Bacterial strain typing in the genomic era

Genetic relatedness of Staphylococcus aureus isolates within food outbreaks by single nucleotide polymorphisms

Investigation of bacterial food outbreaks by whole genome sequencing can rely on the inspection of the genetic relatedness between isolates through the application of single nucleotide polymorphism (SNP) thresholds. However, there is no consensus for Staphylococcus aureus in the context of food outbreaks. In this study, we propose a SNP cut-off by taking into account the mutation rate and the evolution time of this pathogen in food. Through in vitro microevolution, we determined the mutation rate of three S. aureus strains grown under mimicked food stressing conditions. From the mutation rate, we set a cut-off of 28 SNPs considering 30 days as evolution time based on the average shelf-life of foods contaminated by S. aureus and the timeline for identifying this pathogen in outbreaks. The SNP threshold was applied to retrospectively study ten staphylococcal food outbreaks to assess whether isolates from food and/or of human origin from the same outbreak were epidemiologically related. To interpret SNP distances, phylogenetic tree topologies and bootstraps were integrated and showed that isolates differing by up to 28 SNPs were monophyletic. Our suggested cut-off can be used in outbreak management to identify closely related S. aureus strains.

Genotyping of Corynebacterium pseudotuberculosis isolates using PCR-based DNA fingerprinting methods

Phenotypic typing methods are often time consuming and do not adequately discriminate among the strains involved. Innovative molecular techniques can perform direct typing by analyzing DNA and are becoming widespread as important tools for bacterial typing, molecular epidemiology and molecular systematization. The aim of this study was to genotype Corynebacterium pseudotuberculosis strains using PCR-based DNA fingerprinting methods and to evaluate the methods comparatively. Within the scope of the study, 17 C. pseudotuberculosis strains were analyzed. The strains were genotyped by enterobacterial repetitive intergenic consensus (ERIC)-PCR using ERIC2 primer; by random amplified polymorphic (RAPD) DNA-PCR using primers P5, P6, P11, P14, P16, P21 and M13; and by (GTG)5-PCR using (GTG)5 primer. The discrimination power and confidence intervals of the methods were calculated based on the genotyping results using each primer. All strains produced amplification products with the primers used for genotyping. As a result of genotyping with ERIC2, P14, P11, (GTG)5, P21, P5, M13, P6 and P16 primers, the discrimination powers (confidence intervals) were calculated as 0.8603(0.858-0.862), 0.7132(0.709-0.716), 0.6838(0.668-0.699), 0.6397(0.623-0.656), 0.5809(0.560-0.601), 0.3235(0.293-0.353), 0.1176(0.081-0.153), 0.1176(0.081-0.153) and 0.1176(0.081-0.153), respectively. As a result of the comparative evaluation of the results, it was observed that ERIC2 and P14 primers had high discrimination power and confidence interval in genotyping C. pseudotuberculosis strains, while M13, P6 and P16 primers were insufficient in genotyping of strains. It was concluded that genotyping with ERIC2 and P14 primers can be used reliably in investigating the molecular epidemiology of infections and/or outbreaks caused by C. pseudotuberculosis.

An Intensive Care Outbreak Caused by Burkholderia cepacia from Bacterial Filters

BACKGROUND

We report a hospital outbreak caused by Burkholderia cepacia that occurred in 16 patients admitted to intensive care units in Elazığ, Türkiye, between 19 March and 23 April 2024.

METHODS

The outbreak investigation was initiated on 23 March 2024, four days after B. cepacia was detected in four different patients. Environmental samples were collected from various parts of the hospital to find the source of the outbreak. Arbitrarily Primed Polymerase Chain Reaction (AP-PCR) was performed to determine the genetic relationship between environmental and patient samples.

RESULTS

In total, 16 of 18 B. cepacia isolates were obtained from tracheal aspirate culture. A total of 10 of 16 patients developed hospital-acquired pneumonia due to B. cepacia. Among the environmental cultures in the intensive care units, only the respirator bacterial filter grew. The isolate obtained here was in the same cluster as the isolate obtained from patient samples, resulting in a dominant clustering rate of 94.4%.

CONCLUSIONS

Improper and inappropriate use of respirators and equipment can lead to outbreaks. Early detection of the outbreak, identification of the source, and taking appropriate measures quickly to contain the outbreak are key.

Molecular characterization of methicillin-resistant Staphylococcus aureus: Dissemination of multidrug-resistant community-associated MRSA and emergence of LA-MRSA, in a healthcare setting

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) continues to be a significant cause of healthcare-associated infections (HAIs). In this study, we aimed to characterize the MRSA isolates obtained from HAIs.

METHODS

A total of 200 clinical and 13 nasal MRSA isolates were collected and tested. The samples were analyzed for SCCmec typing by using multiplex PCR. Microtiter for biofilm formation were performed and molecular typing for the samples were performed for spa and agr typing.

RESULTS

The isolates showed 100 % sensitivity to vancomycin and linezolid, while 92.5 % were multidrug-resistant. Strong biofilm-forming ability was observed in 47 % of the isolates. SCC mec typing identified 52.5 % of the isolates as classical hospital-associated MRSA or HA-MRSA (SCC mec type III), 23.5 % as community-associated MRSA or CA-MRSA (type IV and V), and 16.5 % as non-typeable, with 7.5 % having multiple SCCmec types.

CONCLUSION

Comparison of HA and CA-MRSA traits revealed that both groups had multidrug resistance, but HA-MRSA was distinguished by its strong capacity for biofilm formation, whereas CA-MRSA was marked by a high count of toxin gene. Our study, to the best of our awareness, documents the presence of LA-MRSA (SCCmec V- t127-agr III) causing HAIs in Indian patients for the first time.

A Multimodal Spectroscopic Approach Combining Mid-infrared and Near-infrared for Discriminating Gram-positive and Gram-negative Bacteria

The rapid and accurate identification of pathogenic bacteria is crucial for combating the growing threat of antibiotic resistance, nosocomial infections, and food safety concerns. This study presents a novel and comprehensive comparison of two vibrational spectroscopic techniques - attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and a low-cost miniature near-infrared (NIR) spectrometer - for distinguishing Gram-positive and Gram-negative bacterial samples grown using the same stock media solution. This is the first report of NIR spectroscopy being applied to differentiate Gram-positive and Gram-negative bacteria, as well as the first direct comparison of ATR-FTIR and NIR for the combined multimodal analysis of clinical bacterial isolates. Using a data set of five Gram-positive and seven Gram-negative species and recording spectra in triplicate, the study employed advanced data fusion and multivariate analysis techniques to classify the spectra and facilitate NIR band assignment. 2D correlation analysis revealed strong positive correlations between key spectral markers identified in both modalities. Partial least-squares- and support vector machine discriminant analysis models were validated using a methodology based on 100 repeated random sampling of calibration and test sets. Models demonstrated that both the standalone ATR-FTIR and the combined ATR-FTIR/NIR approach achieved exceptional classification accuracy (>98%) in differentiating the two bacterial groups. Differences observed in the spectra were attributed to the distinct cell wall compositions of Gram-Positive and Gram-negative bacteria. Notably, the low-cost NIR technique also showed promising performance, with classification accuracy values above 90%. The findings highlight the potential of these rapid, noninvasive, and cost-effective vibrational spectroscopic techniques, particularly the NIR method, for point-of-care applications in clinical microbiology and food safety monitoring. The combination of ATR-FTIR and NIR data further enhances the robustness and reliability of bacterial identification, paving the way for broader adoption of these advanced analytical tools in various healthcare and food safety settings.

Microwave Cooking of Some or All High Starch Ingredients of Cattle Feed Concentrate Improves Nutritional Value and In Vitro Bioavailability

Microwaving has been used to qualitatively improve feed ingredients prior to including them in cattle feed. However, it is not known whether feed ingredients should be microwaved separately or in a mixture before being included in cattle feed concentrates. In the current study, the effects of the partial and full microwaving of high starch ingredients were investigated regarding their impact on the nutritional composition, physicochemical properties, and in vitro digestibility of feed concentrates. The cassava was microwave-irradiated before being mixed with other ingredients (MC, 35% of formulation). A microwave-cooked cassava-corn meal mixture (MCC, 45% of formulation) and a combination of all solid components (MSI, 96% of formulation) were also compared. A feed containing non-microwaved ingredients was formulated and served as the control (NM). Significantly altered proximate compositions and nutritive profiles were observed in all the microwaved components (p < 0.05). The observed modifications in pHs, water absorption capacities, thermal properties (differential scanning calorimetry), diffraction patterns (X-ray diffractometry), and microstructures (scanning electron microscopy) indicated enhanced enzymatic hydrolysis in vitro. A higher cellulase organic matter solubility and digestible organic matter were observed in the MCC and MSIs feeds relative to the control NM (p < 0.05). These findings indicate a combination of components could be added to feedstock before it is microwave processed to potentially include this pretreatment in the feed production process.

PCR-based RFLP and ERIC-PCR patterns of Helicobacter pylori strains linked to multidrug resistance in Egypt

H. pylori infects approximately 50% of the world's population that causes chronic gastritis, and may lead to peptic ulcer disease (PUD). H. pylori-induced chronic infections are associated with gastric adenocarcinoma and low-grade gastric lymphoma. In Egypt, H. pylori strains are widespread and became resistant to antimicrobial agents, thus advanced typing methods are needed to differentiate infectious strains that are resistant to antibiotics, and therefore earlier prognosis and infection control. The main objectives were (i) to determine susceptibility of infectious H. pylori strains to some antimicrobial agents that are currently used in eradication therapy in Egypt; (ii) to identify diverse strains commonly detected in the gastrointestinal (GIT) endoscopy units in Egypt through phenotypic and genotypic analyses. In this observational study we isolated 167 isolates from 232 gastric biopsies (antrum and corpus) of patients who were admitted to the upper GIT endoscopy units in five governmental Egyptian hospitals. Antimicrobial susceptibility patterns were investigated using Kirby Bauer disc diffusion and agar dilution Minimum Inhibitory Concentrations (MICs) methods. Phenotypic characterization was based on biotyping and antibiogram typing techniques. Genotypic characterization was carried out using PCR-based Restriction Fragment Length Polymorphism (RFLP) and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR analyses. H. pylori isolates were highly resistant to diverse antimicrobial agents including Metronidazole, Fluoroquinolones, Macrolides, Amoxycillin, Tetracycline and Gentamicin. Two factors contributed to the increased resistance of H. pylori to the conventional therapy seen in Egypt: (i) Metronidazole and Amoxycillin are inexpensive and available drugs being abused by patients; (ii) the regional prescribing practice of Macrolids commonly used to treat upper respiratory and urinary tract infections. Five different biotypes were identified depending on the ability of the isolates to synthesize different enzymes. Nine antibiogram types were identified. PCR-RFLP analysis revealed fifteen different fingerprints while ERIC-PCR revealed 22 fingerprints. Biotyping alone or in combination with antibiogram typing are highly useful molecular tools in the prognosis of strain relatedness. PCR-RFLP and ERIC-PCR acquired good discriminatory power for identifying H. pylori infectious sub-types.

Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects

Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.

Evaluating Fourier-transform infrared spectroscopy with IR Biotyper as a faster and simpler method for investigating the sources of an outbreak of legionellosis

Fourier-transform infrared (FTIR) spectroscopy using the IR Biotyper and core genome single nucleotide polymorphism (cgSNP) analysis were performed on 12 Legionella isolates associated with an outbreak at a spa house in Kanagawa Prefecture, Japan, and 3 non-outbreak isolates. The discriminative power of FTIR spectroscopy for 48-h incubation conditions of L. pneumophila in this outbreak was lower than cgSNP-based typing but higher than serogroup typing. FTIR spectroscopy could screen outbreak isolates from a group of genetically related isolates and may be useful as an initial typing method in Legionella outbreak investigations.

New Insights and Approach Toward the Genetic Diversity and Strain Typing of Erwinia pyrifoliae Based on rsxC, an Electron Transport Gene

Erwinia pyrifoliae, a causal agent of black shoot blight in apple and pear trees, is a plant pathogenic bacterium first reported in South Korea. The symptoms of black shoot blight are very similar to those of the fire blight disease in apple and pear trees caused by E. amylovora, as E. pyrifoliae has a genetically very close relationship with E. amylovora. Recently, there have been reports that E. pyrifoliae causes disease in European strawberries, resulting in severe fruit loss that aroused great concern about its spread, distribution, and host range. Therefore, it is essential to establish a trustworthy approach to understanding the distribution patterns of E. pyrifoliae based on the genetic background to strengthen the barrier of potential spreading risks, although advanced methods have been provided to accurately detect E. pyrifoliae and E. amylovora. Consequently, this study discovered a noble and noteworthy gene, rsxC, capable of providing the pathogen genotype by comparing E. pyrifoliae genomic sequences in the international representative genome archive. Different numbers of 40-unit amino acid repeats in this gene among the strains induced intraspecific traits in RsxC. By comparing their repeat pattern, E. pyrifoliae isolates were divided into two main groups, branching into several clades via sequence alignment of 35 E. pyrifoliae isolates from various apple orchards from 2020 to 2021 in South Korea. The newly discovered quadraginta amino acid repeat within this gene would be a valuable genetic touchstone for determining the genotype and distribution pattern of E. pyrifoliae strains, ultimately leading to exploring their evolution. The function of amino acid repeats and the biological significance of strains need to be elucidated further.

Determination of antibiotic resistance patterns and genotypes of Escherichia coli isolated from wild birds

BACKGROUND

Curbing the potential negative impact of antibiotic resistance, one of our era's growing global public health crises, requires regular monitoring of the resistance situations, including the reservoir of resistance genes. Wild birds, a possible bioindicator of antibiotic resistance, have been suggested to play a role in the dissemination of antibiotic-resistant bacteria. Therefore, this study was conducted with the objective of determining the phenotypic and genotypic antibiotic resistance profiles of 100 Escherichia coli isolates of gull and pigeon origin by using the Kirby-Bauer disk diffusion method and PCR. Furthermore, the genetic relationships of the isolates were determined by RAPD-PCR.

RESULTS

Phenotypic antibiotic susceptibility testing revealed that 63% (63/100) and 29% (29/100) of E. coli isolates were resistant to at least one antibiotic and multidrug-resistant (MDR), respectively. With the exception of cephalothin, to which the E. coli isolates were 100% susceptible, tetracycline (52%), kanamycin (38%), streptomycin (37%), ampicillin (28%), chloramphenicol (21%), trimethoprim/sulfamethoxazole (19%), gentamicin (13%), enrofloxacin (12%) and ciprofloxacin (12%) resistances were detected at varying degrees. Among the investigated resistance genes, tet(B) (66%), tet(A) (63%), aphA1 (48%), sul3 (34%), sul2 (26%), strA/strB (24%) and sul1 (16%) were detected. Regarding the genetic diversity of the isolates, the RAPD-PCR-based dendrograms divided both pigeon and gull isolates into five different clusters based on a 70% similarity threshold. Dendrogram analysis revealed 47-100% similarities among pigeon-origin strains and 40-100% similarities among gull-origin E.coli strains.

CONCLUSIONS

This study revealed that gulls and pigeons carry MDR E. coli isolates, which may pose a risk to animal and human health by contaminating the environment with their feces. However, a large-scale epidemiological study investigating the genetic relationship of the strains from a "one health" point of view is warranted to determine the possible transmission patterns of antibiotic-resistant bacteria between wild birds, the environment, humans, and other hosts. Video Abstract.

Strain-level detection of Fusobacterium nucleatum in colorectal cancer specimens by targeting the CRISPR-Cas region

IMPORTANCE

Fusobacterium nucleatum is one of the predominant oral bacteria in humans. However, this bacterium is enriched in colorectal cancer (CRC) tissues and may be involved in CRC development. Our previous research suggested that F. nucleatum is present in CRC tissues originating from the oral cavity using a traditional strain-typing method [arbitrarily primed polymerase chain reaction (AP-PCR)]. First, using whole-genome sequencing, this study confirmed an exemplary similarity between the oral and tumoral strains derived from each patient with CRC. Second, we successfully developed a method to genotype this bacterium at the strain level, targeting the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated system, which is hypervariable (defined as F. nucleatum-strain genotyping PCR). This method can identify F. nucleatum strains in cryopreserved samples and is significantly superior to traditional AP-PCR, which can only be performed on isolates. The new methods have great potential for application in etiological studies of F. nucleatum in CRC.

Strain-level bacterial typing directly from patient samples using optical DNA mapping

BACKGROUND

Identification of pathogens is crucial to efficiently treat and prevent bacterial infections. However, existing diagnostic techniques are slow or have a too low resolution for well-informed clinical decisions.

METHODS

In this study, we have developed an optical DNA mapping-based method for strain-level bacterial typing and simultaneous plasmid characterisation. For the typing, different taxonomical resolutions were examined and cultivated pure Escherichia coli and Klebsiella pneumoniae samples were used for parameter optimization. Finally, the method was applied to mixed bacterial samples and uncultured urine samples from patients with urinary tract infections.

RESULTS

We demonstrate that optical DNA mapping of single DNA molecules can identify Escherichia coli and Klebsiella pneumoniae at the strain level directly from patient samples. At a taxonomic resolution corresponding to E. coli sequence type 131 and K. pneumoniae clonal complex 258 forming distinct groups, the average true positive prediction rates are 94% and 89%, respectively. The single-molecule aspect of the method enables us to identify multiple E. coli strains in polymicrobial samples. Furthermore, by targeting plasmid-borne antibiotic resistance genes with Cas9 restriction, we simultaneously identify the strain or subtype and characterize the corresponding plasmids.

CONCLUSION

The optical DNA mapping method is accurate and directly applicable to polymicrobial and clinical samples without cultivation. Hence, it has the potential to rapidly provide comprehensive diagnostics information, thereby optimizing early antibiotic treatment and opening up for future precision medicine management.

Epidemiological Investigation of Hospital Transmission of Corynebacterium striatum Infection by Core Genome Multilocus Sequence Typing Approach

Corynebacterium striatum has recently received increasing attention due to its multiple antimicrobial resistances and its role as an invasive infection/outbreak agent. Recently, whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) has been used in epidemiological studies of specific human pathogens. However, this method has not been reported in studies of C. striatum. In this work, we aim to propose a cgMLST scheme for C. striatum. All publicly available C. striatum genomes, 30 C. striatum strains isolated from the same hospital, and 1 epidemiologically unrelated outgroup C. striatum strain were used to establish a cgMLST scheme targeting 1,795 genes (hereinafter referred to as 1,795-cgMLST). The genotyping results of cgMLST showed good congruence with core genome-based single-nucleotide polymorphism typing in terms of tree topology. In addition, the cgMLST provided a greater discrimination than the MLST method based on 6 housekeeping genes (gyrA, gyrB, hsp65, rpoB, secA1, and sodA). We established a clonal group (CG) threshold based on 104 allelic differences; a total of 56 CGs were identified from among 263 C. striatum strains. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying closely related isolates that could give clues on hospital transmission. According to the results of analysis of drug-resistant genes and virulence genes, we identified CG4, CG5, CG26, CG28, and CG55 as potentially hypervirulent and multidrug-resistant CGs of C. striatum. This study provides valuable genomic epidemiological data on the diversity, resistance, and virulence profiles of this potentially pathogenic microorganism. IMPORTANCE Recently, WGS of many human and animal pathogens has been successfully used to investigate microbial outbreaks. The cgMLST schema are powerful genotyping tools that can be used to investigate potential epidemics and provide classification of the strains precise and reliable. In this study, we proposed the development of a cgMLST typing scheme for C. striatum, and then we evaluated this scheme for its applicability to hospital transmission investigations. This report describes the first cgMLST schema for C. striatum. The analysis of hospital transmission of C. striatum based on cgMLST methods has important clinical epidemiological significance for improving nosocomial infection monitoring of C. striatum and in-depth understanding of its nosocomial transmission routes.

Bacteriocin Production Correlates with Epidemiological Prevalence of Phylotype I Sequevar 18 Ralstonia pseudosolanacearum in Madagascar

Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is a major threat to vegetable crops in Madagascar. For more effective disease management, surveys were carried out in the main vegetable production areas of the country, leading to the collection of 401 new RSSC isolates. Phylogenetic assignment of the isolates revealed a high prevalence of phylotype I sequevar 18. This result contrasts sharply with the epidemiological pattern of RSSC in neighboring islands, including Reunion Island, Comoros, Mayotte, Mauritius, Rodrigues, and the Seychelles, where phylotype I sequevar 31 is widespread. Molecular typing characterization of the Malagasy isolates allowed the identification of 96 haplotypes. Some are found in various plots located in different provinces, which suggests that they were probably disseminated via infected plant material. To find out a potential explanation for the observed epidemiological pattern, we examined the capacity of the Malagasy strains to produce bacteriocin. Interestingly, the highly prevalent genetic lineages I-18 produce bacteriocins that are active against all the genetic lineages present in the country. This work sheds light on the potential impact of bacteriocins in the epidemiology of Malagasy RSSC. IMPORTANCE Knowledge of the epidemiology of a plant pathogen is essential to develop effective control strategies. This study focuses on the epidemiological pattern of Ralstonia pseudosolanacearum phylotype I populations responsible for bacterial wilt in Madagascar. We identified, with the newly collected isolates in three provinces, four genetic lineages probably propagated via infected plant material in Madagascar. We revealed that the epidemiological situation in Madagascar contrasts with that of neighboring Indian Ocean islands. Interestingly, our study on the bacteriocin-producing capacity of Malagasy isolates revealed a correlation between the inhibitory activity of the producing strains and the observed epidemiology. These results suggested that the epidemiology of plant pathogens may be impacted by bacteriocin production.

Isolation and Molecular Characterization of Corynebacterium pseudotuberculosis: Association with Proinflammatory Cytokines in Caseous Lymphadenitis Pyogranulomas

Corynebacterium pseudotuberculosis (C. pseudotuberculosis) is a causative agent of numerous chronic diseases, including caseous lymphadenitis (CLA) in sheep and goats, which has a zoonotic potential in humans in addition to a poor therapeutic response. In this study, out of 120 collected samples, only 12 (10%) were positive for C. pseudotuberculosis by PCR and by intraperitoneal injection of male Guinea pigs and then characterized for antimicrobial susceptibility and its genetic-relatedness by enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR), which showed 2-4 bands ranging from 100 to 3000 bp that can be clustered into four clusters (C1-C4). Despite the serotype biovar 1 only infecting sheep and goats, ERIC-PCR reveals intra-subtyping variation. Examination of affected LNs and organs revealed marked enlargement with either thick creamy green pus or multiple abscesses of variable sizes with a central caseated core surrounded by dense fibrous capsule. A histopathological examination revealed a central necrotic core surrounded by a peripheral mantle of mononuclear cells and a fibrous capsule. Positive immune expression of nuclear factor kappa B (NF-κB/p65) and interleukin-1β (IL-1β) and negative expression of tumor necrosis factor (TNF) in CLA is the first report to our knowledge. Conclusion: In CLA pyogranulomas, IL1β is a more crucial proinflammatory cytokine than TNF in the regulation of C. pseudotuberculosis infection, which is accompanied by marked NF-κB immunoexpression. Therefore, the NF-κB/p65 signaling pathway is involved in the activation of IL1β, and additional immunohistochemical studies are required to determine the various roles of NF-κB/p65 in the inflammatory response within CLA pyogranulomas to control this pathogen.

Genetic diversity of Mycoplasma hyopneumoniae in finishing pigs in Minas Gerais

ABSTRACT: Mycoplasma hyopneumoniae is one of the most challenging respiratory pathogens involved with swine pneumonia worldwide, responsible for a chronic infection with high morbidity, which predisposes secondary bacterial infections in growing and finishing pigs. Advances in diagnostic techniques allowed identification of genetic characteristics associated with high antigenic and proteomic variability among bacterial strains. This study aimed to evaluate the genetic diversity of M. hyopneumoniae strains in lungs with pneumonic lesions obtained from 52 pig farms located in Minas Gerais, one of the largest swine production states in Brazil. Genotyping was performed using multilocus variable number of tandem repeat (VNTR) analysis (MLVA), targeting two loci encoding P97 and P146 adhesins VNTR. The results showed that this agent is widely disseminated in pig farms and there is a high polymorphism of M. hyopneumoniae variants circulating in the state of Minas Gerais. Different M. hyopneumoniae genotypes are randomly distributed in several regions of the state, with no specific geographic population structure pattern. M. hyopneumoniae association with viral agents was sporadic (3.17% with Influenza A and 1.9% with PCV2).

Development of ELISA-based diagnostic methods for the detection of haemorrhagic septicaemia in animals

Haemorrhagic septicaemia (HS) is an acute infection of cattle and buffaloes caused by the B:2 serotype of Pasteurella multocida. This disease is highly endemic in South Asia. In some peracute cases, there is 100% mortality in infected animals within a few hours of infection. Therefore, timely diagnosis of infection may contribute to its treatment and control to minimize economic losses. The current work reported the development of ELISA-based assays for the detection of anti-P. multocida antibodies and pathogen i.e. P. multocida. Owing to high immunogenicity, membrane proteins (MPs) extracted from local isolates of P. multocida serotype B:2 (PM1, PM2, and PM3) were employed as a potential diagnostic antigen for the development of indirect ELISA (i-ELISA) to detect HS antibodies in animals. MPs extracted from PM1, PM2 and PM3 isolates showed very low heterogeneity; hence MPs from the PM3 isolate were selected for the development of i-ELISA. The concentration of MPs (as coating antigen) of 3.13 μg/well and test sera dilution 1:100 was found to be optimal to perform i-ELISA. The developed method was validated through the detection of anti-P. multocida antibodies in sera of mice, immunized with MPs and formalin killed cells from the three local isolates (PM1, PM2 and PM3) of P. multocida. The significantly higher antibody titer in immunized mice was determined compared to unimmunized mice with the cut off value of 0.139. To detect P. multocida directly from the blood of infected animals, whole cell-based ELISA (cb-ELISA) assay was developed. A better detection signal was observed in the assay where bacterial cells were directly adsorbed on plate wells as compared to poly L-lysine (PLL) assisted attachment at a cell concentration of 10⁶ CFU and 10⁷ CFU respectively. The developed assays can be scaled up and potentially be used for the rapid detection of HS antibodies to gauge the immune status of the animal as well as vaccination efficacy and pathogen detection.

Identification of highly variable sequence fragments in unmapped reads for rapid bacterial genotyping

BACKGROUND

Bacterial genotyping is a crucial process in outbreak investigation and epidemiological studies. Several typing methods such as pulsed-field gel electrophoresis, multilocus sequence typing (MLST) and whole genome sequencing are currently used in routine clinical practice. However, these methods are costly, time-consuming and have high computational demands. An alternative to these methods is mini-MLST, a quick, cost-effective and robust method based on high-resolution melting analysis. Nevertheless, no standardized approach to identify markers suitable for mini-MLST exists. Here, we present a pipeline for variable fragment detection in unmapped reads based on a modified hybrid assembly approach using data from one sequencing platform.

RESULTS

In routine assembly against the reference sequence, high variable reads are not aligned and remain unmapped. If de novo assembly of them is performed, variable genomic regions can be located in created scaffolds. Based on the variability rates calculation, it is possible to find a highly variable region with the same discriminatory power as seven housekeeping gene fragments used in MLST. In the work presented here, we show the capability of identifying one variable fragment in de novo assembled scaffolds of 21 Escherichia coli genomes and three variable regions in scaffolds of 31 Klebsiella pneumoniae genomes. For each identified fragment, the melting temperatures are calculated based on the nearest neighbor method to verify the mini-MLST's discriminatory power.

CONCLUSIONS

A pipeline for a modified hybrid assembly approach consisting of reference-based mapping and de novo assembly of unmapped reads is presented. This approach can be employed for the identification of highly variable genomic fragments in unmapped reads. The identified variable regions can then be used in efficient laboratory methods for bacterial typing such as mini-MLST with high discriminatory power, fully replacing expensive methods such as MLST. The results can and will be delivered in a shorter time, which allows immediate and fast infection monitoring in clinical practice.

Pathogenicity and virulence of bacterial strains associated with summer mortality in marine mussels (Perna canaliculus)

The occurrence of pathogenic bacteria has emerged as a plausible key component of summer mortalities in mussels. In the current research, four bacterial isolates retrieved from moribund Greenshell࣪ mussels, Perna canaliculus, from a previous summer mortality event, were tentatively identified as Vibrio and Photobacterium species using morpho-biochemical characterization and MALDI-TOF MS and confirmed as V. celticus, P. swingsii, P. rosenbergii, and P. proteolyticum using whole genome sequencing. These isolates were utilized in a laboratory challenge where mussels were injected with cell concentrations ranging from 105 to 109 CFU/mussel. Of the investigated isolates, P. swingsii induced the highest mortality. Additionally, results from quantitative polymerase chain reaction analysis, focusing on known virulence genes were detected in all isolates grown under laboratory conditions. Photobacterium rosenbergii and P. swingsii showed the highest expression levels of these virulence determinants. These results indicate that Photobacterium spp. could be a significant pathogen of P. canaliculus, with possible importance during summer mortality events. By implementing screening methods to detect and monitor Photobacterium concentrations in farmed mussel populations, a better understanding of the host-pathogen relationship can be obtained, aiding the development of a resilient industry in a changing environment.

Distribution and expression of virulence genes (hlyA, sat) and genotyping of Escherichia coli O25b/ST131 by multi-locus variable number tandem repeat analysis in Tehran, Iran

Escherichia coli ST131 is a pandemic clone with high antibiotic resistance, and it is a major causative agent of urinary tract infection (UTI) and bloodstream infections. This study evaluated the distribution and expression of virulence genes and genotyping of E. coli O25b/ST131 by Multi-locus variable number tandem repeat analysis (MLVA) method among UTI in patients at Tehran hospitals, Iran.A total of 107 E. coli isolates were collected from UTI patients. Polymerase chain reaction (PCR) amplification of the pabB gene was used to identify E. coli O25b/ST131 and the prevalence of sat and hlyA virulence genes was also analyzed. The microtiter method quantified biofilm formation ability in E. coli O25b/ST131. The Real-Time PCR (qRT-PCR) was performed to evaluate the expression of sat and hlyA genes. Finally, MLVA was performed for E. coli O25b/ST131 genotyping by targeting seven tandem repeats. SPSS-16 software was used for statistical analysis. Molecular study showed that 71% of isolates carried the pabB gene and were considered E. coli O25b/ST131 strains. Also, 45.8% and 17.8% of isolates carried sat and hlyA genes, respectively. The 57.9% isolates had biofilm formation ability. Expression of the studied virulence genes showed an increase in strong biofilm producing E. coli O25b/ST131 strains. A total of 76 (100%) E. coli O25b/ST131 strains were typed by the MLVA method.High prevalence of E. coli O25b/ST131 isolates in UTI patients can be a serious warning to the treatment due to the high antibiotic resistance rate, expression of virulence genes, and biofilm formation.

Clonal groups of extended-spectrum β-lactamase and biofilm producing uropathogenic Escherichia coli in Iran

Pathogenicity of a bacterium is affected by the social characteristics of the population and environmental factors. The ability of biofilm formation among β-lactamase-producing uropathogenic Escherichia coli (UPEC) could facilitate the exchange of antibiotic-resistance genes, which resulted in widespread dissemination of antibacterial drug resistance. We investigated the prevalence of biofilm and β-lactamase producing UPECs among patients with urinary tract infection (UTI) in two cities with different demographics and climates in Iran. A total of 265 E. coli was isolated from patients with UTIs from two referral hospitals (n = 191) and two outpatient clinics (n = 74) in Isfahan and Zahedan, Iran. Production of curli and cellulose, and, biofilm formation was investigated using Congo red agar and microtiter plate methods, respectively. Biofilm producing (BFP) isolates (n = 107) were further characterized using rep-PCR, antimicrobial susceptibility testing and extended-spectrum β-lactamase (ESBL)/AmpC phenotypic production. Isolates were also screened for the presence of carbapenemase, ESBL and AmpC genes using multiplex PCR.   High diversity was found among BFP strains in both cities, with 58% strains producing ESBL and 21% producing AmpC. ESBL (98%), AmpC (50%) and carbapenemase genes (40%) were identified in BFP strains with ESBL-positive phenotype, respectively. The prevalence of BFP strains, antibiotic resistance and β-lactamase genes in Zahedan, a low socioeconomic city with a warm climate, was significantly higher than that of Isfahan. High prevalence of biofilm and β-lactamase producing UPEC strains among strains from Zahedan suggests that socioeconomic status and environmental factors might have a role in pathogenicity of the strains.

Listeria monocytogenes in foods-From culture identification to whole-genome characteristics

Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.

Comparison of fast Fourier transform infrared spectroscopy biotyping with whole genome sequencing-based genotyping in common nosocomial pathogens

Early detection of bacterial transmission and outbreaks in hospitals is important because nosocomial infections can result in health complications and longer hospitalization. Current practice to detect outbreaks uses genotyping methods amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS), which are not suitable methods for real-time transmission screening of both susceptible and resistant bacteria. The aim was to assess the typing technique Fourier transform infrared (FTIR) spectroscopy as real-time screening method to discriminate large amounts of susceptible and resistant bacteria at strain level when there is no evident outbreak in comparison with the WGS reference. Isolates of past hospital outbreak strains of Acinetobacter baumannii/calcoaceticus complex (n = 25), Escherichia coli (n = 31), Enterococcus faecium (n = 22), Staphylococcus aureus (n = 37) and Pseudomonas aeruginosa (n = 30) were used for validation of FTIR. Subsequently, Enterococcus faecalis (n = 106) and Enterococcus faecium (n = 104) isolates from weekly routine screening samples when no potential outbreak was present were analysed. FTIR showed reproducibility and congruence of cluster composition with WGS for A. baumannii/calcoaceticus complex and E. faecium outbreak isolates. The FTIR results of E. faecalis and E. faecium isolates from routine samples showed reproducibility, but the congruence of cluster composition with WGS was low. For A. baumannii/calcoaceticus complex and E. faecium outbreak isolates, FTIR appears to be a discriminatory typing tool. However, our study shows the discriminatory power is too low to screen real-time for transmission of E. faecium and E. faecalis at patient wards based on isolates acquired in routine surveillance cultures when there is no clear suspicion of an ongoing outbreak.

Silver nanoparticle effect on Salmonella enterica isolated from Northern West Egypt food, poultry, and calves

A total no. of 65 Salmonella enterica isolates recovered from food samples, feces of diarrheic calves, poultry, and hospital patient in large five cities at Northern West Egypt were obtained from the Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt. The 65 Salmonella enterica isolates had the invA gene were grouped into 11 Salmonella enterica serovars with dominance of S. Enteritidis and S. Kentucky serovars. Their resistance pattern were characterized by using 18 antibiotics from different classes. Approximately 80% of the isolates were multidrug resistant (MDR). Enterobacterial repetitive intergenic consequences polymerase chain reaction (ERIC-PCR) typing of 7 strains of S. Enteritidis showed 5 clusters with dissimilarity 25%. S. Enteritidis clusters in 2 main groups A and B. Group A have 2 human strain (HE2 and HE3) and one food origin (FE7) with a similarity 99%. Group B divided into B1 (FE2) and B2 (FE3) with a similarity ratio ≥ 93%, while ERIC-PCR analysis of 5 strains of S. Kentucky revealed 4 ERIC types, clustered in 2 main groups A and B with similarity 75%. We studied the effect of silver nanoparticles (Ag-NPs) on 10 antibiotic resistant strains of S. Enteritidis and S. Kentucky. The broth microdilution minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were detected. Evaluation of the affection using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) showed different ratios of Ag-NPs and microorganism as well as at different contact time ended finally with morphological alteration of the bacteria. We submitted new method in vivo to explore the activity of nanosilver in chicken. KEY POINTS: • Importance of ERIC-PCR to determine the relatedness between Salmonella isolates. • Effect of silver nanoparticles to confront the antibacterial resistance. • Studying the effect of silver nanoparticles in vivo on infected chicken with Salmonella.

Emergence, Dissemination and Antimicrobial Resistance of the Main Poultry-Associated Salmonella Serovars in Brazil

Salmonella infects poultry, and it is also a human foodborne pathogen. This bacterial genus is classified into several serovars/lineages, some of them showing high antimicrobial resistance (AMR). The ease of Salmonella transmission in farms, slaughterhouses, and eggs industries has made controlling it a real challenge in the poultry-production chains. This review describes the emergence, dissemination, and AMR of the main Salmonella serovars and lineages detected in Brazilian poultry. It is reported that few serovars emerged and have been more widely disseminated in breeders, broilers, and layers in the last 70 years. Salmonella Gallinarum was the first to spread on the farms, remaining as a concerning poultry pathogen. Salmonella Typhimurium and Enteritidis were also largely detected in poultry and foods (eggs, chicken, turkey), being associated with several human foodborne outbreaks. Salmonella Heidelberg and Minnesota have been more widely spread in recent years, resulting in frequent chicken/turkey meat contamination. A few more serovars (Infantis, Newport, Hadar, Senftenberg, Schwarzengrund, and Mbandaka, among others) were also detected, but less frequently and usually in specific poultry-production regions. AMR has been identified in most isolates, highlighting multi-drug resistance in specific poultry lineages from the serovars Typhimurium, Heidelberg, and Minnesota. Epidemiological studies are necessary to trace and control this pathogen in Brazilian commercial poultry production chains.

Using unique ORFan genes as strain-specific identifiers for Escherichia coli

BACKGROUND

Bacterial identification at the strain level is a much-needed, but arduous and challenging task. This study aimed to develop a method for identifying and differentiating individual strains among multiple strains of the same bacterial species. The set used for testing the method consisted of 17 Escherichia coli strains picked from a collection of strains isolated in Germany, Spain, the United Kingdom and Vietnam from humans, cattle, swine, wild boars, and chickens. We targeted unique or rare ORFan genes to address the problem of selective and specific strain identification. These ORFan genes, exclusive to each strain, served as templates for developing strain-specific primers.

RESULTS

Most of the experimental strains (14 out of 17) possessed unique ORFan genes that were used to develop strain-specific primers. The remaining three strains were identified by combining a PCR for a rare gene with a selection step for isolating the experimental strains. Multiplex PCR allowed the successful identification of the strains both in vitro in spiked faecal material in addition to in vivo after experimental infections of pigs and recovery of bacteria from faecal material. In addition, primers for qPCR were also developed and quantitative readout from faecal samples after experimental infection was also possible.

CONCLUSIONS

The method described in this manuscript using strain-specific unique genes to identify single strains in a mixture of strains proved itself efficient and reliable in detecting and following individual strains both in vitro and in vivo, representing a fast and inexpensive alternative to more costly methods.

Genetic characterization and antimicrobial susceptibility of Escherichia coli isolated from household water sources in northern Ghana

The microbial quality of household water is an important issue in developing countries, especially in Ghana, where many people still depend on unimproved sources of water. The present study investigated the prevalence, genetic characteristics, and antimicrobial resistance profile of Escherichia coli from surface water sources. Fifty-two water samples were analyzed by using a spread plate, a biochemical test, and multiplex polymerase chain reactions. E. coli was isolated from each of the 52 water samples. Of these isolates, 75% were noted to possess virulence genes. Approximately 54% of the isolates were characterized as follows: enterotoxigenic E. coli (ETEC, 10.26%), enteropathogenic E. coli (EPEC, 17.95%), verotoxigenic E. coli (VTEC, 23.07%), and enteroinvasive E. coli (EIEC, 2.57%). Eighteen of the fifty-two isolates could not be characterized due to heterogeneity in banding. The disc diffusion method was used to test for antimicrobial susceptibility. The isolates were most resistant to ceftazidime, augmentin, and cefuroxime. Multidrug resistance was recorded in 48.1% of the isolates. In contrast, the isolates were most susceptible to ciprofloxacin (86.5%), nitrofurantoin (84.6%), and ofloxacin (75%). These results revealed a high diversity and widespread of E. coli in northern Ghana. The study provides important data for public health nationwide surveillance of E. coli in surface water across the country.

Biotyping, Virulotyping and Biofilm Formation Ability of ESBL-Klebsiella pneumoniae Isolates from Nosocomial Infections

The aim of this study was to investigate the frequency, molecular characterization, virulence genes, resistance genes and antimicrobial profile of nosocomial extended spectrum beta lactamase producing Klebsiella species. A total of 22 (12.2%) K. pneumoniae strains were isolated from 180 clinical samples collected from hospitalized patients in Egypt. K. pneumoniae biotypes were B1 (72.8%), B3 (13.6%) and B4 (13.6%). The isolates were classified for the capsular serotypes, 86.4% (20/22) were of K1 serotype, while only two isolates (13.64%) were of K2 serotype. Hypermucoviscous K. pneumoniae isolates accounted for 68.2%. Biofilm formation ability of K. pneumoniae was determined by microtitre plate method. The majority of the isolates (40.9%) were moderate biofilm producers, while 27.3% were strong biofilm producers. All K. pneumoniae strains were positive for fimH and traT genes, while magA was identified in only 63.6% of the isolates. The antibiotic susceptibility profile of the isolates (n=22) was determined by the disc diffusion technique using 23 different antibiotics. Streptomycin and imipenem are the most effective antibiotics against 22 tested K. pneumoniae isolates with sensitivity rates of 63.64% and 54.54%, respectively. All tested K. pneumoniae isolates showed high resistance to amoxicillin∕clavulanate (100%), cefuroxime (100%) and ceftazidime (95.45%). Extended spectrum beta lactamases (ESBL) production and the presence of ESBL related genes were tested in the isolates. All the isolates tested positive for blaVIM, NDM1, and blaTEM, while only 81.8 percent tested positive for the blaSHV gene. Increasing antimicrobial resistance in K. pneumoniae causing nosocomial infections limits the use of antimicrobial agents for treatment. Furthermore, the spread of biofilm, multiple drug resistant and ESBL-producing K. pneumoniae isolates is a public threat for hospitalized patients.

Compositional Quality and Possible Gastrointestinal Performance of Marketed Probiotic Supplements

The local pharmacies and shops are brimming with various probiotic products that herald a range of health benefits. The poor quality of probiotic products in both dosage and species is symptomatic of this multi-billion-dollar market making it difficult for consumers to single out reliable ones. This study aims to fill the potential gap in the labeling accuracy of probiotic products intended for human consumption. We describe a combinatorial approach using classical culture-dependent technique to quantify and molecular techniques (16 s rRNA gene sequencing, multilocus sequence, and ribotyping) for strain recognition of the microbial contents. The full gamut of probiotic characteristics including acid, bile and lysozyme tolerances, adhesiveness, anti-pathogenicity, and degree of safeness were performed. Their capacity to endure gastro-intestinal (GIT) stresses and select drugs was assessed in vitro. Our results forced us to declare that the local probiotic market is essentially unregulated. Almost none of the probiotic products tested met the label claim. Some (11%) have no viable cells, and a quarter (27%) showing significant inter-batch variation. A lower microbial count was typical with undesirables constituting a quarter of the total (~ 27%). Half of the products contained antibiotic-resistant strains; the unregulated use of these probiotics carries the risk of spreading antibiotic resistance to gut pathobionts. Poor tolerance to gut conditions and mediocre functionalism make the case worse. The current regulatory systems do not take this discrepancy into account. We recommend an evidence-based regular market surveillance of marketed probiotics to ensure the authenticity of the claims and product effectiveness.

A potentially probiotic strain of Enterococcus faecalis from human milk that is avirulent, antibiotic sensitive, and nonbreaching of the gut barrier

Human milk is a key source of promising probiotic lactic acid bacteria. The Enterococcus species, because of their dual commensal and pathogenic nature, demand critical safety analysis to establish them as probiotic candidates. In this study, eighteen E. faecalis strains from human milk of mothers living in Pakistan were typed at the strain level by riboprinting. The typed strains were then evaluated in vitro for physiological safety and the presence of transmissible antibiotic resistance genes, adhesion genes, biogenic amines, and virulence factors. Selected strains were then checked for tolerance to gastrointestinal acid and bile as criteria for probiotic efficacy. Molecular typing revealed that the strains fell into five distinct clusters or ribotypes. Testing revealed that they were non-hemolytic; however, all strains had gelatinase activity except NPL-493. The isolates were susceptible to most clinically important antibiotics except streptomycin. Molecular screening for antibiotic resistance genes, adhesion genes, biogenic amines, and virulence factors indicated that none of the strains possessed resistance genes for aminoglycosides, vancomycin, bacitracin, tetracycline, or clindamycin. Most virulence factors were absent except for the genes gelE and efaAs associated with gut adhesion and translocation, which were present in all except NPL-493. Strain NPL-493 was the most promising probiotic candidate demonstrating significant tolerance to the acid, bile, and digestive enzymes in the human GIT and antibacterial activity against multiple pathogens. The study concluded that E. faecalis NPL-493 from human milk was safe among all the strains and could be considered a potential probiotic.

Genetic Diversity, Antimicrobial Resistance Pattern, and Biofilm Formation in Klebsiella pneumoniae Isolated from Patients with Coronavirus Disease 2019 (COVID-19) and Ventilator-Associated Pneumonia

Introduction

Patients with acute respiratory distress syndrome caused by coronavirus disease 2019 (COVID-19) are at risk for superadded infections, especially infections caused by multidrug resistant (MDR) pathogens. Before the COVID-19 pandemic, the prevalence of MDR infections, including infections caused by MDR Klebsiella pneumoniae (K. pneumoniae), was very high in Iran. This study is aimed at assessing the genetic diversity, antimicrobial resistance pattern, and biofilm formation in K. pneumoniae isolates obtained from patients with COVID-19 and ventilator-associated pneumonia (VAP) hospitalized in an intensive care unit (ICU) in Iran.

Methods

In this cross-sectional study, seventy K. pneumoniae isolates were obtained from seventy patients with COVID-19 hospitalized in the ICU of Shahid Beheshti hospital, Kashan, Iran, from May to September, 2020. K. pneumoniae was detected through the ureD gene. Antimicrobial susceptibility testing was done using the Kirby-Bauer disc diffusion method, and biofilm was detected using the microtiter plate assay method. Genetic diversity was also analyzed through polymerase chain reaction based on enterobacterial repetitive intergenic consensus (ERIC-PCR). The BioNumerics software (v. 8.0, Applied Maths, Belgium) was used for analyzing the data and drawing dendrogram and minimum spanning tree. Findings. K. pneumoniae isolates had varying levels of resistance to antibiotics meropenem (80.4%), cefepime-aztreonam-piperacillin/tazobactam (70%), tobramycin (61.4%), ciprofloxacin (57.7%), gentamicin (55.7%), and imipenem (50%). Around 77.14% of isolates were MDR, and 42.8% of them formed biofilm. Genetic diversity analysis revealed 28 genotypes (E1-E28) and 74.28% of isolates were grouped into ten clusters (i.e., clusters A-J). Clusters were further categorized into three major clusters, i.e., clusters E, H, and J. Antimicrobial resistance to meropenem, tobramycin, gentamicin, and ciprofloxacin in cluster J was significantly higher than cluster H, denoting significant relationship between ERIC clusters and antimicrobial resistance. However, there was no significant difference among major clusters E, H, and J respecting biofilm formation.

Conclusion

K. pneumoniae isolates obtained from patients with COVID-19 have high antimicrobial resistance, and 44.2% of them have genetic similarity and can be clustered in three major clusters. There is a significant difference among clusters respecting antimicrobial resistance.

Identification of Enterococcus faecalis in Different Clonal Lineages with the Pulsed-Field Gel Electrophoresis Method in Imam Khomeini Hospital, Ilam, Iran

Background: Due to the importance of identifying the source of infectious agents, different typing methods have been developed, among which the pulsed-field gel electrophoresis (PFGE) method is known as the gold standard for bacteria. Also, Enterococcus faecalis is classified as a nosocomial infection. Objectives: The current study aimed to identify the source of E. faecalis by the PFGE method. Methods: Bacteria were collected from all cases of urinary tract infections. Then, the identification process was performed. All isolates were evaluated for vancomycin resistance, and then PFGE was carried out. Results: The results of disk diffusion showed that 54% of the isolates showed resistance to vancomycin. Also, 4% of the isolates were intermediate, and 42% showed sensitivity to vancomycin. Afterwards, the PCR of the VanA gene was performed to confirm the results of disk diffusion. Thus, 48 out of 54 (88.8%) isolates had the VanA gene, and none of the four intermediate isolates had the VanA gene. Our results demonstrated that 54 isolates were vancomycin-resistant, and 50 different pulsotypes groups were identified. Conclusions: Our findings showed the isolates of E. faecalis were from different clonal lineages.

Endophytic Bacteria Pseudomonas aeruginosa PM389 Subsists Host’s (Triticum aestivum) Immune Response for Gaining Entry Inside the Host

The present study was designed to compare the defense response of the host plant towards endophytic bacteria Pseudomonas aeruginosa PM389 and pathogenic bacteria Erwinia carotovora and to correlate the level of defense enzymes vis-a-vis bacterial colonization in the host. Wheat seedlings were treated with 107-108 cells ml-1 endophytic and pathogenic bacteria in the separate experimental set-up, and the level of plant defense enzyme was measured at various time intervals. Comparatively reduced level of most defense enzymes was produced in endophytic bacteria treated plants. While the endophytic bacterial population was almost constant after 24 HAI (hour after inoculation), the population of pathogenic bacteria kept fluctuating during the study period from 24 HAI. Unlike pathogenic bacteria, we observed attenuated defense response in challenged host plants towards endophytic bacteria, which helps endophytes establish inside plant. This study would be useful for understanding the mechanism of colonization and strategies of endophytes to fight against the host defense response.

Establishment of a Publicly Available Core Genome Multilocus Sequence Typing Scheme for Clostridium perfringens

Clostridium perfringens is a spore-forming anaerobic pathogen responsible for a variety of histotoxic and intestinal infections in humans and animals. High-resolution genotyping aiming to identify bacteria at strain level has become increasingly important in modern microbiology to understand pathogen transmission pathways and to tackle infection sources. This study aimed at establishing a publicly available genome-wide multilocus sequence-typing (MLST) scheme for C. perfringens. A total of 1,431 highly conserved core genes (1.34 megabases; 50% of the reference genome genes) were indexed for a core genome-based MLST (cgMLST) scheme for C. perfringens. The scheme was applied to 282 ecologically and geographically diverse genomes, showing that the genotyping results of cgMLST were highly congruent with the core genome-based single-nucleotide-polymorphism typing in terms of resolution and tree topology. In addition, the cgMLST provided a greater discrimination than classical MLST methods for C. perfringens. The usability of the scheme for outbreak analysis was confirmed by reinvestigating published outbreaks of C. perfringens-associated infections in the United States and the United Kingdom. In summary, a publicly available scheme and an allele nomenclature database for genomic typing of C. perfringens have been established and can be used for broad-based and standardized epidemiological studies. IMPORTANCE Global epidemiological surveillance of bacterial pathogens is enhanced by the availability of standard tools and sharing of typing data. The use of whole-genome sequencing has opened the possibility for high-resolution characterization of bacterial strains down to the clonal and subclonal levels. Core genome multilocus sequence typing is a robust system that uses highly conserved core genes for deep genotyping. The method has been successfully and widely used to describe the epidemiology of various bacterial species. Nevertheless, a cgMLST typing scheme for Clostridium perfringens is currently not publicly available. In this study, we (i) developed a cgMLST typing scheme for C. perfringens, (ii) evaluated the performance of the scheme on different sets of C. perfringens genomes from different hosts and geographic regions as well as from different outbreak situations, and, finally, (iii) made this scheme publicly available supported by an allele nomenclature database for global and standard genomic typing.

Genetic diversity and virulence characteristics of biofilm-producing uropathogenic Escherichia coli

Uropathogenic E. coli (UPEC) strains exhibit different levels of biofilm formation that help adhesion of the bacteria to uroepithelial cells. We investigated the genetic diversity and virulence-associated genes (VAGs) of biofilm-producing UPEC. A collection of 107 biofilm-producing (BFP) UPEC strains isolated from patients with UTI in Iran were divided into three groups of strong, moderate, and weak BFPs after a quantitative microtiter plate assay, and the involvement of curli and cellulose in adhesion of the strains to T24 cell line was confirmed by the construction of csgD and yedQ mutants of two representative UPEC strains. BFP strains were tested for their genetic diversity, phylogenetic groups, and the presence of 15 VAGs. A significant decrease in adhesion of csgD and yedQ mutant strains confirmed the role of biofilm production in adhesion to uroepithelial cells. A high diversity was found among all three groups of strong (Di = 0.998), moderate (Di = 0.998), and weak (Di = 0.988) BFPs with majority of the strains belonging to phylogroups B2 (44.9%) and A (24.3%). Strong BFP strains carried significantly higher level papEF, hlyA, and iutA than other BFP groups. In contrast, the presence of fimH, focG, sfaS, set-1, and cvaC was more pronounced among weak BFP strains. There exists a high genetic diversity among the BFP strains with different VGA profiles. However, the high prevalence of phylogroup A among BFP strains suggests the fitness of commensal E. coli strains to cause UTI in this country.

Development of a database and standardized approach for rpoB sequence-based subtyping and identification of aerobic spore-forming Bacillales

Aerobic spore-forming Bacillales are a highly diverse and ubiquitous group that includes organisms that cause foodborne illnesses and food spoilage. Classical microbiological and biochemical identification of members of the order Bacillales represents a challenge due to the diversity of organisms in this group as well as the fact that the phenotypic-based taxonomic assignment of some named species in this group is not consistent with their phylogenomic characteristics. DNA-sequencing-based tools, on the other hand, can be fast and cost-effective, and can provide for a more reliable identification and characterization of Bacillales isolates. In comparison to 16S rDNA, rpoB was shown to better discriminate between Bacillales isolates and to allow for improved taxonomic assignment to the species level. However, the lack of a publicly accessible rpoB database, as well as the lack of standardized protocols for rpoB-based typing and strain identification, is a major challenge. Here, we report (i) the curation of a DNA sequence database for rpoB-based subtype classification of Bacillales isolates; (ii) the development of standardized protocols for generating rpoB sequence data, and a scheme for rpoB-based initial taxonomic identification of Bacillales isolates at the species level; and (iii) the integration of the database in a publicly accessible online platform that allows for the analysis of rpoB sequence data from uncharacterized Bacillales isolates. Specifically, we curated a database of DNA sequences for a 632-nt internal variable region within the rpoB gene from representative Bacillales reference type strains and a large number of isolates that we have previously isolated and characterized through multiple projects. As of May 21, 2021, the rpoB database contained more than 8350 rpoB sequences representing 1902 distinct rpoB allelic types that can be classified into 160 different genera. The database also includes 1129 rpoB sequences for representative Bacillales reference type strains as available on May 21, 2021 in the NCBI database. The rpoB database is integrated into the online Food Microbe Tracker platform (www.foodmicrobetracker.com) and can be queried using the integrated BLAST tool to initially subtype and taxonomically identify aerobic and facultative anaerobic spore-formers. While whole-genome sequencing is increasingly used in bacterial taxonomy, the rpoB sequence-based identification scheme described here provides a valuable tool as it allows for rapid and cost-effective initial isolate characterization, which can help to identify and characterize foodborne pathogens and food spoilage bacteria. In addition, the database and primers described here can also be adopted for metagenomics approaches that include rpoB as a target, improving discriminatory power and identification over what can be achieved using 16S rDNA as a target.

Tracing Clostridium perfringens strains from beef processing of slaughter house by pulsed-field gel electrophoresis, and the distribution and toxinotype of isolates in Shaanxi province, China

The purpose of this study was to investigate the distribution and specify the transmission and cross-contamination of Clostridium perfringens (C. perfringens) in the beef slaughtering and butchering process. The prevalence of 21.2% (150/708) yielded 208 isolates of C. perfringens, including 80.8% type A and 19.2% type D, 0.4% (3/708) samples carried both type A and D strains, and 72.5% type D isolates carried both cpe and atyp.cpb2 genes. C. perfringens were identified through the whole slaughtering process but no type F (cpe and cpa isolates) was found. 69 isolates were further analyzed and classified into 28 PFGE genotypes and clade I contained 94.2% isolates and 24 PFGE genotypes, which showed the genetic diversity and epidemic correlation. Our study traced C. perfringens contamination along the handling processes and showed a gradually ascending contamination rate during the whole process, revealing widespread cross-contamination from the feces and hides of slaughtered cattle to the carcass in the slaughtering workshop, so as from tools and personnel to meat of the cutting workshops. Strains from different slaughterhouses (regions) have high homology, and type A is the predominant toxinotype. It is necessary to monitor and control several key points of cross-contamination during slaughtering process to reduce a risk of C. perfringens infection.

Epidemiologic and molecular characterization of β-lactamase-producing multidrug-resistant uropathogenic Escherichia coli isolated from asymptomatic hospitalized patients

Uropathogenic Escherichia coli (UPECs) are the predominant cause of asymptomatic bacteriuria (ABU) and symptomatic UTI. In this study, multidrug-resistant (MDR) ABU-UPECs from hospitalized patients of Kolkata, India, were characterized with respect to their ESBL phenotype, acquisition of β-lactamase genes, mobile genetic elements (MGEs), phylotype property, ERIC-PCR profile, sequence types (STs), clonal complexes (CCs) and evolutionary and quantitative relationships and compared to the symptomatic ones to understand their epidemiology and evolutionary origin. Statistically significant incidence of ESBL producers, β-lactamase genes, MGEs and novel phylotype property (NPP) among ABU-UPECs similar to the symptomatic ones indicated the probable incidence of chromosomal plasticity on resistance gene acquisition through MGEs due to indiscriminate drug usage. ERIC-PCR typing and MLST analysis showed clonal heterogeneity and predominance of ST940 (CC448) among asymptomatic isolates akin to symptomatic ones along with the evidence of zoonotic transmissions. Minimum spanning tree analysis showed a close association between ABU-UPEC with known and unidentified STs having NPPs with isolates that belonged to phylogroups clade I, D, and B2. This is the first study that reported the occurrence of MGEs and NPPs among ABU-UPECs with the predominance of ESBL production which displayed the deleterious effect of MDR among this pathogen demanding alternative therapeutic interventions. Moreover, this study for the first time attempted to introduce a new approach to ascertain the phylotype property of unassigned UPECs. Withal, increased recognition, proper understanding and characterization of ABU-UPECs with the implementation of appropriate therapeutic measures against them when necessary are the need of the era which otherwise might lead to serious complications in the vulnerable population.

Correlating Genotyping Data of Coxiella burnetii with Genomic Groups

Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. Several distinct genetic lineages or genomic groups have been shown to exist, with evidence for different virulence potential of these lineages. Multispacer Sequence Typing (MST) and Multiple-Locus Variable number tandem repeat Analysis (MLVA) are being used to genotype strains. However, it is unclear how these typing schemes correlate with each other or with the classification into different genomic groups. Here, we created extensive databases for published MLVA and MST genotypes of C. burnetii and analysed the associated metadata, revealing associations between animal host and human disease type. We established a new classification scheme that assigns both MST and MLVA genotypes to a genomic group and which revealed additional sub-lineages in two genomic groups. Finally, we report a novel, rapid genomotyping method for assigning an isolate into a genomic group based on the Cox51 spacer sequence. We conclude that by pooling and streamlining existing datasets, associations between genotype and clinical outcome or host source were identified, which in combination with our novel genomotyping method, should enable an estimation of the disease potential of new C. burnetii isolates.

Population structure and transmission of Mycobacterium bovis in Ethiopia

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis, which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole-genome sequencing to examine the population structure of M. bovis in Ethiopia. A total of 134 M. bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis, based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

minMLST: machine learning for optimization of bacterial strain typing

MOTIVATION

High-resolution microbial strain typing is essential for various clinical purposes, including disease outbreak investigation, tracking of microbial transmission events and epidemiological surveillance of bacterial infections. The widely used approach for multilocus sequence typing (MLST) that is based on the core genome, cgMLST, has the advantage of a high level of typeability and maximal discriminatory power. Yet, the transition from a seven loci-based scheme to cgMLST involves several challenges, that include the need by some users to maintain backward compatibility, growing difficulties in the day-to-day communication within the microbiology community with respect to nomenclature and ontology, issues with typeability, especially if a more stringent approach to loci presence is used, and computational requirements concerning laboratory data management and sharing with end-users. Hence, methods for optimizing cgMLST schemes through careful reduction of the number of loci are expected to be beneficial for practical needs in different settings.

RESULTS

We present a new machine learning-based methodology, minMLST, for minimizing the number of genes in cgMLST schemes by identifying subsets of informative genes and analyzing the trade-off between gene reduction and typing performance. The results achieved with minMLST over eight bacterial species show that despite the reduction in the number of genes up to a factor of 10, the typing performance remains very high and significant with an Adjusted Rand Index that ranges between 0.4 and 0.93 in different species and a P-value < 10-3. The identification of such optimized MLST schemes for bacterial strain typing is expected to improve the implementation of cgMLST by improving interlaboratory agreement and communication.

AVAILABILITY AND IMPLEMENTATION

The python package minMLST is available at https://PyPi.org/project/minmlst/PyPI and supported on Linux and Windows.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Comparative Assessment of Different PCR-Based Typing Methods of Pseudomonas aeruginosa Isolates

Introduction

Pseudomonas aeruginosa is one of the important causes of nosocomial infections. Analyzing the diversity of these isolates is important to control the diseases caused by them. Studies of molecular epidemiology depend on the application of typing methods.

Purpose

This study aims to assess the performance of PCR- based typing techniques (RAPD, ribotyping, tDNA, and ERIC) in determining the genetic diversity of 44 P. aeruginosa urinary isolates.

Methods

Performance parameters were analyzed for each of the tested methods. The banding pattern was assessed by calculating polymorphism, genotypic gene diversity and the effective multiplex ratio. Moreover, strain diversity, typeability, and discriminatory power were used to measure the efficiency of typing methods. The congruence among typing methods was calculated by Rand’s and Wallace coefficients.

Results

P-640 among RAPD primers and Ribo-2 among ribotyping primers were more informative as they gave high strain diversity, the highest number of clusters, and highest discriminatory power (ISD=70.45%, 29 clusters at 70% cutoff, DI=0.97 and ISD=75%, 25 clusters at 70% cutoff DI=0.969, respectively). Comparison of typing methods showed that RAPD-PCR gave the highest mean percent polymorphism per assay (76.85%) followed by ERIC-PCR. ERIC-PCR outperformed in most marker parameters; highest mean number of alleles, number of monomorphic bands per assay unit, mean genotypic gene diversity, effective multiplex ratio, and assay efficiency index. Calculated congruence revealed that individual methods demonstrate moderate to poor predictive power. Interestingly, this power increased by combining data obtained from another method.

Conclusion

RAPD primer (P-640) had more discrimination power followed by ribo-2 and ERIC. The performance and predictive power of typing methods can be improved by combining data obtained from different methods as ERIC+OPA-02 and ERIC+P-640 combinations gave complete typeability and discrimination of isolates. ERIC, ERIC+OPA-02, and ERIC+P-640 combinations can provide finer discrimination and classification of P. aeruginosa strains than the other tested methods.

The structure and diversity of strain-level variation in vaginal bacteria

The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain-level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core genomes for six species of vaginal bacteria: Gardnerella vaginalis, Lactobacillus crispatus, Lactobacillus iners, Lactobacillus jensenii, Lactobacillus gasseri and Atopobium vaginae. Despite inhabiting the same environment, strain diversity and structure varies across species. All species except L. iners are characterized by multiple distinct groups of strains. Even so, strain diversity is lower in the Lactobacillus species, consistent with a more recent colonization of the human vaginal microbiome. Both strain diversity and the frequency of multi-strain samples is related to species-level diversity of the microbiome in which they occur, suggesting similar ecological factors influencing diversity within the vaginal niche. We conclude that the structure of strain-level variation provides both the motivation and means of testing whether strain-level differences contribute to the function and health consequences of the vaginal microbiome.

The Potential Relevance of the Microbiome to Hair Physiology and Regeneration: The Emerging Role of Metagenomics

Human skin and hair follicles are recognized sites of microbial colonization. These microbiota help regulate host immune mechanisms via an interplay between microbes and immune cells, influencing homeostasis and inflammation. Bacteria affect immune responses by controlling the local inflammatory milieu, the breakdown of which can result in chronic inflammatory disorders. Follicular microbiome shifts described in some inflammatory cutaneous diseases suggest a link between their development or perpetuation and dysbiosis. Though the hair follicle infundibulum is an area of intense immunological interactions, bulb and bulge regions represent immune-privileged niches. Immune privilege maintenance seems essential for hair growth and regeneration, as collapse and inflammation characterize inflammatory hair disorders like alopecia areata and primary cicatricial alopecia. Current research largely focuses on immunological aberrations. However, studies suggest that external stimuli and interactions across the follicular epithelium can have profound effects on the local immune system, homeostasis, and cycling. Herein, we review hair follicle bacterial colonization, its possible effects on the underlying tissue, and links to the pathogenesis of alopecia, beyond the pure investigation of specific species abundance. As skin microbiology enters the metagenomics era, multi-dimensional approaches will enable a new level of investigations on the effects of microorganisms and metabolism on host tissue.

Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of bla_OXA-23, bla_OXA-66, bla_ADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.

A new genetic approach to distinguish strains of Anaplasma phagocytophilum that appear not to cause human disease

Genetic diversity of Anaplasma phagocytophilum was assessed in specimens from 16 infected patients and 16 infected Ixodes scapularis ticks. A region immediately downstream of the 16S rRNA gene, which included the gene encoding SdhC, was sequenced. For the A. phagocytophilum strains from patients no sequence differences were detected in this region. In contrast, significantly fewer ticks had a sequence encoding SdhC that was identical to that of the human strains (11/16 vs. 16/16, p = 0.04). This variation is consistent with the premise that not all A. phagocytophilum strains present in nature are able to cause clinical illness in humans. A strain referred to as A. phagocytophilumVariant-1 that is regarded as non-pathogenic for humans was previously described using a different typing method. Data from the current study suggest that both typing methods are identifying the same non-pathogenic strains.

First isolation and molecular phylogenetic analysis of Coxiella burnetii in lactating cows

Q fever is an infectious disease of animals and humans, caused by globally distributed C. burnetii. In Iraq, there are no previous studies associated with the detection of the organism in cattle. An overall of 130 lactating cows were submitted to direct collection of milk samples. Initially, the samples of milk were tested using the molecular polymerase chain reaction (PCR) assay targeting three genes (16S rRNA, IS1111a transposase, and htpB). However, positive results (18.46%; 24/130) were detected only with the 16s rRNA gene. Concerning risk factors, the highest prevalence of C. burnetii was showed in the district of Badra (42.86%), whereas the lowest - in Al-Numaniyah and Al-Suwaira districts (P=0.025). There was no significant variation in positivity between the months of sampling period (P=0.082) and between age groups (P=0.076). Crossbred cows (20.69%) showed a higher positivity than local and pure breeds (P=0.043). Milk of positive samples (n=24) was used for cultivation of C. burnetii into specific pathogen free-embryonated chicken eggs (SPF-ECEs). After three passages into SPF-ECEs, contents of yolk sac were collected, subjected for DNA extraction, and re-tested by PCR assay using the primer of 16s rRNA gene only. Of 24 cultivated milk samples, 12.5% (3/24) were positive for C. burnetii. Finally, the positive local isolates were analysed phylogenetically and reported in NCBI-Genbank under the accession numbers of MN121700.1, MN121701.1, and MN121702.1. In conclusion, this is a unique study as it detected C. burnetii in Iraqi lactating cows, and confirmed that organism was shed actively through milk, suggesting that these animals can play a role as a reservoir for organism with potential risk for transmission of infection from these animals to humans as well as to other animal species.