Advancements in Pathogenic Bacteria: Detection, Genomic Analysis, and Antibiotic Resistance

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 5998

Special Issue Editor


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Guest Editor
Basic Health Sciences Department, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, Brazil
Interests: pathogenic bacteria; microbiology; genomic analysis and molecular biology; antibiotic resistance; detection methods and innovation

Special Issue Information

Dear Colleagues,

The detection of pathogenic, identification and susceptibility testing have been the core of microbiology labs, either in the diagnostic fields or research laboratories.

Bacterial infections can have a devastating effect on patients, especially in cases of sepsis, deep-seated infections and meningitis, which are associated with high rates of mortality. In recent years, immunocompromised patients have challenged microbiologists because even commensal organisms with low pathogenicity can cause serious infections among these patients.

The identification of microorganisms, especially uncommon bacteria, is a challenge for microbiologists, who have been relying mainly on biochemical tests for identification; however, technology has advanced in this field and the use of mass-spectrum (MALDI_TOF) and genomic analysis has revolutionized this field. From specific PCR and real-time PCR assays to whole-genome sequencing, bacterial identification is becoming more sophisticated and challenging for microbiologists and new, reliable and easy-to-use tools are necessary.

The wide spread of antimicrobial resistance (AMR) among even common bacterial isolates has become another significant challenge, not only in terms of the identification of these pathogens but also in the development of faster detection methods, which could detect infected patients or carriers of such organisms, thus aiding in the prevention of dissemination to other patients and helping customize the use of the appropriate antimicrobial agent.

This Special Issue aims to provide a collection of articles that showcase the current issues relating to the detection, genomic analysis and antibiotic resistance of pathogenic bacteria.

Prof. Dr. Vlademir Vicente Cantarelli
Guest Editor

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Keywords

  • bacterial infections
  • immunocompromised patients
  • identification methods
  • mass spectrometry
  • genomic analysis
  • antimicrobial resistance (AMR)
  • faster detection methods
  • pathogenic bacteria
  • new bacterial pathogens

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Published Papers (4 papers)

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Research

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11 pages, 1099 KiB  
Article
Hand Carriage of Yeast in Student of Medicine, Nursing, and Medical Laboratory Science: Impact of Infection Control Measures
by Víctor Silva, Ceidy Silva, Coral Silva, Rodrigo Gacitúa, Hernán Salas, Neftalí Guzmán, Claudio Alburquenque and Viviana Silva-Abello
Microorganisms 2024, 12(9), 1907; https://doi.org/10.3390/microorganisms12091907 - 19 Sep 2024
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Abstract
We studied yeast hand carriage of 260 healthcare students. We isolated yeasts in 27 students (10.4%), without differences between medicine, nursing, and medical laboratory science programs and gender. A significant lower prevalence of carriage was shown in the clinical cycle (2.7%) compared to [...] Read more.
We studied yeast hand carriage of 260 healthcare students. We isolated yeasts in 27 students (10.4%), without differences between medicine, nursing, and medical laboratory science programs and gender. A significant lower prevalence of carriage was shown in the clinical cycle (2.7%) compared to the basic cycle (13.5%) (p = 0.022) and the preclinical cycle (13.5%) (p = 0.014). Increased handwashing frequency and the use of alcohol gel and antiseptic soap decreased yeast carriage. Students who applied moisturizing hand cream two or more times a day had a lower frequency of yeast carriage (3.4%) than those who did not use it or used it once a day (16.5%), showing a significant difference (p = 0.016). The most prevalent species was C. parapsilosis sensu stricto (81.5%), followed by Meyerozyma guilliermondii (C. guillermondii) (7.4%), Trichosporon mucoides (7.4%), and R. mucilagenosa (3.7%). One case showed mixed carriage of C. parapsilosis and C. albicans. All strains were sensitive to voriconazole, caspofungin, and anidulafungin. This study shows hand carriage of yeast in health students, mainly by C. parapsilosis, and the frequency of infection control measures and moisturizing hand cream is associated with colonization control. Full article
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13 pages, 1008 KiB  
Article
Multidisciplinary Effort Leading to Effective Tuberculosis Community Outbreak Containment in Israel
by Inbal Fuchs, Yelena Losev, Zohar Mor, Mor Rubinstein, Marina Polyakov, Tali Wagner, Tamar Gobay, Ester Bayene, Gila Mula, Hasia Kaidar-Shwartz, Zeev Dveyrin, Efrat Rorman, Ehud Kaliner and Sivan Haia Perl
Microorganisms 2024, 12(8), 1592; https://doi.org/10.3390/microorganisms12081592 - 5 Aug 2024
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Abstract
Tuberculosis (TB) is the second-most prevalent cause of mortality resulting from infectious diseases worldwide. It is caused by bacteria belonging to the Mycobacterium tuberculosis complex (MTBC). In Israel, TB incidence is low, acknowledged by the WHO as being in a pre-elimination phase. Most [...] Read more.
Tuberculosis (TB) is the second-most prevalent cause of mortality resulting from infectious diseases worldwide. It is caused by bacteria belonging to the Mycobacterium tuberculosis complex (MTBC). In Israel, TB incidence is low, acknowledged by the WHO as being in a pre-elimination phase. Most cases occur among immigrants from high TB incidence regions like the Horn of Africa and the former Soviet Union (FSU), with occasional outbreaks. The outbreak described in this report occurred between 2018 and 2024, increasing the incidence rate of TB in the region. Control of this outbreak posed challenges due to factors including a diverse population (including Ethiopian immigrants, Israeli-born citizens, and immigrants from other countries), economic and social barriers, and hesitancy to disclose information. The unique multidisciplinary team formed to address these challenges, involving the local TB clinic, district health ministry, health maintenance organization (HMO) infectious disease consultant, neighborhood clinic, and National Mycobacterium Reference Laboratory (NMRL), achieved effective treatment and containment. Whole genome sequencing (WGS) proved pivotal in unraveling patient connections during the outbreak. It pinpointed those patients overlooked in initial field investigations, established connections between patients across different health departments, and uncovered the existence of two distinct clusters with separate transmission chains within the same neighborhood. This study underscores collaborative efforts across sectors that successfully contained a challenging outbreak. Full article
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10 pages, 1352 KiB  
Article
Genomic Characterization of a Clinical NDM-1-Producing Klebsiella michiganensis from Brazil
by Amanda Yaeko Yamada, Andreia Rodrigues de Souza, Amanda Maria de Jesus Bertani, Karoline Rodrigues Campos, Claudio Tavares Sacchi, Denise Brandão de Assis, Enéas de Carvalho, Elizabeth Harummyy Takagi, Marcos Paulo Vieira Cunha, Monique Ribeiro Tiba-Casas and Carlos Henrique Camargo
Microorganisms 2024, 12(7), 1408; https://doi.org/10.3390/microorganisms12071408 - 12 Jul 2024
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Abstract
Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, [...] Read more.
Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, identified as the new ST418. Initially, the isolate from a tracheal secretion was misidentified as K. oxytoca. However, accurate identification was achieved through ANI analyses. Whole-genome sequencing was conducted to characterize the genetic context of the resistance genes, to identify virulence factors, and to construct a phylogenetic tree. The blaNDM-1 gene was found to be harbored on an IncFIB plasmid approximately 112 kb in length, which was transferable in conjugation assays. The detection of carbapenem resistance genes in this species highlights the importance of public health vigilance, as it may serve as a reservoir and disseminator of significant resistance genes. Full article
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10 pages, 433 KiB  
Protocol
The Impact of Non-Dysentery Shigella Infection on the Growth and Health of Children over Time (INSIGHT)—A Prospective Case–Control Study Protocol
by Subhra Chakraborty, Sampa Dash, Nowrin Akbar Antara, Bharati Rani Roy, Shamim Al Mamun, Mohammad Ali, Farina Naz, Fatema-Tuz Johura, Jade Lewis, Farzana Afroze, ABM Ali Hasan, David A. Sack, Malathi Ram, Fahmida Tofail, Tahmeed Ahmed and A. S. G. Faruque
Microorganisms 2024, 12(8), 1677; https://doi.org/10.3390/microorganisms12081677 - 15 Aug 2024
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Abstract
(1) Shigella spp. (Shigella) is known for causing dysentery with blood in stool, but most children infected with Shigella have non-dysentery Shigella-associated diarrhea (NDSD). The World Health Organization recommends the use of antibiotics when diarrhea is bloody, leaving most NDSD cases untreated. The [...] Read more.
(1) Shigella spp. (Shigella) is known for causing dysentery with blood in stool, but most children infected with Shigella have non-dysentery Shigella-associated diarrhea (NDSD). The World Health Organization recommends the use of antibiotics when diarrhea is bloody, leaving most NDSD cases untreated. The absence of dysentery may not indicate a low risk of death and severe morbidity. Rapid diagnosis and treatment of shigellosis in vulnerable, young children may be lifesaving. INSIGHT aims to determine the potential benefit of identifying NDSD cases (n = 296) and their outcomes compared to cases of Shigella dysentery [DS (n = 148)] and non-Shigella watery diarrhea [WD (n = 148)]. (2) Children seeking care at hospitals in Bangladesh will be enrolled and followed for 1 year (NDSD and DS) or 90 days (WD). We will determine the impact of NDSD on morbidity, mortality, gut health, nutritional status, and cognitive development compared to DS and WD in children and whether the simple “Rapid LAMP-based Diagnostic Test (RLDT)” can accelerate the detection and treatment of shigellosis in the clinical settings of rural Bangladesh. (3) INSIGHT will determine the impact of NDSD in children and determine if the treatment guidelines of shigellosis need to be revisited to improve clinical outcomes and the development of these children. Full article
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