Category Archives: Letters in Applied Microbiology

Uncovering the structure and function of specialist bacterial lineages in environments routinely exposed to explosives

Posted on 16 November 2022 by nY. Pal, nS. Mayilraj, nS. Krishnamurthin

Significance and Impact of the Study: This study is the first to provide an overall view of bacterial community structure and associated metabolic pathways in geographically distinct explosives-contaminated sites. In contrast to the previous reports, our findings showed the predominance of Planctomycetes in explosives-contaminated sites. We hypothesized that RDX and HMX concentrations could impart a notable impact on the bacterial community along with the associated metabolic genes.

Abstract

Environmental contamination by hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), the two most widely used compounds for military operations, is a long-standing problem at the manufacturing and decommissioning plants. Since explosives contamination has previously been shown to favour the growth of specific bacterial communities, the present study attempts to identify the specialist bacterial communities and their potential functional and metabolic roles by using amplicon targeted and whole-metagenome sequencing approaches in samples collected from two distinct explosives manufacturing sites. We hypothesize that the community structure and functional attributes of bacterial population are substantially altered by the concentration of explosives and physicochemical conditions. The results highlight the predominance of Planctomycetes in contrast to previous reports from similar habitats. The detailed phylogenetic analysis revealed the presence of operational taxonomic units related to bacterial members known for their explosives degradation. Further, the functional and metabolic analyses highlighted the abundance of putative genes and unidentified taxa possibly associated with xenobiotic biodegradation. Our findings suggest that microbial species capable of utilizing explosives as a carbon, energy or electron source are favoured by certain selective pressures based on the prevailing physicochemical and geographical conditions.

Antibacterial and antibiofilm activities of fosfomycin combined with rifampin against carbapenem‐resistant Pseudomonas aeruginosa

Posted on 16 November 2022 by nY. Liu, nW. Ma, nM. Li, nJ. Wu, nL. Sun, nW. Zhao, nS. Sunn

Significance and Impact of the Study: This study demonstrated for the first time that fosfomycin combined with rifampin showed strong synergistic effects against Pseudomonas aeruginosa, with 100% synergistic rates. Furthermore, we confirmed the antibiofilm activity of fosfomycin combined with rifampin against carbapenem-resistant P. aeruginosa. This study provides new insights that fosfomycin + rifampin may be a promising option for clinical treatment.

Abstract

The increasing prevalence of carbapenem-resistant Pseudomonas aeruginosa (CRPA) strains in the hospital setting represents an emerging challenge to clinical treatment for Pseudomonas aeruginosa (PA) infections, as the range of therapeutic agents active against these pathogens becomes increasingly constrained. This study demonstrated for the first time that fosfomycin (FOS) combined with rifampin (RIF) showed strong synergistic effects against CRPA and carbapenem-susceptible PA, with 100% synergistic rates. Additionally, the time-killing curve further proves the dynamic antibacterial activity of FOS + RIF against CRPA. Further experiments determined that antibacterial mechanisms of FOS + RIF might be inhibition of biofilm formation and eradication of preformed biofilm. The results of the inhibition biofilm formation assay demonstrated that RIF and FOS at 1/8MIC, 1/16MIC and 1/32MIC have better inhibitory effects on CRPA biofilm formation VS FOS alone (96, 90 and 78% vs 29, 24 and 22%) (P < 0·0001) or RIF alone (96, 90 and 78% vs 86, 67 and 29%) (P < 0·01). The rates of eradicating preformed biofilm with combination therapy at 1/2MIC, 1/4MIC and 1/8MIC of both antibiotics, increased 46, 61 and 55% compared with FOS alone (P < 0·001) and 37, 33 and 46% compared with RIF alone (P < 0·01). This finding will provide new insights into the treatment of bacterial infections caused by CRPA, which can be further explored in clinical practice.

The diversity of rhizospheric bacterial communities associated with Trichoderma‐treated rice fields

Posted on 16 November 2022 by

Significance and Impact of The Study: This research will provide new insights into the effects of microbial-based biofertilizers on the rhizospheric microbiota. Through this research, it will help the research community to further understand the usage of biofertilizer as a healthier option to the conventional chemical fertilizers. Using biofertilizer as a more sustainable alternative must be studied thoroughly up to the microbial community level that subsequently contributes to the soil health status. A better understanding allows the scientists and farmers to maximize the usage of the microbe-based products without harming surrounding environments. Moreover, the results that are presented, will convey valuable early information for future research.

Abstract

Microbial-based fertilizer has been widely used as a healthier and better alternative to agrochemical products. However, the effects of biofertilizers on the rhizospheric microbiota has rarely been investigated. Thus, the aim of this study was to investigate the effects of symbiotic fungus Trichoderma asperellum SL2-based inoculant on the soil bacterial population through next generation sequencing using a metabarcoding approach. The treatment plots were treated with T. asperellum SL2 spore suspension, while the control plots were treated with sterilized distilled water. The results showed similar bacterial microbiome profiles in the soil of control and T. asperellum SL2-treated plots. In conclusion, the application of the T. asperellum SL2 inoculant had not exerted a negative impact towards the bacterial population as similar observation was reflected in control plots. Nonetheless, future research should be conducted to investigate the effects of repeated application of T. asperellum SL2 over a longer period on the rice microbiota communities.

Isolation, purification and structural elucidation of Mellein from endophytic fungus Lasiodiplodia theobromae strain (SJF‐1) and its broad‐spectrum antimicrobial and pharmacological properties

Posted on 16 November 2022 by nM. Saraswathi, nS.H. Meshram, nB. Siva, nS. Misra, nK. Suresh Babun

Significance and Impact of the Study: In the present study, the bioactive metabolite Mellein was represented as a broad-spectrum antimicrobial agent produced by Lasiodiplodia theobromae strain (SJF-1) isolated from the medicinal plant Syzygium cumini. In addition, Mellein exhibited drug-like characteristics through in silico absorption, distribution, metabolism, and excretion pharmacological studies. Hence, from the above studies, Mellein could be considered as a potential drug candidate and also a biocontrol agent in the medical, agricultural and pharmaceutical sectors.

Abstract

In an on-going investigation of bioactive metabolites producing potential endophytic fungi, the strain Lasiodiplodia theobromae (SJF-1) was isolated from a medicinal plant Syzygium cumini. The cultural, morphological and molecular identification was done with the SJF-1 strain. The obtained gene sequence was deposited in NCBI with accession number MG 938644. The methanolic extract of SJF-1 strain possessed one major bioactive fraction, and it was purified by column chromatography. Further, it was identified as Mellein by various spectroscopic studies (¹H, ¹³C, DEPT-135°, FT-IR, ESI-HR-MS and 2D NMR). Biologically, Mellein showed potent anti-Xanthomonas activity with minimum inhibitory concentration (MIC) values ranging from 1·9 to 62·5 μg ml⁻¹ against 11 Xanthomonas strains, a broad-spectrum antimicrobial activity with MIC 7·8–31·25 μg ml⁻¹ and 1·9–31·25 μg ml⁻¹ towards both bacterial and fungal strains, respectively. The scanning electron microscope analysis proved the antimicrobial efficacy of a Mellein by rupturing the cell walls of Xanthomonas sp. Molecular docking studies further supported that the Mellein showed good binding interactions with the proteins of Xanthomonas sp. to reduce pathogenicity. Further, in silico pharmacological studies showed that this metabolite exhibited high gastrointestinal absorption properties and promising oral drug bioavailability. We report, anti-Xanthomonas, in silico docking and pharmacological studies of Mellein from (SJF-1) strain for the first time.

Survival of Clostridioides difficile spores in thermal and chemo‐thermal laundering processes and influence of the exosporium on their adherence to cotton bed sheets

Posted on 16 November 2022 by nJ. Tarrant, nL. Owen, nR. Jenkins, nL.J. Smith, nK. Lairdn

Significance and Impact of the Study: Clostridioides difficile spores survive on healthcare linens during industrial laundering. This study demonstrates that C. difficile spores are resistant to thermal and chemo-thermal disinfection parameters recommended for healthcare laundry in the UK. The interactions between soiling, heat and disinfectants on C. difficile spore inactivation were established, which may aid in optimization of healthcare laundry processes. Clostridioides difficile spores attached to cotton over time, with the exosporium playing a role in adherence. These findings may inform novel strategies to prevent attachment to textiles, improving spore removal from linen by detergents during laundering.

Abstract

Clostridioides difficile spores were previously demonstrated to survive industrial laundering. Understanding interactions between heat, disinfectants and soiling (e.g. bodily fluids) affecting C. difficile spore survival could inform the optimization of healthcare laundry processes. Reducing spore attachment to linen could also enhance laundering efficacy. This study aimed to compare the sensitivity of C. difficile spores to heat and detergent, with and without soiling and to investigate adherence to cotton. Survival of C. difficile spores exposed to industrial laundering temperatures (71–90°C), reference detergent and industrial detergent was quantified with and without soiling. The adherence to cotton after 0 and 24 h air drying was determined with the exosporium of C. difficile spores partially or fully removed. Clostridioides difficile spores were stable at 71°C for 20 min (≤0·37 log₁₀ reduction) while 90°C was sporicidal (3 log₁₀ reduction); soiling exerted a protective effect. Industrial detergent was more effective at 71°C compared to 25°C (2·81 vs 0·84 log₁₀ reductions), however, specifications for sporicidal activity (>3 log₁₀ reduction) were not met. Clostridioides difficile spores increasingly adhered to cotton over time, with 49% adherence after 24 h. Removal of the exosporium increased adherence by 19–23% compared to untreated spores. Further understanding of the role of the exosporium in attachment to cotton could enhance spore removal and aid decontamination of linen.

Genetic heterogeneity and predominance of blaCTX‐M‐15 in cefotaxime‐resistant Enterobacteriaceae isolates colonizing hospitalized children in Tunisia

Posted on 16 November 2022 by

Significance and Impact of the Study: Our study showed that extended-spectrum β-lactamase-, plasmidic-AmpC- and carbapenemases-producing Enterobacteriaceae colonized hospitalized children at a rather high incidence and some of them belonged to high-risk clonal lineages. Therefore, it is important to implement and reinforce preventative measures to restrict the selection and spread of such strains.

Abstract

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have emerged as important nosocomial pathogens. Community infections by these organisms have been also reported and were associated with previous intestinal colonization. We aimed to characterize cefotaxime-resistant Enterobacteriaceae (CTX-R-En) isolated from hospitalized children in a Tunisian paediatric ward. Seventy CTX-R-En isolates were collected from 227 rectal swabs from hospitalized children in a paediatric ward. Antimicrobial susceptibility testing was determined according to the EUCAST guidelines. Isolates were characterized by polymerase chain reaction (PCR, genes encoding: ESBLs, pAmpC, carbapenemases, plasmid-mediated quinolone resistance, virulence factors in Escherichia coli and Klebsiella pneumoniae isolates, occurrence of classes 1 and 2 integrons, phylogenetic groups of E. coli isolates, ERIC-PCR and PCR-based replicon typing) and conjugal transfer experiments. In total, 65 out of 227 (28·6%) hospitalized children were colonized with CTX-M-R-En, and 70 isolates were identified. Isolates were 59 ESBL-, 7 plasmidic-AmpC (pAmpC)-, 3 ESBL+pAmpC-, and one ESBL+carbapenemase producers. The following bla genes were identified: bla _CTX-M-15 (n = 54), bla _CTX-M-1 (n = 5), bla _CTX-M-9 (n = 2), bla _CTX-M-13 (n = 1) and bla _CTX-M-14 (n = 1), bla _CMY-2 (n = 5), bla _CMY-4 (n = 4), bla _ACC-1 (n = 1) and bla _OXA-48 (n = 1). Our results showed that hospitalized children were colonized with various CTX-R-En-producing several beta-lactamase enzymes.

Detection of optrA and poxtA genes in linezolid‐resistant Enterococcus isolates from fur animals in China

Posted on 16 November 2022 by nW. Sun, nH. Liu, nJ. Liu, nQ. Jiang, nY. Pan, nY. Yang, nX. Zhu, nJ. Gen

Significance and Impact of the Study: In this study, we first reported linezolid-resistant (LR) Enterococcus isolates from foxes and minks in the north of China and explored the resistance mechanism. Notably, linezolid is not allowed for treatment of fur animals in China. Resistance genes may come from the environment or other species. What's more, we found a LR Enterococcus faecium isolate and carrying the optrA gene represented a novel ST type ST2010, indicating an involvement of fur animals in the spread of LR bacteria.

Abstract

The emergence of linezolid-resistant (LR) enterococci found in food of animal origin arouses attention, but little is known about LR enterococci in fur animals. A total of 342 Enterococcus faecalis and 265 E. faecium strains isolated from fur animals in China from 2015 to 2017 were investigated to determine if LR enterococci (≥16 μg ml⁻¹) are present. Overall, two E. faecalis and 12 E. faecium among these isolates were resistant to linezolid. In addition, all LR isolates were classified as multidrug-resistant isolates. We further explore the resistance genes of the LR enterococci, four E. faecalis and two E. faecium isolates contained optrA gene. Two of them co-harboured optrA and poxtA genes. We detected virulence genes in LR enterococci were the following: asa1, cylA, esp, gelE and hyl, among which the highest carrying rate gene was asa1. Besides, all of the LR enterococci we tested had the biofilm-forming ability. It is worth noting that we detected a novel ST type ST2010 from E. faecium 82-2. These data show LR enterococci exist in fur animals and have unique characteristics.

Efficacy of hydrogen peroxide wipes for decontamination of AZD1222 adenovirus COVID‐19 vaccine strain on pharmaceutical industry materials

Posted on 16 November 2022 by

Significance and Impact of Study: The disinfection procedure with hydrogen peroxide® wipes (HPW) resulted in complete decontamination of AZD1222 chimpanzee adenovirus strain in formulated recombinant COVID-19 vaccine (≥7·46 and ≥7·49 log₁₀ infectious unit [IFU] ml⁻¹ for stainless steel [SS] and low-density-polyethylene [LDP] carriers respectively) and active pharmaceutical ingredient (≥8·79 and ≥8·78 log₁₀ IFU ml⁻¹ for SS and LDP carriers respectively). HPW can be a good option for disinfection processes in pharmaceutical industry facilities during recombinant COVID-19 vaccine production. This procedure is simple and can be also applied on safety unit cabins and sampling bags made of LDP as well.

Abstract

This study aimed to evaluate the performance of accelerated hydrogen peroxide® wipes (HPW) for decontamination of the chimpanzee adenovirus AZD1222 vaccine strain used in the production of recombinant COVID-19 vaccine in a pharmaceutical industry. Two matrices were tested on stainless-steel (SS) and low-density-polyethylene (LDP) surfaces: formulated recombinant COVID-19 vaccine (FCV) and active pharmaceutical ingredient (API). The samples were spiked, dried and the initial inoculum, possible residue effect (RE) and titre reduction after disinfection with HPW were determined. No RE was observed. The disinfection procedure with HPW resulted in complete decontamination the of AZD1222 adenovirus strain in FCV (≥7·46 and ≥7·49 log₁₀ infectious unit [IFU] ml⁻¹ for SS and LDP carriers respectively) and API (≥8·79 and ≥8·78 log₁₀ IFU ml⁻¹ for SS and LDP carriers respectively). In conclusion, virucidal activity of HPW was satisfactory against the AZD1222 adenovirus strain and can be a good option for disinfection processes of SS and LPD surfaces in pharmaceutical industry facilities during recombinant COVID-19 vaccine production. This procedure is simple and can be also applied on safety unit cabins and sampling bags made of LDP as well.

Temporal dysregulation of genes in lamb testis cell during sheeppox virus infection

Posted on 16 November 2022 by

Significance and Impact of Study: The host cellular processes, particularly the immune response, are highly influenced during virus infection. Previously, we have conducted a transcriptomics study of the sheeppox virus (SPPV) infection in lamb testis cell during the immediate-early (0·5 h) phase when only the immediate-early pox viral genes are expressed. However, the SPPV expresses its early genes within 1–2 h and late genes within 8 h in the cell cytoplasm, both of which in turn affect the expression of the host genes. These host–pathogen interactions tend to activate various cell signalling pathways involved in several cellular processes.

Abstract

The present study was aimed to elucidate the host–virus interactions using RNA-Seq analysis at 1 h and 8 h of post-infection of sheeppox virus (SPPV) in lamb testis cell. The differentially expressed genes (DEGs) and the underlying mechanisms linked to the host immune responses were obtained. The protein–protein interaction (PPI) network analysis and ingenuity pathway analysis (IPA) illustrated the interaction between the DEGs and their involvement in cell signalling responses. Highly connected hubs viz. AURKA, CHEK1, CCNB2, CDC6 and MAPK14 were identified through PPI network analysis. IPA analysis showed that IL-6- and ERK5-mediated signalling pathways were highly enriched at both time points. The TP53 gene was identified to be the leading upstream regulator that directly responded to SPPV infection, resulting in downregulation at both time points. The study provides an overview of how the lamb testis genes and their underlying mechanisms link to growth and immune response during SPPV infection.

Enzymatic and antifungal susceptibility profiles of Candida glabrata isolates from paediatric patients and their genetic diversity based on microsatellite length polymorphism

Posted on 16 November 2022 by nH. Jafarian, nA.K. Hardani, nA.A. Asnafi, nA.Z. Mahmoudabadin

Significance and Impact of the Study: The current study provides a detailed characterization of enzymatic activity, antifungal susceptibility, and genotypes of Candida glabrata recovered from urine or oral culture from paediatric patients with/without neutropenia, environmental samples, and normal adult population oral samples. Although a high proteinase activity was observed in all isolates, multi-drug resistance was observed amongst normal population isolates. Furthermore, neutropenic patient isolates were genetically divergent from other populations. Detected genotypes were mainly related to previously reported Iranian, Spanish, and Chinese genotypes. Candida glabrata has a critical distinction due to its haploid genome. Improving our knowledge about the antifungal susceptibility profile associated with this species is essential, especially in neutropenic patients.

Abstract

This study aimed to detect different genotypes of Candida glabrata isolates in paediatric patients with and without neutropenia utilizing microsatellite length polymorphism (MLP) and its correlation with drug resistance and enzymatic activity were assessed. Samples from neutropenic and non-neutropenic patients were collected from November 2020 to November 2021. Thirty-six C. glabrata strains were isolated and identified using classical and molecular methods. Then, C. glabrata isolates were genotyped by the MLP technique, and their antifungal susceptibility was performed based on the CLSI M27 guideline. Eighteen different multi-loci genotypes (G1–G18) were detected based on MLP analysis. Analysis of molecular variance revealed high genetic variation within populations (94%) and low genetic differentiation amongst populations (6%). Also, 40% (n = 4) of isolates from neutropenic patients were non-wild-type for posaconazole, and 30% (n = 3) were resistant to caspofungin. Very strong hemolytic and proteinase activity were seen in 97·2 and 86·1% of isolates. Candida glabrata strains from neutropenic patients were genetically divergent from other populations. The minimum spanning tree shows that observed genotypes were mainly related to previously reported genotypes from Iran, Spain, and China.