distribution of ARGs were found and 5 of the 6 genera included potential pathogens. This is the first study on the fate of ARGs in STP using metagenomic analysis with high-throughput sequencing and hopefully would enhance our knowledge on fate of ARGs in STP.

The spread of carbapenemase-producing bacteria in Africa: a systematic review

BACKGROUND

Carbapenems are the last line of defence against ever more prevalent MDR Gram-negative bacteria, but their efficacy is threatened worldwide by bacteria that produce carbapenemase enzymes. The epidemiology of bacteria producing carbapenemases has been described in considerable detail in Europe, North America and Asia; however, little is known about their spread and clinical relevance in Africa.

METHODS

We systematically searched in PubMed, EBSCOhost, Web of Science, Scopus, Elsevier Masson Consulte and African Journals Online, international conference proceedings, published theses and dissertations for studies reporting on carbapenemase-producing bacteria in Africa. We included articles published in English or French up to 28 February 2014. We calculated the prevalence of carbapenemase producers only including studies where the total number of isolates tested was at least 30.

RESULTS

Eighty-three studies were included and analysed. Most studies were conducted in North Africa (74%, 61/83), followed by Southern Africa (12%, 10/83), especially South Africa (90%, 9/10), West Africa (8%, 7/83) and East Africa (6%, 6/83). Carbapenemase-producing bacteria were isolated from humans, the hospital environment and community environmental water samples, but not from animals. The prevalence of carbapenemase-producing isolates in hospital settings ranged from 2.3% to 67.7% in North Africa and from 9% to 60% in sub-Saharan Africa.

CONCLUSIONS

Carbapenemase-producing bacteria have been described in many African countries; however, their prevalence is poorly defined and has not been systematically studied. Antibiotic stewardship and surveillance systems, including molecular detection and genotyping of resistant isolates, should be implemented to monitor and reduce the spread of carbapenemase-producing bacteria.

Antimicrobial resistance among Enterobacteriaceae in South America: history, current dissemination status and associated socioeconomic factors

South America exhibits some of the higher rates of antimicrobial resistance in Enterobactericeae worldwide. This continent includes 12 independent countries with huge socioeconomic differences, where the ample access to antimicrobials, including counterfeit ones, coexists with ineffective health systems and sanitation problems, favoring the emergence and dissemination of resistant strains. This work presents a literature review concerning the evolution and current status of antimicrobial resistance threats found among Enterobacteriaceae in South America. Resistance to β-lactams, fluoroquinolones and aminoglycosides was emphasized along with description of key epidemiological studies that highlight the success of specific resistance determinants in different parts of the continent. In addition, a discussion regarding political and socioeconomic factors possibly related to the dissemination of antimicrobial resistant strains in clinical settings and at the community is presented. Finally, in order to assess the possible sources of resistant bacteria, we compile the current knowledge about the occurrence of antimicrobial resistance in isolates in South American' food, food-producing animals and off-hospitals environments. By addressing that intensive intercontinental commerce and tourism neutralizes the protective effect of geographic barriers, we provide arguments reinforcing that globally integrated efforts are needed to decelerate the emergence and dissemination of antimicrobial resistant strains.

Four structural subclasses of the antivirulence drug target disulfide oxidoreductase DsbA provide a platform for design of subclass-specific inhibitors

By catalyzing oxidative protein folding, the bacterial disulfide bond protein A (DsbA) plays an essential role in the assembly of many virulence factors. Predictably, DsbA disruption affects multiple downstream effector molecules, resulting in pleiotropic effects on the virulence of important human pathogens. These findings mark DsbA as a master regulator of virulence, and identify the enzyme as a target for a new class of antivirulence agents that disarm pathogenic bacteria rather than killing them. The purpose of this article is to discuss and expand upon recent findings on DsbA and to provide additional novel insights into the druggability of this important disulfide oxidoreductase by comparing the structures and properties of 13 well-characterized DsbA enzymes. Our structural analysis involved comparison of the overall fold, the surface properties, the conformations of three loops contributing to the binding surface and the sequence identity of residues contributing to these loops. Two distinct structural classes were identified, classes I and II, which are differentiated by their central β-sheet arrangements and which roughly separate the DsbAs produced by Gram-negative from Gram-positive organisms. The classes can be further subdivided into a total of four subclasses on the basis of surface features. Class Ia is equivalent to the Enterobacteriaceae class that has been defined previously. Bioinformatic analyses support the classification of DsbAs into 3 of the 4 subclasses, but did not pick up the 4th subclass which is only apparent from analysis of DsbA electrostatic surface properties. In the context of inhibitor development, the discrete structural subclasses provide a platform for developing DsbA inhibitory scaffolds with a subclass-wide spectrum of activity. We expect that more DsbA classes are likely to be identified, as enzymes from other pathogens are explored, and we highlight the issues associated with structure-based inhibitor development targeting this pivotal mediator of bacterial virulence. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.

Differentiating anthropogenic impacts on ARGs in the Pearl River Estuary by using suitable gene indicators

Antibiotic resistance genes (ARGs) are increasingly a focus of concern because they pose a potential health risk. The Pearl River (PR) and Pearl River Estuary (PRE) show a distinct gradient in anthropogenic impacts, in particular associated with the use of antibiotics, from the river, to the estuary, and on to the coast. In this study, two surveys were conducted in the PR and PRE areas during the winter and summer of 2011, respectively. Seven tet genes consisting of efflux pump (tetA, tetC, and tetH) and ribosomal protection proteins (tetB, tetM, tetO, and tetW) were analyzed using the polymerase chain reaction (PCR) technique. The tet genes, with the exception of tetA and tetH, were widely detected in the PR and PRE environments. The tet genes exhibited a trend of an increase in total concentration and diversity with the degree of anthropogenic impacts from the river to the coast, indicating that riverine input was the main source of ARGs in the region. Significant correlations were observed between tet genes and antibiotic concentrations, as well as among different environmental compartments (water and sediments). The distribution patterns of tet genes were similar between the potential sources of pollution and the highly-impacted sites, but were significantly different between less-impacted sites and highly-impacted ones or pollution sources. The results suggest that ARGs and antibiotics may be released from identical sources, and transported in a similar manner in estuary/coastal environments close to sources of pollution.

Effect of wastewater colloids on membrane removal of antibiotic resistance genes

Recent studies have demonstrated that wastewater treatment plants (WWTPs) significantly alter the magnitude and distribution of antibiotic resistance genes (ARGs) in receiving environments, indicating that wastewater treatment represents an important node for limiting ARG dissemination. This study examined the potential for membrane treatment of microconstituent ARGs and the effect of native wastewater colloids on the extent of their removal. Plasmids containing vanA (vancomycin) and bla(TEM) (β-lactam) ARGs were spiked into three representative WWTP effluents versus a control buffer and tracked by quantitative polymerase chain reaction through a cascade of microfiltration and ultrafiltration steps ranging from 0.45 μm to 1 kDa. Significant removal of ARGs was achieved by membranes of 100 kDa and smaller, and presence of wastewater colloids resulted in enhanced removal by 10 kDa and 1 kDa membranes. ARG removal was observed to correlate significantly with the corresponding protein, polysaccharide, and total organic carbon colloidal fractions. Alumina membranes removed ARGs to a greater extent than polyvinylidene fluoride membranes of the same pore size (0.1 μm), but only in the presence of wastewater material. Control studies confirmed that membrane treatment was the primary mechanism of ARG removal, versus other potential sources of loss. This study suggests that advanced membrane treatment technology is promising for managing public health risks of ARGs in wastewater effluents and that removal may even be enhanced by colloids in real-world wastewaters.

Ocular penetration of topically applied 1% daptomycin in a rabbit model

PURPOSE

To evaluate the ocular penetration of daptomycin, a new antibiotic agent targeted against Gram-positive organisms.

METHODS

Thirty-two New Zealand white rabbits were divided into 4 equal groups. One drop of 50 μL 1% daptomycin was administered to group 1. In group 2, 1 drop of 1% daptomycin was administered after the corneal epithelium was scraped. In group 3, 1 drop of 1% daptomycin was administered every 15 min for 1 h (keratitis protocol). In group 4, the keratitis protocol was applied after the corneal epithelium was scraped. In groups 1 and 2, aqueous humor samples were collected 30 min, 1 h, and 2 h after the single drop under general anesthesia. All the animals in groups 3 and 4 were humanely killed. Cornea, aqueous humor, and vitreous samples were collected 1 and 2 h after the last drop. Daptomycin concentrations were measured by high-performance liquid chromatography.

RESULTS

Each group comprised 8 rabbits. Daptomycin was not detected in the aqueous humor in groups 1 and 2. In group 3, the mean values at 1 h in the aqueous humor and cornea, respectively, were 1.90±0.15 μg/mL and 3.93±0.67 μg/g, and at 2 h were 1.71±0.42 μg/mL and 4.13±0.46 μg/g. In group 4, the mean values at 1 h were 5.19±0.50 μg/mL and 7.10±0.35 μg/g, and at 2 h were 4.96±0.47 μg/mL and 7.22±0.34 μg/g. Daptomycin was not detected in vitreous samples in groups 3 and 4.

CONCLUSIONS

Single-drop administration does not yield a detectable daptomycin concentration in aqueous humor in neither nonscraped nor scraped group. In the multiple-drop regimen, daptomycin seems to penetrate well into the aqueous humor and cornea both in nonscraped and scraped groups. However, this concentration may not cover the minimum inhibitory concentration (MIC) of organisms such as Enterococcus fecalis.