Investigation of Raman Spectroscopic Signatures with Multivariate Statistics: An Approach for Cataloguing Microbial Biosignatures

Spectroscopic instruments are increasingly being implemented in the search for extraterrestrial life. However, microstructural spectral analyses of alien environments could prove difficult without knowledge on the molecular identification of individual spectral signatures. To bridge this gap, we introduce unsupervised K-means clustering as a statistical approach to discern spectral patterns of biosignatures without prior knowledge of spectral regions of biomolecules. Spectral profiles of bacterial isolates from analogous polar ice sheets were measured with Raman spectroscopy. Raman analysis identified carotenoid and violacein pigments, and key cellular features including saturated and unsaturated fats, triacylglycerols, and proteins. Principal component analysis and targeted spectra integration biplot analysis revealed that the clustering of bacterial isolates was attributed to spectral biosignatures influenced by carotenoid pigments and ratio of unsaturated/saturated fat peaks. Unsupervised K-means clustering highlighted the prevalence of the corresponding spectral peaks, while subsequent supervised permutational multivariate analysis of variance provided statistical validation for spectral differences associated with the identified cellular features. Establishing a validated catalog of spectral signatures of analogous biotic and abiotic materials, in combination with targeted supervised tools, could prove effective at identifying extant biosignatures.

Investigation of a cluster of Bacillus cereus bacteremia in neonatal care units

BACKGROUND

Bacillus cereus is a well-known pathogen for self-limited foodborne illness, and rarely an opportunistic pathogen associated with invasive infections among immunocompromised patients. Nosocomial outbreaks have been rarely reported.

METHODS

Between August and November 2019, four preterm neonates in neonatal care units of a medical center developed late-onset B. cereus bacteremia. An investigation was carried out. Forty-eight environmental specimens were obtained from these neonatal units, skin surface and environmental objects of Patient 4 for the detection of this organism 19 days after the onset of illness of Patient 4. B. cereus isolates from Patient 4, five unrelated patients and environmental objects if identified were further characterized by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

RESULTS

All four infants survived after vancomycin-containing treatment. Patient 4 developed diffuse cerebritis, brain abscess with severe neurologic sequelae. Of the 48 environmental samplings, 26 specimens showed positive for B. cereus, with one major clone (sequence type 365) accounting for 73%. The isolate from Patient 4 (ST427) was identical to one isolate collected from environmental objects in the same unit. After extensive cleaning of the environment and re-institution of the sterilization procedure of hospital linens, which was ceased since two months before the outbreak, no more cases was identified in these units for at least one year.

CONCLUSIONS

We documented a cluster of B. cereus bacteremia involving four preterm infants, which might be associated with cessation of the procedure for linen sterilization and was successfully controlled by re-institution of this procedure.

The trend of environmental and clinical methicillin-resistant Staphylococcus aureus in a hospital in Taiwan: Impact of USA300

BACKGROUND

The environment may facilitate transmission of health care-associated methicillin-resistant Staphylococcus aureus (MRSA) and the pathogen is frequently shed by patients. However, the molecular characteristics and genetic relatedness between clinical and environmental MRSA isolates remain largely unclear in the clinical setting.

METHODS

A total of 100 hospitalized patients with MRSA infection and 25 hospitalized patients without MRSA infection were enrolled in a medical center, Taiwan in 2019. Environmental and clinical MRSA isolates were characterized by antibiotic susceptibility testing and molecular methods.

RESULTS

In the study, we detected 17 MRSA isolates in the environment that surrounded 15 MRSA-infected patients and one environmental MRSA isolate from one patient without MRSA infection. The molecular analysis revealed a high genetic diversity within either environmental or clinical MRSA isolates, while the USA300 clone (pulsotype AI, SCCmec IV, ST8, PVL-positive) accounts for 39% (7/18) of environmental and 33% (7/21) of clinical MRSA isolates. Moreover, 13 of the 15 MRSA-infected patients had identical paired clinical-environmental MRSA isolates, which exhibited indistinguishable genetic relatedness and highly similar antibiotic susceptibility phenotype, suggesting a possible transmission cycle of MRSA in the hospital.

CONCLUSIONS

The environmental MRSA was closely linked to MRSA isolated from patients, suggesting that the environment may act as a reservoir of MRSA. Besides, the USA300 MRSA has become a major clone in the hospital setting. An effective and rigorous approach to environmental cleaning and decontamination is suggested to eradicate MRSA in the hospital.

Diversity in gene arrangement in a DNA region lacking aerA in clinical and environmental Aeromonas hydrophila isolates

Aquatic pathogen Aeromonas hydrophila produces an array of virulence factors, many of which are excreted proteins that causes infectious disease in fish, reptiles, and humans. Aerolysin, a haemolytic toxin, is the most well-known of the A. hydrophila virulence factors and is encoded by aerA. Although used as a virulence gene marker in several studies, recent whole-genome sequencing data suggest there may be some variation in aerolysin genes, as well as in the genetic environment of these genes, among A. hydrophila strains. Here, we used PCR-based assays to examine gene arrangement in the traditional aerA region of 42 aerA-minus clinical and environmental A. hydrophila isolates. PCR primers were designed based on known genes from within the target regions of reference strains carrying non-aerA aerolysin genes. Analyses revealed four different gene arrangement patterns among the isolates, indicating considerable genetic diversity in the target region. While 19 of the 21 environmental isolates showed the same gene pattern, all four patterns were represented among the clinical isolates, implying that the gene pattern is highly conserved in the target region among environmental isolates. Further analysis of the gene regions showed that the predominant pattern among environmental isolates, which did not contain an aerolysin gene, appeared to be the progenitor of the other three patterns, which likely arose as a result of gene acquisition, deletion, and rearrangement events during the evolution of A. hydrophila, and may be linked to the acquisition of aerolysin genes. These findings shed light on the evolution of virulence in A. hydrophila.

In vitro expression of vital virulent genes of clinical and environmental isolates of Cryptococcus neoformans/gattii in endothelial cells of human blood-brain barrier

BACKGROUND

Evaluation of the pathogenesis of clinical and environmental cryptococcal isolates to the central nervous system is necessary for understanding the risk. This study was designed to determine the in vitro expression of six important virulent genes of Cryptococcus neoformans/gattii in Human Brain Microvascular Endothelial cells (hBMEC).

METHODS

The hBMEC were infected with Cryptococcus to determine invasion and survival rate at 3, 12 and 24hours by subsequent colony count of internalized yeasts. The whole RNA of the intracellular Cryptococcus was extracted to quantify the expression of CAP10, PLB1, ENA1, URE1, LAC1, and MATα genes by real-time quantitative PCR for 3 and 12hours of infection.

RESULTS

Invasion and survival rates were higher in clinical and standard strains of C. neoformans. A significant difference was observed among the clinical and environmental isolates for the expression of CAP10, ENA1, LAC1, MATα and URE1 at 3hours, and ENA1, LAC1, MATα, PLB1 and URE1 at 12hours. Clinical isolates showed significant upregulation of all the genes except PLB1, which was higher in environmental isolates. Relative expressions at the two time-points showed statistically significant (P=0.043) changes for the clinical isolates and no significance (P=0.063) for environmental isolates.

CONCLUSION

The C. gattii (VGI) isolates showed significantly lower invasion and survival than C. neoformans (VNI, and VNII) irrespective of their sources. Clinical isolates exhibited higher expression for the majority of the virulent genes until 12hours of infection, probably due to their better adaptation in the host system and enhanced pathogenicity than the environmental counterparts.

Rapid dereplication of microbial isolates using matrix-assisted laser desorption ionization time-of-flight mass spectrometry: A mini-review

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MALDI-TOF MS is applicable as high-resolution and high-throughput tool.

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The classification and characterization of cultivable microorganisms is targeted.

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Advantageous are its simple sample preparation and short measurement time.

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It accelerates the dereplication of isolates from large-scale screening campaigns.

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Applications for studying microbial diversity and future trends are discussed.

Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid, cost-effective and accurate classification and characterization of cultivable microorganisms. Due to its simple sample preparation and short measurement time, MALDI-TOF MS is an excellent choice for the high-throughput study of microbial isolates from rhizospheres or plants grown under diverse environmental conditions. While clinical isolates have a higher identification rate than environmental isolates due to the focus of commercial mass spectral libraries on the former, no identification is necessary in the dereplication step of large environmental studies. The grouping of large sets of isolates according to their intact protein profiles can be performed without knowledge of their taxonomy. Thus, this method is easily applicable to environmental samples containing microorganisms from yet undescribed phylogenetic origins. The main strategies applied to achieve effective dereplication are, first, expanding existing mass spectral libraries and, second, using an additional statistical analysis step to group measured mass spectra and identify unique isolates. In this review, these aspects are addressed. It closes with a prospective view on how MALDI-TOF MS-based microbial characterisation can accelerate the exploitation of plant-associated microbiota.

Enumerating Antibiotic Susceptibility Patterns of Pseudomonas aeruginosa Isolated from Different Sources in Dhaka City

Background:

Pseudomonas aeruginosa is a ubiquitous free-living bacterium and is responsible for severe nosocomial infections, life-threatening infections in immune compromised persons. The bacterium, along with its natural resistance, can acquire resistance to many antibiotics by a variety of methods.

Method:

Therefore, to compare the antibiotic sensitivity pattern of Pseudomonas aeruginosa, a total of seventeen isolates of P. aeruginosa were isolated from different sources; for example environmental sources, frozen food sources, clinical sources and medical waste materials. Isolates were confirmed to be P. aeruginosa by cultural and biochemical properties.

Result:

The isolates were tested against seventeen commercially available antibiotics to observe the antibiotic susceptibility patterns. Imipenem and meropenem were the most potent antibiotics (100% sensitivity) followed by amikacin and piperacillin with maximum sensitivity. Among others, gentamicin, ciprofloxacin, levofloxacin and aztreonam were found to be fairly active. A good number of isolates were intermediately resistant to ceftriaxone. The rates of resistance to aztreonam, cefotaxime and ceftazidime were 11.76%, 82.35% and 5.88% respectively. Complete resistance was observed against penicillin, ampicillin, cefixime and cefpodoxime.

Conclusion:

It can be concluded that the clinical isolates including isolate from medical waste, were multi-drug resistant than environmental and food isolates indicating the risk of transmission of resistance to the environmental isolates of P. aeruginosa.

Enzymatic characterization of clinical and environmental Cryptococcus neoformans strains isolated in Italy

BACKGROUND

Cryptococcus neoformans is an encapsulated yeast causing mainly opportunistic infections. The virulence factors involved in cryptococcosis pathogenesis include the presence and the size of the polysaccharide capsule, the production of melanin by phenoloxidase, the growth at 37°C and the enzyme secretion like proteinase, phospholipase and urease. Many other enzymes are secreted by C. neoformans but their role in the fungus virulence is not yet known.

AIMS

In order to investigate this topic, we compared the phospholipase production between strains from patients and from bird droppings, and we examined its relationship to phenoloxidase production. We further characterized the strains by determining the activity of 19 different extracellular enzymes.

METHODS

Two hundred and five Italian C. neoformans clinical isolates and 32 environmental isolates were tested. Phenoloxidase production was determined by the development of brown colonies on Staib's agar. Extracellular phospholipase activity was performed using the semiquantitative egg-yolk plate method. API ZYM commercial kit was used to observe the production and the activity of 19 different extracellular enzymes.

RESULTS

Statistical analysis of the results showed a significantly higher phospholipase activity in the clinical isolates than in the environmental isolates. No significant difference about the phenoloxidase production between both groups was found. Regarding the 19 extracellular enzymes tested using the API ZYM commercial kit, acid phosphatase showed the highest enzymatic activity in both groups. Concerning the enzyme α-glucosidase, the clinical isolates presented a significantly higher positivity percentage than the environmental isolates. A hundred percent positivity in the enzyme leucine arylamidase production was observed in both groups, but the clinical isolates metabolized a significantly greater amount of substrate.

CONCLUSIONS

The higher phospholipase production in the clinical isolates group confirms the possible role of this enzyme in the cryptococcosis pathogenesis. The extracellular activities of the enzymes acid phosphatase, α-glucosidase and leucine arylamidase, tested by means of the API ZYM commercial kit, appear to be very interesting. Many studies indicate that these enzymes are involved in the virulence of bacteria and parasites; our results suggest their possible role as virulence factors in Cryptococcus infections too.

Thermal and Starvation Stress Response of Escherichia coli O157:H7 Isolates Selected from Agricultural Environments

Pathogens exposed to agricultural production environments are subject to multiple stresses that may alter their survival under subsequent stress conditions. The objective of this study was to examine heat and starvation stress response of Escherichia coli O157:H7 strains isolated from agricultural matrices. Seven E. coli O157:H7 isolates from different agricultural matrices-soil, compost, irrigation water, and sheep manure-were selected, and two ATCC strains were used as controls. The E. coli O157:H7 isolates were exposed to heat stress (56°C in 0.1% peptone water for up to 1 h) and starvation (in phosphate-buffered saline at 37°C for 15 days), and their survival was examined. GInaFiT freeware tool was used to perform regression analyses of the surviving populations. The Weibull model was identified as the most appropriate model for response of the isolates to heat stress, whereas the biphasic survival curves during starvation were fitted using the double Weibull model, indicating the adaptation to starvation or a resistant subpopulation. The inactivation time during heating to achieve the first decimal reduction time (δ) calculated with the Weibull parameters was the highest (45 min) for a compost isolate (Comp60A) and the lowest (28 min) for ATCC strain 43895. Two of the nine isolates (ATCC 43895 and a manure isolate) had β < 1, indicating that surviving populations adapted to heat stress, and six strains demonstrated downward concavity (β > 1), indicating decreasing heat resistance over time. The ATCC strains displayed the longest δ₂ (>1,250 h) in response to starvation stress, compared with from 328 to 812 h for the environmental strains. The considerable variation in inactivation kinetics of E. coli O157:H7 highlights the importance of evaluating response to stress conditions among individual strains of a specific pathogen. Environmental isolates did not exhibit more robust response to stress conditions in this study compared with ATCC strains.

Discovery of keratinases using bacteria isolated from marine environments

Bacteria are important for the biodegradation of keratin. Thus, a workflow to isolate keratin-degrading bacteria utilizing an optimized azo-keratin assay was established. Deteriorated feather samples, collected in marine shoreline environments from the intertidal zone, yielded 50 unique bacterial isolates exhibiting keratin degradation when feather meal was supplied as keratin substrate. The majority of isolates, identified by 16S sequencing, belonged to genera previously reported to produce keratinases: Bacillus spp. (42%) and Stenotrophomonas spp. (40%). The remaining 18% represented the genera Alcaligenes, Chryseobacterium, Salinivibrio, Delftia, Stappia, and Microbacterium, genera not previously been associated with keratinase production. The workflow, also applied to 21 Bacilli from our in-house culture collection, additionally revealed four Bacilli with remarkable feather degradation potential. The industrial applicability of their associated keratinases was evaluated and the most active keratinase expressed in E. coli to confirm keratinase expression. Enriched keratinase fractions demonstrated activity up to 75°C and retained viability when stored lyophilized at 20°C for up to 200d.