Editorial

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5 pages, 177 KiB

Open AccessEditorial

Recent Advances in the Epidemiology of Pathogenic Agents

by Wei-Chuan Chen and Yusen Eason Lin

Pathogens 2024, 13(3), 263; https://doi.org/10.3390/pathogens13030263 - 19 Mar 2024

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Abstract

The COVID-19 pandemic has underscored the pivotal role of epidemiology in studying pathogenic agents [...] Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

Research

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16 pages, 2476 KiB

Open AccessArticle

A Retrospective Assessment of Sputum Samples and Antimicrobial Resistance in COVID-19 Patients

by Talida Georgiana Cut, Adelina Mavrea, Alin Adrian Cumpanas, Dorin Novacescu, Cristian Iulian Oancea, Felix Bratosin, Adelina Raluca Marinescu, Ruxandra Laza, Alexandra Mocanu, Alexandru Silvius Pescariu, Diana Manolescu, Raluca Dumache, Alexandra Enache, Elena Hogea and Voichita Elena Lazureanu

Pathogens 2023, 12(4), 620; https://doi.org/10.3390/pathogens12040620 - 19 Apr 2023

Cited by 6 | Viewed by 1703

Abstract

Data on bacterial or fungal pathogens and their impact on the mortality rates of Western Romanian COVID-19 patients are scarce. As a result, the purpose of this research was to determine the prevalence of bacterial and fungal co- and superinfections in Western Romanian [...] Read more.

Data on bacterial or fungal pathogens and their impact on the mortality rates of Western Romanian COVID-19 patients are scarce. As a result, the purpose of this research was to determine the prevalence of bacterial and fungal co- and superinfections in Western Romanian adults with COVID-19, hospitalized in in-ward settings during the second half of the pandemic, and its distribution according to sociodemographic and clinical conditions. The unicentric retrospective observational study was conducted on 407 eligible patients. Expectorate sputum was selected as the sampling technique followed by routine microbiological investigations. A total of 31.5% of samples tested positive for Pseudomonas aeruginosa, followed by 26.2% having co-infections with Klebsiella pneumoniae among patients admitted with COVID-19. The third most common Pathogenic bacteria identified in the sputum samples was Escherichia coli, followed by Acinetobacter baumannii in 9.3% of samples. Commensal human pathogens caused respiratory infections in 67 patients, the most prevalent being Streptococcus penumoniae, followed by methicillin-sensitive and methicillin-resistant Staphylococcus aureus. A total of 53.4% of sputum samples tested positive for Candida spp., followed by 41.1% of samples with Aspergillus spp. growth. The three groups with positive microbial growth on sputum cultures had an equally proportional distribution of patients admitted to the ICU, with an average of 30%, compared with only 17.3% among hospitalized COVID-19 patients with negative sputum cultures (p = 0.003). More than 80% of all positive samples showed multidrug resistance. The high prevalence of bacterial and fungal co-infections and superinfections in COVID-19 patients mandates for strict and effective antimicrobial stewardship and infection control policies. Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

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13 pages, 761 KiB

Open AccessArticle

Serotypes and Antibiotic Resistance of Streptococcus pneumoniae before and after the Introduction of the 13-Valent Pneumococcal Conjugate Vaccine for Adults and Children in a Rural Area in Japan

by Takashi Ono, Masahiro Watanabe, Koichi Hashimoto, Yohei Kume, Mina Chishiki, Hisao Okabe, Masatoki Sato, Sakurako Norito, Bin Chang and Mitsuaki Hosoya

Pathogens 2023, 12(3), 493; https://doi.org/10.3390/pathogens12030493 - 21 Mar 2023

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Abstract

The increase in non-vaccine serotypes of Streptococcus pneumoniae and their multidrug resistance have become an issue following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). In this study, we investigated the serotypes and drug resistance of S. pneumoniae detected in adult and [...] Read more.

The increase in non-vaccine serotypes of Streptococcus pneumoniae and their multidrug resistance have become an issue following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). In this study, we investigated the serotypes and drug resistance of S. pneumoniae detected in adult and pediatric outpatients at a hospital in a rural area of Japan between April 2012 and December 2016. Serotypes of the bacterium were identified using the capsular swelling test and multiplex polymerase chain reaction testing of DNA extracted from the specimens. Antimicrobial susceptibility was determined using the broth microdilution method. The serotype 15A was classified using multilocus sequence typing. The results showed that the prevalence of non-vaccine serotypes increased significantly in children from 50.0% in 2012–2013 to 74.1% in 2016 (p ≤ 0.006) and in adults from 15.8% in 2012–2013 to 61.5% in 2016 (p ≤ 0.026), but no increase in drug-resistant isolates was evident. However, an increase in the drug-resistant serotypes 15A and 35B was observed in children. Although isolates of these two serotypes showed cefotaxime susceptibility, cefotaxime resistance was confirmed for the serotype 15A isolates. Future trends in the spread of these isolates should be monitored with caution. Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

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14 pages, 754 KiB

Open AccessArticle

High Burden of Co-Infection with Multiple Enteric Pathogens in Children Suffering with Diarrhoea from Rural and Peri-Urban Communities in South Africa

by Natasha Potgieter, Lee Heine, Jean Pierre Kabue Ngandu, Solanka Ellen Ledwaba, Tinyiko Zitha, Lutendo Sylvia Mudau, Piet Becker, Afsatou Ndama Traore and Tobias George Barnard

Pathogens 2023, 12(2), 315; https://doi.org/10.3390/pathogens12020315 - 14 Feb 2023

Cited by 5 | Viewed by 2154

Abstract

Infectious diarrhoea contributes to high morbidity and mortality in young children from sub-Saharan Africa. The aim of this study was to assess the prevalence of single and multiple diarrhoeal-causing pathogen combinations in children suffering from diarrhoea from rural and peri-urban communities in South [...] Read more.

Infectious diarrhoea contributes to high morbidity and mortality in young children from sub-Saharan Africa. The aim of this study was to assess the prevalence of single and multiple diarrhoeal-causing pathogen combinations in children suffering from diarrhoea from rural and peri-urban communities in South Africa. A total of 275 diarrhoea stool specimens were collected between 2014 and 2016 from Hospitals and Primary Health Care clinics. The BioFire^® FilmArray^® Gastrointestinal panel was used to simultaneously detect 22 diarrhoea pathogens (viruses, bacteria, parasites) known to cause diarrhoea. A total of 82% (226/275) enteric pathogens were detected in the stool specimens. The two most detected bacterial, viral and parasitic pathogens each included: EAEC (42%), EPEC (32%), Adenovirus F40/41 (19%), Norovirus (15%), Giardia (8%) and Cryptosporidium (6%), respectively. Single enteric pathogen infections were recorded in 24% (65/275) specimens with EAEC, and Norovirus was found in 26% (17/65) and 14% (9/65) of the specimens, respectively. Multiple enteric pathogen combinations were recorded in 59% (161/275) of the stool specimens with 53% (85/161) containing two pathogens, 22% (35/161) containing three pathogens and 25% (41/161) containing four or more pathogens. The results from this study demonstrated the complex nature of pathogen co-infections in diarrhoeal episodes which could have an impact on treatment effectiveness. Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

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12 pages, 859 KiB

Open AccessArticle

Helicobacter pylori Virulence Factors and Clarithromycin Resistance-Associated Mutations in Mexican Patients

by Judit Alarcón-Millán, José Bonilla-Delgado, Gloria Fernández-Tilapa, Nayeli Goreti Nieto-Velázquez, Mónica Sierra-Martínez, Víctor Manuel Alvarado-Castro and Enoc Mariano Cortés-Malagón

Pathogens 2023, 12(2), 234; https://doi.org/10.3390/pathogens12020234 - 02 Feb 2023

Cited by 3 | Viewed by 2058

Abstract

Persistent infection with Helicobacter pylori (H. pylori) is an important factor in gastric diseases. The vacA and cagA virulence factors of H. pylori contribute to the development of these diseases. Triple therapy containing clarithromycin has been used to eradicate this infection. Unfortunately, resistance [...] Read more.

Persistent infection with Helicobacter pylori (H. pylori) is an important factor in gastric diseases. The vacA and cagA virulence factors of H. pylori contribute to the development of these diseases. Triple therapy containing clarithromycin has been used to eradicate this infection. Unfortunately, resistance to this antibiotic is the primary cause of treatment failure. This study aimed to determine the prevalence of clarithromycin resistance-associated mutations and to assess the relationship between virulence factors and Mexican patients infected with H. pylori. The cagA and vacA genotypes were determined by multiplex PCR. Furthermore, a qPCR was used to identify mutations of the 23S rRNA gene. This study reported a prevalence of 84.3% of H. pylori among patients with gastric diseases, and the vacA s1m1/cagA+ genotype was the most frequent (44.8%) in antrum and corpus. Analysis of the 23S rRNA gene revealed a 19.8% prevalence of clarithromycin resistance-associated mutations. The most prevalent mutations were A2143G (56%) and A2142C (25%). A significant association (p < 0.05) between the A2142G and the vacA s1m1/cagA+ genotype was detected. In conclusion, we report a high prevalence (>15%) of clarithromycin resistance-associated mutations, and we found an association between the genotypes of virulence factors and a mutation in the 23S rRNA gene. Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

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11 pages, 8560 KiB

Open AccessArticle

Hematological Parameters as Potential Markers for Distinguishing Pulmonary Tuberculosis from Genitourinary Tuberculosis

by Hui-Zin Tu, Tsung-Jen Lai, Yao-Shen Chen, Herng-Sheng Lee and Jin-Shuen Chen

Pathogens 2023, 12(1), 84; https://doi.org/10.3390/pathogens12010084 - 04 Jan 2023

Cited by 2 | Viewed by 1990

Abstract

Mycobacterium tuberculosis complex (MTBC) infection is an important public health concern in Taiwan. In addition to pulmonary tuberculosis (PTB), MTBC can also cause genitourinary tuberculosis (GUTB). This study aimed to examine the role of laboratory data and the values that can be calculated [...] Read more.

Mycobacterium tuberculosis complex (MTBC) infection is an important public health concern in Taiwan. In addition to pulmonary tuberculosis (PTB), MTBC can also cause genitourinary tuberculosis (GUTB). This study aimed to examine the role of laboratory data and the values that can be calculated from them for the early detection of GUTB. Patients admitted from 2011 to 2020 were retrospectively recruited to analyze their associated clinical data. Statistical significance was analyzed using the chi-square test and univariate analysis for different variables. A receiver operating characteristic (ROC) curve analysis was used to evaluate the performances of the examined laboratory data and their calculated items, including the neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), neutrophil-to-monocyte-plus-lymphocyte ratio (NMLR), and platelet-to-lymphocyte ratio (PLR), in diagnosing PTB or GUTB. A p-value of <0.05 was considered significant. The ROC curve showed that the discriminative power of the neutrophil count, NLR, and MLR was within the acceptable level between patients with both PTB and GUTB and those with GUTB alone (area under the curve [AUC] values = 0.738, 0.779, and 0.725; p = 0.024, 0.008, and 0.033, respectively). The discriminative power of monocytes and the MLR was within the acceptable level (AUC = 0.782 and 0.778; p = 0.008 and 0.010, respectively). Meanwhile, the neutrophil and lymphocyte counts, NLR, NMLR, and PLR had good discriminative power (AUC = 0.916, 0.896, 0.898, 0.920, and 0.800; p < 0.001, <0.001, <0.001, <0.001, and 0.005, respectively) between patients with GUTB and those with PTB alone. In conclusion, the neutrophil count, lymphocyte count, NLR, NMLR, and PLR can be used as potential markers for distinguishing PTB from GUTB. Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

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10 pages, 619 KiB

Open AccessArticle

High Rates of Antimicrobial Resistance in Rapidly Growing Mycobacterial Infections in Taiwan

by Hui-Zin Tu, Herng-Sheng Lee, Yao-Shen Chen and Susan Shin-Jung Lee

Pathogens 2022, 11(9), 969; https://doi.org/10.3390/pathogens11090969 - 25 Aug 2022

Cited by 3 | Viewed by 1426

Abstract

Rapidly growing mycobacteria (RGM) has gained increasing clinical importance, and treatment is challenging due to diverse drug resistance. The minimum inhibitory concentrations (MIC) of 13 antimicrobial agents using modified broth microdilution and E-test were determined for 32 clinical isolates of RGM, including Mycobacterium [...] Read more.

Rapidly growing mycobacteria (RGM) has gained increasing clinical importance, and treatment is challenging due to diverse drug resistance. The minimum inhibitory concentrations (MIC) of 13 antimicrobial agents using modified broth microdilution and E-test were determined for 32 clinical isolates of RGM, including Mycobacterium abscessus (22 isolates) and Mycobacterium fortuitum (10 isolates). Our results showed high rates of resistance to available antimicrobial agents. Amikacin remained highly susceptible (87.5%). Clarithromycin was active against the isolates of M. abscessus (95.5%), and M. fortuitum (50%), but 36.4% and 20% had inducible macrolide resistance, respectively. Rates of susceptibility to tigecycline were 68.2–70%, and linezolid 45.5–50%, respectively. The quinolones (ciprofloxacin and moxifloxacin) showed better in vitro activity against M. fortuitum isolates (50% susceptibility) than the M. abscessus isolates (31.8% susceptibility). The susceptibilities to other conventional anti-mycobacterial agents were poor. The MICs of E-test were higher than broth microdilution and may result in reports of false resistance. In conclusion, the implementation of the modified broth microdilution plates into the routine clinical laboratory workflow to provide antimicrobial susceptibility early, allows for the timely selection of appropriate treatment of RGM infections to improve outcome. Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

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11 pages, 1245 KiB

Open AccessCase Report

Dermatological Manifestations in COVID-19: A Case Study of SARS-CoV-2 Infection in a Genetic Thrombophilic Patient with Mthfr Mutation

by Gabriela Gomes Celestino, Marla Karine Amarante, Eliana Carolina Vespero, Eliandro Reis Tavares, Lucy Megumi Yamauchi, Érika Donizetti Candido, Danielle Bruna Leal de Oliveira, Edison Luiz Durigon, Sueli Fumie Yamada-Ogatta and Ligia Carla Faccin-Galhardi

Pathogens 2023, 12(3), 438; https://doi.org/10.3390/pathogens12030438 - 10 Mar 2023

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Abstract

The present case study describes the dermatological manifestations of COVID-19 in a patient with genetic thrombophilia (MTHFR–C677T mutation) and the identification of a SARS-CoV-2 variant of interest (VOI). A female patient, 47 years old, unvaccinated, with thrombophilia, was diagnosed with COVID-19. She presented [...] Read more.

The present case study describes the dermatological manifestations of COVID-19 in a patient with genetic thrombophilia (MTHFR–C677T mutation) and the identification of a SARS-CoV-2 variant of interest (VOI). A female patient, 47 years old, unvaccinated, with thrombophilia, was diagnosed with COVID-19. She presented with urticarial and maculopapular eruptions from the seventh day of symptoms, which progressed to multiple lesions with dark centers (D-dimer value > 1450 ng/mL). The dermatological manifestations disappeared after 30 days, corroborating the reduction in D-dimer levels. Viral genome sequencing revealed infection by the VOI Zeta (P.2). Antibody testing, performed 30 days after the onset of symptoms, detected only IgG. The virus neutralization test showed the highest neutralizing titer for a P.2 strain, validating the genotypic identification. Lesions were suggested to be due to infection in skin cells causing a direct cytopathic effect or release of pro-inflammatory cytokines triggering erythematous and urticarial eruptions. In addition, vascular complications are also proposed to be due to the MTHFR mutation and increased D-dimer values. This case report is an alert about COVID-19 in patients with pre-existing vascular diseases, especially in unvaccinated patients, by VOI. Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

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8 pages, 1959 KiB

Open AccessCase Report

Epidemiological, Clinical, and Virological Investigation of the First Four Cases of Monkeypox in Cartagena during the 2022 Outbreak

by Steev Loyola, Mashiel Fernández-Ruiz and Doris Gómez-Camargo

Pathogens 2023, 12(2), 159; https://doi.org/10.3390/pathogens12020159 - 18 Jan 2023

Cited by 2 | Viewed by 1527

Abstract

Since early May 2022, numerous cases of Monkeypox (Mpox) have been reported globally in non-endemic areas. However, despite numerous reports worldwide, the epidemiological and genomic information related to the 2022 multi-country outbreak remains scarce in South America. By late June 2022, the first [...] Read more.

Since early May 2022, numerous cases of Monkeypox (Mpox) have been reported globally in non-endemic areas. However, despite numerous reports worldwide, the epidemiological and genomic information related to the 2022 multi-country outbreak remains scarce in South America. By late June 2022, the first Mpox cases were detected in Colombia. Cartagena is a Colombian Caribbean city with high domestic and international connectivity, and, therefore, is vulnerable to the introduction of the Monkeypox virus (MPXV). This report provides an in-depth description of the epidemiological, clinical, and virological characteristics of the first four cases detected in Cartagena including three cases with no history of recent travel and one imported case. Using various laboratory tools based on PCR, next-generation sequencing, and viral isolation and quantification methods, the MPXV clade IIB was detected and isolated. Importantly, infectious viral particles were identified in lesion swabs collected from all cases and in oropharyngeal swabs collected from two cases. Blood samples tested negative using PCR and isolation. In summary, our work contributes complete genomic, clinical, and epidemiological information that will be useful for a number of studies going forward, and it also documents local information that contributes to our understanding of Mpox at the local level. Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

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19 pages, 2429 KiB

Open AccessSystematic Review

Syphilis as Re-Emerging Disease, Antibiotic Resistance, and Vulnerable Population: Global Systematic Review and Meta-Analysis

by Yaneth Citlalli Orbe-Orihuela, Miguel Ángel Sánchez-Alemán, Adriana Hernández-Pliego, Claudia Victoria Medina-García and Dayana Nicté Vergara-Ortega

Pathogens 2022, 11(12), 1546; https://doi.org/10.3390/pathogens11121546 - 15 Dec 2022

Cited by 8 | Viewed by 4173

Abstract

Syphilis is a sexually transmitted disease that has become a public health problem, especially in vulnerable populations. A systematic review and time-free meta-analysis of the publications on the molecular detection of syphilis and mutations associated with antibiotic resistance, CORE group, and syphilis genotypes [...] Read more.

Syphilis is a sexually transmitted disease that has become a public health problem, especially in vulnerable populations. A systematic review and time-free meta-analysis of the publications on the molecular detection of syphilis and mutations associated with antibiotic resistance, CORE group, and syphilis genotypes in PubMed databases, Scielo, and Cochrane was performed, and the last search was conducted in June 2022. Proportions were calculated, and standard errors and confidence intervals were reported for all results of interest. We included 41 articles for quantitative extraction and data synthesis. An increase was observed in the proportion of subjects diagnosed with syphilis and the presence of the A2058G mutation during the 2018–2021 period compared to 2006 (70% _95%CI 50–87 vs. 58% _95%CI 12–78), and we observed that the greater the proportion of the population participating in men who have sex with men (MSM) (<50% and >50%) syphilis increased (78% _95%CI 65–90 vs. 33% _95%CI 19–49). In conclusion, we suggest that there are a set of characteristics that are contributing to the resurgence of syphilis and the selective pressure of bacteria. The MSM population could be a vulnerable factor for this scenario and the global presence of A2058G and A2059G mutations that confer resistance to macrolides. Full article

(This article belongs to the Special Issue Epidemiology of Pathogenic Agents)

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