High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis

ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets

Methods that measure the transcriptomic state of thousands of individual cells have transformed our understanding of cellular heterogeneity in eukaryotic cells since their introduction in the past decade. While simple and accessible protocols and commercial products are now available for the processing of mammalian cells, these existing technologies are incompatible with use in bacterial samples for several fundamental reasons including the absence of polyadenylation on bacterial messenger RNA, the instability of bacterial transcripts and the incompatibility of bacterial cell morphology with existing methodologies. Recently, we developed ProBac sequencing (ProBac-seq), a method that overcomes these technical difficulties and provides high-quality single-cell gene expression data from thousands of bacterial cells by using messenger RNA-specific probes. Here we provide details for designing large oligonucleotide probe sets for an organism of choice, amplifying probe sets to produce sufficient quantities for repeated experiments, adding unique molecular indexes and poly-A tails to produce finalized probes, in situ probe hybridization and single-cell encapsulation and library preparation. This protocol, from the probe amplification to the library preparation, requires ~7 d to complete. ProBac-seq offers several advantages over other methods by capturing only the desired target sequences and avoiding nondesired transcripts, such as highly abundant ribosomal RNA, thus enriching for signal that better informs on cellular state. The use of multiple probes per gene can detect meaningful single-cell signals from cells expressing transcripts to a lesser degree or those grown in minimal media and other environmentally relevant conditions in which cells are less active. ProBac-seq is also compatible with other organisms that can be profiled by in situ hybridization techniques.

Recent Advances in the Use of Molecular Methods for the Diagnosis of Bacterial Infections

Infections caused by bacteria have a major impact on public health-related morbidity and mortality. Despite major advances in the prevention and treatment of bacterial infections, the latter continue to represent a significant economic and social burden worldwide. The WHO compiled a list of six highly virulent multidrug-resistant bacteria named ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) responsible for life-threatening diseases. Taken together with Clostridioides difficile, Escherichia coli, Campylobacter spp., (C. jejuni and C. coli), Legionella spp., Salmonella spp., and Neisseria gonorrhoeae, all of these microorganisms are the leading causes of nosocomial infections. The rapid and accurate detection of these pathogens is not only important for the early initiation of appropriate antibiotic therapy, but also for resolving outbreaks and minimizing subsequent antimicrobial resistance. The need for ever-improving molecular diagnostic techniques is also of fundamental importance for improving epidemiological surveillance of bacterial infections. In this review, we aim to discuss the recent advances on the use of molecular techniques based on genomic and proteomic approaches for the diagnosis of bacterial infections. The advantages and limitations of each of the techniques considered are also discussed.

Escherichia coli Causing Neonatal Meningitis During 2001-2020: A Study in Eastern China

Background and Objective

Neonatal meningitis (NM) caused by Escherichia coli remains a major health problem in industrialized countries. Currently, information on the epidemiology and antimicrobial susceptibility patterns of NM in developing countries such as China is relatively scarce. Therefore, the present study investigated changes in the antimicrobial susceptibility of E. coli causing NM in a perinatal center in eastern China over the past 20 years.

Methods

This survey was conducted during three periods: 2001–2006, 2007–2012, and 2013–2020. NM was diagnosed according to the number of white blood cells in the cerebrospinal fluid (CSF) and the presence of a single potential pathogenic bacterium in the culture prepared from the blood or CSF of a newborn baby. Changes in the antimicrobial susceptibility of E. coli were analyzed.

Results

In total, 182 NM cases were identified. E. coli was identified in 69 of these cases, and in 21 of these cases, extended-spectrum beta-lactamase (ESBL) production was detected. E. coli was the main cause of NM identified in this study. The overall susceptibility of E. coli to third-generation cephalosporins such as cefotaxime decreased from 100% during 2001–2006 to 50% during 2007–2012 and, subsequently, increased to 71.0% during 2013–2020. This pattern of change is correlated with bacterial ESBL production. Only 8.3% of E. coli found in samples collected from infants with early onset meningitis (EOM) produced ESBL, while 37.3% of E. coli isolated from children with late-onset meningitis (LOM) produced ESBL.

Conclusion

E. coli remains the primary pathogen of NM. Compared with that isolated from infants with LOM, the percentage of ESBL-producing multidrug-resistant E. coli isolated from infants with EOM is significantly lower. Clinicians should consider this trend when determining appropriate and effective antibiotics as empirical treatment for NM.

Proteomics-based discrimination of differentially expressed proteins in antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium, Klebsiella pneumoniae, and Staphylococcus aureus

This study was designed to compare the differentially expressed proteins between antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium, Klebsiella pneumonia, and Staphylococcus aureus. The susceptibilities of wild-type (WT), ciprofloxacin (CIP) and/or oxacillin (OXA)-induced, and clinically isolated resistant (CCARM) S. Typhimurium (ST^WT, ST^CIP, and ST^CCARM), K. pneumoniae (KP^WT, KP^CIP, and KP^CCARM), and S. aureus (SA^WT, SA^CIP, SA^OXA, and SA^CCARM) to antibiotics were determined using broth microdilution assay. ST^CIP was highly resistant to piperacillin (MIC > 512 μg/ml), KP^CIP was resistant to chloramphenicol (128 μg/ml) and norfloxacin (16 μg/ml), SA^CIP was resistant to fluoroquinolones (32 μg/ml), and SA^OXA was resistant to ceftriaxone (32 μg/ml). The protein profiles of antibiotic-sensitive and antibiotic-resistant strains were determined using 2-DE analysis followed by LC-MS/MS. The commonly expressed proteins of ST^WT-ST^CIP, ST^WT-ST^CCARM, KP^WT-KP^CIP, KP^WT-KP^CCARM, SA^WT-SA^CIP, SA^WT-SA^OXA, and SA^WT-SA^CCARM were 763, 677, 677, 469, 261, 259, and 226, respectively. The unique protein spots were observed 57 (6.5%), 80 (11.5%), and 68 (13.9%), respectively, for ST^CCARM, KP^CCARM, and SA^CCARM. The highly up-regulated protein, PrsA (10-fold), was observed in ST^CIP resistant to ciprofloxacin (128-fold), levofloxacin (32-fold), norfloxacin (64-fold), and piperacillin (> 16-fold). The up-regulated proteins (YadC, FimA, and RplB) in KP^CIP resistant to chloramphenicol (> 32-fold), ciprofloxacin (32-fold), levofloxacin (6-fold), norfloxacin (128-fold), and sparfloxacin (64-fold). AcrB and RpoB were up-regulated in SA^CCARM resistant to multiple antibiotics. The differentially expressed proteins were related to the antibiotic resistance of ST^WT, ST^CIP, ST^CCARM, KP^WT, KP^CIP, KP^CCARM, SA^WT, SA^CIP, SA^OXA, and SA^CCARM. The resistance-associated proteins could be useful biomarkers for detecting antibiotic-resistant pathogens.

Nanoliter deposition on star-shaped hydrophilic-superhydrophobic patterned surfaces

Nanoliter sized droplet deposition has gained increasing importance in many biomedical, chemical, and microfluidic applications and in materials synthesis. In this paper, we report a simple method for rapid and high-throughput deposition of nanoliter-sized droplets by dragging a larger droplet on star-shaped hydrophilic-superhydrophobic patterned surfaces. Dragging a droplet on the patterned surface causes water to adhere to hydrophilic patterns. As the larger mother droplet detaches from a star-shaped pattern, a small daughter droplet is deposited on the pattern. Star-shaped hydrophilic patterns with a distinct number of spikes are fabricated and investigated. Systematic tests are carried out to study the influence of different process parameters including the volume of a mother droplet, the dragging velocity, the number of spikes and the dragging directions to the deposition process. The results indicate that creating microarrays by dragging large droplets on patterned hydrophilic-superhydrophobic surfaces yield a reliable, cost-efficient, high-accuracy and easily scalable deposition. The volume of the daughter droplet grows with the velocity of the mother droplet and the number of spikes in a pattern, and decreases with the volume of the mother droplet.

Five-Year Multicenter Study of Clinical Tests of Neonatal Purulent Meningitis

This study aimed to provide more data support for early diagnosis and treatment of neonatal purulent meningitis through retrospective analysis of its clinical diagnosis and treatment, pathogen distribution, and drug resistance in 5 third-class A hospitals in Southwest and Northwest China from January 2011 to December 2015. It was found that both the positive rates of blood and cerebrospinal fluid culture were low, and Escherichia coli should be the main pathogenic bacteria. Drug-resistant strains with varying degrees to the third generation of cephalosporin antibiotics have appeared currently.

Nanotools and molecular techniques to rapidly identify and fight bacterial infections

Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.

Multidrug-Resistant Escherichia coli Strains Isolated from Patients Are Associated with Class 1 and 2 Integrons

Background:Escherichia coli isolates displaying multidrug-resistance (MDR) are a major health care problem that results in mortality and morbidity. Integrons are DNA elements in E.coli that are related to antibiotic resistance. The aim of this study was to determine class 1 and 2 integrons and MDR in E. coli isolates obtained from patients in two Sanandaj hospitals, located in Iran. Materials and Methods: 120 isolates of E. coli were obtained from clinical specimens (from November 2013 to April 2014), and the susceptibility of E. coli antimicrobial agents was determined using the Kirby-Bauer disk diffusion method according to the CLSI. PCR were applied for detection of class 1 and 2 integrons in E. coli isolates. SPSS software v16 and the χ2 test were used for statistical analysis in order to calculate the association between antibiotic resistance and the presence of integrons (p < 0.05). Results: In a total of 120 E. coli isolates, 42.5% had MDR. Integrons were found in 50.9% of the MDR isolates, and included 47.05% class 1 and 3.92% class 2 integrons. The strains did not have both classes of integrons simultaneously. An association between resistance to antibiotics and integrons was found. Conclusion: Our results showed that int1 and int2 genes present in E. coli isolates obtained from patients cause MDR in this isolates. Since such bacteria are a reservoir for the transmission of MDR bacteria, appropriate programs are necessary to reduce this problem.

Detection of integrons among multi-drug resistant (MDR) Escherichia coli strains isolated from clinical specimens in northern west of Iran

Transference of resistance determinants by integrons is one of the important factors that can contribute to the increase in multi-resistant bacteria. We determined the prevalence and class of integrons among multi-drug resistant (MDR) Escherichia coli strains isolated from clinical specimens in Tabriz teaching hospitals. Firstly, susceptibility of 140 isolates to 13 antibiotics was determined using the disc diffusion method. Then, prevalence and class of integrons was detected in MDR strains by PCR-RFLP. One hundred five (75%) of total 140 isolates were uropathogenic Escherichia coli (UPEC). Other pathotypes included were: diarrheagenic Escherichia coli (13; 9.3%), sepsis-associated E. coli (5; 3.6%) and newborn meningitis-associated E. coli (2; 1.4%). Antibiotic resistance patterns were as follows: amoxicillin 99.3%, gentamicin 33.6%, tetracycline 72.8%, ceftazidime 46.4%, co-trimoxazole 75%, imipenem 1.4%, ciprofloxacin 47.6%, norfloxacin 50.7%, cephalothin 77.8%, amikacin 12.1%, nitrofurantoin 12.9%, chloramphenicol 20.7% and nalidixic acid 60.7%. One hundred eighteen (84.2%) of tested isolates were multi-drug resistant. Prevalence of integrons was confirmed in 27.1% of MDR isolates. intI1 and intI2 were detected respectively in 22.05% and 5.08% of MDR strains. No intI3 was detected. Resistance to gentamicin, amikacin and chloramphenicol was significantly associated with the presence of integrons. These results showed high resistance of E. coli to routine antibiotics, however, in consideration of low prevalence of integrons among these strains, we can conclude that antibiotic resistance genes in these strains presumably carried on elements other than integrons.

Transcriptional and functional analysis of trifluoromethionine resistance in Entamoeba histolytica

OBJECTIVES

Drug resistance in parasitic protozoa is an obstacle to successful chemotherapy. Understanding how pathogens respond to drugs is crucial in preventing resistance. Previously, we have shown that in Entamoeba histolytica, methionine γ-lyase (EhMGL) downregulation results in trifluoromethionine resistance. The transcriptional response, however, of this parasite to the drug is not known. In this study, we used microarray analysis to determine whether additional genes are involved.

METHODS

The expression profiles of 9230 genes in wild-type and trifluoromethionine-resistant strains were compared. Episomal overexpression of EhBspA1 was performed to verify its role in trifluoromethionine resistance. The transcriptomes of a trifluoromethionine-resistant strain cultured with or without trifluoromethionine, an EhMGL gene-silenced strain, a strain with reduced susceptibility to metronidazole and a wild-type strain under cysteine-deprived conditions were compared to determine the specificity of the changes observed in the trifluoromethionine-resistant strain.

RESULTS

The expression of 35 genes differed at least 3-fold between trifluoromethionine-resistant and wild-type strains. Some of the genes play roles in metabolism, the stress response and gene regulation. EhMGL and EhBspA1 were found to be highly downregulated and upregulated, respectively. Overexpression of EhBspA1 conferred partial resistance to trifluoromethionine. Comparative transcriptome analysis showed that genes modulated in trifluoromethionine-resistant strains were specific.

CONCLUSIONS

E. histolytica has few known resistance mechanisms against drugs. In this study, we showed that aside from EhMGL downregulation, induction of EhBspA1 plays a role in trifluoromethionine resistance. We also showed a unique set of induced genes that could represent the signature profile of trifluoromethionine resistance in E. histolytica.

Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens

Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples.