Ventilator-Associated Pneumonia: The Role of Emerging Diagnostic Technologies

AbstractAntibiotic resistance has emerged as a key determinant of outcome in patients with serious infections along with the virulence of the underlying pathogen. Within the intensive care unit (ICU) setting, ventilator-associated pneumonia (VAP) is a common nosocomial infection that is frequently caused by multidrug-resistant bacteria. Antimicrobial resistance is a growing challenge in the care of critically ill patients. Escalating rates of antibiotic resistance add substantially to the morbidity, mortality, and cost related to infection in the ICU. Both gram-positive organisms, such as methicillin-resistant Staphylococcus aureus and vancomycin-intermediate S. aureus, and gram-negative bacteria, including Pseudomonas aeruginosa, Acinetobacter species, carbapenem-resistant Enterobacteriaceae, such as the Klebsiella pneumoniae carbapenemase–producing bacteria, and extended spectrum β-lactamase organisms, have contributed to the escalating rates of resistance seen in VAP and other nosocomial infections. The rising rates of antimicrobial resistance have led to the routine empiric administration of broad-spectrum antibiotics even when bacterial infection is not documented. Moreover, there are several new broader-spectrum antibiotics that have recently become available and others scheduled for approval in the near future. The challenge to ICU clinicians is how to most effectively utilize these agents to maximize patient benefits while minimizing further emergence of resistance. Use of rapid diagnostics may hold the key for achieving this important balance. There is an urgent need for integrating the administration of new and existing antibiotics with the emerging rapid diagnostic technologies in a way that is both cost-effective and sustainable for the long run.

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Genomic Surveillance for Antimicrobial Resistance inMannheimia haemolyticaUsing Nanopore Single Molecule Sequencing Technology

10.1101/395087 ◽

2018 ◽

Author(s):

Alexander Lim ◽

Bryan Naidenov ◽

Haley Bates ◽

Karyn Willyerd ◽

Timothy Snider ◽

...

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Single Molecule ◽

Resistant Strain ◽

De Novo ◽

Gene Annotation ◽

Cost Effective ◽

Multidrug Resistant ◽

Oxford Nanopore ◽

Long Read

AbstractDisruptive innovations in long-range, cost-effective direct template nucleic acid sequencing are transforming clinical and diagnostic medicine. A multidrug resistant strain and a pan-susceptible strain ofMannheimia haemolytica, isolated from pneumonic bovine lung samples, were respectively sequenced at 146x and 111x coverage with Oxford Nanopore Technologies MinION.De novoassembly produced a complete genome for the non-resistant strain and a nearly complete assembly for the drug resistant strain. Functional annotation using RAST (Rapid Annotations using Subsystems Technology), CARD (Comprehensive Antibiotic Resistance Database) and ResFinder databases identified genes conferring resistance to different classes of antibiotics including beta lactams, tetracyclines, lincosamides, phenicols, aminoglycosides, sulfonamides and macrolides. Antibiotic resistance phenotypes of theM. haemolyticastrains were confirmed with minimum inhibitory concentration (MIC) assays. The sequencing capacity of highly portable MinION devices was verified by sub-sampling sequencing reads; potential for antimicrobial resistance determined by identification of resistance genes in the draft assemblies with as little as 5,437 MinION reads corresponded to all classes of MIC assays. The resulting quality assemblies and AMR gene annotation highlight efficiency of ultra long-read, whole-genome sequencing (WGS) as a valuable tool in diagnostic veterinary medicine.

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Novel Approaches to Hasten Detection of Pathogens and Antimicrobial Resistance in the Intensive Care Unit

Seminars in Respiratory and Critical Care Medicine ◽

10.1055/s-0039-1693160 ◽

2019 ◽

Vol 40 (04) ◽

pp. 454-464 ◽

Cited By ~ 2

Author(s):

M. Cristina Vazquez Guillamet ◽

Jason P. Burnham ◽

Marin H. Kollef

Keyword(s):

Intensive Care Unit ◽

Antibiotic Resistance ◽

Intensive Care ◽

Antimicrobial Resistance ◽

Critically Ill ◽

Broad Spectrum ◽

Critically Ill Patients ◽

Resistant Bacteria ◽

Acinetobacter Species ◽

Broad Spectrum Antibiotics

AbstractAntibiotic resistance is recognized as a key determinant of outcome in patients with serious infections influencing empiric antibiotic practices especially for critically ill patients. Within the intensive care unit (ICU), nosocomial infections and increasingly community-onset infections are caused by multidrug-resistant bacteria. Escalating rates of antibiotic resistance adds substantially to the morbidity, mortality, and cost related to infections treated in the ICU. Both gram-positive organisms, such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci, and gram-negative bacteria, including Pseudomonas aeruginosa, Acinetobacter species, carbapenem-resistant Enterobacteriaceae, and extended spectrum β-lactamase producing organisms, are urgent threats. The rising rates of antimicrobial resistance have resulted in routine empiric administration of broad-spectrum antibiotics by clinicians to critically ill patients even when bacterial infection is microbiologically absent. Moreover, new broad-spectrum antibiotics are a challenge to use effectively while avoiding emergence of further resistance. Use of rapid diagnostic technologies (RDTs) will likely provide an important methodology for achieving this important balance. There is an urgent need for integrating the administration of new and existing antibiotics with RDTs in a way that is safe, cost-effective, applicable in all countries, and sustainable.

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Animal source food eating habits of outpatients with antimicrobial resistance in Bukavu, D.R. Congo

Antimicrobial Resistance and Infection Control ◽

10.1186/s13756-021-00991-y ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Ghislain Bilamirwa Ngaruka ◽

Brigitte Bora Neema ◽

Theophile Kashosi Mitima ◽

Antoine Sadiki Kishabongo ◽

Olivier Basole Kashongwe

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Eating Habits ◽

Multidrug Resistant ◽

Health Concern ◽

Diffusion Method ◽

Resistant Bacteria ◽

Animal Source ◽

Drinking Milk ◽

Animal Source Food

Abstract Background Antibiotic resistance is a public health concern in Democratic Republic Congo and worldwide. It is usually caused by antibiotic over prescription or dispensing practices. The consumption of animal source food (ASF) could be another source of antibiotic resistance but is rarely studied. The objective of the study was to evaluate the eating habits of ASF by outpatients with antimicrobial resistance through an analysis of (i) the association of their antimicrobial resistance with ASF consumption; (ii) the influence of the types of ASF on their antimicrobial resistance. Methods This is a retrospective analytical study conducted at three major Hospitals in Bukavu City (D. R. Congo). A total number of 210 patients, whose samples (mainly faeces and urine) had been subjected to bacterial examination, was included in this study. Morphological, biochemical and antibiotic susceptibility (using disc diffusion method) tests were performed on the samples. This served to isolate and identify resistant bacteria. Afterwards, patients responded to questions about the types and quantity of ASF eaten in the last week. We analysed data using descriptive statistics, logistic regression and non-parametric ranking tests. Results Escherichia coli (37.1%), Klebsiella pneumonae (14.7%), and Staphylococcus aureus (13.8%) were the most prevalent bacteria. E. coli (68.4%) and K. pneumonae (87.5%) were multidrug resistant (MDR), while S. aureus (7.7%) was minor. Low beef (O.R. 0.737, C.I. 0.542–1.002) and pork (O.R. 0.743, C.I. 0.560 – 0.985) consumption led to significantly (p < 0.05) lower risks of resistance to ciprofloxacin. Patients eating three different ASF per week had the highest resistance score (20.67) and high consumption rates of goat meat, pork and milk (41.5%). Conclusion The findings of this study suggest a contribution of human nutrition to antimicrobial resistance frequency. Our results show the existence of a high prevalence of multi-drug resistant bacteria in patients for which eating beef, pork and drinking milk are major risk factors. Therefore, a stricter control of antibiotic usage in livestock production and of their presence in ASF is recommended.

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Animal Source Food Eating Habits of Outpatients With Antimicrobial Resistance in Bukavu, D.R. Congo

10.21203/rs.3.rs-313184/v1 ◽

2021 ◽

Author(s):

Olivier Basole Kashongwe ◽

Bilamirwa Reagan Ngaruka ◽

Sarcelles Bora Brigitte Neema ◽

Theophile Kashosi Mitima ◽

Antoine Sadiki Kishabongo

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Eating Habits ◽

Multidrug Resistant ◽

Health Concern ◽

Diffusion Method ◽

Resistant Bacteria ◽

Animal Source ◽

Drug Resistant Bacteria ◽

Animal Source Food

Abstract Background: Antibiotic resistance is a public health concern in Democratic Republic Congo and worldwide. It is usually caused by antibiotic over prescription or dispensing practices. The consumption of animal source food (ASF) could be another source of antibiotic resistance but is rarely studied. The objective of the study was to evaluate the eating habits of ASF by outpatients with antimicrobial resistance through an analysis of (i) the association of their antimicrobial resistance with ASF consumption; (ii) the influence of the types of ASF on their antimicrobial resistance.Methods: This is a retrospective analytical study conducted at three major Hospitals in Bukavu City (D. R. Congo). A total number of 210 patients, whose samples (mainly faeces and urine) had been subjected to bacterial examination, was included in this study. Morphological, biochemical and antibiotic susceptibility (using disc diffusion method) tests were performed on the samples. This served to isolate and identify resistant bacteria. Afterwards, patients responded to questions about the types and quantity of ASF eaten in the last week. We analysed data using descriptive statistics, logistic regression and non-parametric ranking tests.Results: Escherichia coli (37.1%), Klebsiella pneumonae (14.7%), and Staphylococcus aureus (13.8%) were the most prevalent bacteria. E. coli (68.4%) and K. pneumonae (87.5%) were multidrug resistant (MDR), while S. aureus (7.7%) was minor. Low beef (O.R. 0.737, C.I. 0.542-1.002) and pork (O.R. 0.743, C.I. 0.560 – 0.985) consumption led to significantly (p<0.05) lower risks of resistance to ciprofloxacin. Patients eating three different ASF per week had the highest resistance score (20.67) and high consumption rates of goat meat, pork and milk (41.5%). Conclusion: The findings of this study suggest a contribution of human nutrition to antimicrobial resistance frequency. Our results show the existence of a high prevalence of multi-drug resistant bacteria in patients frequently consuming ASF in Bukavu. Therefore, a stricter control of antibiotic usage in livestock production and of their presence in ASF is recommended.

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Antimicrobial Resistance and Presence of Class 1 Integrons Among Different Serotypes of Salmonella spp. Recovered From Children with Diarrhea in Tehran, Iran

Infectious Disorders - Drug Targets ◽

10.2174/1871526519666190130171020 ◽

2020 ◽

Vol 20 (2) ◽

pp. 160-166

Author(s):

Seyedeh Hanieh Eshaghi Zadeh ◽

Hossein Fahimi ◽

Fatemeh Fardsanei ◽

Mohammad Mehdi Soltan Dallal

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Multidrug Resistant ◽

Salmonella Spp ◽

Class 1 Integron ◽

Class 1 Integrons ◽

Food Borne ◽

Class 1 ◽

Resistance Patterns ◽

C 30

Background: Salmonellosis is a major food-borne disease worldwide. The increasing prevalence of antimicrobial resistance among food-borne pathogens such as Salmonella spp. is concerning. Objective: The main objective of this study is to identify class 1 integron genes and to determine antibiotic resistance patterns among Salmonella isolates from children with diarrhea. Methods: A total of 30 Salmonella isolates were recovered from children with diarrhea. The isolates were characterized for antimicrobial susceptibility and screened for the presence of class 1 integron genes (i.e. intI1, sulI1, and qacEΔ1). Results: The most prevalent serotype was Enteritidis 36.7%, followed by Paratyphi C (30%), and Typhimurium (16.7%). The highest rates of antibiotic resistance were obtained for nalidixic acid (53.3%), followed by streptomycin (40%), and tetracycline (36.7%). Regarding class 1 integrons, 36.7%, 26.7%, and 33.3% of the isolates carried intI1, SulI, and qacEΔ1, respectively, most of which (81.8%) were multidrug-resistant (MDR). Statistical analysis revealed that the presence of class 1 integron was significantly associated with resistance to streptomycin and tetracycline (p = 0.042). However, there was no association between class 1 integron and other antibiotics used in this study (p > 0.05). Conclusion: The high frequency of integron class 1 gene in MDR Salmonella strains indicates that these mobile genetic elements are versatile among different Salmonella serotypes, and associated with reduced susceptibility to many antimicrobials.

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The Role of Aquatic Ecosystems (River Tua, Portugal) as Reservoirs of Multidrug-Resistant Aeromonas spp.

Water ◽

10.3390/w13050698 ◽

2021 ◽

Vol 13 (5) ◽

pp. 698

Author(s):

Sónia Gomes ◽

Conceição Fernandes ◽

Sandra Monteiro ◽

Edna Cabecinha ◽

Amílcar Teixeira ◽

...

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Nalidixic Acid ◽

Water Samples ◽

Aquatic Ecosystems ◽

Anthropogenic Activities ◽

Aquatic Organisms ◽

Resistant Bacteria ◽

Anthropogenic Pressures ◽

Resistance Rates

The inappropriate use of antibiotics, one of the causes of the high incidence of antimicrobial-resistant bacteria isolated from aquatic ecosystems, represents a risk for aquatic organisms and the welfare of humans. This study aimed to determine the antimicrobial resistance rates among riverine Aeromonas spp., taken as representative of the autochthonous microbiota, to evaluate the level of antibacterial resistance in the Tua River (Douro basin). The prevalence and degree of antibiotic resistance was examined using motile aeromonads as a potential indicator of antimicrobial susceptibility for the aquatic environment. Water samples were collected from the middle sector of the river, which is most impacted area by several anthropogenic pressures. Water samples were plated on an Aeromonas-selective agar, with and without antibiotics. The activity of 19 antibiotics was studied against 30 isolates of Aeromonas spp. using the standard agar dilution susceptibility test. Antibiotic resistance rates were fosfomycin (FOS) 83.33%, nalidixic acid (NA) 60%, cefotaxime (CTX) 40%, gentamicin (CN) 26.67%, tobramycin (TOB) 26.67%, cotrimoxazole (SXT) 26.67%, chloramphenicol (C) 16.67%, and tetracycline (TE) 13.33%. Some of the nalidixic acid-resistant strains were susceptible to fluoroquinolones. Multiple resistance was also observed (83.33%). The environmental ubiquity, the natural susceptibility to antimicrobials and the zoonotic potential of Aeromonas spp. make them optimal candidates for studying antimicrobial resistance (AMR) in aquatic ecosystems. Aquatic environments may provide an ideal setting for the acquisition and dissemination of antibiotic resistance because anthropogenic activities frequently impact them. The potential risk of multi- and pan-resistant bacteria transmission between animals and humans should be considered in a “One Health—One World” concept.

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Testudines as Sentinels for Monitoring the Dissemination of Antibiotic Resistance in Marine Environments: An Integrative Review

Antibiotics ◽

10.3390/antibiotics10070775 ◽

2021 ◽

Vol 10 (7) ◽

pp. 775

Author(s):

Kezia Drane ◽

Roger Huerlimann ◽

Michelle Power ◽

Anna Whelan ◽

Ellen Ariel ◽

...

Keyword(s):

Antibiotic Resistance ◽

Anthropogenic Activities ◽

Sea Turtles ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Marine Environments ◽

Beta Lactam ◽

Antibiotic Resistant ◽

Sensitivity Tests ◽

Standard Culture

Dissemination of antibiotic resistance (AR) in marine environments is a global concern with a propensity to affect public health and many ecosystems worldwide. We evaluated the use of sea turtles as sentinel species for monitoring AR in marine environments. In this field, antibiotic-resistant bacteria have been commonly identified by using standard culture and sensitivity tests, leading to an overrepresentation of specific, culturable bacterial classes in the available literature. AR was detected against all major antibiotic classes, but the highest cumulative global frequency of resistance in all represented geographical sites was against the beta-lactam class by a two-fold difference compared to all other antibiotics. Wastewater facilities and turtle rehabilitation centres were associated with higher incidences of multidrug-resistant bacteria (MDRB) accounting for an average of 58% and 49% of resistant isolates, respectively. Furthermore, a relatively similar prevalence of MDRB was seen in all studied locations. These data suggest that anthropogenically driven selection pressures for the development of AR in sea turtles and marine environments are relatively similar worldwide. There is a need, however, to establish direct demonstrable associations between AR in sea turtles in their respective marine environments with wastewater facilities and other anthropogenic activities worldwide.

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Rethinking Manure Application: Increase in Multidrug-Resistant Enterococcus spp. in Agricultural Soil Following Chicken Litter Application

Microorganisms ◽

10.3390/microorganisms9050885 ◽

2021 ◽

Vol 9 (5) ◽

pp. 885

Author(s):

Dorcas Oladayo Fatoba ◽

Akebe Luther King Abia ◽

Daniel G. Amoako ◽

Sabiha Y. Essack

Keyword(s):

Antimicrobial Resistance ◽

Agricultural Soil ◽

Multidrug Resistant ◽

Diffusion Method ◽

Resistant Bacteria ◽

Manure Application ◽

Unamended Soil ◽

Enterococcus Spp ◽

Chicken Litter ◽

Amended Soil

The current study investigated the impact of chicken litter application on the abundance of multidrug-resistant Enterococcus spp. in agricultural soil. Soil samples were collected from five different strategic places on a sugarcane farm before and after manure application for four months. Chicken litter samples were also collected. Enterococci were enumerated using the Enterolert®/Quanti-Tray 2000® system and confirm and differentiated into species using real-time PCR. The antibiotic susceptibility profile of the isolates was determined using the disk diffusion method following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The overall mean bacterial count was significantly higher (p < 0.05) in manure-amended soil (3.87 × 107 MPN/g) than unamended soil (2.89 × 107 MPN/g). Eight hundred and thirty-five enterococci (680 from soil and 155 from litter) were isolated, with E. casseliflavus being the most prevalent species (469; 56.2%) and E. gallinarum being the least (16; 1.2%). Approximately 56% of all the isolates were resistant to at least one antibiotic tested, with the highest resistance observed against tetracycline (33%) and the lowest against chloramphenicol (0.1%); 17% of E. faecium were resistant to quinupristin-dalfopristin. Additionally, 27.9% (130/466) of the isolates were multidrug-resistant, with litter-amended soil harbouring more multidrug-resistant (MDR) isolates (67.7%; 88/130) than unamended soil (10.0%; 13/130). All isolates were susceptible to tigecycline, linezolid and gentamicin. About 7% of the isolates had a multiple antimicrobial resistance index > 0.2, indicative of high antibiotic exposure. Although organic fertilizers are regarded as eco-friendly compared to chemical fertilizers for improving soil fertility, the application of untreated animal manure could promote the accumulation of antibiotics and their residues and antibiotic-resistant bacteria in the soil, creating an environmental reservoir of antimicrobial resistance, with potential human and environmental health risks.

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Liposomes as Antibiotic Delivery Systems: A Promising Nanotechnological Strategy against Antimicrobial Resistance

Molecules ◽

10.3390/molecules26072047 ◽

2021 ◽

Vol 26 (7) ◽

pp. 2047

Author(s):

Magda Ferreira ◽

Maria Ogren ◽

Joana N. R. Dias ◽

Marta Silva ◽

Solange Gil ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Bacterial Infections ◽

Private Investment ◽

Therapeutic Index ◽

Multidrug Resistant ◽

Current Treatment ◽

Delivery Systems ◽

Resistant Bacteria ◽

Bacterial Cells ◽

Antimicrobial Drugs

Antimicrobial drugs are key tools to prevent and treat bacterial infections. Despite the early success of antibiotics, the current treatment of bacterial infections faces serious challenges due to the emergence and spread of resistant bacteria. Moreover, the decline of research and private investment in new antibiotics further aggravates this antibiotic crisis era. Overcoming the complexity of antimicrobial resistance must go beyond the search of new classes of antibiotics and include the development of alternative solutions. The evolution of nanomedicine has allowed the design of new drug delivery systems with improved therapeutic index for the incorporated compounds. One of the most promising strategies is their association to lipid-based delivery (nano)systems. A drug’s encapsulation in liposomes has been demonstrated to increase its accumulation at the infection site, minimizing drug toxicity and protecting the antibiotic from peripheral degradation. In addition, liposomes may be designed to fuse with bacterial cells, holding the potential to overcome antimicrobial resistance and biofilm formation and constituting a promising solution for the treatment of potential fatal multidrug-resistant bacterial infections, such as methicillin resistant Staphylococcus aureus. In this review, we aim to address the applicability of antibiotic encapsulated liposomes as an effective therapeutic strategy for bacterial infections.

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Antibiotic Resistance in Pediatric Infections: Global Emerging Threats, Predicting the Near Future

Antibiotics ◽

10.3390/antibiotics10040393 ◽

2021 ◽

Vol 10 (4) ◽

pp. 393

Author(s):

Alessandra Romandini ◽

Arianna Pani ◽

Paolo Andrea Schenardi ◽

Giulia Angela Carla Pattarino ◽

Costantino De Giacomo ◽

...

Keyword(s):

Antibiotic Resistance ◽

Pediatric Population ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Pediatric Age ◽

Carbapenem Resistant ◽

Pediatric Infections ◽

Surgical Treatments ◽

Developing System ◽

Near Future

Antibiotic resistance is a public health threat of the utmost importance, especially when it comes to children: according to WHO data, infections caused by multidrug resistant bacteria produce 700,000 deaths across all ages, of which around 200,000 are newborns. This surging issue has multipronged roots that are specific to the pediatric age. For instance, the problematic overuse and misuse of antibiotics (for wrong diagnoses and indications, or at wrong dosage) is also fueled by the lack of pediatric-specific data and trials. The ever-evolving nature of this age group also poses another issue: the partly age-dependent changes of a developing system of cytochromes determine a rather diverse population in terms of biochemical characteristics and pharmacokinetics profiles, hard to easily codify in an age- or weight-dependent dosage. The pediatric population is also penalized by the contraindications of tetracyclines and fluoroquinolones, and by congenital malformations which often require repeated hospitalizations and pharmacological and surgical treatments from a very young age. Emerging threats for the pediatric age are MRSA, VRSA, ESBL-producing Enterobacteriaceae, carbapenem-resistant Enterobacteriaceae and the alarming colistin resistance. Urgent actions need to be taken in order to step back from a now likely post-antibiotic era, where simple infections might cause infant death once again.

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