scholarly journals Evaluation of MicroScan Bacterial Identification Panels for Low-Resource Settings

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 349
Author(s):  
Sien Ombelet ◽  
Alessandra Natale ◽  
Jean-Baptiste Ronat ◽  
Olivier Vandenberg ◽  
Liselotte Hardy ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Ease Of Use ◽  
Bacterial Identification ◽  
Gram Positive ◽  
Gram Negative ◽  
Low Resource Settings ◽  
Low Resource ◽  
Bacillus Spp ◽  
Gram Negative Organisms ◽  
Instructions For Use

Bacterial identification is challenging in low-resource settings (LRS). We evaluated the MicroScan identification panels (Beckman Coulter, Brea, CA, USA) as part of Médecins Sans Frontières’ Mini-lab Project. The MicroScan Dried Overnight Positive ID Type 3 (PID3) panels for Gram-positive organisms and Dried Overnight Negative ID Type 2 (NID2) panels for Gram-negative organisms were assessed with 367 clinical isolates from LRS. Robustness was studied by inoculating Gram-negative species on the Gram-positive panel and vice versa. The ease of use of the panels and readability of the instructions for use (IFU) were evaluated. Of species represented in the MicroScan database, 94.6% (185/195) of Gram-negative and 85.9% (110/128) of Gram-positive isolates were correctly identified up to species level. Of species not represented in the database (e.g., Streptococcus suis and Bacillus spp.), 53.1% out of 49 isolates were incorrectly identified as non-related bacterial species. Testing of Gram-positive isolates on Gram-negative panels and vice versa (n = 144) resulted in incorrect identifications for 38.2% of tested isolates. The readability level of the IFU was considered too high for LRS. Inoculation of the panels was favorably evaluated, whereas the visual reading of the panels was considered error-prone. In conclusion, the accuracy of the MicroScan identification panels was excellent for Gram-negative species and good for Gram-positive species. Improvements in stability, robustness, and ease of use have been identified to assure adaptation to LRS constraints.

The Natural History of Bacterial Colonization of the Newborn in a Maternity Hospital (Part I)

1974 ◽  
Vol 19 (3) ◽  
pp. 119-124 ◽  
Author(s):  
T. A. McAllister ◽  
J. Givan ◽  
A. Black ◽  
M. J. Turner ◽  
M. M. Kerr ◽  
...  
Keyword(s):  
Bacterial Colonization ◽  
Bacterial Species ◽  
Maternity Hospital ◽  
Gram Positive ◽  
Gram Negative ◽  
Large Numbers ◽  
History Of ◽  
Gram Negative Organisms ◽  
The Individual ◽  
High Level

Bacteriological examinations were performed on 1103 infants to determine the ages at which the newborn are colonized at different sites by bacteria, and with which organisms. On the day of birth, specimens for culture included aspirated gastric contents, and swabs from nose, throat, groin and rectum; on Day 3 the umbilical cord clamp with a section of the cord, swabs from nose, throat, groin and rectum; on days 5 and 1, and weekly thereafter, swabs from the same 4 sites. These examinations included identification of the individual bacterial species. The mass of information so obtained was analysed by computer. The high level of bacterial colonization by day 3 was striking and, indeed, large numbers of potential pathogens were grown from infants within one hour of birth. Staphylococcus aureus was found only in very small numbers of infants, e.g. only 2.6 per cent of infants' umbilical cords on day 3, and 4 per cent of infants' noses on day 7. If the levels of colonization reflect the risks of infection, Pseudomonas aeruginosa ranks close to Staph. aureus in the newborn nursery of the modern maternity hospital. Forty two different species of bacteria were isolated from these infants of which 24 were potential pathogens and of the latter, gram-negative organisms greatly outnumbered the gram-positive. This high incidence of gram-negative colonization in a large series of hospitalized neonates may be a normal phenomenon but it suggests that the risk of infection is today greater with gram-negative than with gram-positive bacteria. The figures for carriage of pathogenic staphylococci in the present investigation contrast markedly with the figures reported by many workers between 1950 and 1960.

scholarly journals Linearized esculentin-2EM shows pH dependent antibacterial activity with an alkaline optimum

2021 ◽  
Author(s):  
Erum Malik ◽  
David A. Phoenix ◽  
Timothy J. Snape ◽  
Frederick Harris ◽  
Jaipaul Singh ◽  
...  
Keyword(s):  
Helical Structure ◽  
Food Preservation ◽  
Forming Process ◽  
Gram Positive ◽  
Gram Negative ◽  
Bacterial Membranes ◽  
Gram Positive Bacteria ◽  
Alkaline Conditions ◽  
Ph Dependent ◽  
Gram Negative Organisms

AbstractHere the hypothesis that linearized esculentin 2EM (E2EM-lin) from Glandirana emeljanovi possesses pH dependent activity is investigated. The peptide showed weak activity against Gram-negative bacteria (MLCs ≥ 75.0 μM) but potent efficacy towards Gram-positive bacteria (MLCs ≤ 6.25 μM). E2EM-lin adopted an α-helical structure in the presence of bacterial membranes that increased as pH was increased from 6 to 8 (↑ 15.5–26.9%), whilst similar increases in pH enhanced the ability of the peptide to penetrate (↑ 2.3–5.1 mN m−1) and lyse (↑ 15.1–32.5%) these membranes. Theoretical analysis predicted that this membranolytic mechanism involved a tilted segment, that increased along the α-helical long axis of E2EM-lin (1–23) in the N → C direction, with −  < µH > increasing overall from circa − 0.8 to − 0.3. In combination, these data showed that E2EM-lin killed bacteria via novel mechanisms that were enhanced by alkaline conditions and involved the formation of tilted and membranolytic, α-helical structure. The preference of E2EM-lin for Gram-positive bacteria over Gram-negative organisms was primarily driven by the superior ability of phosphatidylglycerol to induce α-helical structure in the peptide as compared to phosphatidylethanolamine. These data were used to generate a novel pore-forming model for the membranolytic activity of E2EM-lin, which would appear to be the first, major reported instance of pH dependent AMPs with alkaline optima using tilted structure to drive a pore-forming process. It is proposed that E2EM-lin has the potential for development to serve purposes ranging from therapeutic usage, such as chronic wound disinfection, to food preservation by killing food spoilage organisms.

scholarly journals 1554. Epidemiology of Adult Bacterial Hand Infections at Two Urban Hospitals

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S777-S778
Author(s):  
Arsheena Yassin ◽  
Christine Stavropoulos ◽  
Krystina L Woods ◽  
Jiashan Xu ◽  
Justin Carale ◽  
...  
Keyword(s):  
New York ◽  
Staphylococcus Aureus ◽  
Antibiotic Regimen ◽  
Gram Positive ◽  
Gram Negative ◽  
Streptococcus Species ◽  
Urban Hospitals ◽  
Haemophilus Parainfluenzae ◽  
Empiric Antibiotic ◽  
Gram Negative Organisms

Abstract Background Hand infections represent a major source of morbidity, which can result in hand stiffness and amputation. Early appropriate empiric antibiotic regimen may reduce the associated morbidity, hence the importance to examine local epidemiology. The aim of this study was to define the current epidemiology of adult hand infections at two urban hospitals in New York City. Methods We performed a double center, retrospective study of adult patients hospitalized from March 2018 to May 2020. Patients with positive cultures associated with the hand infections were included. Retrospectively, 100 patients were reviewed. Data on baseline demographic, clinical, surgical, microbiology, and treatment parameters were collected. Results Of the 100 patients, 76% were male, with median age of 47.5 years (35, 58.25) and average C-reactive protein (CRP) of 50.66 mg/L (± 64.64) on admission (see Table 1). Previous hospitalization within 1 year (38%), previous surgical procedures (39%) and recent IV medication use (26%) were common. 130 bacterial isolates were identified (see Table 2). The most frequent organisms were Gram-positive, with Methicillin susceptible Staphylococcus aureus (MSSA, 25.38%), Streptococcus species (20.08%), and Methicillin resistant Staphylococcus aureus (MRSA, 15.38%) being the most common. Gram-negative organisms were infrequent, with Haemophilus parainfluenzae (3.85%), Enterobacter cloacae (3.85) and Pseudomonas aeruginosa (3.08%) being the most prevalent. Of the 100 patients, 27% had polymicrobial infections, associated with trauma (6%), illicit IV use (6%) and unknown (7%) etiologies. Table 1: Baseline demographics and co-morbid conditions Table 2: Types and numbers of organisms in relation to etiologies Conclusion Within our population, the most common organisms associated with hand infections were Gram-positive, with Staphylococcus aureus and Streptococcus species being the most prevalent. Gram-negative pathogens were infrequently isolated. The results within this study can provide guidance to clinicians on assessing the appropriate empiric antibiotic regimen in patients with hand infections, and can serve as a basis for further studies identifying risk factors associated with isolation of organisms associated with hand infections. Disclosures All Authors: No reported disclosures

scholarly journals The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms

Micromachines ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 367 ◽  
Author(s):  
Yuguang Liu ◽  
Dirk Schulze-Makuch ◽  
Jean-Pierre de Vera ◽  
Charles Cockell ◽  
Thomas Leya ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Bacterial Species ◽  
Cell Manipulation ◽  
Microfluidic Platforms ◽  
Gram Positive ◽  
Gram Negative ◽  
Genome Amplification ◽  
Single Cell Sequencing ◽  
Wide Range

Single-cell sequencing is a powerful technology that provides the capability of analyzing a single cell within a population. This technology is mostly coupled with microfluidic systems for controlled cell manipulation and precise fluid handling to shed light on the genomes of a wide range of cells. So far, single-cell sequencing has been focused mostly on human cells due to the ease of lysing the cells for genome amplification. The major challenges that bacterial species pose to genome amplification from single cells include the rigid bacterial cell walls and the need for an effective lysis protocol compatible with microfluidic platforms. In this work, we present a lysis protocol that can be used to extract genomic DNA from both gram-positive and gram-negative species without interfering with the amplification chemistry. Corynebacterium glutamicum was chosen as a typical gram-positive model and Nostoc sp. as a gram-negative model due to major challenges reported in previous studies. Our protocol is based on thermal and chemical lysis. We consider 80% of single-cell replicates that lead to >5 ng DNA after amplification as successful attempts. The protocol was directly applied to Gloeocapsa sp. and the single cells of the eukaryotic Sphaerocystis sp. and achieved a 100% success rate.

scholarly journals Evaluating Flinders Technology Associates card for transporting bacterial isolates and retrieval of bacterial DNA after various storage conditions

2020 ◽  
Vol 13 (10) ◽  
pp. 2243-2251
Author(s):  
Azhar G. Shalaby ◽  
Neveen R. Bakry ◽  
Abeer A. E. Mohamed ◽  
Ashraf A. Khalil
Keyword(s):  
Nucleic Acid ◽  
Bacterial Species ◽  
Storage Conditions ◽  
Animal Origin ◽  
Cell Detection ◽  
Bacterial Cells ◽  
Gram Positive ◽  
Bacterial Dna ◽  
Gram Negative ◽  
Fta Cards

Background and Aim: Flinders Technology Associates (FTA) cards simplify sample storage, transport, and extraction by reducing cost and time for diagnosis. This study evaluated the FTA suitability for safe transport and storage of Gram-positive and Gram-negative bacterial cells of animal origin on its liquid culture form and from organ impression smears (tissues) under the same routine condition of microbiological laboratory along with detecting their nucleic acid over different storage conditions. Materials and Methods: Increase in bacterial count from 104 to 107 (colony-forming units/mL) of 78 isolates representing seven bacterial species was applied onto cards. FTA cards were grouped and inoculated by these bacteria and then stored at different conditions of 24-27°C, 4°C, and –20°C for 24 h, for 2 weeks, for 1 and 3 month storage, respectively. Bacteriological examination was done, after which bacterial DNA was identified using specific primers for each bacterial type and detected by polymerase chain reaction (PCR). Results: The total percentage of recovered bacteria from FTA cards was 66.7% at 24-27–C for 24 h, the detection limit was 100% in Gram-positive species, while it was 57.4% in Gram-negative ones. Regarding viable cell detection from organ impression smears, it was successful under the previous conditions. No live bacterial cells were observed by bacteriological isolation rather than only at 24-27°C for 24 h storage. All bacterial DNA were sufficiently confirmed by the PCR technique at different conditions. Conclusion: Overall, the FTA card method was observed to be a valid tool for nucleic acid purification for bacteria of animal origin in the form of culture or organ smears regardless of its Gram type and is used for a short time only 24 h for storage and transport of live bacteria specifically Gram-positive type. Moreover, the bacterial nucleic acid was intact after storage in –20°C for 3 months and was PCR amplifiable.

A 10-YEAR REVIEW OF COMPARISON BETWEEN GRAM-POSITIVE AND GRAM-NEGATIVE ORGANISMS IN ACUTE THORACIC EMPYEMA

CHEST Journal ◽  
2009 ◽  
Vol 136 (4) ◽  
pp. 45S
Author(s):  
Abhijit Duggal ◽  
Konstantinos Marmagkiolis ◽  
Lawrence Goldstein
Keyword(s):  
Gram Positive ◽  
Gram Negative ◽  
Thoracic Empyema ◽  
Gram Negative Organisms

P1173PERITONEAL DIALYSIS INFECTIONS IN MALTA - TRENDS OVER ELEVEN YEARS

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Angela Borg Cauchi ◽  
Maria Angela Gauci ◽  
Theresia Dalli ◽  
James Gauci ◽  
James Farrugia ◽  
...  
Keyword(s):  
Peritoneal Dialysis ◽  
Coagulase Negative Staphylococcus ◽  
Distributed Data ◽  
Dialysis Modality ◽  
Gram Positive ◽  
Gram Negative ◽  
Male Predominance ◽  
E Coli ◽  
Number Of Patients ◽  
Gram Negative Organisms

Abstract Background and Aims Infections related to peritoneal dialysis (PD) are still a cause of morbidity and mortality. We describe an overview of PD peritonitis and catheter-related infections (CRI) in Malta over a period of eleven years. We also describe trends in dialysis modality over the years. Method All patients undergoing PD in Malta during 2008 and 2018 were analysed. Data from 2008-2012 was retrospective, shown as mean, that from 2013-2018 prospective. International Society for Peritoneal Dialysis (ISPD) definitions were used. Results for categorical responses were summarized using absolute numbers and percentages. Medians (range) were used to describe continuous non-normally distributed data. Results The total number of patients undergoing PD from 2008 till 2018 were 137 (2008-2012), 91, 80, 126, 117, 102, 103 respectively. There was an overall male predominance of 63.5% (61-67). Patient years at risk were 85.80, 85.25, 89.71, 83.70, 79.69, 72.88 since 2013 respectively. The overall incidence of diabetes mellitus was 45.3% (41.8-50), cardiovascular disease 34.2% (33.8-35), hypertension 79.3% (73.8-84.6). PD was used in 50% of dialysis modality prior to 2012, 39% in 2018. Initially 51% used Automated PD (APD), with 21% assisted PD, in 2018 39% used APD, with 6% assisted PD. PD peritonitis rates from 2008 were 0.38, 0.31, 0.35, 0.46, 0.43, 0.57, 0.54, 0.43, 0.39, 0.40, 0.46 episodes/patient year respectively There was marked dominance of Gram-positive peritonitis, mainly Staphylococcal, with a reduction of coagulase-negative-Staphylococcus from 0.26 episodes/patient in 2013 to 0.03 in 2017, 0.11 in 2018. Methicillin-resistant S. aureus (MRSA) peritonitis decreased from 0.03 episodes/patient to nil in 2016, 2017, 0.01 episodes/patient in 2018. Amongst Gram-negative peritonitis, Pseudomonas rates decreased from 0.06 to 0.03 episodes/patient in 2018, nil in 2016. Escherichia coli rates decreased from 0.02 episodes/patient to nil in the last three years. Fungal rates from 0.03 to 0.01 episodes/patient/year, with nil in 2016, 2017. Catheter-related infection rates were 0.39 (2008-2012), 0.35, 0.91, 0.37, 0.38, 0.25, 0.50 episodes/patient/year respectively. There was a higher incidence of recurrent infections in 2014, none in 2015 and 2016. Gram-negative organisms accounted for 57% of all CRI, predominantly Pseudomonas at 0.12 (2008-2012), 0.06, 0.09, 0.09, 0.14, 0.03, 017 episodes/patient/year respectively. Gram-positive CRI were mostly Staphylococcus aureus, peaking in 2014 at 0.38 episodes/patient/year. MRSA rates declined from 0.15 to 0.01 episodes/patient/year in 2018. Conclusion PD peritonitis rates in Malta between 2008 and 2018 were below the ISPD recommended threshold. There were no episodes of MRSA in 2016, 2017, no Pseudomonas in 2016, no E coli in the last three years and no fungal PD peritonitis in 2016, 2017. CRI rates also declined, with an overall predominance of Gram-negative infections.

Diversity profiling of xenic cultures of Dientamoeba fragilis following systematic antibiotic treatment and prospects for genome sequencing

Parasitology ◽  
2019 ◽  
Vol 147 (1) ◽  
pp. 29-38
Author(s):  
Rory Gough ◽  
Joel Barratt ◽  
Damien Stark ◽  
John Ellis
Keyword(s):  
Antibiotic Treatment ◽  
Genome Sequencing ◽  
Ribosomal Dna ◽  
Bacterial Species ◽  
Nutritional Requirement ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
Dientamoeba Fragilis ◽  
The Impact

AbstractThe presence of bacterial DNA in Dientamoeba fragilis DNA extracts from culture poses a substantial challenge to sequencing the D. fragilis genome. However, elimination of bacteria from D. fragilis cultures has proven difficult in the past, presumably due to its dependence on some unknown prokaryote/s. This study explored options for removal of bacteria from D. fragilis cultures and for the generation of genome sequence data from D. fragilis. DNA was extracted from human faecal samples and xenic D. fragilis cultures. Extracts were subjected to 16S ribosomal DNA bacterial diversity profiling. Xenic D. fragilis cultures were then subject to antibiotic treatment regimens that systematically removed bacterial species depending on their membrane structure (Gram-positive or Gram-negative) and aerobic requirements. The impact of these treatments on cultures was assessed by 16S amplicon sequencing. Prior to antibiotic treatment, the cultures were dominated by Gram-negative bacteria. Addition of meropenem to cultures eliminated anaerobic Gram-negative bacteria, but it also led to protozoan death after 5 days incubation. The seeding of meropenem resistant Klebsiella pneumoniae strain KPC-2 into cultures before treatment by meropenem prevented death of D. fragilis cells beyond this 5 day period, suggesting that one or more species of Gram-negative bacteria may be an essential nutritional requirement for D. fragilis. Gram-positive cells were completely eliminated using vancomycin without affecting trophozoite growth. Finally, this study shows that genome sequencing of D. fragilis is feasible following bacterial elimination from cultures as the result of the major advances occurring in bioinformatics. We provide evidence on this fact by successfully sequencing the D. fragilis 28S large ribosomal DNA subunit gene using culture-derived DNA.

scholarly journals INCREASED RESISTANCE TO INFECTION AND ACCOMPANYING ALTERATION IN PROPERDIN LEVELS FOLLOWING ADMINISTRATION OF BACTERIAL LIPOPOLYSACCHARIDES

1956 ◽  
Vol 104 (3) ◽  
pp. 383-409 ◽  
Author(s):  
Maurice Landy ◽  
Louis Pillemer
Keyword(s):  
Defense Mechanisms ◽  
Bacterial Species ◽  
Complex Nature ◽  
Gram Negative ◽  
Resistance To Infection ◽  
Bacterial Lipopolysaccharides ◽  
Gram Negative Organisms ◽  
Incomplete Picture ◽  
Time Of Administration

It has been shown that injection of lipopolysaccharides, derived from a variety of Gram-negative bacterial species, evokes in mice a rapidly developing rise in resistance to infection with Gram-negative pathogens. This is accompanied by an elevation in properdin titer, at times to levels 2 to 3 times the normal. The rate, magnitude, and duration of these responses are dependent on many factors, the most important of which are the quantity and timing of the lipopolysaccharide administered. The increased resistance to infection evoked in mice by lipopolysaccharides was effective against infections produced by endotoxin-bearing organisms-bacterial species highly susceptible in vitro to the bactericidal action of the properdin system. Properdin titers of mice prior to infection provide an incomplete picture of the subsequent reaction of the host to the infective agent. Following infection with Gram-negative organisms, properdin levels accurately reflect the bacteriologic course and outcome of the infection. Thus, in control animals, properdin titers progressively declined and the animals died, while in mice appropriately treated with lipopolysaccharide, properdin levels were either maintained in the normal range or increased, depending on the dose and time of administration of lipopolysaccharide; this was always accompanied by successful management of the infection. The complex nature of the alterations produced in the host by lipopolysaccharides is stressed. It is pointed out that the increase in the ability of the host to cope with Gram-negative infections may be the result of stimulation of other defense mechanisms, in addition to the properdin system.

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