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Pathogens
Special Issues
Nosocomial Infection and Antimicrobial Resistance
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Nosocomial Infection and Antimicrobial Resistance

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Epidemiology of Infectious Diseases".

Deadline for manuscript submissions: 15 September 2024 | Viewed by 8352

Special Issue Editors

Prof. Dr. Graciela Castro-Escarpulli

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Guest Editor
Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
Interests: molecular epidemiology; nosocomial outbreaks; antimicrobial resistance; diagnostic medical bacteriology, infectious diseases
Dr. Juan Manuel Bello-López

E-Mail Website
Guest Editor
División de Investigación, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Ciudad de México 07760, Mexico
Interests: epidemiology; molecular epidemiology; healthcare-associated infections; nosocomial outbreaks; antimicrobial resistance
Dr. Cecilia Hernandez-Cortez

E-Mail Website
Guest Editor
Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
Interests: microbial metabolism; pigment production; molecular methods; antimicrobial resistance

Special Issue Information

Dear Colleagues,

Nosocomial infections, which are also called healthcare-associated infections (HAI), are those infectious diseases that are acquired during the hospital stay but which are not present at the time of admission of the patient or in the incubation period of the infectious agent. These types of infections are characterized by their tendency to appear after the first 48 hours post-admission and, depending on the type of infection, may be accompanied by specific signs and symptoms. Among HAIs are urinary tract infections associated with catheter use, ventilator-associated pneumonia, surgical site infection and catheter-associated bloodstream infection.

According to the scientific literature, no country in the world is free from these types of conditions, even though developing countries may be the most affected by these adverse events. Undoubtedly, the COVID-19 pandemic caused by the SARS-CoV-2 coronavirus was one of the main factors that contributed significantly in the last three years to the increase in this type of nosocomial infections regardless of the country's development, and in many cases the spread of these infections led to the appearance of outbreaks among COVID-19 patients.

It is known that the nosocomial microbiological reservoir is directly related to these types of infections where ESKAPE group bacteria are recognized as the main causative agents of nosocomial infections. The ESKAPE group of bacteria is a heterogeneous group of potentially pathogenic Gram-negative and Gram-positive bacteria consisting of various bacterial genera and species such as: Enterobacter spp. species, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and the group of Enterocuccus spp. and Enterobacterales. The latter group includes a significant number of enterobacterial genera of medical importance.

Technological advances in the field of health in recent decades have made it possible to mitigate these ailments; however, another public health problem has arisen: antimicrobial resistance. Antimicrobial resistance generates additional problems that hinder antimicrobial therapies and consequently increase morbidity and mortality rates. In this changing context, Pathogens is launching a Special Issue entitled “Nosocomial Infection and Antimicrobial Resistance”.

Both original research and review articles. Potential topics include:

  • Identification and genetic characterization of nosocomial outbreaks;
  • Detection of antimicrobial resistance mechanisms in pathogens causing healthcare-associated infections;
  • Classical and molecular epidemiology in the detection and containment of nosocomial outbreaks;
  • Implementation and/or validation of diagnostic tests for resistance mechanisms in nosocomial pathogens;
  • Antimicrobial susceptibility studies with new antimicrobials in nosocomial pathogens;
  • Epidemiological surveillance of high-risk nosocomial clones;
  • Interhospital dissemination studies of nosocomial pathogens.

Prof. Dr. Graciela Castro-Escarpulli
Dr. Juan Manuel Bello-López
Dr. Cecilia Hernandez-Cortez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pathogens is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (6 papers)

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Research

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11 pages, 1480 KiB  
Article
Acquired blaVIM and blaGES Carbapenemase-Encoding Genes in Pseudomonas aeruginosa: A Seven-Year Survey Highlighting an Increasing Epidemiological Threat
by María Guadalupe Martínez-Zavaleta, Diana Fernández-Rodríguez, Melissa Hernández-Durán, Claudia A. Colín-Castro, María de Lourdes García-Hernández, Noé Becerra-Lobato, Rafael Franco-Cendejas and Luis Esaú López-Jácome
Pathogens 2023, 12(10), 1256; https://doi.org/10.3390/pathogens12101256 - 18 Oct 2023
Viewed by 1165
Abstract
(1) Background: Pseudomonas aeruginosa is a Gram-negative bacterium with several intrinsic and acquired antimicrobial resistance mechanisms. The spread of carbapenemase-encoding genes, an acquired mechanism, enables carbapenem resistance in clinical settings. Detection of the carbapenemase-producer strains is urgent. Therefore, we aimed to characterize carbapenemase [...] Read more.
(1) Background: Pseudomonas aeruginosa is a Gram-negative bacterium with several intrinsic and acquired antimicrobial resistance mechanisms. The spread of carbapenemase-encoding genes, an acquired mechanism, enables carbapenem resistance in clinical settings. Detection of the carbapenemase-producer strains is urgent. Therefore, we aimed to characterize carbapenemase production in the clinical strains of P. aeruginosa at a tertiary-care center. (2) Methods: We included clinical strains of P. aeruginosa (from August 2011 to December 2018) with resistance towards at least one carbapenem. Strains were isolated in a tertiary-care center in Mexico City. Antimicrobial susceptibility profiles were determined by broth microdilution. Screening for carbapenemase-encoding genes was performed in all strains. Phenotypic assays (CarbaNP and mCIM) were conducted. Additional modifications to mCIM were also tested. (3) Results: One-hundred seventy-one P. aeruginosa strains out of 192 included in this study were resistant towards at least one of the carbapenems tested. Forty-seven of these strains harbored a carbapenemase-encoding gene. VIM (59.6%) and GES (23.4%) were the most frequently found carbapenemases in our study, followed by IMP (14.9%). (4) Among the most frequent carbapenemase genes identified, metallo-ß-lactamases were the most prevalent, which impair new treatment options. Searching for carbapenemase genes should be performed in resistant isolates to stop transmission and guide antimicrobial treatment. Full article
(This article belongs to the Special Issue Nosocomial Infection and Antimicrobial Resistance)
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16 pages, 2270 KiB  
Article
Typing of Candida spp. from Colonized COVID-19 Patients Reveal Virulent Genetic Backgrounds and Clonal Dispersion
by Edith Quiroga-Vargas, Miguel Ángel Loyola-Cruz, Araceli Rojas-Bernabé, Mario Adán Moreno-Eutimio, Rodolfo Pastelin-Palacios, Clemente Cruz-Cruz, Emilio Mariano Durán-Manuel, Claudia Calzada-Mendoza, Graciela Castro-Escarpulli, Geovanni Hernández-Hernández, Mónica Alethia Cureño-Díaz, Verónica Fernández-Sánchez and Juan Manuel Bello-López
Pathogens 2023, 12(10), 1206; https://doi.org/10.3390/pathogens12101206 - 29 Sep 2023
Viewed by 887
Abstract
Advances in the knowledge of the pathogenesis of SARS-CoV-2 allowed the survival of COVID-19 patients in intensive care units. However, due to the clinical characteristics of severe patients, they resulted in the appearance of colonization events. Therefore, we speculate that strains of Candida [...] Read more.
Advances in the knowledge of the pathogenesis of SARS-CoV-2 allowed the survival of COVID-19 patients in intensive care units. However, due to the clinical characteristics of severe patients, they resulted in the appearance of colonization events. Therefore, we speculate that strains of Candida spp. isolated from COVID-19 patients have virulent genetic and phenotypic backgrounds involved in clinical worsening of patients. The aim of this work was to virutype Candida spp. strains isolated from colonized COVID-19 patients, analyze their genomic diversity, and establish clonal dispersion in care areas. The virulent potential of Candida spp. strains isolated from colonized COVID-19 patients was determined through adhesion tests and the search for genes involved with adherence and invasion. Clonal association was done by analysis of intergenic spacer regions. Six species of Candida were involved as colonizing pathogens in COVID-19 patients. The genotype analysis revealed the presence of adherent and invasive backgrounds. The distribution of clones was identified in the COVID-19 care areas, where C. albicans was the predominant species. Evidence shows that Candida spp. have the necessary genetic tools to be able colonize the lungs, and could be a possible causal agent of coinfections in COVID-19 patients. The detection of dispersion of opportunistic pathogens can be unnoticed by classical epidemiology. Epidemiological surveillance against opportunistic fungal pathogens in COVID-19 patients is an immediate need, since the findings presented demonstrate the potential virulence of Candida spp. Full article
(This article belongs to the Special Issue Nosocomial Infection and Antimicrobial Resistance)
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28 pages, 10137 KiB  
Article
Non-Structural Proteins (Nsp): A Marker for Detection of Human Coronavirus Families
by María Concepción Tamayo-Ordóñez, Ninfa María Rosas-García, Benjamín Abraham Ayil-Gutiérrez, Juan Manuel Bello-López, Francisco Alberto Tamayo-Ordóñez, Francisco Anguebes-Franseschi, Siprian Damas-Damas and Yahaira de Jesús Tamayo-Ordóñez
Pathogens 2023, 12(9), 1185; https://doi.org/10.3390/pathogens12091185 - 21 Sep 2023
Cited by 2 | Viewed by 1559
Abstract
SARS-CoV-2 was the cause of the global pandemic that caused a total of 14.9 million deaths during the years 2020 and 2021, according to the WHO. The virus presents a mutation rate between 10−5 and 10−3 substitutions per nucleotide site per cell infection [...] Read more.
SARS-CoV-2 was the cause of the global pandemic that caused a total of 14.9 million deaths during the years 2020 and 2021, according to the WHO. The virus presents a mutation rate between 10−5 and 10−3 substitutions per nucleotide site per cell infection (s/n/c). Due to this, studies aimed at knowing the evolution of this virus could help us to foresee (through the future development of new detection strategies and vaccines that prevent the infection of this virus in human hosts) that a pandemic caused by this virus will be generated again. In this research, we performed a functional annotation and identification of changes in Nsp (non-structural proteins) domains in the coronavirus genome. The comparison of the 13 selected coronavirus pangenomes demonstrated a total of 69 protein families and 57 functions associated with the structural domain’s differentials between genomes. A marked evolutionary conservation of non-structural proteins was observed. This allowed us to identify and classify highly pathogenic human coronaviruses into alpha, beta, gamma, and delta groups. The designed Nsp cluster provides insight into the trajectory of SARS-CoV-2, demonstrating that it continues to evolve rapidly. An evolutionary marker allows us to discriminate between phylogenetically divergent groups, viral genotypes, and variants between the alpha and betacoronavirus genera. These types of evolutionary studies provide a window of opportunity to use these Nsp as targets of viral therapies. Full article
(This article belongs to the Special Issue Nosocomial Infection and Antimicrobial Resistance)
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Review

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12 pages, 261 KiB  
Review
New Frontier on Antimicrobial Therapy: Long-Acting Lipoglycopeptides
by Valentina Siciliano, Flavio Sangiorgi, Pierluigi Del Vecchio, Layla Vahedi, Maya Manuela Gross, Angela Saviano and Veronica Ojetti
Pathogens 2024, 13(3), 189; https://doi.org/10.3390/pathogens13030189 - 20 Feb 2024
Viewed by 921
Abstract
Long-acting lipoglycopeptides (LGPs), such as dalbavancin and oritavancin, are semisynthetic antibiotics known for their strong effectiveness against a wide array of Gram-positive bacteria. This includes Staphylococcus aureus, both methicillin-sensitive (MSSA) and methicillin-resistant (MRSA) strains, coagulase-negative Staphylococci (CoNS), streptococci, and vancomycin-sensitive Enterococcus faecalis [...] Read more.
Long-acting lipoglycopeptides (LGPs), such as dalbavancin and oritavancin, are semisynthetic antibiotics known for their strong effectiveness against a wide array of Gram-positive bacteria. This includes Staphylococcus aureus, both methicillin-sensitive (MSSA) and methicillin-resistant (MRSA) strains, coagulase-negative Staphylococci (CoNS), streptococci, and vancomycin-sensitive Enterococcus faecalis. A literature search was conducted on PubMed and on ClinicalTrials.gov to identify articles published until July 2023 investigating the use of oritavancin and dalbavancin in clinical practice. The review included case reports, case series, observational studies, and clinical studies. Although more consistent data are needed, LGPs seem to be a good alternative that may provide a quicker hospital discharge and reduce long-term intravenous access and therapy. This is attributed to their unique pharmacologic and pharmacokinetic characteristics. More quality data (i.e., number of patients treated with clinical success) are needed before clinicians may use these therapies more widely. Full article
(This article belongs to the Special Issue Nosocomial Infection and Antimicrobial Resistance)
17 pages, 767 KiB  
Review
Clostridioides difficile Infection: Diagnosis and Treatment Challenges
by John E. Markantonis, John T. Fallon, Rajat Madan and Md Zahidul Alam
Pathogens 2024, 13(2), 118; https://doi.org/10.3390/pathogens13020118 - 27 Jan 2024
Viewed by 1936
Abstract
Clostridioides difficile is the most important cause of healthcare-associated diarrhea in the United States. The high incidence and recurrence rates of C. difficile infection (CDI), associated with high morbidity and mortality, pose a public health challenge. Although antibiotics targeting C. difficile bacteria are [...] Read more.
Clostridioides difficile is the most important cause of healthcare-associated diarrhea in the United States. The high incidence and recurrence rates of C. difficile infection (CDI), associated with high morbidity and mortality, pose a public health challenge. Although antibiotics targeting C. difficile bacteria are the first treatment choice, antibiotics also disrupt the indigenous gut flora and, therefore, create an environment that is favorable for recurrent CDI. The challenge of treating CDI is further exacerbated by the rise of antibiotic-resistant strains of C. difficile, placing it among the top five most urgent antibiotic resistance threats in the USA. The evolution of antibiotic resistance in C. difficile involves the acquisition of new resistance mechanisms, which can be shared among various bacterial species and different C. difficile strains within clinical and community settings. This review provides a summary of commonly used diagnostic tests and antibiotic treatment strategies for CDI. In addition, it discusses antibiotic treatment and its resistance mechanisms. This review aims to enhance our current understanding and pinpoint knowledge gaps in antimicrobial resistance mechanisms in C. difficile, with an emphasis on CDI therapies. Full article
(This article belongs to the Special Issue Nosocomial Infection and Antimicrobial Resistance)
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Other

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11 pages, 1084 KiB  
Brief Report
Phenotypic and Genotypic Drug Resistance of Mycobacterium tuberculosis Strains Isolated from HIV-Infected Patients from a Third-Level Public Hospital in Mexico
by Daniel Valencia-Trujillo, Amanda Marineth Avila-Trejo, Rocío Liliana García-Reyes, Luis Narváez-Díaz, Mario Alberto Mújica-Sánchez, Addy Cecilia Helguera-Repetto, Eduardo Becerril-Vargas, Mónica Maribel Mata-Miranda, Sandra Rivera-Gutiérrez and Jorge Francisco Cerna-Cortés
Pathogens 2024, 13(2), 98; https://doi.org/10.3390/pathogens13020098 - 23 Jan 2024
Viewed by 1073
Abstract
Background: Drug-resistant tuberculosis (TB) is associated with higher mortality rates in patients with human immunodeficiency virus (HIV). In Mexico, the number of deaths due to TB among the HIV-positive population has tripled in recent years. Methods: Ninety-three Mycobacterium tuberculosis strains isolated from the [...] Read more.
Background: Drug-resistant tuberculosis (TB) is associated with higher mortality rates in patients with human immunodeficiency virus (HIV). In Mexico, the number of deaths due to TB among the HIV-positive population has tripled in recent years. Methods: Ninety-three Mycobacterium tuberculosis strains isolated from the same number of HIV-infected patients treated in a public hospital in Mexico City were studied to determine the drug resistance to first- and second-line anti-TB drugs and to identify the mutations associated with the resistance. Results: Of the 93 patients, 82.7% were new TB cases, 86% were male, and 73% had extrapulmonary TB. Most patients (94%) with a CD4 T-lymphocyte count <350 cells/mm3 were associated with extrapulmonary TB (p <0.0001), whilst most patients (78%) with a CD4 T-lymphocyte count >350 cells/mm3 were associated with pulmonary TB (p = 0.0011). Eighty-two strains were pan-susceptible, four mono-resistant, four poly-resistant, two multidrug-resistant, and one was extensively drug-resistant. In the rifampicin-resistant strains, rpoB S531L was the mutation most frequently identified, whereas the inhA C15T and katG S315T1 mutations were present in isoniazid-resistant strains. The extensively drug-resistant strain also contained the mutation gyrA D94A. Conclusions: These data highlight the need to promptly diagnose the drug resistance of M. tuberculosis among all HIV-infected patients by systematically offering access to first- and second-line drug susceptibility testing and to tailor the treatment regimen based on the resistance patterns to reduce the number of deaths in HIV-infected patients. Full article
(This article belongs to the Special Issue Nosocomial Infection and Antimicrobial Resistance)
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