Enterobacteriaceae Research Articles

Bacterial contamination of autologous blood salvaged during deceased donor liver transplantation: a prospective observational study.

Decompensated cirrhotic patients experience severely increased intestinal permeability and bacterial translocation. Thus, autologous blood salvaged during deceased donor liver transplantation (DDLT) may be contaminated with enteric bacteria. We aimed to evaluate bacterial contamination of autologous blood salvaged during DDLT and its association with post-transplant bacteremia. In 30 patients undergoing DDLT, bacterial culture was performed in salvaged autologous blood samples: one before graft reperfusion (non-leukoreduced) and two after graft reperfusion (non-leukoreduced and leukoreduced). The primary outcome was bacterial contamination of salvaged autologous blood. Seven of 30 patients (23.3%) were positive for bacteria (3 enteric/4 non-enteric) before graft reperfusion while 11 patients (36.7%) were positive (5 enteric/6 non-enteric) after graft reperfusion. Six of 7 patients who were positive for bacteria before graft reperfusion were positive after graft reperfusion with the same bacteria. Only 4 of 11 contaminated blood samples were converted to negative after leukoreduction. Post-transplant bacteremia risk was insignificantly greater in patients who received autologous blood with bacteria than in patients without bacteria (30.0% vs. 5.0%, P = 0.06). We found contamination of salvaged autologous blood with enteric bacteria throughout DDLT and incomplete performance of leukoreduction, indicating high bacterial load. The potential association between contaminated autotransfusion and post-transplant bacteremia warrants further validation in a larger prospective study.Clinical trial notation: This study was registered at the Clinical Research Information Service (CRiS; https://cris.nih.go.kr ; No. KCT0007223; principal registration investigator: Sangbin Han, date of registration: April 25, 2022).

Investigating the role of PmrB mutation on Colistin antibiotics drug resistance in Klebsiella Pneumoniae

Klebsiella pneumoniae, a member of the Enterobacteriaceae family, naturally resides in the digestive tracts of both healthy animals and humans. Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant health risk for hospitalized patients worldwide, greatly reducing the effectiveness of commonly used antibiotics. This leaves healthcare providers with limited treatment options, often relying on colistin. PmrB is important for the survival of Klebsiella pneumonia and, a mutation in the PmrB protein is accountable for the development of colistin antibiotic resistance in Klebsiella pneumonia. This is especially important because colistin is a fundamental component in the treatment of pneumonia. Three mutated residues—T157P, G207D, and T246A—are responsible for colistin resistance. The structural alterations and underlying mechanisms in the PmrB protein that cause resistance owing to mutation remain unclear. As a result, this study is focused to the exploration of the putative mechanism of resistance resulting from these mutations, as well as the structure modification of normal and mutant PmrB proteins, using molecular docking and molecular dynamics simulations analysis. Our results demonstrated that the interaction paradigm for the mutants has been altered and thus showing a significant effect upon the hydrogen bonding network. Interestingly, the binding of Colistin with the three mutant demonstrate unstable behavior as compared with WT+Colistin. The proposed drug-resistance mechanism will help to guide the development of PmrB drugs. These finding may give a new framework for developing novel drugs against the mutant version of PmrB.

Characteristics of the Gut Microbiota Composition of the Arctic Zone Residents in the Far Eastern Region

Background. In many studies over the past decade, scientists have made a connection between the composition of gut microbiota and human health. A number of publications have shown that gut bacteria are involved in many metabolic and physiological processes of the organism. The composition of the gut microbiome is unique for each person and is formed under the influence of various factors associated with both the individual characteristics of the body and the characteristics of the environment. Different regional characteristics make it necessary for the body to adapt to certain conditions, including temperature fluctuations. Living in areas with low temperatures, such as the Arctic zone, dictates the need for increased energy consumption, which affects the composition of the gut microbiome. Methods. In our study, an extensive questionnaire was conducted among the participants, where many questions were included about the dietary preferences of the study participants, which allowed them us to further divide them into groups according to their diets. Stool samples were collected from participants from 3 groups: Arctic native, Arctic newcomer and the control group. The next step was the isolation of bacterial DNA and sequencing the 16S rRNA gene. The analysis of the results of the diversity of the intestinal microbiota was carried out both with and without taking into account the dietary preferences of the participants. Results. As a result of comparing the intestinal microbiota obtained from residents of the Arctic zone with the gut microbiota of residents of other regions with a milder climate, significant differences are found. These differences may be related to limited food resources and a reduction in the variety of food products characteristic of this Arctic region. t was also found that representatives of the bacterial families Christensenellaceae and Muribaculaceae dominated the control group, both with traditional nutrition and with a dairy-free diet in comparison with the Arctic groups. The control group was dominated by representatives of the Prevotellaceae, Enterobacteriaceae and Comamonadaceae families compared to the Arctic group (with a traditional diet). The results also show that the number of representatives of the families Desulfovibrionaceae (with traditional diet) and Enterobacteriaceae (with milk-free diet) is growing in the Arctic group. Conclusions. In the course of this work, bacterial families characteristic of people living in the Arc-tic zone of the Far Eastern region of the Russian Federation were identified. Poor diet, difficult climatic conditions, and problems with logistics and medical care can have a strong impact on the health of this population. The main type of diet for the inhabitants of the Arctic is the traditional type of diet. They consume a large number of low-cost products, obtainget animal protein from poultry and canned food, and also eat a small number of fresh vegetables and fruits. Such a diet is due to the social status of the study participants and the climatic and geographical features of the region (difficulties in agriculture). With such a diet, we observe a decrease in representatives of the Christensenellaceae, Muribaculaceae, Eubacteriaceae, and Prevotellaceae families and an increase in representatives of the Enterobacteriaceae and Desulfovibrionaceae families among Arctic residents. This imbalance in the futuremay cause, this population may to develop various diseases in the future, including chronic diseases such as obesity, intestinal dysbiosis, inflammatory bowel diseases, and type 2 diabetes.

Assessment of Nitrate Reduction by Microbes in Artificial Groundwater Medium

There are significant reasons for nitrate contamination in groundwater (Delhi, India): sewage, runoff from landfill sites, nitrogenous chemical fertilisers, and pesticides from agricultural lands. The highest recorded concentration of nitrate in Delhi’s groundwater is reported to be 1500 mg/l. Consumption of high nitrate through water may pose serious health problems in humans, especially children (below five years). The study’s primary objective was to isolate and identify nitrate-remediating microbes from the nitrate-contaminated site Okhla Barrage, located on the Yamuna River in Delhi, India. A total of 11 different strains were isolated from this site. Among these four strains exhibited 40%–50% remediation efficiency at a nitrate concentration of 1000 mg/l. Molecular characterisation revealed that these four strains, Enterobacter aerogenes, E. coli K12, <i>Klebsiella oxytoca</i> and <i>Lelliottia amnigena</i>, belong to the Enterobacteriaceae family. This study assessed the nitrate remediation potential of isolated microbes in groundwater with 1000 and 1500 mg/l nitrate concentrations. By using a 2% inoculum, the microbes were incubated anaerobically at room temperature for ten days. Nitrate concentrations were monitored every 48 hours. <i>Lelliottia</i>, <i>E. coli</i>, and <i>Enterobacter</i> reduced nitrate (1500 mg/l) by approximately 42%, 24%, and 29%, respectively, while <i>K. oxytoca</i> showed minimal reduction. <i>L. amnigena</i> exhibited superior nitrate removal efficiency compared to other strains. According to the reported data, these strains are known to reduce nitrate concentrations of 620 mg/l. However, our findings demonstrate a remarkable nitrate remediation capacity of 1500 mg/l, showcasing a novel contribution to this study. Further detailed analysis for condition optimisation and association of microbe-microbe could be more helpful.

Cedecea lapagei as an emerging extensively drug-resistant microorganism: A case report in a patient with pleural empyema and literature review

Cedecea lapagei is a Gram-negative bacterium that belongs to the Enterobacteriaceae family and is said to be pathogenic for humans. Herein, we report a case of extensively drug-resistant C. lapagei in a patient with pleural empyema and offer a literature review of the already documented case reports on individuals infected with C. lapagei. A 60-year-old female patient was brought to the emergency department at AIIMS Bathinda with a history of breathing difficulty since one day after she sustained multiple injuries from a road accident. She was diagnosed with pleural empyema. Subsequently, an intercostal drain tube was inserted into the patient, and the drain content was sent for culture, which revealed growth of C. lapagei. Our literature retrieval work gathered a total of 13 relevant cases. In conclusion, early identification of C. lapagei and administering suitable treatment is important for good patient outcome.

Identification of pathogenic bacteria from eggshell of leatherback sea turtle (Dermochelys coriacea) in Lampuuk Beach, Aceh Besar using 16S rRNA gene

Currently, the leatherback turtle population in Indonesia tends to decline. One of the factors that cause turtles' existence is the turtle eggs that fail to hatch because bacteria contaminate them, 80% of the reasons turtle eggs fail to hatch are due to infection by microorganisms found on the eggshell. Turtle eggs have a soft structure and there are pores that function for gas exchange and water absorption. Microorganisms in sand can infect turtle eggs through the pores and cause hatching failure. This study aims to isolate and identify pathogenic bacteria found in leatherback turtle eggshell (Dermochelys coriacea) from Lampuuk Beach, Aceh Besar, based on the 16S rRNA gene analysis. Eight eggshell samples from leatherback turtle eggs that failed and hatched were cultured on Nutrient Agar (NA) medium. Then, the samples were inoculated on a blood agar medium for haemolysis test. Molecular identification of the 16S rRNA gene was also carried out to determine bacterial species. A total of five bacterial colonies from leatherback turtle eggshells were successfully isolated consisting of two Gram-negative bacteria (Penyu Belimbing Aceh (PBA) = PBA-1 and PBA-2 and three Gram-positive bacteria (PBA-3, PBA-4, and PBA-5). Based on the haemolysis test, the five bacterial isolates were unable to haemolyze blood. Bacterial DNA of PBA-1 and PBA-2 were successfully isolated and amplified using polymerase chain reaction (PCR) with a DNA target of ~1500 bp. Analysis using BLASTN and phylogenetic tree construction showed that PBA-1 isolate had 98.64% similarity with Acinetobacter baumannii, while PBA-2 isolate had 97.82% similarity with Enterobacter kobei. Both bacteria are members of the Enterobacteriaceae family. It can be concluded that, there were two pathogenic bacteria can potentially be opportunistic pathogens found in leatherback turtle eggshells that failed or succeeded in hatching, namely A. baumannii and E. Kobei

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality.

The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the model organism Escherichia coli, as well as major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, with the Keio E. coli single-gene deletion library often regarded as a gold standard. However, it remains unclear how gene essentiality varies between related strains and species. To investigate this, we have assembled a collection of 13 sequenced high-density transposon mutant libraries from five genera within the Enterobacteriaceae. We first assess several gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations, we develop a new classifier for gene essentiality. Using this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes. Despite the presence of a large cohort of variably essential genes, we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the σE extracytoplasmic stress response, which appears to have independently acquired essentiality multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts that have emerged from within the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival and identifies several instances of essential stress responses masked by redundancy in free-living bacteria.IMPORTANCEThe essential genome, that is the set of genes absolutely required to sustain life, is a core concept in genetics. Essential genes in bacteria serve as drug targets, put constraints on the engineering of biological chassis for technological or industrial purposes, and are key to constructing synthetic life. Despite decades of study, relatively little is known about how gene essentiality varies across related bacteria. In this study, we have collected gene essentiality data for 13 bacteria related to the model organism Escherichia coli, including several human pathogens, and investigated the conservation of essentiality. We find that approximately a third of the genes essential in any particular strain are non-essential in another related strain. Surprisingly, we do not find evidence for essential genes unique to specific genera; rather it appears a substantial fraction of the essential genome rapidly gains or loses essentiality during evolution. This suggests that essentiality is not an immutable characteristic but depends crucially on the genomic context. We illustrate this through a comparison of our essential genes in free-living bacteria to genes conserved in 34 insect endosymbionts with naturally reduced genomes, finding several cases where genes generally regarded as being important for specific stress responses appear to have become essential in endosymbionts due to a loss of functional redundancy in the genome.

Differential gut microbiota composition in β-Thalassemia patients and its correlation with iron overload

Recent research highlights the significant impact of the gut microbiota on health and disease. Thalassemia, a hereditary blood disorder, requires regular blood transfusions, leading to an accumulation of iron in the body. Such changes could potentially alter the intestinal microbiota, thereby increasing the susceptibility of thalassemic patients to infection. In this study, we analyzed the fecal microbiota of 70 non-transfusion-dependent (NTDT) β-thalassemia/HbE patients and 30 healthy controls. Our findings indicate that iron chelation intervention had no detectable effect on the microbiome profile of thalassemic patients. However, the cross-sectional analysis revealed that the bacterial diversity and community structure in patients were significantly less diverse and distinct compared to those of healthy subjects. Using reference frames, we were also able to demonstrate that bacterial taxa that are known to produce short chain fatty acids, from the genera Alistipes, Coprococcus, and Oscillospira, and those from the family Ruminococcaceae, were less prevalent in the patients. In contrast, bacterial taxa associated with an unhealthy gut, including the genus Clostridium and those from the families Fusobacteriaceae, Enterobacteriaceae, and Peptostrptococcaceae, were more prevalent in patients and found to be correlated with higher levels of ferritin. Collectively, these changes in the microbiota could be regarded as markers of raised ferritin levels, and therefore, awareness should be exercised as they could interfere, albeit indirectly, with the treatment of the co-morbidities of thalassemia.

Safety and security of household water purifiers against pathogenic microbial contamination and bio-risk evaluation of their microbial community structures

Household water filters, particularly point-of-use systems, are crucial to ensure safe drinking water consumption by eliminating microbial contaminants. This study evaluated the efficacy of three types of water purifiers (ultrafiltration [UF], nanofiltration [NF], and reverse osmosis [RO]) against microbial contamination. In our experiments, Escherichia coli and bacteriophage MS2 were used as two microbial indicators in daily household settings to track the spatial and temporal profiles of their behavior from the filter inlets to in-UF, NF, and RO water purifiers, and then to effluents. The results showed that both NF and RO water purifiers removed 100 % of the indicator organisms. The UF water purifier achieved 100 % removal of E. coli, but the removal of MS2 phage was poor. The presence of coexisting ions and natural organic matter in tap water can significantly affect the behavior of MS2 phages during the water treatment process. Their presence reduces the charge repulsion effect of the UF membrane on the MS2 phage as well as promotes the migration of the MS2 phage on the post-activated carbon cartridge that was placed in the last unit of the water purifier system, which could increase the pathogen transmission risks in drinking water supplies. The bacterial community structures of the cartridge materials and cartridge effluents from each unit were analyzed by 16S rRNA gene sequencing, which revealed distinct microbial profiles of the different purifiers. Environmental conditions such as pH, nutrient availability, materials, and operational parameters can affect the composition of bacterial communities. Scanning electron microscopy-energy-dispersive X-ray spectroscopy (SEM-EDS) was used to examine the surface morphology of the membranes after they were exposed to water contaminants, which demonstrated that the inherent differences in the membrane structure influenced the retention of pollutants and microorganisms on the surfaces. In summary, this study demonstrates that both NF and RO water purifiers can significantly reduce the presence of various enteric and opportunistic pathogenic bacteria in drinking water, leading to safer potable water, whereas UF water purifiers may have certain risks owing to their UF membranes and post-activated carbon. In addition, secondary microbial contamination may be introduced by the post-activated carbon units of water purifiers, especially after long-term usage. Therefore, we concluded that addressing the secondary microbial pollution caused by post-activated carbon after prolonged use and long-term shutdown is essential for maintaining the safety and quality of drinking water.

Investigation of Shiga toxin-producing Escherichia coli and evaluation of the microbiological quality of raw vegetable sal-ads

Foodborne diseases (FBD) are a significant public health concern worldwide, affecting millions of people annually. Symptoms of FBD range from mild gastrointestinal discomfort to more severe conditions, which in some cases can lead to death. Raw vegetables, especially those consumed in ready-to-eat (RTE) salads, are particularly susceptible to microbial contamination. This study aimed to investigate the presence of Shiga toxin-producing Escherichia coli (STEC) and to evaluate the microbiological quality of 77 RTE raw vegetable salads from 20 restaurants in Niterói, RJ, Brazil. None samples presented STEC, nor the safety indicators (SI) Salmonella spp. and Listeria monocytogenes. However, 89.6% of the samples were considered unfit for human consumption, since they presented at least one hygiene indicator (HI) outside the established standards. The majority of samples (95.5%) were unsatisfactory for Enterobacteriaceae (EB), followed by total aerobic bacteria (TAB) (76.6%), thermotolerant coliforms (C45) (32.5%) and Escherichia coli (EC) (1.3%). The difference between the occurrences of hygiene indicators was not significant. Given the high percentage of inadequate samples found in the study, it is clear that there is a need for stricter surveillance and adequate hygiene practices in restaurants. To reduce the risks of microbial contamination in RTE raw vegetable salads, several approaches can be implemented. These include continuous training of food handlers, implementation of food safety management systems such as Hazard Analysis and Critical Control Points (HACCP), and regular inspections. In addition, consumers also play an important role by demanding safe food and following safe food handling and consumption practices at home.

Impact of Enteric Nervous Cells on Irritable Bowel Syndrome: Potential Treatment Options.

Irritable bowel syndrome (IBS) is a condition that significantly impacts the lifestyle, health, and habits of numerous individuals worldwide. Its diagnosis and classification are based on the Rome criteria, updated periodically to reflect new research findings in this field. IBS can be classified into different types based on symptoms, each with distinct treatment approaches and some differences in their pathophysiology. The exact pathological background of IBS remains unclear, with many aspects still unknown. Recent research developments suggest that disorders in the brain-gut-microbiota axis are key contributors to the symptoms and severity of IBS. The central nervous system (CNS) interacts bidirectionally with intestinal processes within the lumen and the intestinal wall, with the autonomic nervous system, particularly the vagus nerve, playing an important role. However, the enteric nervous system (ENS) is also crucial in the pathophysiological pathway of IBS. The apeline-corticotropin-releasing factor (CRF)-toll-like receptor 4 (TLR4) signaling route via enteric glia and serotonin production in enteroendocrine cells at the enteric barrier are among the most well-understood new findings that affect IBS through the ENS. Additionally, the microbiota regulates neuronal signals, modifying enteric function by altering the number of enteric bacteria and other mechanisms. Given the limited therapeutic options currently available, it is essential to identify new treatment targets, with the brain-gut axis, particularly the enteric nervous system, being a promising focus. This study aims to delineate the molecular mechanisms that induce IBS and to suggest potential targets for future research and treatment of this potentially debilitating disease.

Bakteri Penyebab Gingivitis dan Sensitivitas Antibiotik Pada Pasien Diabetes Melitus

Gingivitis is an inflammation of the gingiva caused by plaque and poor oral hygiene, including in patients with long-term diabetes mellitus and uncontrolled blood glucose. Gingivitis is caused by various bacteria such as Streptococcus sp, Staphylococcus aureus, Enterococcus faecalis, Streptococcus pneumoniae, Streptococcus pyogenes, Neisseria meningitidis and also the Enterobacteriaceae family, Haemophilus influenzae and Actinomycetes. Management of infection with antibiotics, especially beta-lactam class. The study aimed to determine the characteristics of the research subjects, the type of bacteria, and their sensitivity to the bacteria that cause gingivitis in diabetes mellitus (DM) patients. The research was a cross-sectional descriptive study at the internal medicine polyclinic at Arifin Achmad Hospital, Riau Province, and the Microbiology Laboratory of Medical Faculty, Universitas Riau. The research sample was a gingivitis plaque swab in DM patients who signed an informed consent. Samples were cultured, identified, and tested for antibiotic sensitivity. The results of the study obtained 34 samples with characteristics aged 33-67 years, most of them were women, high school education/equivalent, civil servants/army/police/retired. Most aerobic bacteria Klebsiella sp. The highest sensitivity to levofloxacin, amikacin, ciprofloxacin, trimethoprim-sulfamethoxazole, and meropenem, the lowest sensitivity to amoxicillin, ceftazidim, and amoxicillin-clavulanic acid.

A Study on Extended Spectrum β-Lactamase Producing (ESBL) and Fluoroquinolone-Resistant Escherichia coli in the Japanese Quails

Antimicrobial resistance (AMR) is a growing public health threat worldwide, and members of the Enterobacteriaceae family are among the clinically important bacteria rapidly developing resistance to available antibacterial agents. The development of extended-spectrum β-lactamase (ESBL) enzymes is the primary cause of resistance to third-generation cephalosporins among Enterobacteriaceae. Quails also represent a source of animal protein deficiency in developing countries including India. This study aimed to detect the presence of extended-spectrum β-lactamases (ESBLs) and fluoroquinolone-resistant Escherichia coli from fecal samples of quails in Puducherry. A total of 36 fecal samples of quails from six different retail outlets were collected. E. coli could be isolated from 27 fecal samples and confirmed as E. coli by polymerase chain reaction by targeting the uspA gene. The isolates were preliminarily screened for ESBL production by indicator antimicrobial disc and phenotypic ESBL production was confirmed by combination disc method. The isolates were subjected to genotypic detection of ESBL (bla CTX-M, bla TEM, and bla SHV) by PCR. Out of 27 isolates, 16 isolates were positive for the presence of ESBL-producing genes, in which, 9 harbored bla CTX-M, 2 harbored bla TEM, and 5 harboured bla SHV genes. Similarly, out of 27 isolates 13 isolates were found positive for fluoroquinolone resistance in which 13 (48.18%) isolates harbored the qnrS gene, and 11 (40.74%) isolates harbored the qnrB gene. Antimicrobial susceptibility test showed that the isolates exhibited a high level of resistance against Cefpodoxime (90%), Amoxycillin/clavulanic acid (70%), Ceftriaxone (60%), Cefotaxime (55%), Ceftazidime (45%), Ciprofloxacin (40%) and Aztreonam (30%).

The Enteric Bacterium Enterococcus faecalis Elongates and Incorporates Exogenous Short and Medium Chain Fatty Acids Into Membrane Lipids.

Enterococcus faecalis incorporates and elongates exogeneous short- and medium-chain fatty acids to chains sufficiently long to enter membrane phospholipid synthesis. The acids are activated by the E. faecalis fatty acid kinase (FakAB) system and converted to acyl-ACP species that can enter the fatty acid synthesis cycle to become elongated. Following elongation the acyl chains are incorporated into phospholipid by the PlsY and PlsC acyltranferases. This process has little effect on de novo fatty acid synthesis in the case of short-chain acids, but a greater effect with medium-chain acids. Incorporation of exogenous short-chain fatty acids in E. faecalis was greatly increased by overexpression of either AcpA, the acyl carrier protein of fatty acid synthesis, or the phosphate acyl transferase PlsX. The PlsX of Lactococcus lactis was markedly superior to the E. faecalis PlsX in incorporation of short-chain but not long-chain acids. These manipulations also allowed unsaturated fatty acids of lengths too short for direct transfer to the phospholipid synthesis pathway to be elongated and support growth of E. faecalis unsaturated fatty acid auxotrophic strains. Short- and medium-chain fatty acids can be abundant in the human gastrointestinal tract and their elongation by E. faecalis would conserve energy and carbon by relieving the requirement for total de novo synthesis of phospholipid acyl chains.

Early changes in the gut microbiome among HIV-infected Individuals in Uganda initiating daily TMP/SMX.

Daily cotrimoxazole (TMP/SXT) prophylaxis is part of the HIV treatment package for all new HIV-infected individuals in Uganda. Although this treatment has shown reduced morbidity and mortality in HIV, it remains controversial due to its contribution to developing antibiotic-resistant bacteria. Moreover, the effects of daily use of a broad-spectrum antibiotic on the gut microbiome remain unknown. To study the early effects, we analysed shotgun metagenome sequence data from stool samples of five newly HIV-infected individuals initiating TMP/SXT prophylaxis longitudinally for the first 30 days of treatment. Using shotgun metagenomics sequencing, we generated both taxonomic and functional profiles from each patient and compared gut microbial changes Pre-TMP/SXT and post-TMP/SXT on Day 5, Day 14, and Day 30. Daily TMP/SXT prophylaxis resulted in a shift characterised by an enrichment of Prevetollea and Ruminococcus genera members and the depletion of Lactococcus and Bacteroides genera members. Furthermore, these microbial shifts were associated with changes in the functional profile revealed by a differential abundance of pathways of amino acid metabolism, carbohydrate metabolism, and nucleotide biosynthesis linked to members of the Bacteroidaceae and Enterobacteriaceae families. TMP/SXT daily prophylaxis in HIV-infected individuals is associated with dramatic changes in microbial composition and functional profiles; however, other factors such as Age, Gender, HIV clinical stage, and ART regiment are at play. Further investigation is needed to examine the implication of these shifts on clinical management and outcomes among HIV patients.

Assessment of bacterial diversity in hand rinse, stored and drinking water in low-income neighbourhoods of Ibule-Soro, Nigeria

ABSTRACT The microbiological quality of hand rinse, stored and drinking water in selected households in Ibule-Soro, Nigeria was assessed for six months. Culture-based, 16S rRNA gene sequencing and molecular methods were used to identify culturable and non-culturable bacterial species in the water samples. The results revealed that bacteria in the phyla Proteobacteria, Firmicutes and Bacteroidetes were predominant in the water samples. The order Sphingomonadales had the highest read count of 5,065 with 30.60%. The highest mean bacterial loads include Klebsiella (3.60 log10 cfu/100 mL) in hand rinse water, E. coli (3.62 log10 cfu/100 mL) in stored water and Enterobacter (2.60 log10 cfu/100 mL) in the drinking water. While E. coli had the highest percentage frequency of occurrence of 19.9% in drinking water, Klebsiella had the highest percentage frequency of occurrence of 29 and 23.6% in hand rinse and stored water, respectively. The findings of this study provided a more comprehensive understanding of the microbiome of household hand rinse, stored and drinking water. The high load of enteric bacteria in the hand rinse water suggests poor hand hygiene practices. Stored and drinking water must be treated before consumption to protect residents from potential risks of gastrointestinal illnesses.

Detection of the CTX-M Gene Associated with Extended-Spectrum β-Lactamase (ESBL) in Broiler Chickens in Surabaya Traditional Markets

A common indicator used to examine the frequency and distribution of antibiotic resistance against other enteric bacteria in humans and animals is the commensal enteric bacterium, Escherichia coli. The transmission of plasmids harboring ESBL enzymes, primarily generated by E. coli, is the cause of this resistance. The purpose of this study was to identify the CTX-M gene in ESBL-producing E. coli from broiler chicken cloacal swabs in traditional Surabaya markets. The samples used were 96 cloacal swabs from broiler chickens in the traditional markets of Dukuh Kupang, Keputran, Pacar Keling, and Pucang. The antibiotic disks used in this study belonged to five different antibiotic classes; they are aztreonam (monobactam), chloramphenicol (phenicol), kanamycin (aminoglycoside), ciprofloxacin (fluoroquinolone), and tetracycline (tetracycline). Presumptive ESBL strains were then molecularly screened for the presence of CTX-M gene. Results revealed that out of the 96 chicken cloacal swab samples collected, 58 (60.42%) were positive for E. coli based on morphological culture, Gram staining, and biochemical tests. Additionally, 15 out of the 58 E. coli isolates recovered from broiler chicken cloacal swabs were multidrug-resistant (MDR) while 7 of E. coli isolates harbored CTX-M gene. Conclusively, this study has shown that broiler chickens sold in traditional Surabaya markets harbor MDR E. coli which possess CTX-M gene. Conditions in traditional markets with low levels of cleanliness and chickens placed close together can spread resistance genes with serious public health consequences. Therefore, it is imperative to observe good hygienic practices in Surabaya traditional markets in order to curtail the spread of MDR bacterial pathogens in the food chain.

A-277 Viability of multi-drug resistant organisms in a fecal collection and transport system stored at ultra-low temperature

Abstract Background Epidemiological studies are constantly investigating new, easier ways to collect and store patient specimens that allow for flexible testing windows and long-term storage as well as accurate quantification of organisms of interest. The FecalSwabTM system (Copan, Brescia, Italy) is intended for the collection and preservation of rectal and fecal specimens. This system includes a preservation medium which serves to maintain the viability of enteric pathogens during transport to a clinical laboratory for up to 72 hours at 4oC. The objective of this study was to assess the continued viability of multi-drug resistant organisms (MDROs) suspended in the FecalSwab sample format when frozen at -80°C and the impact of freeze-thaw cycles. Methods A total of 40 organisms were chosen spanning methicillin-resistant Staphylococcus aureus (MRSA, n=10), carbapenem-resistant Pseudomonas aeruginosa (CRPA, n=5), carbapenem-resistant Enterobacterales (CRE, n=5), vancomycin-resistant Enterobacterales (VRE, n=10) and extended-spectrum beta-lactamase containing Enterobacterales (ESBL, n=10). Each organism was spiked into FecalSwab at standardized concentrations. At each time point, FecalSwab media was plated onto blood agar and colonies were quantified. Each of the 40 organisms were assessed one-week post-freeze and over the course of freeze-thaw cycles at days 3 and 5. The survival of each MDRO was evaluated by calculating a difference between the concentration of organisms recovered (CFU per 10uL media) at each time point and the concentration of organisms confirmed present at the time of inoculation. Percent recovery was calculated from this difference. Results One week after freezing, the percent recovery for MRSA, VRE, ESBL, CRE, and CRPA averaged to 102%, 201%, 17.8%, 7.6%, and 0.8%, respectively (Kruskal Wallis p < 0.001), with significant differences noted between gram positive and gram negative organisms (Kruskal Wallis p <0.001). Conclusions Epidemiological studies interested in MDRO surveillance rely on methodologies that allow for accurate quantification of viable organisms. In this study, we’ve evaluated the viability of several multi-drug resistant organisms when frozen at -80°C in the FecalSwab. The FecalSwab system is intended for the collection of rectal swab and fecal specimens and to preserve the viability of enteric pathogenic bacteria for testing in the clinical laboratory. Although it was not specifically designed to preserve MDROs, it performed well with MRSA and VRE, but less well with CRE, CRPA and ESBL organisms. When using the FecalSwab system, the observed gram-specific differences may inform the suitability of this system depending on the organism(s) of interest.

Assessing the causal relationship between gut microbiota and prostate cancer: A two-sample Mendelian randomization study

BackgroundNumerous studies indicate that the gut microbiome is closely associated with prostate cancer (PCa), however, owing to various confounding factors, the causal relationship between gut microbiota and PCa remains unclear. MethodsA 2-sample Mendelian randomization (MR) analysis utilized genome-wide association study (GWAS) data on the gut microbiota of 18,340 participants and GWAS summary statistics on PCa involving 46,3010 participants. Inverse variance weighted (IVW) served as the primary method, complemented by the MR-Egger method, weighted median method (WME), simple mode method (SM), and weighted mode method (WM). Finally, to confirm the robustness of the results, heterogeneity test, pleiotropy test, and leave-one-out sensitivity test were conducted. ResultsIVW analysis revealed that 12 specific gut microbial taxa were potentially causally associated with PCa; the genera Victivallis, Akkermansia, Odoribacter, Butyrivibrio, and the families Enterobacteriaceae, Verrucomicrobiaceae, as well as the orders Verrucomicrobiales, Enterobacteriales and the class Verrucomicrobiae, were found to be positively associated with PCa risk. Conversely, the genera Eubacterium ruminantium group, Candidatus Soleaferrea, and RuminococcaceaeUCG003 were negatively associated with PCa risk. ConclusionsOur MR study's results support a genetically predicted causal relationship between the gut microbiota and PCa, and we identified 12 specific gut microbial taxa. These findings could offer new targets for PCa screening and treatment.

Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut.

Resource competition is a driver of gut microbiota composition. Bacteria can outcompete metabolically similar rivals through the limitation of shared growth-fuelling nutrients. The mechanisms underlying this remain unclear for bacteria with identical sets of metabolic genes. Here we analysed the lactose utilization operon in the murine commensal Escherichia coli 8178. Using in vitro and in vivo approaches, we showed that translation of the lactose utilization repressor gene lacI from its native non-canonical GTG start codon increases the basal expression of the lactose utilization cluster, enhancing adaptation to lactose consumption. Consequently, a strain carrying the wild type lacI GTG start codon outperformed the lacI ATG start codon mutant in the mouse intestine. This advantage was attenuated upon limiting host lactose intake through diet shift or altering the mutant frequency, emphasizing the context-dependent effect of a single nucleotide change on the bacterial fitness of a common member of the gut microbiota. Coupled with a genomic analysis highlighting the selection of non-ATG start codons in sugar utilization regulator genes across the Enterobacteriaceae family, our data exposed an unsuspected function of non-canonical start codons in metabolic competition.