Pathogens最新文献

During the COVID-19 pandemic, SARS-CoV-2 caused an alarming number of cases and deaths worldwide. Brazil was severely affected from late 2020 onward, especially after the emergence of variants of concern (VOCs) and variants of interest (VOIs). Although much is known about the dynamics and evolution of SARS-CoV-2 VOIs and VOCs in the country, information is still lacking on how the cocirculation of several SARS-CoV-2 lineages, along with the lack of vaccination and low adherence to social isolation measures, shaped the first year of the COVID-19 pandemic in Brazil. We used a combination of genomic and epidemiological data to understand the transmission dynamics of SARS-CoV-2 variants from March to November 2020 within a medium-sized city in São Paulo state. By generating 627 SARS-CoV-2 whole genomes, we were able to identify 10 different SARS-CoV-2 lineages that were cocirculating in the municipality. Although many introduction events have been identified, B.1.1.28 and B.1.1.33 variants were the most frequent during the sampling period. We also detected the presence of the Zeta and N.9 variants earlier than had previously been reported in Brazil. These findings reinforce the need for active genomic surveillance to detect new viral introductions that may impact health systems during public health emergencies.

Urinary tract infections (UTIs) are among the most common pediatric infections. This study evaluated the antimicrobial susceptibility patterns of 3511 uropathogenic E. coli (UPEC) isolated from pediatric patients in the United States from 2014 to 2023. The database from the SENTRY antimicrobial surveillance program from 89 medical centers was utilized as a data source. The antimicrobial susceptibility was tested using the microbroth dilution technique against 24 antimicrobial agents. MICs were determined using the CLSI/EUCAST/FDA breakpoint criteria. All the antimicrobials reported susceptibility rates above 80% except for tetracycline (76.2%), trimethoprim-sulfamethoxazole (69.7%), and ampicillin-sulbactam (55.7%). During the study period, the susceptibility rates remained stable for most antimicrobial agents. However, significant differences were observed among age, gender, and U.S. census regions, with the Middle Atlantic showing the lowest and the Mountain region the highest susceptibility rates, for most antimicrobials. The incidence of ESBL UPEC increased from 7.1% to 10.8% between 2014 and 2023, while the prevalence of the MDR phenotype remained relatively stable. The prevalence of both ESBL and MDR phenotypes was highest among infants and young children (0-24 months), with the highest resistance rates from the Pacific region. Knowledge of the landscape of antibiotic resistance in pediatric UPEC will help healthcare providers to better tailor empiric treatment regimens for most UTI infections.

Florida is home to a vast number of wildlife species that come into close contact with residents and domestic animals. As mammals are competent hosts for many zoonotic diseases, it is important to understand what exposure risks are present for both people and animals. Using Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, this review analyzed published literature spanning 1963 through 2023 documenting zoonotic enteric parasites in synanthropic wild mammals of Florida, excluding mice and rats. Between an initial search conducted in 2022 and updated search in 2024, 10,563 titles were reviewed. Using predetermined inclusion and exclusion criteria, 26 titles were included in the final analysis examining a range of acanthocephala, cestode, nematode, protozoa, and trematode parasite species. Of the results, most studies found at least one parasite in Florida raccoons (n = 14) with additional studies in opossums (n = 8), armadillos (n = 4), bobcats (n = 4), coyotes (n = 3), squirrels (n = 3), gray foxes (n = 1), red foxes (n = 1), an undeclared fox type (n = 1), and bats (n = 1). No studies were found documenting zoonotic enteric parasites in rabbits or moles. The transmission pathways for each parasite and the zoonotic exposure risks varied significantly. Coordinated One Health prevention and control efforts must be targeted for effectiveness.

Fusarium verticillioides is an important plant pathogen in maize and other cereals that is seldom detected as the cause of human fusariosis. Here, we provide the analysis of the available diversity of F. verticillioides sequenced worldwide and report the first two genome assemblies and annotations (including mitochondrial DNA) of Fusarium verticillioides from clinical settings. Fusarium verticillioides 05-0160 (IUM05-0160) and Fusarium verticillioides 09-1037 (IUM09-1037) strains were obtained from the bone marrow and blood of two immunocompromised patients, respectively. The phylogenomic analysis confirmed the species identity of our two strains. Comparative genomic analyses among the reannotated F. verticillioides genomes (n = 46) did not lead to the identification of unique genes specific to the clinical samples. Two subgroups in the F. verticillioides clade were also identified and confirmed by a mitochondrial diversity study. Clinical strains (n = 4) were positioned in the multigene phylogenetic tree without any correlation between the host and the tree branches, grouping with plant-derived strains. To investigate the existence of a potential fitness advantage of our two clinical strains, we compared demethylase inhibitor fungicides susceptibility against the reference Fusarium verticillioides 7600, showing, on average, lower susceptibility to agricultural and medical-used antifungals. A significant reduction in susceptibility was observed for itraconazole and tetraconazole, which might be explained by structural changes in CYP51A and CYP51C sequences. By providing the first two annotated genomes of F. verticillioides from clinical settings comprehensive of their mitogenomes, this study can serve as a base for exploring the fitness and adaptation capacities of Fusarium verticillioides infecting different kingdoms.

Brucellosis is a neglected zoonotic disease affecting livestock and humans that remains endemic in Ethiopia. Despite its prevalence, only a few studies have identified Brucella species circulating in livestock in the country. This study aimed to determine the Brucella species responsible for infections in livestock in the Afar region of Ethiopia and characterize the isolates using whole-genome single nucleotide polymorphism (wgSNP) analysis and in silico multi-locus sequence typing (MLST). Comparisons were made between Ethiopian Brucella and regional and global isolates to determine their phylogenetic relationships. Surveys conducted in May and October-November 2022 in six villages of the Amibara district involved the collection of vaginal swabs (n = 231) and milk samples (n = 17) from 32 sheep and 199 goats kept by 143 pastoral households reporting recent abortions in the animals. Brucella melitensis was detected in three sheep and 32 goats, i.e., 15% (35/231) of animals across 20% (29/143) of households using bacterial culture and PCR-based methods (bcsp31, AMOS, and Bruce-ladder multiplex PCR). Of the 35 positive animals, B. melitensis was isolated from 24 swabs, while the remaining 11 were culture-negative and detected only by PCR. The genomic DNA of the 24 isolates was sequenced using Illumina Novaseq 6000 and assembled using the SPAdes pipeline. Nine- and 21-locus MLST identified 23 isolates as genotype ST12, while one isolate could not be typed. The wgSNP-based phylogenetic analysis revealed that the Ethiopian isolates clustered within the African clade and were closely related to isolates from Somalia. Several virulence factors responsible for adhesion, intracellular survival, and regulatory functions were detected in all isolates. No antimicrobial resistance genes associated with resistance to drugs commonly used for treating brucellosis were detected. Since B. melitensis is prevalent in sheep and goats, vaccination with the B. melitensis Rev-1 vaccine is the recommended strategy in these pastoral systems to protect animal and human health.

Concatemeric viral DNA is packaged into bacteriophage P22 procapsids via a headful packaging mechanism mediated by a molecular machine consisting of small (gp3) and large (gp2) terminase subunits. Although a negative stain reconstruction exists for the terminase holoenzyme, it is not clear how this complex binds the dodecameric portal protein located at a 5-fold mismatch vertex. Herein, we describe new assemblies for the holoenzyme. Both native mass spectrometry and transmission electron microscopy reveal that the P22 terminase complex adopts three main assemblies, which include a nonameric S-terminase bound to two L-terminase 1(gp3)₉:2(gp2), two nonameric S-terminase bound to five L-terminase 2(gp3)₉:5(gp2), and three nonameric S-terminase bound to seven L-terminase 3(gp3)₉:7(gp2). Native agarose gel electrophoresis shows that the terminase complex interacts with procapsids with mild crosslinking. These results herein illustrate the P22 terminase complex can adopt a variety of conformations and assembly states.

Diagnosing non-tuberculous mycobacterial pulmonary disease (NTM-PD) in patients unable to produce sputum spontaneously requires invasive procedures to obtain valid respiratory specimens. In this retrospective study, we evaluated the results of microbiological tests performed on respiratory samples of 132 patients affected by NTM-PD. In the diagnostic workout, 98 patients performed both induced sputum (IS) and bronchoalveolar lavage (BAL) and were enrolled in our study. A total of 93 out of 98 BAL samples (95%) were culture-positive for mycobacteria, whereas only 67/153 (44%) induced sputum cultures were positive for NTM (p < 0.001). Molecular identification of NTM with real-time polymerase chain reaction (PCR) was positive in 48/64 BAL (75%) and in 47/139 (34%) IS samples (p < 0.001). Patients affected by nodular-bronchiectatic form were 65/98 (66%): BAL culture was positive in 95% of cases (62/65 BAL), while only 30/99 IS cultures were positive (30%; p < 0.001). PCR was positive in 76% of BAL samples examined (26/34) and in 26% of the IS samples (24 out of 91) (p < 0.001). Among 33 patients with a fibro-cavitary radiological pattern, 65% of IS (35/54) were culture-positive for NTM, whereas 94% of cases (31/33) had a positive culture for NTM from BAL (p = 0.002). PCR was positive in 73% of BAL samples tested (22/30) and 48% of IS samples tested (23/48) (p = 0.031). Our results confirm BAL mycobacterial culture as the gold standard for the diagnosis of pulmonary mycobacteriosis. FBS with BAL should be performed in every patient with a strong suspicion of NTM-PD, if other respiratory samples are repeatedly negative. Sputum induction is a useful technique to obtain valid respiratory samples when patients are unable to produce spontaneous sputum, especially in the outpatient setting. However, during the diagnostic workup of NTM-PD, we should not forget that PCR and mycobacterial culture of induced sputum have a lower yield than when performed on BAL, especially in the nodular-bronchiectatic form of the disease.

Zoonotic spillover events pose a significant and growing threat to global health. By focusing on preventing these cross-species transmissions, we can significantly mitigate pandemic risks. This review aims to analyze the mechanisms of zoonotic spillover events, identify key risk factors, and propose evidence-based prevention strategies to reduce future pandemic threats. Through a comprehensive literature review and analysis of major databases including PubMed, Web of Science, and Scopus from 1960-2024, we examined documented spillover events, their outcomes, and intervention strategies. This article emphasizes that targeting the root cause-the spillover event itself-is key to averting future pandemics. By analyzing historical and contemporary outbreaks, we extract crucial insights into the dynamics of zoonotic transmission. Factors underlying these events include increased human-animal contact due to habitat encroachment, agricultural intensification, and wildlife trade. Climate change, global travel, and inadequate healthcare infrastructure exacerbate risks. The diversity of potential viral reservoirs and rapid viral evolution present major challenges for prediction and prevention. Solutions include enhancing surveillance of wildlife populations, improving biosecurity measures, investing in diagnostic capabilities, and promoting sustainable wildlife management. A "One Health" approach integrating human, animal, and environmental health is crucial. Predictive modelling, international cooperation, and public education are key strategies. Developing pre-exposure prophylactics and post-exposure treatments is essential for mitigating outbreaks. While obstacles remain, advances in genomics and ecological modelling offer hope. A proactive, comprehensive approach addressing the root causes of spillover events is vital for safeguarding global health against future pandemics.

The number of older adults undergoing organ transplantation, and waiting lists are increasing. The epidemiological data on infections in older transplant patients are scarce. The objective of the study was to investigate the incidence and distribution of infectious complications in older patients according to post-transplant periods. This retrospective study was conducted in a university hospital between 1 January 2018 and 31 March 2023. All infectious episodes were analyzed over three post-transplant periods. Forty-four patients were enrolled. The median age was 67 years (min: 65 and max: 87 years). Patients experienced a total of 98 infectious episodes. The median number of infectious events per patient was 1.0 (min: 0 and max: 8). The overall incidence rate of infectious events was 2.18 infectious episodes per 1000 transplant days. Of the patients at risk, 18.2% had 12 (12.4% of all infections) infections in the first month (9.09 episodes per 1000 transplant days), 56.8% had 52 (53.1%) infections between 1 and 6 months (7.88 episodes per 1000 transplant days), and 40.9% had 34 (35%) infections >6-12 months post-transplant (0.92 episodes per 1000 transplant days) The most prevalent type of infection was bacterial (79.6%, n = 78) followed by viral (18.4%, n = 18) and fungal (2.0%, n = 2) infections. The overall mortality rate of the 44 patients was 13.6%. The bacterial infections were more prevalent, and the incidence of infection was high during all post-transplant periods. These results may guide infection management in older transplant patients.

Thalassemia is an inherited hematological disorder characterized by a decrease in the synthesis of or absence of one or more globin chains. Hepatitis E virus (HEV) is a major cause of acute viral hepatitis, constituting a major global health burden and emerging as a critical public health concern. HEV infection is mainly transmitted via the fecal-oral route; however, parenteral transmission through blood components has been reported in both developing and developed countries. Although HEV infection is typically self-limiting, immunocompromised individuals, patients with chronic liver disease, and thalassemic patients are at a heightened risk of contracting the infection and may develop chronic hepatitis and life-threatening complications that require treatment. The reported prevalence rates of HEV in thalassemia patients vary significantly by country. Age, gender, residential area, and the cumulative amount of blood transfusions received have been identified as associated risk factors for HEV infection. In order to enhance blood safety and ensure the protection of vulnerable patient populations, such as thalassemia patients, several countries have introduced universal or targeted HEV screening policies in blood donations. Other preventive measures include vigilant monitoring of thalassemic patients and screening for anti-HEV antibodies. The aim of this review is to explore the prevalence, risk factors, clinical impact and management of HEV infection in patients with thalassemia.