Microbiology spectrum最新文献

{"title":"Changes in the pharyngeal and nasal microbiota in pediatric patients with adenotonsillar hypertrophy.","authors":"Federica Del Chierico, Antonia Piazzesi, Ersilia Vita Fiscarelli, Maria Vittoria Ristori, Ilaria Pirona, Alessandra Russo, Nicoletta Citerà, Gabriele Macari, Sara Santarsiero, Fabrizio Bianco, Valeria Antenucci, Valerio Damiani, Luigi Mercuri, Giovanni Carlo De Vincentis, Lorenza Putignani","doi":"10.1128/spectrum.00728-24","DOIUrl":"https://doi.org/10.1128/spectrum.00728-24","url":null,"abstract":"<p><p>The present study aimed to investigate the pharyngeal and nasal microbiota composition in children with adenotonsillar hypertrophy (AH) and assess longitudinal alterations in both microbiota after a probiotic oral spray treatment. A cohort of 57 AH patients were enrolled and randomly assigned to the probiotic and placebo groups for a 5-month treatment course. Pharyngeal and nasal swabs were collected before and after treatment and analyzed by 16S rRNA-based metataxonomics and axenic cultures for pathobiont identification. 16S rRNA sequences from pharyngeal and nasal swabs of 65 healthy children (HC) were used as microbiota reference profiles. We found that the pharyngeal and nasal microbiota of AH children were similar. When compared to HC, we observed an increase of the genera <i>Rothia</i>, <i>Granulicatella</i>, <i>Streptococcus</i>, <i>Neisseria</i>, and <i>Haemophilus</i>, as well as a reduction of <i>Corynebacterium</i>, <i>Pseudomonas, Acinetobacter,</i> and <i>Moraxella</i> in both microbiota of AH patients. After probiotic treatment, we confirmed the absence of adverse effects and a reduction of upper respiratory tract infections (URTI). Moreover, the composition of pharyngeal microbiota was positively influenced by the reduction of potential pathobionts, like <i>Haemophilus</i> spp., with an increase of beneficial microbial metabolic pathways. Finally, the probiotic reduced the abundance of the pathobionts <i>Streptococcus mitis</i> and <i>Gemella haemolysans</i> in relation to AH severity. In conclusion, our results highlight the alterations of the pharyngeal and nasal microbiota associated with AH. Moreover, probiotic administration conferred protection against URTI and reduced the presence of potential pathobionts in patients with AH.</p><p><strong>Importance: </strong>Adenotonsillar hypertrophy (AH) is considered the main cause of breathing disorders during sleep in children. AH patients, after significant morbidity and often multiple courses of antibiotics, often proceed to tonsillectomy and/or adenoidectomy. Given the potential risks associated with these procedures, there is a growing interest in the use of nonsurgical adjuvant therapies, such as probiotics, that could potentially reduce their need for surgical intervention. In this study, we investigated the pharyngeal and nasal microbiota in patients with AH compared with healthy children. Furthermore, we tested the effects of probiotic spray administration on both disease symptoms and microbiota profiles, to evaluate the possible use of this microbial therapy as an adjuvant for AH patients.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effects of <i>Pinus sylvestris</i> L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment.","authors":"Pulak Maitra, Katarzyna Hrynkiewicz, Agnieszka Szuba, Adrianna Niestrawska, Joanna Mucha","doi":"10.1128/spectrum.00807-24","DOIUrl":"https://doi.org/10.1128/spectrum.00807-24","url":null,"abstract":"<p><p>Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of <i>Pinus sylvestris</i> L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different <i>P. sylvestris</i> origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within <i>P. sylvestris</i> also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments.</p><p><strong>Importance: </strong>This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (<i>Pinus sylvestris</i>). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Flagellum-deficient <i>Pseudomonas aeruginosa</i> is more virulent than non-motile but flagellated mutants in a cystic fibrosis mouse model.","authors":"Dina A Moustafa, Kayla M Fantone, Samantha L Tucker, Nael A McCarty, Arlene A Stecenko, Joanna B Goldberg, Balázs Rada","doi":"10.1128/spectrum.01325-24","DOIUrl":"https://doi.org/10.1128/spectrum.01325-24","url":null,"abstract":"<p><p>Loss of the flagellum marks the pathoadaptation of <i>Pseudomonas aeruginosa</i> to the cystic fibrosis (CF) airway environment during lung disease. Losing the flagellum is advantageous to the bacterium as the flagellum can be recognized by immune cells. The primary purpose of the flagellum is, however, to provide motility to the bacterium. Our goal was to determine whether the loss of flagellar motility or the loss of flagellum expression contributes to <i>P. aeruginosa</i> lung infection in CF. To address this, wild-type and gut-corrected FABP-human cystic fibrosis transmembrane conductance regulator (hCFTR) mice deficient in the murine <i>Cftr</i> gene were infected intratracheally with lethal doses of wild-type or flagellum-deficient <i>P. aeruginosa</i>. While there was no significant difference in the survival of wild-type mice after infection with either of the bacterial strains, a significantly higher mortality was observed in FABP-hCFTR mice infected with flagellum-deficient <i>P. aeruginosa</i>, compared to mice infected with their flagellated counterparts. When FABP-hCFTR mice were infected with isogenic, motility-deficient flagellated mutants, animal survival and lung bacterial titers were similar to those observed in mice infected with the wild-type bacterium. Airway levels of neutrophils and the amount neutrophil elastase were similar in mice infected with either the wild-type bacteria or the flagellum-deficient <i>P. aeruginosa</i>. Our results show that FABP-hCFTR mice have a different response to flagellum loss in <i>P. aeruginosa</i> compared to wild-type animals. The loss of flagellum expression, rather than the loss of motility, is the main driver behind the increased virulence of flagellum-deficient <i>P. aeruginosa</i> in CF. These observations provide new insight into <i>P. aeruginosa</i> virulence in CF.IMPORTANCE<i>Pseudomonas aeruginosa</i>, a major respiratory pathogen in cystic fibrosis, is known to lose its flagellum during the course of infection in the airways. Here, we show that the loss of flagellum leads to a more enhanced virulence in Cftr-deficient cystic fibrosis mice than in control animals. Loss of flagellum expression, rather than the loss of flagellar swimming motility, represents the main driver behind this increased virulence suggesting that this appendage plays a specific role in <i>P. aeruginosa</i> virulence in cystic fibrosis airways.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hepatitis B surface antigen impairs TLR4 signaling by upregulating A20 expression in monocytes.","authors":"Cong Wang, Chenlu Huang, Yaming Li, Jinjin Bai, Kuangjie Zhao, Zhong Fang, Jieliang Chen","doi":"10.1128/spectrum.00909-24","DOIUrl":"https://doi.org/10.1128/spectrum.00909-24","url":null,"abstract":"<p><p>Toll-like receptors (TLRs) play a crucial role in eliminating viral infection. Conversely, viruses have evolved various strategies to disrupt TLR signaling during chronic infection. In the case of hepatitis B virus (HBV), we previously reported that plasma hepatitis B surface antigen (HBsAg) is closely associated with impaired TLR responses in peripheral blood mononuclear cells from chronic hepatitis B (CHB) patients, but the reasons remain unclear. In this study, we investigated the mechanism by which HBsAg suppresses TLR4 signaling in monocyte cell lines. The monocyte cell line THP-1 was pretreated with HBsAg, followed by lipopolysaccharide (LPS) stimulation. Levels of proinflammatory cytokines and the activation of NF-κB, c-JNK, and ERK were examined. We found that HBsAg did not influence the LPS-induced activation of p65, but it disrupted NF-κB promoter activity through the ectopic expression of myeloid differentiation factor 88 (MyD88) and TAK1, suggesting that HBsAg can block downstream TLR4 signaling. Furthermore, we proved that LPS-induced polyubiquitination of tumor necrosis factor receptor-associated factor 6 (TRAF6) and the formation of the TRAF6-TAB2 complex were inhibited in HBsAg-pretreated cells. Interestingly, HBsAg led to a significant upregulation of A20, a ubiquitin-editing enzyme. Correspondingly, downregulation of A20 using siRNA restored LPS-mediated cytokines production, reflecting its crucial role in HBsAg-mediated inhibition of TLR4 signaling. These results demonstrated a novel mechanism by which HBsAg disrupts TLR4 signaling through the upregulation of A20, suggesting that targeting A20 may be a potential strategy to help restore monocyte functions.</p><p><strong>Importance: </strong>Clearance HBsAg indicates a functional cure of HBV infection, but in chronic hepatitis B (CHB), it is hard to achieve. HBsAg has been found to regulate anti-viral immune responses, such as the activation of TLR. Our previous jobs proved that HBsAg negatively correlates with TLR2/4 activation in monocytes from CHB patients and blocks TLR2 ligand-indcuced IL-12 production in monocytes. However, how TLR4 signaling is affected by HBsAg remains unknown. In this study, we not only observed impaired TLR4 activation after pretreated monocytes with HBsAg but also identified HBsAg-induced A20 play a role in this impairment, which suggests that targeting A20 may be a viable strategy to restore monocyte functions in CHB.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Penicillin susceptibility among <i>Staphylococcus aureus</i> skin and soft tissue infections at a children's hospital.","authors":"J Chase McNeil, Lauren M Sommer, Marritta Joseph, Kristina G Hulten, Sheldon L Kaplan","doi":"10.1128/spectrum.00869-24","DOIUrl":"https://doi.org/10.1128/spectrum.00869-24","url":null,"abstract":"<p><p>Shortly after its introduction into clinical practice, <i>Staphylococcus aureus</i> isolates gained resistance to penicillin via the acquisition of β-lactamases. A number of centers have recently described an increase in the proportion of invasive methicillin-susceptible <i>S. aureus</i> (MSSA), which are also susceptible to penicillin (PSSA). Little data are available regarding the prevalence or impact of PSSA in skin and soft tissue infections (SSTI). Community-acquired MSSA SSTI isolates were obtained through a surveillance study at Texas Children's Hospital from January 2017 to December 2021. A total of 200 random isolates underwent PCR for <i>blaZ</i> β-lactamase; <i>blaZ</i>-negative isolates then underwent penicillin susceptibility testing using macrobroth dilution. Isolates which were <i>blaZ</i> negative and had a penicillin MIC ≤0.125 µg/mL were regarded as PSSA with the remainder regarded as penicillin-resistant MSSA (PR-MSSA). All PSSA underwent multilocus sequence typing. Medical records were reviewed. The median age of subjects was 4.2 years (IQR: 1.6-10.5). PSSA accounted for 9% of isolates during the study period. PSSA and PR-MSSA cases were similar with respect to age, demographics, and rates of prior antibiotic exposure. PSSA isolates less often had vancomycin MIC ≥1.5 µg/mL. Furthermore, 39% of PSSA were variants of sequence type 1. In multivariable analyses, penicillin susceptibility was independently associated with both hospital admission and surgical intervention. PSSA account for a small but significant proportion of MSSA SSTI in children. Clinically distinguishing patients with PSSA and PR-MSSA SSTI is challenging. However, PSSA SSTI were independently associated with higher rates of hospital admission as well as the need for surgical intervention suggesting a significant clinical impact.IMPORTANCEThe vast majority of <i>Staphylococcus aureus</i> in the US are penicillin resistant with most clinical labs no longer reporting penicillin susceptibility for this organism. A number of centers, however, have reported increasing penicillin susceptibility among invasive <i>S. aureus</i> infections. Skin and soft tissue infections (SSTI) are far more common than invasive infections, yet the frequency and impact of penicillin-susceptible <i>S. aureus</i> (PSSA) in this population are uncertain. Through active surveillance at a children's hospital, we found that 9% of methicillin-susceptible <i>S. aureus</i> SSTI isolates were PSSA. PSSA were independently associated with hospital admission for the management of SSTI as well as the need for debridement in the operating room. Given that most SSTI are managed in the outpatient setting, these findings suggest a clinical impact of this phenotype and the need for a reassessment of the value in susceptibility testing and potentially even treatment with penicillin.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Acinetobacter calcoaceticus-baumannii</i> complex prevalence, spatial-temporal distribution, and contamination sources in Canadian aquatic environments.","authors":"Thomas Benoit, Dania Sajjad, Michel Cloutier, David R Lapen, Emilia Craiovan, Ellen M E Sykes, Ayush Kumar, Izhar U H Khan","doi":"10.1128/spectrum.01509-24","DOIUrl":"https://doi.org/10.1128/spectrum.01509-24","url":null,"abstract":"<p><p><i>Acinetobacter calcoaceticus-baumannii</i> (ACB) complex has been identified as a group of emerging opportunistic pathogens that cause nosocomial infections. The current study investigates the prevalence, distribution, and diversity of pathogenic ACB complex in various aquatic systems with different uses. Of the total 157 agricultural, raw drinking water intake, recreational beach, and wastewater treatment plant (WWTP) effluent samples, acinetobacters were isolated, quantified, and confirmed by genus- and ACB complex-specific PCR assays. Of all agricultural surface water samples, <i>A. calcoaceticus</i> (65%) was more frequently detected than <i>A. pittii</i> (14%), <i>A. nosocomialis</i> (9%), and <i>A. baumannii</i> (3%). In WWTP effluent samples, <i>A. baumannii</i> was more prevalent in de-chlorinated (60%) samples compared to both <i>A. pittii</i> and <i>A. nosocomialis</i> (40%). Interestingly<i>, A. nosocomialis</i> (43%), <i>A. calcoaceticus</i> (29%), and <i>A. baumannii</i> (14%) were detected in raw drinking water intake samples, whereas <i>A. pittii</i> (50%) and <i>A. nosocomialis</i> (25%) were detected in beach samples. Although no sampling location-specific differences were recorded, significant (<i>P</i> < 0.05) seasonal differences were observed when agricultural surface water samples collected in spring were compared with the summer and fall. Whereas effluent chlorination significantly impacted the degree of prevalence of <i>Acinetobacter</i> in WWTP effluent samples, overall, the prevalence of ACB complex in all sampling locations and seasons indicates that these water sources, containing human-associated ACB complex, may pose potential health risks as community-acquired opportunistic infections.IMPORTANCE<i>Acinetobacter calcoaceticus-baumannii</i> (ACB) complex is a group of organisms known to cause problematic nosocomial opportunistic infections. A member of the species complex, <i>A. baumannii</i>, is becoming a global threat to infection treatment as strains are increasingly develop resistance to antibiotics. The prevalence and distribution of potentially pathogenic <i>Acinetobacter calcoaceticus-baumannii</i> complex species remain poorly understood, and there is a need to better understand the occurrence of <i>A. baumannii</i> in non-nosocomial environments. Our research details the spatial-temporal distribution of ACB complex species in a regional watershed and highlights the presence of ACB complex in wastewater effluent that is discharged into a river. These findings deepen our understanding of this group of species in non-nosocomial environments and encourage the development of monitoring programs for these species in regional waters.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142140549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial efficiency and cytocompatibility of resveratrol and naringin as chemical decontaminants on SLA surface.","authors":"You Zhou, Zhe Shen, Yan Xu, Xin-Na Qian, Wei Chen, Jing Qiu","doi":"10.1128/spectrum.03679-23","DOIUrl":"https://doi.org/10.1128/spectrum.03679-23","url":null,"abstract":"<p><p>Bacterial biofilms are the major etiology agent of peri-implant disease. Chemical decontamination is a promising treatment strategy against bacterial biofilms; however, its applications are limited by its low efficiency and poor biocompatibility. In contrast to three conventional cleaners (sterile saline, hydrogen peroxide, and chlorhexidine), this study used resveratrol and naringin solutions to remove mature <i>Staphylococcus aureus</i> and <i>Porphyromonas gingivalis</i> biofilm on sandblasted (with large grit and acid-etched (SLA) titanium surface. To determine changes in surface characteristics, the surface wettability and roughness were measured, and micromorphology was observed by scanning electron microscopy. With crystal violet (CV) and live/dead bacterial staining, residual plaque quantity and composition were measured. The biocompatibility was tested using pH and cytotoxicity, as well as by osteoblasts (MC3T3-E1) adhesion, proliferation, and differentiation, and fibroblasts (L-929) proliferation were also analyzed. It was found that resveratrol and naringin solutions were more effective in restoring surface characteristics and also showed that less plaque and viable bacteria were left. Naringin removed <i>S. aureus</i> biofilms better than chlorhexidine. Alkaline resveratrol and naringin solutions increased cell adhesion, proliferation, and osteogenic differentiation without any cytotoxicity. Resveratrol increased the expression of mRNA and protein associated with osteogenesis. In conclusion, resveratrol and naringin effectively restored SLA titanium surface characteristics and decontaminated the biofilm with good biocompatibility, suggesting their therapeutic potential as chemical decontaminants.</p><p><strong>Importance: </strong>Bacterial biofilms are considered the primary etiology of peri-implant disease. Physical cleaning is the most common way to remove bacterial biofilm, but it can cause grooving, melting, and deposition of chemicals that alter the surface of implants, which may hamper biocompatibility and re-osseointegration. Chemical decontamination is one of the most promising treatments but is limited by low efficiency and poor biocompatibility. Our study aims to develop safer, more effective chemical decontaminants for peri-implant disease prevention and treatment. We focus on resveratrol and naringin, two natural compounds, which have shown to be more effective in decontaminating biofilms on dental implant surfaces and exerting better biocompatibility. This research is groundbreaking as it is the first exploration of natural plant extracts' impact on mature bacterial biofilms on rough titanium surfaces. By advancing this knowledge, we seek to contribute to more effective and biocompatible strategies for combating peri-implant diseases, enhancing oral health, and prolonging implant lifespan.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142140551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical and pathogen features of COVID-19-associated infections during an Omicron strain outbreak in Guangzhou, China.","authors":"Lin-Ling Cheng, Zheng-Tu Li, Hong-Kai Wu, Feng Li, Ye Qiu, Tao Wang, Hui Peng, Zi-Hao Liu, Pan-Rui Huang, Lu Zhou, Li-Fen Gao, Hui-Ju Huang, Bin Zhang, Xi-Long Deng, Xin Chen, Feng Ye, Xiao-Qing Liu, Wei-Jie Guan, Yue-Ping Li, Yi-Min Li, Shi-Yue Li, Nan-Shan Zhong","doi":"10.1128/spectrum.03406-23","DOIUrl":"https://doi.org/10.1128/spectrum.03406-23","url":null,"abstract":"<p><p>Although the Omicron variant has been associated with greater transmissibility and tropism of the upper respiratory tract, the clinical and pathogenic features of patients infected with the Omicron variant during an outbreak in China have been unclear. Adults with COVID-19 were retrospectively enrolled from seven medical centers in Guangzhou, China, and clinical information and specimens ( BALF, sputum, and throat swabs) from participants were collected. Conventional detection methods, metagenomics next-generation sequencing (mNGS), and other methods were used to detect pathogens in lower respiratory tract samples. From December 2022 to January 2023, we enrolled 836 patients with COVID-19, among which 56.7% patients had severe/critical illness. About 91.4% of patients were infected with the Omicron strain (BA.5.2). The detection rate of possible co-infection pathogens was 53.4% by mNGS, including <i>Klebsiella pneumoniae</i> (16.3%), <i>Aspergillus fumigatus</i> (12.2%), and <i>Pseudomonas aeruginosa</i> (11.8%). The co-infection rate was 19.5%, with common pathogens being <i>Streptococcus pneumoniae</i> (11.5%), <i>Haemophilus influenzae</i> (9.2%), and <i>Adenovirus</i> (6.9%). The superinfection rate was 75.4%, with common pathogens such as <i>Klebsiella pneumoniae</i> (26.1%) and <i>Pseudomonas aeruginosa</i> (19.4%). <i>Klebsiella pneumoniae</i> (27.1%% vs 6.1%, <i>P</i> < 0.001), <i>Aspergillus fumigatus</i> (19.6% vs 5.3%, <i>P</i> = 0.001), <i>Acinetobacter baumannii</i> (18.7% vs 4.4%, <i>P</i> = 0.001), <i>Pseudomonas aeruginosa</i> (16.8% vs 7.0%, <i>P</i> = 0.024), <i>Staphylococcus aureus</i> (14.0% vs 5.3%, <i>P</i> = 0.027), and <i>Streptococcus pneumoniae</i> (0.9% vs 10.5%, <i>P</i> = 0.002) were more common in severe cases. Co-infection and superinfection of bacteria and fungi are common in patients with severe pneumonia associated with Omicron variant infection. Sequencing methods may aid in the diagnosis and differential diagnosis of pathogens.</p><p><strong>Importance: </strong>Our study has analyzed the clinical characteristics and pathogen spectrum of the lower respiratory tract associated with co-infection or superinfection in Guangzhou during the outbreak of the Omicron strain, particularly after the relaxation of the epidemic prevention and control strategy in China. This study will likely prompt further research into the specific issue, which will benefit clinical practice.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142140553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial resistance and prevalence of extended-spectrum beta-lactamase-producing <i>Klebsiella</i> species in East Tennessee dairy farms.","authors":"Benti Deresa Gelalcha, Aga E Gelgie, Oudessa Kerro Dego","doi":"10.1128/spectrum.03537-23","DOIUrl":"https://doi.org/10.1128/spectrum.03537-23","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Klebsiella&lt;/i&gt; species commonly reside in dairy cattle guts and are consistently exposed to beta-lactam antibiotics, including ceftiofur, which are frequently used on the U.S. dairy farms. This may impose selection pressure and result in the emergence of extended-spectrum beta-lactamase (ESBL)-producing strains. However, information on the status and antimicrobial resistance (AMR) profile of ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. in the U.S. dairy farms is largely unknown. This study aimed to determine the prevalence and AMR profile of ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. and the factors affecting their occurrence in dairy cattle farms. Rectal fecal samples (&lt;i&gt;n&lt;/i&gt; = 508) and manure, feed, and water samples (&lt;i&gt;n&lt;/i&gt; = 64) were collected from 14 dairy farms in Tennessee. Samples were directly plated on CHROMagar ESBL, and presumptive &lt;i&gt;Klebsiella&lt;/i&gt; spp. were confirmed using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Antimicrobial susceptibility testing was performed on the isolates against panels of 14 antimicrobial agents from 10 classes using minimum inhibitory concentration. Of 572 samples, 57 (10%) were positive for ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. The fecal prevalence of ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. was 7.2% (95% CI: 6.5-8.0). The herd-level fecal prevalence of ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. was 35.7% (95% CI: 12.7-64.8). The fecal prevalence of ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. was significantly higher in calves than in cows and higher in cows with higher parity (≥3) as compared to cows with low parity (&lt;i&gt;P&lt;/i&gt; &lt; 0.001). Most (96.5%, &lt;i&gt;n&lt;/i&gt; = 57) ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. were resistant to ceftriaxone. The highest level of acquired co-resistance to ceftriaxone in ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. was to sulfisoxazole (66.7%; 38/57). About 19% of ESBL-K&lt;i&gt;lebsiella&lt;/i&gt; spp. were multidrug resistant. The presence of ESBL-producing &lt;i&gt;Klebsiella&lt;/i&gt; spp. in dairy cattle, feed, and water obtained from troughs could play a crucial epidemiological role in maintaining and spreading the bacteria on farms and serving as a point source of transmission.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;We collected 572 samples from dairy farms, including rectal feces, manure, feed, and water. We isolated and identified extended-spectrum beta-lactamase (ESBL)-&lt;i&gt;Klebsiella&lt;/i&gt; spp. and conducted an antimicrobial susceptibility test and analyzed different variables that may be associated with ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. in dairy farms. The results of our study shed light on how ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. are maintained through fecal-oral routes in dairy farms and possibly exit from the farm into the environment. We determine the prevalence of ESBL-&lt;i&gt;Klebsiella&lt;/i&gt; spp. and their antimicrobial susceptibility profiles, underscoring their potential as a vehicle for multiple resistance gene dissemination within dairy farm settings. We also collected data on variables affecting their occurrence and spread in dairy farms. These findings have significant impli","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142140552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs.","authors":"Philip Sweet, Matthew Burroughs, Sungyeon Jang, Lydia Contreras","doi":"10.1128/spectrum.03838-23","DOIUrl":"https://doi.org/10.1128/spectrum.03838-23","url":null,"abstract":"<p><p>The trait of ionizing radiation (IR) tolerance is variable between bacterium, with species succumbing to acute doses as low as 60 Gy and extremophiles able to survive doses exceeding 10,000 Gy. While survival screens have identified multiple highly radioresistant bacteria, such systemic searches have not been conducted for IR-sensitive bacteria. The taxonomy-level diversity of IR sensitivity is poorly understood, as are genetic elements that influence IR sensitivity. Using the protein domain (Pfam) frequencies from 61 bacterial species with experimentally determined <i>D</i>₁₀ values (the dose at which only 10% of the population survives), we trained TolRad, a random forest binary classifier, to distinguish between radiosensitive (<i>D</i>₁₀ < 200 Gy) and radiation-tolerant (<i>D</i>₁₀ > 200 Gy) bacteria. On untrained species, TolRad had an accuracy of 0.900. We applied TolRad to 152 UniProt-hosted bacterial proteomes associated with the human microbiome, including 37 strains from the ATCC Human Microbiome Collection, and classified 34 species as radiosensitive. Whereas IR-sensitive species (<i>D</i>₁₀ < 200 Gy) in the training data set had been confined to the phylum <i>Proteobacterium</i>, this initial TolRad screen identified radiosensitive bacteria in two additional phyla. We experimentally validated the predicted radiosensitivity of a <i>Bacteroidota</i> species from the human microbiome. To demonstrate that TolRad can be applied to metagenome-assembled genomes (MAGs), we tested the accuracy of TolRad on Egg-NOG assembled proteomes (0.965) and partial proteomes. Finally, three collections of MAGs were screened using TolRad, identifying further phyla with radiosensitive species and suggesting that environmental conditions influence the abundance of radiosensitive bacteria.</p><p><strong>Importance: </strong>Bacterial species have vast genetic diversity, allowing for life in extreme environments and the conduction of complex chemistry. The ability to harness the full potential of bacterial diversity is hampered by the lack of high-throughput experimental or bioinformatic methods for characterizing bacterial traits. Here, we present a computational model that uses <i>de novo</i>-generated genome annotations to classify a bacterium as tolerant of ionizing radiation (IR) or as radiosensitive. This model allows for rapid screening of bacterial communities for low-tolerance species that are of interest for both mechanistic studies into bacterial sensitivity to IR and biomarkers of IR exposure.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}