Iranian Journal of Microbiology

Antibiotic susceptibility profile of Pseudomonas species isolated from clinical specimens to access, watch and reserve drugs across various hospital settings at a tertiary care hospital of central India

2024-05-08T08:59:58+0430

Background and Objectives: Over the last decade, hospital-acquired infections, particularly in the critical care setting, have become more common, with Gram-negative bacterial infections having the highest prevalence. This study aims to determine the prevalence and antibiotic susceptibility pattern of Pseudomonas species to WHO’s, aware class of antibiotics, which are commonly prescribed across various ICU’s, medical and surgical wards of our tertiary care teaching hospital.
Materials and Methods: This prospective study conducted from January 2021 to June 2022 at a tertiary care centre of central India identified Pseudomonas species from clinical samples using standard procedures and antimicrobial susceptibility testing performed as per Clinical Laboratory Standards Institute (CLSI) guidelines (M100; 32^th Edition).
Results: A total of 1490 non duplicate Pseudomonas species isolates were grown from 21,019 culture positive clinical samples, of which 1247 were Pseudomonas aeruginosa. Out of these 1247 Pseudomonas aeruginosa 384 were MDR (30.7%). Pseudomonas aeruginosa were most commonly isolated from the pus samples (85%). ICU isolates were significantly more resistant to antibiotics than those from other units. P. aeruginosa strains from ICUs showed the highest rates of resistance to ceftazidime (93.9%). Reserve drug colistin showed good susceptibility (98.2%). All the 18 colistin resistant strains were found to be negative for plasmid mediated mcr-1,2,3 genes.
Conclusion: The study shall help to generate and disseminate the data so that proper antibiotic policy can be made for judicious use of Access, Watch and Reserve antibiotics and antibiotic de-escalation plan can be put forth.

Antibacterial and antibiofilm activities of diclofenac against levofloxacin-resistant Stenotrophomonas maltophilia isolates; emphasizing repurposing of diclofenac

2024-05-08T08:59:57+0430

Background and Objectives: Stenotrophomonas maltophilia is an opportunistic pathogen causing nosocomial infections. Diclofenac is an anti-inflammatory drug that is considered a non-antibiotic drug. This study assessed the antibacterial and antibiofilm effects of diclofenac and levofloxacin/diclofenac combination against levofloxacin resistant isolates.
Materials and Methods: Minimum inhibitory concentration was determined using broth microdilution method for levofloxacin, diclofenac, and levofloxacin/diclofenac combination. Biofilm forming capacity and biofilm inhibition assay were determined. Relative gene expression was measured for efflux pump genes; smeB, and smeF genes and biofilm related genes rmlA, spgM, and rpfF without and with diclofenac and the combination.
Results: Diclofenac demonstrated MIC of 1 mg/ml. The combination-with ½ MIC diclofenac- showed synergism where levofloxacin MIC undergone 16-32 fold decrease. All the isolates that overexpressed smeB and smeF showed a significant decrease in gene expression in presence of diclofenac or the combination. The mean percentage inhibition of biofilm formation with diclofenac and the combination was 40.59% and 46.49%, respectively. This agreed with biofilm related genes expression investigations.
Conclusion: Diclofenac showed an antibacterial effect against Stenotrophomonas maltophilia. The combination showed in-vitro synergism, significant reduction in biofilm formation and in the relative level of gene expression. Furthermore, it can potentiate the levofloxacin activity or revert its resistance.

Sequence-subtype association of multi-drug-resistant diarrheagenic Escherichia coli

2024-05-08T08:59:57+0430

Background and Objectives: Multi-drug-resistant pathogens pose a significant threat as they can rapidly spread, leading to severe healthcare-associated invasive infections. In developing countries, diarrheagenic Escherichia coli (DEC) is a major bacterial pathogen responsible for causing diarrhea. However, the outbreak of resistant strains has made the treatment of DEC infections much more challenging. This study aimed to investigate the relationship between antibiotic resistance genes and other virulence categories in E. coli strains that cause diarrhea, particularly DEC.
Materials and Methods: The phylogenetic grouping was defined using PCR and multi-locus sequence type (MLST) methods.
Results: Among the isolates analyzed, 14 were identified as resistant and were classified into eight distinct sequence types: ST3, ST53, ST77, ST483, ST512, ST636, ST833, and ST774, indicating genetic diversity among the resistant strains. Certain sequence types, notably ST512 and ST636, were found to be associated with multiple antibiotic resistance in DEC. Regarding antibiotic susceptibility, strains showed the highest resistance to amoxicillin, suggesting that this antibiotic may not be effective in treating DEC infections. On the other hand, the isolates demonstrated susceptibility to amikacin and chloramphenicol, implying that these antibiotics could be more suitable treatment options for DEC infections.
Conclusion: The findings underscore the importance of promptly identifying antibiotic resistance patterns and their correlation with specific pathogenic virulence categories, as this knowledge can aid in selecting the most appropriate antibiotics for treating DEC infections. Considering the antibiotic resistance profiles and associated resistance genes is crucial in managing and containing diarrheal outbreaks and in selecting effective antibiotic therapies for DEC infections.

Phenotypic and genotypic evaluation of aminoglycoside resistance in Escherichia coli isolated from patients with blood stream infections in Tehran, Iran

2024-05-08T08:59:56+0430

Background and Objectives: Escherichia coli is a significant causative agent of bloodstream infections (BSIs). Aminoglycoside antibiotics play a crucial role in treating severe infections such as sepsis and pneumonia. However, resistance to these antibiotics often occurs due to the production of aminoglycoside-modifying enzymes (AMEs). This study was conducted to assess antimicrobial susceptibility patterns against various aminoglycosides and to determine the prevalence of common AME genes in E. coli strains isolated from BSIs.
Materials and Methods: Sixty-five E. coli isolates were obtained from blood samples in a referral hospital in Tehran, Iran. The susceptibility patterns of aminoglycosides were determined using disk diffusion method and AMEs genes were investigated using PCR assay.
Results: Resistance to aminoglycosides was observed in 64.6% (42/65) of the isolates. The most frequent resistance rate was found for kanamycin (44.6%) and gentamicin (38.5%), followed by tobramycin (29.2%) and amikacin (4.6%). The most frequent AME gene was aac(3)-IVa, which detected in 49.2% isolates, followed by aac(6)-Ib (40%), aac(3)-IIa (32.3%), and ant(2)-Ia (30.8%), respectively.
Conclusion: Athough the findings of this survey are based on specimens collected from a single hospital, our study shows that the high prevalence of aminoglycoside resistance is primarily attributed to the presence of the aac(3)-Iva, aac(6)-Ib and aac(3)-IIa genes. The low rate of resistance to amikacin makes this antibiotic a good candidate for treatment of BSIs due to E. coli.

Plasmid-mediated quinolone resistance in Escherichia coli isolates from commercial broiler chickens in Semnan, Iran

2024-05-08T08:59:55+0430

Background and Objectives: Antibiotic resistance within the poultry sector presents a considerable health concern due to treatment inefficacy and resistance transmission to humans and the environment. The investigation of plasmid-mediated quinolone resistance (PMQR) in Escherichia coli, acknowledged for its role in advancing resistance, remains inadequately studied in Iranian poultry. This study aimed to evaluate PMQR gene prevalence as well as to determine correlation between resistance phenotype and genotype in E. coli obtained from poultry colibacillosis.
Materials and Methods: A collection of 100 E. coli isolates from the viscera of broilers suspected to colibacillosis was assessed. Using the Kirby-Bauer disk diffusion method, antimicrobial susceptibility tests were conducted for ofloxacin, nalidixic acid, levofloxacin, ciprofloxacin, and ampicillin. Additionally, PCR was employed to screen for qnrS, qnrB, and aac(6)Ib-cr genes.
Results: Among the analyzed E. coli isolates, 51% demonstrated resistance to at least one of the tested antibiotics, with 17% exhibiting resistance to four different antibiotics. Nalidixic acid displayed the highest resistance rate at 48%, while ampicillin had the lowest at 16%. PMQR genes were detected in 28% of the E. coli isolates, with aac(6′)-Ib-cr being the most prevalent at 14%, followed by qnrB in 13%, and qnrS in 7%.
Conclusion: The study underscores the vital need for careful antibiotic usage in poultry to curb the emergence of antibiotic-resistant bacteria. The results illuminate the prevalence of PMQR genes and their association with resistance trends in Iranian poultry, forming a pivotal basis for forthcoming approaches to combat antibiotic resistance within the poultry sector.

Study of behavioral and psychosocial factors relating to needle stick injuries in nursing staff of a tertiary care cancer hospital of Punjab, India

2024-05-08T08:59:54+0430

Background and Objectives: Needle stick injury (NSI) is the most dreaded occupational health hazard affecting a healthcare worker (HCW) psychologically and physically. The risk of infection post needle stick injury ranges between 1.9% to greater than 40% for HBV infections, 2.7-10% for HCV and 0.2-0.44% for HIV infections. As per National AIDS Control Organisation (NACO) records, nursing staff is at highest risk (43%) followed by physicians (28%). The main objective of this study was to evaluate knowledge of nursing staff about needle stick injuries and to study factors leading to such incidents in their working areas, impart them knowledge regarding the same and fill gaps in knowledge.
Materials and Methods: This is a cross-sectional retrospective analysis involving nursing staff and students. p values were calculated using SPSS software.
Results: Overall NSI prevalence among nursing staff and students was 51.6% whereas in more exposed and less exposed group was 47.45% and 10.16% respectively (p=0.2056). The most common cause of NSI incident was recapping of needle (38.5%) followed by transferring needle to sharp container (35%).
Conclusion: Consequences of NSI are serious and this study has tried to emphasize on the need to study the factors leading to NSI.

Antibacterial activity of Shallots (Allium xwakegi Araki.) cultivars in Palu Valley against Salmonella Typhi ATCC 27870 through in vitro and in silico evaluation

2024-05-08T08:59:54+0430

Background and Objectives: Shallots, recognized for their minimal toxicity, cost-effectiveness, and widespread availability, are increasingly considered a viable source of biological activity. This study evaluates the antibacterial efficacy of a specific shallot cultivar from Palu Valley, Indonesia, against Salmonella typhi, the pathogen responsible for typhoid fever.
Materials and Methods: Utilizing thin-layer chromatography (TLC-bioautography) and gas chromatography-mass spectroscopy (GC-MS), the study identifies active compounds in shallot ethanol extract and employs molecular docking to assess interactions between receptors and ligands.
Results: Findings indicate significant antibacterial activity, with a notable inhibition zone diameter of 31.5 mm at spot Rf 0.28 in TLC bioautography and an optimum concentration of 2% yielding an average clear zone diameter of 28.27 mm in the agar diffusion test. GC-MS analysis reveals 41 compounds, predominantly dodecanoic acid and 1,2,3-propanetriyl ester. Additionally, molecular docking reveals the lowest binding affinity (-7.3 kcal/mol) for Ergost-8-En-3-Ol, 14-Methyl-, (3.Beta,5.Alpha.) against DNA gyrase.
Conclusion: This study confirms Palu Valley shallot extract's potent antibacterial effect against Salmonella typhi, highlighting its therapeutic potential.

Cytotoxic activity and apoptosis induction by supernatant of Lentilactobacillus buchneri on HT-29 colon cancer cells

2024-05-08T08:59:53+0430

Background and Objectives: Colorectal cancer (CRC) is the fourth most commonly diagnosed cancer and the third most deadly cancer in the world. According to recent experimental reports, probiotics and their derivatives protect CRC patients from treatment-related side effects. Therefore, the present study aimed to investigate the cytotoxic impact of the cell-free supernatant (CFS) of Lentilactobacillus buchneri on the HT-29 cancer cell line.
Materials and Methods: In the current study, we used the L. buchneri CFS, which was well isolated and identified in our previous investigation from traditional yogurt in the Arak region of Iran. The apoptosis induction in HT-29 cancer cells was assessed by cell cytotoxicity, flow cytometry, and qRT-PCR.
Results: L. buchneri CFS inhibited the proliferation of HT-29 cancer cells in a time- and dose-dependent manner. The apoptotic effect of CFS was further supported by the flow cytometry data, which showed that the maximum incidence of apoptosis was observed in HT-29 cancer cells treated with the IC₅₀ concentration of CFS after 72 hours. CFS of L. buchneri also exerted the up-regulating effect on the expression of pro-apoptotic genes including BAX, CASP9, and CASP3. L. buchneri CFS at an IC₅₀ dose induced cell cycle arrest in the G0/G1 phase in HT-29 cells.
Conclusion: This study indicates that L. buchneri CFS can prevent colorectal cancer (CRC) development in patients by inducing cancer cell apoptosis. This finding suggests that the CFS of L. buchneri could be used as a therapeutic agent for the control of CRC.

The phenotypic and genotypic antibiotic susceptibility of vaginal Lactobacillus with potential probiotic properties isolated from healthy women in northern Iran

2024-05-08T08:59:52+0430

Background and Objectives: This study assesses the antibiotic susceptibility of vaginal Lactobacillus strains and provides data for determining the prevalence of certain antibiotic resistance genes in the new strains of lactobacilli serving as probiotics and selected from healthy women in northern Iran.
Materials and Methods: One hundred premenopausal non-pregnant women in the reproductive age range of 22-50 years participated in this study. The potential probiotic vaginal lactobacilli used in the study included Lactobacillus crispatus (34.2%), Lactobacillus gasseri (26.3%), Lactobacillus johnsonii (10.5%), Lactobacillus acidophilus (15.7%) and Lactobacillus jensenii (13.1%). The phenotypic antibiotic susceptibility of the strains was determined by E test and DNA extraction and PCR were performed to examine the antibiotic resistance genes.
Results: 38 potential probiotic vaginal lactobacilli were isolated. All the strains of lactobacilli were resistant to metronidazole and trimethoprim/sulfamethoxazole and all of the strains were susceptible to ampicillin and chloramphenicol antibiotics. The results showed that ermB, ermC, and ermA genes were observed in the strains of Lactobacillus acidophilus. Metronidazole resistance (nim) gene was also found in one strain of Lactobacillus crispatus and Lactobacillus johnsonii. The aminoglycoside resistance (aac6'-aph2") gene was observed in 8% of the strains. Also, tetM, tetK and tetW genes were found in more than 80% of the Lactobacillus strains.
Conclusion: The antimicrobial susceptibility of vaginal lactobacilli is an important criterion for establishing whether or not the organism is a probiotic. A high level of resistance to clinical antibiotics, such as metronidazole and aminoglycosides, was demonstrated. Antibiotic resistant genes also appeared widely in vaginal lactobacilli.

Risk analysis of candidemia and its effect on mortality in COVID 19 and non COVID 19 patients

2024-05-08T08:59:51+0430

Background and Objectives: Candidemia is the most common serious fungal infection in critically ill patients in intensive care units (ICU). It series fourth among bloodstream infectious agents. In this study, candidemia risk analysis was examined in COVID 19 and non-COVID 19 patients during the pandemic period.
Materials and Methods: COVID 19 and non-COVID 19 cases who were followed up with candidemia in the ICU of our hospital were retrospectively screened. Demographic data, intubation, central venous catheter (CVC), medications, and total parenteral nutrition (TPN) status were evaluated in terms of risk between the two groups. Isolated Candida species and susceptibilty were evaluated.
Results: When age, gender, medication, intubation, TPN and CVC were evaluated, no difference was seen in terms of risk. Differences were detected in terms of comorbidities. While the most frequently identified Candida species was C. albicans, the most frequently detected species in the COVID19 patient group was C. parapsilosis.
Conclusion: There was no difference in candidemia incidence and risk factors between the two groups. Since candidemias were evaluated in terms of comorbidities, it was determined that Diabetes Mellitus (DM) and chronic obstructive pulmoner disease (COPD) were more common in patients with COVID 19 and less common in coronary artery disease (CAD) and malignancy.

Molecular characterization and evolutionary dynamics of influenza A(H1N1) strains isolated from 2015 to 2017 in North India

2024-05-08T08:59:51+0430

Background and Objectives: The influenza A(H1N1) virus is known for large outbreaks, epidemics and pandemics worldwide owing to its genome plasticity which evolves constantly. In the year 2015 and then in 2017, India witnessed an upsurge in cases.
Materials and Methods: The study was carried out in this period (2015-2017) with samples from 5 states across north India. The hemagglutinin 1 (HA1) and non-structural 1 (NS1) gene segments of the viral genome were characterised by phylogenetic analysis, selection pressure analysis, prediction of potential glycosylation sites and phylodynamic analysis of the study strains.
Results: The study strains belonged to genogroup 6B. A total of 12 mutations were observed, half of which were located on the key receptor binding region of the HA1 protein. Established virulence markers D222G, S183P were observed in 2017 samples. Acquisition of an extra glycosylation site was observed in few strains from 2017 and 2016. Selection pressure analysis found the average dN/dS (v) ratio of 0.2106 and few codon sites in particular showed significant evidence of being under negative selection.
Conclusion: The genogroup 6B continues to be the dominant circulating strain in Indian subcontinent region however the presence of pathogenic mutations in the 2017 strains from north India underlines the importance of continued molecular surveillance.

In vitro anti-HSV1 activity of aqueous extract of Areca catechu L.

2024-05-08T08:59:50+0430

Background and Objectives: HSV-1 is known as a very contagious virus and the main cause of cold sores or fever blisters. Herein, the aqueous extract of Areca catechu L. was evaluated for its anti-HSV-1 activity, compared to the standard control (acyclovir). Also, the effect of extract on the expression of UL46 and US6 genes that accumulate late in viral infection, was studied.
Materials and Methods: The aqueous extract was obtained by the maceration of powdered plant in boiling water. Its antiviral activity was evaluated on Vero cells infected with HSV-1 at different times: 2 h pre-infection, simultaneous infection, and 4 h post-infection, using MTT assay. The effect of extract on the expression of genes was investigated with quantitative real-time PCR.
Results: The aqueous extract of A. catechu induced the inhibition of infection with the IC₅₀ value of 110.52 ± 1.36 μg/ml. Also, it reduced the expression of UL46 when it was added 2 h pre-infection at 100 μg/ml. Moreover, reduction of expression of US6 was observed at the same concentration when the extract was used simultaneously with the occurrence of infection and 4 h post-infection.
Conclusion: A. catechu can be considered an essential element of natural-based anti-HSV-1 agents.

Transfusion transmissible malaria: seroprevalence of malaria parasitemia in blood donors in Garhwal region of Uttarakhand, India

2024-05-08T08:59:49+0430

Background and Objectives: Malaria was the first ever reported case of transfusion transmitted infection (TTI). Transfusion transmissible malaria (TTM) can result in febrile transfusion reaction in the recipient. TTM can be fatal if the blood transfusion recipient is from vulnerable population i.e. pregnant women or young children. Therefore, the present study was done to estimate the seroprevalence of malaria parasitemia among blood donors in Garhwal region.
Materials and Methods: Study subjects were healthy blood donors who had passed the screening criteria for blood donation. Donors with a history of malaria were temporarily deferred for 3 months following full recovery. Screening of the donated blood units for malaria parasite was done using immunochromatography based rapid diagnostic test. Thin smear examination was performed for malaria parasite species identification.
Results: A total of 1984 blood donations were screened for TTI. The seroprevalence of HBV, HCV HIV and syphilis was 0.3% (n=6), 0.25% (n=5), 0% (n=0) and 0% (n=0) respectively. The seroprevalence of malaria parasite was 0.05% (n=1). Plasmodium vivax was identified upon thin smear examination. The donor reactive for malaria parasite was a replacement donor and gave no recent history of fever or any past history of malaria.
Conclusion: Meticulous donor screening combined with rapid diagnostic tests for malaria parasite is the most practical strategy to prevent TTM in Garhwal region of India.

Time to positivity of blood cultures causing candidemia and its relation to mortality

2024-05-08T08:59:48+0430

Background and Objectives: Early diagnosis of candidemia is of vital importance in reducing mortality and morbidity. The main objective of the study was to determine the TTP (Time to Positivity) of different species of Candida causing bloodstream infection and to see whether TTP can help differentiate Candida glabrata which is frequently fluconazole resistant from Fluconazole sensitive Candida.
Materials and Methods: TTP (Time to positivity) and AAT (Appropriate Antifungal therapy) were noted for Blood cultures becoming positive for Candida. Presence of Risk factors for candidemia like prolonged ICU stay, neutropenia, Total Parenteral Nutrition (TPN), use of steroids , broad spectrum antibiotics, use of Central Venous Catheter, Foleys catheter were also analyzed.
Results: The most frequent isolates were Candida parapsilosis, Candida tropicalis and Candida albicans. The median TTP for all Candida isolates in our study was 34 hours. The diagnostic sensitivity of TTP for detecting C. glabrata and C. tropicalis in patients with candidemia was 88% and 85% respectively. TTP showed that there was no difference in survival between TTP <24 hrs. and > 24hrs. Initiation of antifungal therapy <24 hours and > 24hrs after onset of candidemia had no association with survival.
Conclusion: Longer TTP maybe predictive of C. glabrata while shorter TTP may be predictive of C. tropicalis. In our study we found that fluconazole resistant Candida causing blood stream infection is quite unlikely if the TTP of the isolate is <48hrs.

Identification and assessment of antifungal susceptibility of Candida species based on bronchoalveolar lavage in immunocompromised and critically ill patients

2024-05-08T08:59:48+0430

Background and Objectives: The presence of fungi in the respiratory tract as mycobiome, particularly Candida species (spp.), remains a serious problem due to increasing numbers of immunocompromised pa-tients. The confirmed reliable existence of these pathogens due to frequent colonization is essential. This investigation aimed to recognize Candida spp. among isolates from bron-choalveolar lavage of immunocompromised and critically ill patients and to evaluate their susceptibility to antimycotic drugs.
Materials and Methods: Bronchoalveolar lavage fluid was collected from 161 hospitalized patients presenting with suspected respiratory fungal infection /colonization. The specimens were examined by standard molecular and mycological assays. Candida spp. were recognized with sequence assessment of the D1-D2 section of the large subunit ribosomal DNA. The susceptibility of Candida isolates to common antimycotic drugs was distinguished by standard broth micro-dilution.
Results: Seventy-one clinical isolates of Candida spp. were recognized. Candida albicans was the most frequent, followed by C. glabrata, C. krusei (Pichia kudriavzevii), C. dubliniensis, C. parapsilosis, and C. tropicalis. We found 5.1% of C. albicans isolates and 8% of C. glabrata isolates to show resistance to fluconazole. The whole of the Candida spp. were sensitive to amphotericin B and caspofungin.
Conclusion: This study demonstrated that C. albicans and C. glabrata are the most common isolates of bronchoalveolar lavage fluid in patients, and the drug susceptibility screening confirmed that amphotericin B and caspofungin are effective against Candida spp. but some C. glabrata and C. albicans isolates showed resistance to fluconazole.

First report of amphotericin B resistant Candida haemulonii isolated from the ICU of a referral hospital in Indonesia

2024-05-08T08:59:47+0430

Background and Objectives: Amphotericin B is a broad-spectrum antifungal agent commonly used to treat Candida haemulonii infection. C. haemulonii was isolated from patients reported to be intrinsically resistant to amphotericin B, encoded by the ERG2 and ERG11 genes. However, there have been limited studies concerning amphotericin B-resistant C. haemulonii in Indonesia. The objective of this study is to explore the phenotypic and genotypic characteristics (ERG2 and ERG11) of C. haemulonii isolated from the ICU of a referral hospital in Indonesia.
Materials and Methods: Identification and susceptibility tests were conducted using VITEK2. Thereafter, DNA was extracted and amplified using conventional PCR followed by DNA sequencing (Sanger method).
Results: The results of the phenotypic susceptibility test showed that all C. haemulonii were resistant to amphotericin B. ERG2 and ERG11 sequences showed the same amino acid sequence and corresponded to references that are resistant to amphotericin B.
Conclusion: The resistant properties of C. haemulonii against amphotericin B found in this study require further exploration, including comparing resistant and sensitive C. haemulonii to amphotericin B. In addition, it is necessary to analyze other genes besides ERG2 and ERG11.