Microorganisms

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15 pages, 4878 KiB

Open AccessArticle

Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods

by Verónica Fernández-Sánchez, Estibeyesbo Said Plascencia-Nieto, Mónica Alethia Cureño-Díaz, Emilio Mariano Durán-Manuel, Aida Verónica Rodríguez-Tovar, Claudia Camelia Calzada-Mendoza, Clemente Cruz-Cruz, Miguel Ángel Loyola-Cruz, María Elizbeth Álvarez-Sánchez, Juan Carlos Bravata-Alcántara, Enzo Vásquez-Jiménez, Víctor Hugo Gutiérrez-Muñoz, Dulce Milagros Razo Blanco-Hernández, Liliana Nicolás-Sayago, Araceli Rojas-Bernabé, Omar García-Hernández, Erika Gómez-Zamora, Mireya Ruíz-Valdés, Graciela Castro-Escarpulli and Juan Manuel Bello-López

Microorganisms 2025, 13(1), 131; https://doi.org/10.3390/microorganisms13010131 - 10 Jan 2025

Viewed by 969

Abstract

Pyogenic liver abscesses (PLAs) are serious infections in which doctors often fail in identifying the causative agent due to microbiological limitations. These limitations in detecting uncommon pathogens complicate the treatment and recovery. Molecular techniques, like massive sequencing, enable the detection of uncommon pathogens [...] Read more.

Pyogenic liver abscesses (PLAs) are serious infections in which doctors often fail in identifying the causative agent due to microbiological limitations. These limitations in detecting uncommon pathogens complicate the treatment and recovery. Molecular techniques, like massive sequencing, enable the detection of uncommon pathogens and highlight the shortcomings of traditional cultures. The aim of this work was to characterise the bacterial composition of PLAs through massive sequencing of the V3-V4 hypervariable region of the 16S rRNA gene in cases where conventional culture methods were negative. Purulent material was collected from three patients with PLAs at Hospital Juárez de México. Classical and molecular microbiological cultures were performed in parallel. Metagenomic DNA was extracted and massively sequenced (16S rRNA gene) using the Illumina MiSeq platform. A bioinformatic analysis was performed to determine the diversity at six different taxa levels and the relative abundances. The culture methods were not sufficient to detect the causative agent of the PLAs. However, the massive sequencing revealed the causative agents of the monomicrobial and polymicrobial infectious foci, with Gardnerella vaginalis, Lactobacillus iners, and Prevotella timonensis as the dominant bacteria. The massive sequencing revealed the presence of unusual pathogens that traditional culture failed to detect. There is an immediate need for molecular or comprehensive microbiological culture techniques to search for unusual bacteria in the diagnosis of PLAs. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

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12 pages, 1252 KiB

Open AccessArticle

Clostridioides difficile Infections in Children: What Is the Optimal Laboratory Diagnostic Method?

by Mohammed Suleiman, Patrick Tang, Omar Imam, Princess Morales, Diyna Altrmanini, Jill C. Roberts and Andrés Pérez-López

Microorganisms 2024, 12(9), 1785; https://doi.org/10.3390/microorganisms12091785 - 28 Aug 2024

Cited by 1 | Viewed by 1412

Abstract

The diagnosis of Clostridioides difficile infection (CDI) in the pediatric population is complicated by the high prevalence of asymptomatic colonization, particularly in infants. Many laboratory diagnostic methods are available, but there continues to be controversy over the optimal laboratory testing approach to diagnose [...] Read more.

The diagnosis of Clostridioides difficile infection (CDI) in the pediatric population is complicated by the high prevalence of asymptomatic colonization, particularly in infants. Many laboratory diagnostic methods are available, but there continues to be controversy over the optimal laboratory testing approach to diagnose CDI in children. We evaluated commonly used C. difficile diagnostic commercial tests in our pediatric hospital population at Sidra Medicine in Doha, Qatar. Between June and December 2023, 374 consecutive stool samples from pediatric patients aged 0–18 years old were tested using: Techlab C. diff Quik Chek Complete, Cepheid GeneXpert C. difficile, QIAstat-Dx Gastrointestinal Panel, and culture using CHROMagar C. difficile. The results of these tests as standalone methods or in four different testing algorithms were compared to a composite reference method on the basis of turnaround time, ease of use, cost, and performance characteristics including specificity, sensitivity, negative predictive value, and positive predictive value. Our study showed variability in test performance of the different available assays in diagnosing CDI. In our population, a testing algorithm starting with Cepheid GeneXpert C. difficile PCR assay or QIAstat-Dx Gastrointestinal panel as a screening test followed by toxin immunoassay for positive samples using the Techlab C. diff Quik Chek Complete kit showed the best performance (100% specificity and 100% positive predictive value) when combined with clinical review of the patient to assess risk factors for CDI, clinical presentation, and alternative causes of diarrhea. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

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7 pages, 696 KiB

Open AccessCommunication

Evaluation of Direct Antimicrobial Susceptibility Testing of Gram-Negative Bacilli and Staphylococcus aureus from Positive Pediatric Blood Culture Bottles Using BD Phoenix M50

by Princess Morales, Patrick Tang, Elaine Mariano, Arun Gopalan, Nisha Aji, Andrés Pérez-López and Mohammed Suleiman

Microorganisms 2024, 12(8), 1704; https://doi.org/10.3390/microorganisms12081704 - 18 Aug 2024

Viewed by 1622

Abstract

Bloodstream infections (BSIs) are life-threatening infections for which a timely initiation of appropriate antimicrobial therapy is critical. Antibiotic susceptibility testing (AST) directly performed on positive blood culture broths can help initiate targeted antibiotic therapy sooner than the standard AST performed on colonies isolated [...] Read more.

Bloodstream infections (BSIs) are life-threatening infections for which a timely initiation of appropriate antimicrobial therapy is critical. Antibiotic susceptibility testing (AST) directly performed on positive blood culture broths can help initiate targeted antibiotic therapy sooner than the standard AST performed on colonies isolated on solid media after overnight incubation. Faster antimicrobial susceptibility testing (AST) results can improve clinical outcomes, and reduce broad-spectrum antimicrobial consumption and healthcare-associated costs in sepsis. In this study, we evaluated the accuracy of a direct AST inoculation method on the BD Phoenix M50 system using serum separator tubes to harvest bacteria from positive pediatric blood culture bottles. Direct AST was performed on 132 monomicrobial pediatric blood culture bottles that were positive for Enterobacterales (65; 49.2%), Staphylococcus aureus (46; 34.8%), and non-fermenting Gram-negative bacilli (21; 16%). Overall, the categorical and essential agreements between the direct method and standard method were 99.6% and 99.8%, respectively. Very major, major, and minor error rates were 0.1%, 0.09%, and 0.20% respectively. Direct AST performed on pediatric blood culture bottles using BD Phoenix M50 can quickly provide accurate susceptibility information to guide antimicrobial therapy in patients with BSI. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

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15 pages, 2093 KiB

Open AccessArticle

Streptococcus thermophilus iHA318 Improves Dry Eye Symptoms by Mitigating Ocular Surface Damage in a Mouse Model

by Yu-Wei Chang, Yen-Ling Sun, Evelyn Chu, Yi-Yun Hung, Wei-Chieh Liao, Su-Min Tsai, Tsung-Han Lu, Pin-Chao Huang, Chin-Hsiu Yu, Shao-Yu Lee, Han-Hsin Chang and David Pei-Cheng Lin

Microorganisms 2024, 12(7), 1306; https://doi.org/10.3390/microorganisms12071306 - 27 Jun 2024

Cited by 3 | Viewed by 2283

Abstract

Dry eye is a complicated ocular surface disease that causes discomfort, visual disturbance, and frequently observed ocular surface damage. Emerging hypotheses suggest probiotics may help relieve dry eye symptoms by modulating inflammation and oxidative stress. This study aimed to investigate the therapeutic effects [...] Read more.

Dry eye is a complicated ocular surface disease that causes discomfort, visual disturbance, and frequently observed ocular surface damage. Emerging hypotheses suggest probiotics may help relieve dry eye symptoms by modulating inflammation and oxidative stress. This study aimed to investigate the therapeutic effects of Streptococcus thermophilus iHA318 probiotics on dry eye using in vitro assays and an in vivo murine model of ultraviolet B (UVB) radiation-induced dry eye. In vitro analyses revealed that S. thermophilus iHA318^® exhibited antioxidant activity and anti-inflammatory effects by inhibiting reactive oxygen species production and suppressing inflammatory cytokines. For the in vivo study, female ICR mice were assigned to normal control, UVB-induced dry eye, and UVB+iHA318 treatment groups. UVB exposure significantly decreased tear volume and tear film breakup time (TBUT) compared to normal controls. Supplementation with S. thermophilus iHA318^® via oral gavage markedly improved tear production and TBUT on day 7 post-UVB exposure. Ocular surface photography demonstrated improved gradings of corneal opacity, smoothness, and lissamine green staining in the iHA318 group versus the UVB group. Topographical analysis further revealed improvement in the UVB-induced corneal irregularities by iHA318 treatment. Collectively, these results indicate that S. thermophilus iHA318 exerts a protective effect against dry eye symptoms by mitigating oxidative stress and inflammation, thereby preserving tear film stability and ocular surface integrity. This probiotic strain represents a promising therapeutic approach for managing dry eye syndrome. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

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8 pages, 1584 KiB

Open AccessCommunication

Use of PCR Cycle Threshold and Clinical Interventions to Aid in the Management of Pediatric Clostridioides difficile Patients

by Mohammed Suleiman, Patrick Tang, Omar Imam, Princess Morales, Diyna Altrmanini, Kelli L. Barr, Jill C. Roberts and Andrés Pérez-López

Microorganisms 2024, 12(6), 1181; https://doi.org/10.3390/microorganisms12061181 - 11 Jun 2024

Viewed by 1219

Abstract

Better diagnostic tools are needed to improve the diagnosis of Clostridioides difficile infections (CDI) and reduce the overtreatment of colonized children. In this study, we evaluated two polymerase chain reaction (PCR) assays (Cepheid GeneXpert C. difficile and the Gastroenteritis PCR Panel by QIAstat-Dx) [...] Read more.

Better diagnostic tools are needed to improve the diagnosis of Clostridioides difficile infections (CDI) and reduce the overtreatment of colonized children. In this study, we evaluated two polymerase chain reaction (PCR) assays (Cepheid GeneXpert C. difficile and the Gastroenteritis PCR Panel by QIAstat-Dx) as a standalone method in combination with the PCR cycle threshold (Ct) value in positive samples to predict the presence of free toxins. We also evaluated the clinical impact of reporting toxin production results and provided comments alongside the PCR results in our pediatric population. PCR-positive stool samples from pediatric patients (aged 2 to 18 years old) were included in our study and tested for the presence of toxins A and B using the C. difficile Quik Chek Complete kit. For the clinical intervention, the CDI treatment rates 6 months pre- and post-intervention were compared. The use of PCR Ct value showed excellent sensitivity (100%) at a Ct value cutoff of 26.1 and 27.2 using the Cepheid GeneXpert C. difficile and the Gastroenteritis PCR Panel by QIAstat-Dx, respectively, while the toxin test showed inferior sensitivity of 64% in the PCR-positive samples. In addition, CDI treatment rates were decreased by 23% post-intervention. The results of our study suggest that nucleic acid amplification test (NAAT) assays supplemented by the use of PCR Ct value for positive samples can be used as standalone tests to differentiate CDI from colonization. Furthermore, the reporting of toxin production along with the PCR results can help reduce the unnecessary treatment of colonized children. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

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13 pages, 245 KiB

Open AccessArticle

Nocardiosis in Solid Organ Transplant Recipients: 10-Year Single Center Experience and Review of Literature

by Julia Bini Viotti, Jacques Simkins, John M. Reynolds, Gaetano Ciancio, Giselle Guerra, Lilian Abbo and Shweta Anjan

Microorganisms 2024, 12(6), 1156; https://doi.org/10.3390/microorganisms12061156 - 6 Jun 2024

Viewed by 1162

Abstract

Solid organ transplant recipients (SOTRs) are at an increased risk of nocardiosis, a rare but life-threatening opportunistic infection. Universal PCP prophylaxis with trimethoprim–sulfamethoxazole (TMP-SMX) is used at our center, which is active in vitro against most species of the Nocardia genus and may [...] Read more.

Solid organ transplant recipients (SOTRs) are at an increased risk of nocardiosis, a rare but life-threatening opportunistic infection. Universal PCP prophylaxis with trimethoprim–sulfamethoxazole (TMP-SMX) is used at our center, which is active in vitro against most species of the Nocardia genus and may have a role in preventing early infections. This is a single-center retrospective cohort study of nocardiosis in adult SOTRs at a large transplant center between January 2012 and June 2022, with comprehensive review of literature. Out of 6179 consecutive cases, 13 (0.2%) were diagnosed with nocardiosis. The patients were predominantly male (76.9%) and kidney transplant recipients (62%). Infection was diagnosed at median of 8.8 months (range, 3.7–98) after transplant. Patients were followed for a median of 457 days (range 8–3367). Overall mortality within one year after diagnosis was 46% (6/13), of which 17% (1/6) of deaths was attributable to Nocardia infection. No recurrence was reported. Nocardia infections were noted in a small proportion of our SOTRs and carried significant morbidity and mortality. TMP-SMX prophylaxis may be protective in some cases given low incidence of cases. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

6 pages, 189 KiB

Open AccessCommunication

Antibiotic Resistance Profiles in Eye Infections: A Local Concern with a Retrospective Focus on a Large Hospital in Northern Italy

by Lorenzo Drago, Vincenzo Minasi, Andrea Lembo, Angela Uslenghi, Sofia Benedetti, Matteo Covi, Paolo Nucci and Loredana Deflorio

Microorganisms 2024, 12(5), 984; https://doi.org/10.3390/microorganisms12050984 - 14 May 2024

Cited by 2 | Viewed by 1644

Abstract

The emergence of antibiotic resistance poses a significant threat to public health worldwide, affecting various medical fields, including ophthalmology. Eye infections, ranging from conjunctivitis to more severe conditions like keratitis, are commonly treated with antibiotics. However, the misuse and overuse of these drugs [...] Read more.

The emergence of antibiotic resistance poses a significant threat to public health worldwide, affecting various medical fields, including ophthalmology. Eye infections, ranging from conjunctivitis to more severe conditions like keratitis, are commonly treated with antibiotics. However, the misuse and overuse of these drugs have led to the development of resistant strains of bacteria, allowing traditional treatments ineffective. This paper aims to examine the current situation of antibiotic resistance in eye infections globally, with a specific focus on a large group of hospitals located in Milan (Italy) with considerable experience in cataract and cornea surgery as well as in retinopathy. The results of the study show the prevalence of Gram-positives in the tested samples and a low resistance of fluoroquinolones and glycopeptides. The results also highlight the need to implement sample collection methods for ocular infections, as the quantity of positive samples is rather low compared to the total number of samples. In conclusion, the study, although with limited data, shows that resistance to aminoglycosides and cephalosporins is a situation to be monitored. These data also show the critical need to improve and guide the biological sample collection modalities in order to make the diagnosis more reliable. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

17 pages, 937 KiB

Open AccessArticle

Prospective Longitudinal Study of Dynamics of Human Papillomavirus 6 and 11 Infection in Anogenital Hairs and Eyebrows of Male Patients with Anogenital Warts and Age-Matched Controls

by Vesna Tlaker, Lea Hošnjak, Mateja Kolenc, Tomaž Mark Zorec, Boštjan Luzar, Marko Potočnik, Jovan Miljković, Katja Seme and Mario Poljak

Microorganisms 2024, 12(3), 466; https://doi.org/10.3390/microorganisms12030466 - 25 Feb 2024

Viewed by 1405

Abstract

To better understand the natural history of anogenital warts (AGWs) and the dynamics of HPV6/11 infection in regional hairs, 32 newly diagnosed male patients with AGWs and 32 age-matched healthy controls were closely followed. During enrollment and six follow-up visits (every 2.6 months), [...] Read more.

To better understand the natural history of anogenital warts (AGWs) and the dynamics of HPV6/11 infection in regional hairs, 32 newly diagnosed male patients with AGWs and 32 age-matched healthy controls were closely followed. During enrollment and six follow-up visits (every 2.6 months), 43 AGW tissues and 1232 anogenital and eyebrow hair samples were collected. This is the closest longitudinal monitoring of AGW patients to date. Patients were treated according to standards of care. The HPV6/11 prevalence was 19.9% in the patients’ hair samples (HPV6 B1 in 53.1%) and 0% in the controls. The highest HPV6/11 prevalence was found in pubic hairs (29.0%) and the lowest in eyebrows (7.1%). The odds of having HPV6/11-positive hairs increased with smoking, shaving the anogenital region, and age. A close association between HPV6/11 presence in hairs and clinically visible AGWs was observed. The proportion of patients with visible AGWs and HPV6/11-positive hairs declined during follow-up with similar trends. No particular HPV6/11 variant was linked with an increased AGW recurrence, but the sublineage HPV6 B1 showed significantly higher clearance from hairs. Despite treatment, 78.1% and 62.5% of the AGW patients experienced one and two or more post-initial AGW episodes, respectively. The patients with HPV6/11-positive hairs or visible AGWs at a preceding visit demonstrated substantially higher odds of presenting with visible AGWs at a subsequent visit. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

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Review

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22 pages, 3802 KiB

Open AccessReview

The Role of Bacteria in Central Nervous System Tumors: Opportunities and Challenges

by Rui Zhang, Xueying Li and Si Zhang

Microorganisms 2024, 12(6), 1053; https://doi.org/10.3390/microorganisms12061053 - 23 May 2024

Cited by 2 | Viewed by 2498

Abstract

Tumors of the central nervous system (CNS) are severe and refractory diseases with poor prognosis, especially for patients with malignant glioblastoma and brain metastases. Currently, numerous studies have explored the potential role of bacteria and intestinal flora in tumor development and treatment. Bacteria [...] Read more.

Tumors of the central nervous system (CNS) are severe and refractory diseases with poor prognosis, especially for patients with malignant glioblastoma and brain metastases. Currently, numerous studies have explored the potential role of bacteria and intestinal flora in tumor development and treatment. Bacteria can penetrate the blood–brain barrier (BBB), targeting the hypoxic microenvironment at the core of tumors, thereby eliminating tumors and activating both the innate and adaptive immune responses, rendering them promising therapeutic agents for CNS tumors. In addition, engineered bacteria and derivatives, such as bacterial membrane proteins and bacterial spores, can also be used as good candidate carriers for targeted drug delivery. Moreover, the intestinal flora can regulate CNS tumor metabolism and influence the immune microenvironment through the “gut–brain axis”. Therefore, bacterial anti-tumor therapy, engineered bacterial targeted drug delivery, and intervention of the intestinal flora provide therapeutic modalities for the treatment of CNS tumors. In this paper, we performed a comprehensive review of the mechanisms and therapeutic practices of bacterial therapy for CNS tumors and discussed potential future research directions in this field. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

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13 pages, 1570 KiB

Open AccessReview

Bacteria Living in Biofilms in Fluids: Could Chemical Antibiofilm Pretreatment of Culture Represent a Paradigm Shift in Diagnostics?

by Lorenzo Drago, Andrea Fidanza, Alessio Giannetti, Alessio Ciuffoletti, Giandomenico Logroscino and Carlo Luca Romanò

Microorganisms 2024, 12(2), 259; https://doi.org/10.3390/microorganisms12020259 - 26 Jan 2024

Cited by 7 | Viewed by 2221 | Correction

Abstract

Biofilms are multicellular aggregates of bacteria immersed in an extracellular matrix that forms on various surfaces, including biological tissues and artificial surfaces. However, more and more reports point out the fact that even biological fluids and semifluid, such as synovial liquid, blood, urine, [...] Read more.

Biofilms are multicellular aggregates of bacteria immersed in an extracellular matrix that forms on various surfaces, including biological tissues and artificial surfaces. However, more and more reports point out the fact that even biological fluids and semifluid, such as synovial liquid, blood, urine, or mucus and feces, harbor “non-attached” biofilm aggregates of bacteria, which represent a significant phenomenon with critical clinical implications that remain to be fully investigated. In particular, biofilm aggregates in biological fluid samples have been shown to play a relevant role in bacterial count and in the overall accuracy of microbiological diagnosis. In line with these observations, the introduction in the clinical setting of fluid sample pretreatment with an antibiofilm chemical compound called dithiothreitol (DTT), which is able to dislodge microorganisms from their intercellular matrix without killing them, would effectively improve the microbiological yield and increase the sensitivity of cultural examination, compared to the current microbiological techniques. While other ongoing research continues to unveil the complexity of biofilm formation in biological fluids and its impact on infection pathogenesis and diagnosis, we here hypothesize that the routine use of a chemical antibiofilm pretreatment of fluid and semi-solid samples may lead to a paradigm shift in the microbiological approach to the diagnosis of biofilm-related infections and should be further investigated and eventually implemented in the clinical setting. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

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Other

Jump to: Research, Review

1 pages, 173 KiB

Open AccessCorrection

Correction: Drago et al. Bacteria Living in Biofilms in Fluids: Could Chemical Antibiofilm Pretreatment of Culture Represent a Paradigm Shift in Diagnostics? Microorganisms 2024, 12, 259

by Lorenzo Drago, Andrea Fidanza, Alessio Giannetti, Alessio Ciuffoletti, Giandomenico Logroscino and Carlo Luca Romanò

Microorganisms 2024, 12(12), 2577; https://doi.org/10.3390/microorganisms12122577 - 13 Dec 2024

Cited by 1 | Viewed by 450

Abstract

In the original publication [...] Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

6 pages, 655 KiB

Open AccessCase Report

Community-Acquired Solitary Brain Abscesses Caused by Hypervirulent Klebsiella pneumoniae in a Healthy Adult

by Joo-Hee Hwang, Jung Soo Park, Tae Won Bae, Jeong-Hwan Hwang and Jaehyeon Lee

Microorganisms 2024, 12(5), 894; https://doi.org/10.3390/microorganisms12050894 - 29 Apr 2024

Cited by 2 | Viewed by 1576

Abstract

A 42-year-old man was admitted to the emergency room complaining of fever and headache. His cerebrospinal fluid showed a cloudy appearance, and his white blood cell count was elevated at 2460/mm³, with a predominance of neutrophils (81%), and abnormal protein and [...] Read more.

A 42-year-old man was admitted to the emergency room complaining of fever and headache. His cerebrospinal fluid showed a cloudy appearance, and his white blood cell count was elevated at 2460/mm³, with a predominance of neutrophils (81%), and abnormal protein and glucose levels (510.7 mg/dL and 5 mg/dL, respectively). A lobulated lesion with rim enhancement, suggestive of abscess, was detected through magnetic resonance imaging. Klebsiella pneumoniae was detected in nasopharyngeal swab and blood cultures. The capsular serotype of K. pneumoniae was K2 and the sequence type determined by multilocus sequence typing was 23. The hypervirulent phenotype was associated with multiple virulent genes, including rmpA, rmpA2, entB, ybtS, kfu, iucA, iutA, iroB mrkD, allS, peg-344, peg-589, and peg-1631. After six weeks of receiving appropriate antibiotics and exhibiting clinical resolution of the brain abscesses, the patient was discharged. We present the first reported case of a healthy community-dwelling adult with solitary brain abscesses, and no other invasive abscesses, related to hypervirulent K. pneumoniae. Full article

(This article belongs to the Special Issue Advances in Medical Microbiology)

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