Routine wastewater-based monitoring of antibiotic resistance in two Finnish hospitals: focus on carbapenem resistance genes and genes associated with bacteria causing hospital-acquired infections

ABSTRACT In addition to having a reputation as the causative agent of several types of hospital-acquired infections, Klebsiella pneumoniae has gained widespread attention as a pathogen with a propensity for acquiring antibiotic resistance. It is capable of causing a range of infections, including urinary tract infections, pneumonia, and sepsis. Because of the rapid emergence of carbapenem resistance among Klebsiella strains, there is a dire need for a better understanding of virulence mechanisms and identification of new drug targets. Here, we identify the periplasmic transporter FepB as one such potential target. Klebsiella pneumoniae is considered a significant public health threat because of the emergence of multidrug-resistant strains and the challenge associated with treating life-threatening infections. Capsule, siderophores, and adhesins have been implicated as virulence determinants of K. pneumoniae, yet we lack a clear understanding of how this pathogen causes disease. In a previous screen for virulence genes, we identified a potential new virulence locus and constructed a mutant (smr) with this locus deleted. In this study, we characterize the smr mutant and show that this mutation renders K. pneumoniae avirulent in a pneumonia model of infection. The smr mutant was expected to have a deletion of three genes, but subsequent genome sequencing indicated that a much larger deletion had occurred. Further analysis of the deleted region indicated that the virulence defect of the smr mutant could be attributed to the loss of FepB, a periplasmic protein required for import of the siderophore enterobactin. Interestingly, a ΔfepB mutant was more attenuated than a mutant unable to synthesize enterobactin, suggesting that additional processes are affected. As FepB is highly conserved among the members of the family Enterobacteriaceae, therapeutic targeting of FepB may be useful for the treatment of Klebsiella and other bacterial infections. IMPORTANCE In addition to having a reputation as the causative agent of several types of hospital-acquired infections, Klebsiella pneumoniae has gained widespread attention as a pathogen with a propensity for acquiring antibiotic resistance. It is capable of causing a range of infections, including urinary tract infections, pneumonia, and sepsis. Because of the rapid emergence of carbapenem resistance among Klebsiella strains, there is a dire need for a better understanding of virulence mechanisms and identification of new drug targets. Here, we identify the periplasmic transporter FepB as one such potential target.

Download Full-text

Carriage of two carbapenem-resistance genes in Pseudomonas aeruginosa isolated from hospital-acquired infections in children from Costa Rica: the importance of local epidemiology

Antimicrobial Resistance and Infection Control ◽

10.1186/s13756-021-00942-7 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Cristian Pérez-Corrales ◽

Valeria Peralta-Barquero ◽

Christopher Mairena-Acuña

Keyword(s):

Pseudomonas Aeruginosa ◽

Costa Rica ◽

Resistance Genes ◽

Carbapenem Resistance ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Middle Income ◽

Hospital Acquired Infections ◽

Antimicrobial Resistance Genes ◽

Hospital Acquired

Abstract Background The assessment of Hospital-acquired infections due to multidrug-resistant bacteria involves the use of a variety of commercial and laboratory-developed tests to detect antimicrobial resistance genes in bacterial pathogens; however, few are evaluated for use in low- and middle-income countries. Methods We used whole-genome sequencing, rapid commercial molecular tests, laboratory-developed tests and routine culture testing. Results We identified the carriage of the metallo-β-lactamase blaVIM-2 and blaIMP-18 alleles in Carbapenem-Resistant Pseudomonas aeruginosa infections among children in Costa Rica. Conclusions The blaIMP-18 allele is not present in the most frequently used commercial tests; thus, it is possible that the circulation of this resistance gene may be underdiagnosed in Costa Rica.

Download Full-text

Antibiotic resistance: a modern view of the problem by the example of a multi-profile hospital

Vrač skoroj pomoŝi (Emergency Doctor) ◽

10.33920/med-02-2102-01 ◽

2021 ◽

pp. 19-25

Author(s):

L. Yu. Kulagina ◽

I. R. Valiullina ◽

E. R. Kadyseva ◽

M. L. Maksimov

Keyword(s):

Mass Spectrometry ◽

Antibiotic Resistance ◽

Antibiotic Sensitivity ◽

Hospital Infections ◽

Strategic Decisions ◽

Hospital Acquired Infections ◽

Empirical Antibacterial Therapy ◽

Inflammatory Processes ◽

Hospital Acquired ◽

Inpatient Department

Relevance. Conducting microbiological monitoring allows controlling hospital-acquired infections and making timely strategic decisions for epidemiologists and clinical pharmacologists. Objective of the work is to determine the tendency of prevailing problem microflora and to develop a strategy of empirical antibacterial therapy for severe nosocomial infections and inflammatory processes. Materials and methods. The article analyzes the main groups of pathogens of hospital infections in dynamics for the first quarter of 2018, 2019 and 2020. The relation of positive cultures to the total number of investigated samples was taken for the analysis. Antibiotic sensitivity was isolated, identified and determined using conventional mass spectrometry methods. The results. The stable sowing rate of Acinetobacter baumannii and Klebsiella pneumoniae in the intensive care and surgical departments was noted for the analyzed periods. To solve the issue of antibiotic resistance in the inpatient department, a strategy to contain it has been developed.

Download Full-text

819. Antibiotic Resistance in Pathogens Causing Hospital Acquired Infections in Brazil: A Multicenter Study

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab466.1015 ◽

2021 ◽

Vol 8 (Supplement_1) ◽

pp. S502-S503

Author(s):

Carlos Starling ◽

Bráulio R G M Couto ◽

Estevão Urbano Silva ◽

Virginia Andrade ◽

Edna M M Leite ◽

...

Keyword(s):

Antibiotic Resistance ◽

Tertiary Care ◽

Healthcare Associated Infections ◽

Gram Positive ◽

Resistance Profile ◽

Hospital Acquired Infections ◽

Microbiological Methods ◽

Belo Horizonte ◽

Healthcare Associated ◽

Hospital Acquired

Abstract Background In the present study we determined the prevalence of antibiotic resistance in the most common organisms causing healthcare-associated infections in tertiary-care hospitals in Belo Horizonte, a 3,000,000 inhabitants city from Brazil. Methods Microbiology data of hospital acquired infections (HAI) defined by the National Healthcare Safety Network (NHSN)/CDC protocols of seven general hospitals were analyzed: three public institutions, two philanthropic, and two private hospitals. Samples from different topographies were plate in an ideal culture medium and after growth, the microorganisms were identified by standard biochemical and microbiological methods, using the VITEK 2 compact system (Biomerieux), which allows the simultaneous identification of Gram-positive and Gram bacteria -negative and combine the identification and TSA results in a single report. Six hospitals used automated methods and one institution used manual method for antimicrobial susceptibility testing. Results Samples of seven Gram-negative and two Gram-positive bacteria collected between Dec/2019-Nov/2020 from HAI isolates were analyzed: 565 Klebsiella, 293 Escherichia coli, 153 Proteus, 403 Pseudomonas, 275 Acinetobacter, 174 Serratia, 153, 361 Staphylococcus aureus, and 176 Enterococcus. Antibiotic resistance profile of each strain is summarized in Figures 1, 2, and 3. Resistance profile: Klebsiella, E. coli, Proteus. ATB profile: Pseudomonas, Acinetobacter, Serratia. ATB profile: Enterobacter, S. aureus, Enterococcus . Conclusion Benchmarks for antibiotic resistance in the most common organisms causing healthcare-associated infections were defined, and can be used as indicators for healthcare assessment, specially in developing countries institutions. Disclosures All Authors: No reported disclosures

Download Full-text

Clinical metagenomics bioinformatics pipeline for the identification of hospital-acquired pneumonia pathogens antibiotic resistance genes from bronchoalveolar lavage samples

10.1101/2020.02.26.966309 ◽

2020 ◽

Author(s):

Maud Tournoud ◽

Etienne Ruppé ◽

Guillaume Perrin ◽

Stéphane Schicklin ◽

Ghislaine Guigon ◽

...

Keyword(s):

Antibiotic Resistance ◽

Bronchoalveolar Lavage ◽

Resistance Genes ◽

Direct Sequencing ◽

Antibiotic Resistance Genes ◽

Traditional Culture ◽

Reference Database ◽

Bioinformatics Pipeline ◽

Hospital Acquired ◽

Taxonomic Binning

AbstractBackgroundShortening the time-to-result for pathogen detection and identification and antibiotic susceptibility testing for patients with Hospital-Acquired and Ventilator-Associated pneumonia (HAP-VAP) is of great interest. For this purpose, clinical metagenomics is a promising non-hypothesis driven alternative to traditional culture-based solutions: when mature, it would allow direct sequencing all microbial genomes present in a BronchoAlveolar Lavage (BAL) sample with the purpose of simultaneously identifying pathogens and Antibiotic Resistance Genes (ARG). In this study, we describe a new bioinformatics method to detect pathogens and their ARG with good accuracy, both in mono- and polymicrobial samples.MethodsThe standard approach (hereafter called TBo), that consists in taxonomic binning of metagenomic reads followed by an assembly step, suffers from lack of sensitivity for ARG detection. Thus, we propose a new bioinformatics approach (called TBwDM) with both models and databases optimized for HAP-VAP, that performs reads mapping against ARG reference database in parallel to taxonomic binning, and joint reads assembly.ResultsIn in-silico simulated monomicrobial samples, the recall for ARG detection increased from 51% with TBo to 97.3% with TBwDM; in simulated polymicrobial infections, it increased from 41.8% to 82%. In real sequenced BAL samples (mono and polymicrobial), detected pathogens were also confirmed by traditional culture approaches. Moreover, both recall and precision for ARG detection were higher with TBwDM than with TBo (35 points difference for recall, and 7 points difference for precision).ConclusionsWe present a new bioinformatics pipeline to identify pathogens and ARG in BAL samples from patients with HAP-VAP, with higher sensitivity for ARG recovery than standard approaches and the ability to link ARG to their host pathogens.

Download Full-text

Etiologic Agents and Antibiotic Resistance Pattern of Community- and Hospital-Acquired Infections

Avicenna Journal of Clinical Medicine ◽

10.21859/ajcm.25.1.41 ◽

2018 ◽

Vol 25 (1) ◽

pp. 41-48

Author(s):

Mohammad Mahdi Majzoobi ◽

Azar Pirdehghan ◽

Zahra Rashidian ◽

Ali Saadatmand ◽

◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Pattern ◽

Hospital Acquired Infections ◽

Antibiotic Resistance Pattern ◽

Etiologic Agents ◽

Hospital Acquired

Download Full-text

Antibiotic resistance in Acinetobacter baumannii as agent of surgery infection and approaches to its overcoming by means of deca-methoxinum antiseptic

Perioperaciina Medicina ◽

10.31636/prmd.v1i2.2 ◽

2019 ◽

Vol 1 (2) ◽

pp. 18-22

Author(s):

O A Nazarchuk ◽

V I Nahaichuk

Keyword(s):

Antibiotic Resistance ◽

Antibiotic Sensitivity ◽

Antibiotic Resistant ◽

Clinical Strains ◽

Minimal Inhibitory Concentrations ◽

Hospital Acquired Infections ◽

Causative Agents ◽

Resistant Strains ◽

Burn Disease ◽

Hospital Acquired

Introduction. Non-fermenting Gram-negative bacilli are known as one of the most frequent causative agents of hospital-acquired infections. Acinetobacter baumannii, as causative agent of infection complications of different localization, has obtained recently high resistance to anti-biotics and has belonged to ESKAPE group of pathogens. Antimicrobials, recommended for the prophylaxis and therapy of hospital-acquired infections, have been failing in their effectiveness and lead to selection of antibiotic resistant strains of A. baumannii. The aim of this research was to substantiate the way of overcoming of resistance in clinical strains of A. baumannii, by means of synergic antimicrobial activity of antibiotics and antiseptic decamethoxinum®. Material and methods. The research was carried out on 190 clinical strains of A. baumannii, isolated from patients with burn disease during the period 2011–2015. The sensitivity of clinical strains of A. baumannii was determined to such antibiotics as ampicillin/sulbactam, cefoperazone, cefoperazone/sulbactam, meropenem, imipenem, amikacin, ciprofloxacin, gatifloxacin and antiseptic decamethoxinum® (DCM; Registration certificate No UA/14444/01/01 since 24.06.2015. Order of the Ministry of Health of Ukraine No 373). The sensitivity of A. baumannii to antibiotics and DCM was determined by means of disk diffusion test and serial dilution (Order of the Ministry of Health of Ukraine No167 since 05.04.2007; EUCAST expert rules).The study of the influence of antiseptic DCM on the sensitivity of acinetobacteria to antibiotics was studied on 35 clinical strains of A. baumannii, drafted from the general number of isolates enrolled in the research. For this, the sensitivity of A. baumannii to antibiotics in the presence of sub-minimal inhibitory concentrations (subMIC) of DCM was identified. The received experimental data were analyzed by “Statistica 6.0”. Results and discussion. The changes of antibiotic sensitivity profile of A. baumannii for five years were shown. It was found that the sensitivity of A. baumannii to majority of antibiotics, selected for study, decreased significantly. But the only ampicillin/sulbactam was found to have vice versa tendency. We found the rising quantity of antibiotic resistant strains of A. baumannii. At the same time, high resistance of acinetobacteria to fluoroquinolones (ciprofloxacin– 96,1%; gatifloxacin– 95,8%) was found in 2015. The in vitro research of combined activity of DCM antiseptic remedy and early mentioned antibiotics against clinical strains of A. baumannii demonstrated the reveal antibiotic effectiveness. As follows, minimal inhibitory concentrations of antibiotics decreased in 1.5–4 times in the mediums which contained subMIC of DCM. Especially this tendency was found in resistant clinical strains. Conclusion. Under selective influence of antibiotics protected by β-lactamase inhibitors, carbapenems, fluoroquinolones aminoglycosides increase the antibiotic resistance in A. baumannii, causative agents of infectious complications in patients with burn disease. The antiseptic remedy decamethoxinum® helps to improve antibiotic sensitivity in resistant A. baumannii.

Download Full-text

The human microbiota: novel targets for hospital-acquired infections and antibiotic resistance

Annals of Epidemiology ◽

10.1016/j.annepidem.2016.02.007 ◽

2016 ◽

Vol 26 (5) ◽

pp. 342-347 ◽

Cited By ~ 20

Author(s):

Melinda M. Pettigrew ◽

J. Kristie Johnson ◽

Anthony D. Harris

Keyword(s):

Antibiotic Resistance ◽

Hospital Acquired Infections ◽

Human Microbiota ◽

Novel Targets ◽

Hospital Acquired

Download Full-text

Use of 16s rRNA to identify non-lactose-fermenting bacilli and molecular detection of ESBL resistance genes associated with hospital-acquired infection in Soba University Hospital, Sudan

F1000Research ◽

10.12688/f1000research.22541.1 ◽

2020 ◽

Vol 9 ◽

pp. 1311

Author(s):

Wissam Ahmed Al Hag ◽

Hana Elbadawi ◽

Muzamil Mahdi Abdel Hamid

Keyword(s):

Pseudomonas Aeruginosa ◽

16S Rrna ◽

Resistance Genes ◽

University Hospital ◽

16S Rrna Genes ◽

Rrna Genes ◽

Biochemical Tests ◽

Gram Negative ◽

Hospital Acquired Infections ◽

Hospital Acquired

Background: Non-lactose-fermenting gram-negative bacilli (NLFGNB) have become significant nosocomial pathogens and often exhibit intrinsic multidrug resistance. Sequencing of 16s rRNA genes could be utilized for robust identification of NLFGNB. This study aimed to identify resistant NLFGNB associated with hospital-acquired infections using 16s rRNA sequencing and to detect the extended-spectrum β-lactamase (ESBL) genes of isolates in Soba Hospital, Khartoum State, Sudan. Methods: A prospective, cross-sectional, laboratory-based study was conducted from October 2017 to March 2018 at the Microbiology Department of Soba University Hospital. A total of 100 randomly selected NLFGNB samples were isolated from blood and urine during the time of the study. All the isolates were identified using standard biochemical tests and antimicrobial sensitivity testing, 16s rRNA gene sequencing, and bioinformatics techniques. Results: The biochemical tests revealed that, out of the 100 NLFGNB isolates, the Pseudomonas species was predominant (57 isolates), followed by gram-negative bacilli (33 isolates), Coccobacilli (9 isolates) and Coliform (1 isolate) species. Sequencing of 16s rRNA genes identified all the resistant isolates at the species level: Pseudomonas aeruginosa (26%), Acinetobacter baumannii (22%), Burkholderia cepacia (13%), Stenotrophomonas maltophilia (10%), Enterococcus species (E. faecalis, E. faecium) (10%), and other GNB (Acinetobacter variabilis, Klebsiella pneumoniae, Morganella morganii, Escherichia fergusonii, Enterobacter hormaechei and Pseudomonas stutzeri) (19%). The antimicrobial susceptibility tests indicated that 31 isolates were resistant to at least three classes of antibiotics and contain the highest level of ESBL resistance genes. Conclusions: Pseudomonas aeruginosa and Acinetobacter baumannii were the most widely recognized NLFGNB identified from hospital-acquired infections in Soba hospital. Among the NLFGNB, antimicrobial resistance and ESBL resistance genes were observed at a high frequency.

Download Full-text

Identification of Two Regulators of Virulence That Are Conserved inKlebsiella pneumoniaeClassical and Hypervirulent Strains

mBio ◽

10.1128/mbio.01443-18 ◽

2018 ◽

Vol 9 (4) ◽

Cited By ~ 18

Author(s):

Michelle Palacios ◽

Taryn A. Miner ◽

Daniel R. Frederick ◽

Victoria E. Sepulveda ◽

Joshua D. Quinn ◽

...

Keyword(s):

Gene Expression ◽

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Virulence Factors ◽

Content Type ◽

Hospital Acquired Infections ◽

Capsule Type ◽

Capsule Production ◽

Invasive Infections ◽

Hospital Acquired

ABSTRACTKlebsiella pneumoniaeis widely recognized as a pathogen with a propensity for acquiring antibiotic resistance. It is capable of causing a range of hospital-acquired infections (urinary tract infections [UTI], pneumonia, sepsis) and community-acquired invasive infections. The genetic heterogeneity ofK. pneumoniaeisolates complicates our ability to understand the virulence ofK. pneumoniae. Characterization of virulence factors conserved between strains as well as strain-specific factors will improve our understanding of this important pathogen. The MarR family of regulatory proteins is widely distributed in bacteria and regulates cellular processes such as antibiotic resistance and the expression of virulence factors.Klebsiellaencodes numerous MarR-like proteins, and they likely contribute to the ability ofK. pneumoniaeto respond to and survive under a wide variety of environmental conditions, including those present in the human body. We tested loss-of-function mutations in all themarRhomologues in a murine pneumonia model and found that two (kvrAandkvrB) significantly impacted the virulence of K1 and K2 capsule type hypervirulent (hv) strains and thatkvrAaffected the virulence of a sequence type 258 (ST258) classical strain. In thehvstrains,kvrAandkvrBmutants displayed phenotypes associated with reduced capsule production, mucoviscosity, and transcription fromgalFandmanCpromoters that drive expression of capsule synthesis genes. In contrast,kvrAandkvrBmutants in the ST258 strain had no effect on capsule gene expression or capsule-related phenotypes. Thus, KvrA and KvrB affect virulence in classical andhvstrains but the effect on virulence may not be exclusively due to effects on capsule production.IMPORTANCEIn addition to having a reputation as the causative agent for hospital-acquired infections as well as community-acquired invasive infections,Klebsiella pneumoniaehas gained widespread attention as a pathogen with a propensity for acquiring antibiotic resistance. Due to the rapid emergence of carbapenem resistance amongK. pneumoniaestrains, a better understanding of virulence mechanisms and identification of new potential drug targets are needed. This study identified two novel regulators (KvrA and KvrB) of virulence inK. pneumoniaeand demonstrated that their effect on virulence in invasive strains is likely due in part to effects on capsule production (a major virulence determinant) and hypermucoviscosity. KvrA also impacts the virulence of classical strains but does not appear to affect capsule gene expression in this strain. KvrA and KvrB are conserved amongK. pneumoniaestrains and thus could regulate capsule expression and virulence in diverse strains regardless of capsule type.

Download Full-text