Review

17 pages, 917 KiB

Open AccessReview

Chronic Granulomatous Disease (CGD): Commonly Associated Pathogens, Diagnosis and Treatment

by Angel A. Justiz-Vaillant, Arlene Faye-Ann Williams-Persad, Rodolfo Arozarena-Fundora, Darren Gopaul, Sachin Soodeen, Odalis Asin-Milan, Reinand Thompson, Chandrashekhar Unakal and Patrick Eberechi Akpaka

Microorganisms 2023, 11(9), 2233; https://doi.org/10.3390/microorganisms11092233 - 05 Sep 2023

Cited by 2 | Viewed by 2197

Abstract

Chronic granulomatous disease (CGD) is a primary immunodeficiency caused by a defect in the phagocytic function of the innate immune system owing to mutations in genes encoding the five subunits of the nicotinamide adenine dinucleotide phosphatase (NADPH) oxidase enzyme complex. This review aimed [...] Read more.

Chronic granulomatous disease (CGD) is a primary immunodeficiency caused by a defect in the phagocytic function of the innate immune system owing to mutations in genes encoding the five subunits of the nicotinamide adenine dinucleotide phosphatase (NADPH) oxidase enzyme complex. This review aimed to provide a comprehensive approach to the pathogens associated with chronic granulomatous disease (CGD) and its management. Patients with CGD, often children, have recurrent life-threatening infections and may develop infectious or inflammatory complications. The most common microorganisms observed in the patients with CGD are Staphylococcus aureus, Aspergillus spp., Candida spp., Nocardia spp., Burkholderia spp., Serratia spp., and Salmonella spp. Antibacterial prophylaxis with trimethoprim-sulfamethoxazole, antifungal prophylaxis usually with itraconazole, and interferon gamma immunotherapy have been successfully used in reducing infection in CGD. Haematopoietic stem cell transplantation (HCT) have been successfully proven to be the treatment of choice in patients with CGD. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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32 pages, 1503 KiB

Open AccessReview

Uropathogenic Escherichia coli (UPEC)-Associated Urinary Tract Infections: The Molecular Basis for Challenges to Effective Treatment

by Shane Whelan, Brigid Lucey and Karen Finn

Microorganisms 2023, 11(9), 2169; https://doi.org/10.3390/microorganisms11092169 - 28 Aug 2023

Cited by 6 | Viewed by 6207

Abstract

Urinary tract infections (UTIs) are among the most common bacterial infections, especially among women and older adults, leading to a significant global healthcare cost burden. Uropathogenic Escherichia coli (UPEC) are the most common cause and accounts for the majority of community-acquired UTIs. Infection [...] Read more.

Urinary tract infections (UTIs) are among the most common bacterial infections, especially among women and older adults, leading to a significant global healthcare cost burden. Uropathogenic Escherichia coli (UPEC) are the most common cause and accounts for the majority of community-acquired UTIs. Infection by UPEC can cause discomfort, polyuria, and fever. More serious clinical consequences can result in urosepsis, kidney damage, and death. UPEC is a highly adaptive pathogen which presents significant treatment challenges rooted in a complex interplay of molecular factors that allow UPEC to evade host defences, persist within the urinary tract, and resist antibiotic therapy. This review discusses these factors, which include the key genes responsible for adhesion, toxin production, and iron acquisition. Additionally, it addresses antibiotic resistance mechanisms, including chromosomal gene mutations, antibiotic deactivating enzymes, drug efflux, and the role of mobile genetic elements in their dissemination. Furthermore, we provide a forward-looking analysis of emerging alternative therapies, such as phage therapy, nano-formulations, and interventions based on nanomaterials, as well as vaccines and strategies for immunomodulation. This review underscores the continued need for research into the molecular basis of pathogenesis and antimicrobial resistance in the treatment of UPEC, as well as the need for clinically guided treatment of UTIs, particularly in light of the rapid spread of multidrug resistance. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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22 pages, 1305 KiB

Open AccessReview

International Clones of High Risk of Acinetobacter Baumannii—Definitions, History, Properties and Perspectives

by Andrey Shelenkov, Vasiliy Akimkin and Yulia Mikhaylova

Microorganisms 2023, 11(8), 2115; https://doi.org/10.3390/microorganisms11082115 - 19 Aug 2023

Cited by 2 | Viewed by 1713

Abstract

Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of [...] Read more.

Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of A. baumannii is driven by several lineages named ‘international clones of high risk’ (ICs), two of which were first revealed in the 1970s. Epidemiological surveillance is a crucial tool for controlling the spread of this pathogen, which currently increasingly involves whole genome sequencing. However, the assignment of a particular A. baumannii isolate to some IC based on its genomic sequence is not always straightforward and requires some computational skills from researchers, while the definitions found in the literature are sometimes controversial. In this review, we will focus on A. baumannii typing tools suitable for IC determination, provide data to easily determine IC assignment based on MLST sequence type (ST) and intrinsic bla_OXA-51_-like gene variants, discuss the history and current spread data of nine known ICs, IC1-IC9, and investigate the representation of ICs in public databases. MLST and cgMLST profiles, as well as OXA-51-like presence data are provided for all isolates available in GenBank. The possible emergence of a novel A. baumannii international clone, IC10, will be discussed. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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14 pages, 1959 KiB

Open AccessReview

Fungal Osteomyelitis: A Systematic Review of Reported Cases

by Erika Asperges, Giuseppe Albi, Francesco Truffelli, Andrea Salvaderi, Flavia Puci, Aurelia Sangani, Valentina Zuccaro, Valeria Scotti, Paolo Orsolini, Enrico Brunetti and Raffaele Bruno

Microorganisms 2023, 11(7), 1828; https://doi.org/10.3390/microorganisms11071828 - 17 Jul 2023

Cited by 1 | Viewed by 2212

Abstract

Fungal osteomyelitis is considered a rare disease, and the published literature mainly comprises case reports, case series and narrative reviews. A systematic review was undertaken to provide a practice-based global perspective on this disease, focusing on epidemiology and treatment strategies. We searched MEDLINE, [...] Read more.

Fungal osteomyelitis is considered a rare disease, and the published literature mainly comprises case reports, case series and narrative reviews. A systematic review was undertaken to provide a practice-based global perspective on this disease, focusing on epidemiology and treatment strategies. We searched MEDLINE, EMBASE and Cochrane Library between the 3rd and 8th of March 2023 using a predefined search string. We included studies with at least one patient with a diagnosis of fungal osteomyelitis published before the 1st of January 2023. We included all study designs except for reviews, and we excluded non-English languages and grey literature. After exclusion, 678 studies, mostly case reports, were included. Descriptive analysis was performed on 1072 patients. The most common aetiological agent was Aspergillus (26.5%), followed by Candida (20.7%) and Mucor (16.8%), and the bones most frequently involved were the vertebrae. We described the characteristics of patients divided by site of infection, and we found that diabetes mellitus, disseminated fungal infection, surgery and local lesion were major risk factors. We also successfully associated duration of treatment with outcome. We provided a general overview of this rare disease, and we highlighted the need for high-quality investigations on the subject. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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28 pages, 3444 KiB

Open AccessReview

Milk Transmission of Mammalian Retroviruses

by Laura M. Kemeter, Alexandra Birzer, Stefanie Heym and Andrea K. Thoma-Kress

Microorganisms 2023, 11(7), 1777; https://doi.org/10.3390/microorganisms11071777 - 08 Jul 2023

Cited by 1 | Viewed by 2919

Abstract

The transmission of viruses from one host to another typically occurs through horizontal or vertical pathways. The horizontal pathways include transmission amongst individuals, usually through bodily fluids or excretions, while vertical transmission transpires from mother to their offspring, either during pregnancy, childbirth, or [...] Read more.

The transmission of viruses from one host to another typically occurs through horizontal or vertical pathways. The horizontal pathways include transmission amongst individuals, usually through bodily fluids or excretions, while vertical transmission transpires from mother to their offspring, either during pregnancy, childbirth, or breastfeeding. While there are more than 200 human pathogenic viruses to date, only a small number of them are known to be transmitted via breast milk, including cytomegalovirus (CMV), human immunodeficiency virus type 1 (HIV-1), and human T cell lymphotropic virus type 1 (HTLV-1), the latter two belonging to the family Retroviridae. Breast milk transmission is a common characteristic among mammalian retroviruses, but there is a lack of reports summarizing our knowledge regarding this route of transmission of mammalian retroviruses. Here, we provide an overview of the transmission of mammalian exogenous retroviruses with a focus on Orthoretrovirinae, and we highlight whether they have been described or suspected to be transmitted through breast milk, covering various species. We also elaborate on the production and composition of breast milk and discuss potential entry sites of exogenous mammalian retroviruses during oral transmission. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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16 pages, 834 KiB

Open AccessReview

Pulmonary Tuberculosis in Children: A Forgotten Disease?

by Umberto Pelosi, Roberta Pintus, Salvatore Savasta and Vassilios Fanos

Microorganisms 2023, 11(7), 1722; https://doi.org/10.3390/microorganisms11071722 - 30 Jun 2023

Cited by 2 | Viewed by 2534

Abstract

Even today, tuberculosis in childhood is a disease that is often undiagnosed and undertreated. In the absence of therapy with antituberculosis drugs, children in the first years of life have a high degree of severe forms and mortality. In these children, symptoms are [...] Read more.

Even today, tuberculosis in childhood is a disease that is often undiagnosed and undertreated. In the absence of therapy with antituberculosis drugs, children in the first years of life have a high degree of severe forms and mortality. In these children, symptoms are often not very specific and can easily be confused with other diseases of bacterial, viral or fungal etiology, making diagnosis more difficult. Nevertheless, the introduction of new diagnostic techniques has allowed a more rapid identification of the infection. Indeed, Interferon gamma release assay (IGRA) is preferred to the Mantoux, albeit with obvious limitations in children aged <2 years. While the Xpert Mtb/RIF Ultra test is recommended as an initial diagnostic investigation of the gastric aspirate and/or stools in children with signs and symptoms of pulmonary tuberculosis. The drugs used in the treatment of susceptible and resistant TB are the same as those used in adults but doses and combinations are different in the pediatric age. In children, brief therapy is preferable in both the latent infection and the active disease, as a significant reduction in side effects is obtained. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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21 pages, 817 KiB

Open AccessReview

Eradication of Drug-Tolerant Mycobacterium tuberculosis 2022: Where We Stand

by Alessio Lanni, Angelo Iacobino, Lanfranco Fattorini and Federico Giannoni

Microorganisms 2023, 11(6), 1511; https://doi.org/10.3390/microorganisms11061511 - 06 Jun 2023

Cited by 2 | Viewed by 1671

Abstract

The lungs of tuberculosis (TB) patients contain a spectrum of granulomatous lesions, ranging from solid and well-vascularized cellular granulomas to avascular caseous granulomas. In solid granulomas, current therapy kills actively replicating (AR) intracellular bacilli, while in low-vascularized caseous granulomas the low-oxygen tension stimulates [...] Read more.

The lungs of tuberculosis (TB) patients contain a spectrum of granulomatous lesions, ranging from solid and well-vascularized cellular granulomas to avascular caseous granulomas. In solid granulomas, current therapy kills actively replicating (AR) intracellular bacilli, while in low-vascularized caseous granulomas the low-oxygen tension stimulates aerobic and microaerophilic AR bacilli to transit into non-replicating (NR), drug-tolerant and extracellular stages. These stages, which do not have genetic mutations and are often referred to as persisters, are difficult to eradicate due to low drug penetration inside the caseum and mycobacterial cell walls. The sputum of TB patients also contains viable bacilli called differentially detectable (DD) cells that, unlike persisters, grow in liquid, but not in solid media. This review provides a comprehensive update on drug combinations killing in vitro AR and drug-tolerant bacilli (persisters and DD cells), and sterilizing Mycobacterium tuberculosis-infected BALB/c and caseum-forming C3HeB/FeJ mice. These observations have been important for testing new drug combinations in noninferiority clinical trials, in order to shorten the duration of current regimens against TB. In 2022, the World Health Organization, following the results of one of these trials, supported the use of a 4-month regimen for the treatment of drug-susceptible TB as a possible alternative to the current 6-month regimen. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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16 pages, 2972 KiB

Open AccessReview

A Putative Role of Candida albicans in Promoting Cancer Development: A Current State of Evidence and Proposed Mechanisms

by Jasminka Talapko, Tomislav Meštrović, Branko Dmitrović, Martina Juzbašić, Tatjana Matijević, Sanja Bekić, Suzana Erić, Josipa Flam, Dino Belić, Anamarija Petek Erić, Andrea Milostić Srb and Ivana Škrlec

Microorganisms 2023, 11(6), 1476; https://doi.org/10.3390/microorganisms11061476 - 01 Jun 2023

Cited by 6 | Viewed by 3172

Abstract

Candida albicans is a commensal fungal species that commonly colonizes the human body, but it is also a pervasive opportunistic pathogen in patients with malignant diseases. A growing body of evidence suggests that this fungus is not only coincidental in oncology patients, but [...] Read more.

Candida albicans is a commensal fungal species that commonly colonizes the human body, but it is also a pervasive opportunistic pathogen in patients with malignant diseases. A growing body of evidence suggests that this fungus is not only coincidental in oncology patients, but may also play an active role in the development of cancer. More specifically, several studies have investigated the potential association between C. albicans and various types of cancer, including oral, esophageal, and colorectal cancer, with a possible role of this species in skin cancer as well. The proposed mechanisms include the production of carcinogenic metabolites, modulation of the immune response, changes in cell morphology, microbiome alterations, biofilm production, the activation of oncogenic signaling pathways, and the induction of chronic inflammation. These mechanisms may act together or independently to promote cancer development. Although more research is needed to fully grasp the potential role of C. albicans in carcinogenesis, the available evidence suggests that this species may be an active contributor and underscores the importance of considering the impact of the human microbiome on cancer pathogenesis. In this narrative review, we aimed to summarize the current state of evidence and offer some insights into proposed mechanisms. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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19 pages, 1571 KiB

Open AccessReview

Chlamydia Infection Remodels Host Cell Mitochondria to Alter Energy Metabolism and Subvert Apoptosis

by Heng Choon Cheong, Sofiah Sulaiman, Chung Yeng Looi, Li-Yen Chang and Won Fen Wong

Microorganisms 2023, 11(6), 1382; https://doi.org/10.3390/microorganisms11061382 - 24 May 2023

Cited by 1 | Viewed by 1908

Abstract

Chlamydia infection represents an important cause for concern for public health worldwide. Chlamydial infection of the genital tract in females is mostly asymptomatic at the early stage, often manifesting as mucopurulent cervicitis, urethritis, and salpingitis at the later stage; it has been associated [...] Read more.

Chlamydia infection represents an important cause for concern for public health worldwide. Chlamydial infection of the genital tract in females is mostly asymptomatic at the early stage, often manifesting as mucopurulent cervicitis, urethritis, and salpingitis at the later stage; it has been associated with female infertility, spontaneous abortion, ectopic pregnancy, and cervical cancer. As an obligate intracellular bacterium, Chlamydia depends heavily on host cells for nutrient acquisition, energy production, and cell propagation. The current review discusses various strategies utilized by Chlamydia in manipulating the cell metabolism to benefit bacterial propagation and survival through close interaction with the host cell mitochondrial and apoptotic pathway molecules. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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14 pages, 2471 KiB

Open AccessReview

Relative Abundance and Detection of Pseudomonas aeruginosa from Chronic Wound Infections Globally

by Sang Phan, Cafrey He Feng, Raymond Huang, Zeng X. Lee, Yer Moua, Olivia J. Phung and Justin R. Lenhard

Microorganisms 2023, 11(5), 1210; https://doi.org/10.3390/microorganisms11051210 - 05 May 2023

Cited by 4 | Viewed by 3209

Abstract

Pseudomonas aeruginosa is a difficult-to-treat pathogen that is frequently involved with chronic wound infections. Here, we conducted a literature search of world-wide studies published between 2005 and 2022 that described the microbiological profiles of chronic wound infections. For each continent, a hierarchy of [...] Read more.

Pseudomonas aeruginosa is a difficult-to-treat pathogen that is frequently involved with chronic wound infections. Here, we conducted a literature search of world-wide studies published between 2005 and 2022 that described the microbiological profiles of chronic wound infections. For each continent, a hierarchy of pathogens was created to define the organisms that were most frequently isolated in each region. Except for South America, P. aeruginosa was the second most common organism in each major continent, with Staphylococcus aureus being the most abundant pathogen overall. When individual countries were evaluated, P. aeruginosa was the most frequently isolated organism in several Southeast Asia nations including India and Malaysia. P. aeruginosa was less commonly isolated from diabetic foot infections in North America, Europe, and Africa in comparison to other types of chronic wound infections. Additionally, the Levine wound swab technique may be a quick and painless way to isolate P. aeruginosa from wound infections, but the isolation of P. aeruginosa does not seem to be an informative predictor of the patient’s clinical course. A multivariate risk assessment that accounts for the regional frequency of P. aeruginosa isolation may be an appropriate way to guide empiric management of chronic wound infections. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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29 pages, 864 KiB

Open AccessReview

Paediatric Asthma and the Microbiome: A Systematic Review

by Marwh G. Aldriwesh, Abrar M. Al-Mutairi, Azzah S. Alharbi, Hassan Y. Aljohani, Nabeel A. Alzahrani, Reham Ajina and Abdullah M. Alanazi

Microorganisms 2023, 11(4), 939; https://doi.org/10.3390/microorganisms11040939 - 03 Apr 2023

Cited by 3 | Viewed by 2089

Abstract

Evidence from the literature suggests an association between the microbiome and asthma development. Here, we aimed to identify the current evidence for the association between asthma and the upper airway, lower airway and/or the gut microbiome. An electronic systemic search of PubMed, EBSCO, [...] Read more.

Evidence from the literature suggests an association between the microbiome and asthma development. Here, we aimed to identify the current evidence for the association between asthma and the upper airway, lower airway and/or the gut microbiome. An electronic systemic search of PubMed, EBSCO, Science Direct and Web of Science was conducted until February 2022 to identify the eligible studies. The Newcastle–Ottawa Scale and the Systematic Review Centre for Laboratory Animal Experimentation risk of the bias tools were used to assess quality of included studies. Twenty-five studies met the inclusion criteria. Proteobacteria and Firmicutes were identified as being significantly higher in the asthmatic children compared with the healthy controls. The high relative abundance of Veillonella, Prevotella and Haemophilus in the microbiome of the upper airway in early infancy was associated with a higher risk of asthma development later in life. The gut microbiome analyses indicated that a high relative abundance of Clostridium in early childhood might be associated with asthma development later in life. The findings reported here serve as potential microbiome signatures associated with the increased risk of asthma development. There is a need for large longitudinal studies to further identify high-risk infants, which will help in design strategies and prevention mechanisms to avoid asthma early in life. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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