International Journal of Microbiology

Background. Cryptococcosis is the most common opportunistic fungal infection. High morbidity and mortality are frequently observed among hospitalized HIV/AIDS patients, particularly having CD4 count ≤100 cells/μl. Therefore, this study aimed to determine the prevalence of cryptococcal antigenemia and associated factors among HIV/AIDS patients. Methods. A hospital-based cross-sectional study was conducted among 140 HIV/AIDS patients. A cryptococcal antigen test was performed for all patients along with medical chart and laboratory registration book review. Cryptococcal antigen was detected from serum by using Remel Cryptococcal Antigen Test Kit. Data related to possible associated factors were extracted from patients’ charts and laboratory registration book. Data were coded, entered, and analyzed using SPSS version 20. Logistic regression analysis was done to see the association between dependent and independent variables. A value <0.05 was considered statistically significant. Finally, data were presented in the form of texts, figures, and tables. Result. Among 140 serum cryptococcal antigenemia-tested study subjects, 16 (11.43%) were positive for serum cryptococcal antigen. Of them, 43.8% (7/16) were pulmonary tuberculosis coinfected, 31.2% (5/16) were extrapulmonary tuberculosis positive, and 25% (4/16) had bacterial bloodstream infections. In addition, 68.7% (11/16) had CD4 count less than 100 cells/μl, 18.7% (3/16) had CD4 count 100–150 cells/μl, 50% (8/16) were antiretroviral therapy defaulters, and 31.3% (5/16) were naïve. In this study, the majority, 75% (12/16), of the serum cryptococcal antigen-positive subjects were clinical stage IV. Of the assessed associated factors, tuberculosis coinfection (AOR: 0.04; 95% CI [0.005–0.25]) and antiretroviral therapy status (AOR: 0.02; 95% CI [0.001–0.5]) were significantly associated factors enhancing serum cryptococcal antigenemia. Conclusion. In this study, the high rate of cryptococcal antigenemia was observed among hospitalized HIV/AIDS patients, and it is alarming and highlights the need for improving CD4 status, expanding serum cryptococcal antigen screening, and strengthening regular cryptococcal antigenemia surveillance systems.

Background and Aims. Bloodstream infections (BSIs) are one of the most frequently observed hospital-acquired infections (HAIs). We sought to describe the epidemiology and drug resistance secondary Enterobacterales BSIs in surgical patients and check for any correlation with the type of hospital ward. Materials and Methods. This multicenter (13 hospitals in southern Poland) laboratory-based retrospective study evaluated adults diagnosed with BSI secondary to surgical site infection (SSI) hospitalized in 2015–2018; 121 Enterobacterales strains were collected. The drug resistance was tested according to the EUCAST recommendations. Tests confirming the presence of extended-spectrum β-lactamases (ESBLs) and bla resistance genes were carried out. The occurrence of possible clonal epidemics among K. pneumoniae strains was examined. Results. The prevalence of Enterobacterales in secondary BSI was 12.1%; the most common strains were E. coli (n = 74, 61.2%) and Klebsiella spp. (n = 33, 27.2%). High resistance involved ampicillin and ampicillin/sulbactam (92, 8–100%), fluoroquinolones (48–73%), and most cephalosporins (29–50%). Carbapenems were the antimicrobials with the susceptibility at 98%. The prevalence of ESBL strains was 37.2% (n = 45). All the ESBL strains had bla_CTX-M gene, 26.7% had the bla_SHV gene, and 24.4% had bla_TEM gene. The diversity of Klebsiella strains was relatively high. Only 4 strains belonged to one clone. Conclusions. What is particularly worrying is the high prevalence of Enterobacterales in BSI, as well as the high resistance to antimicrobial agents often used in the empirical therapy. To improve the effectiveness of empirical treatment in surgical departments, we need to know the epidemiology of both surgical site infection and BSI, secondary to SSI. We were surprised to note high heterogeneity among K. pneumoniae strains, which was different from our previous experience.

Introduction. Cancer patients being immunosuppressed are vulnerable to develop infections. Knowledge of the changing epidemiology of infections has a pivotal role in its management. Aims and Objectives. The study is undertaken to assess the types of bacterial infections in cancer patients undergoing anticancer treatment, the associated bacterial pathogens, and their antibiotic sensitivity patterns. Materials and Methods. A retrospective surveillance study was undertaken in our center. Positive culture reports and other clinical details of cancer patients diagnosed with infection during a stay in the tertiary care center from 1st January 2015 to 31st December 2016 were analysed by descriptive statistical methods chi-square test and odds ratio to study the association. Results. Out of 638 cancer patients diagnosed with infections in the 2-year period, 140 patients had positive cultures, representing 272 specimens and 306 isolates. Common specimens sent for culture were blood sputum, urine, and pus. 214 isolates (69.9%) were gram-negative bacilli, and 92 (30.1%) were gram-positive cocci. The most common isolates were Klebsiella spp. (18.30%), Pseudomonas spp. (17.65%), and Escherichia coli (14.71%) followed by Staphylococcus aureus (13.72%). Among the gram-negative organisms, the antibiotic resistance rates reported to fluoroquinolones, aminoglycosides, and third-generation cephalosporins were 45.13%, 39.20%, and 48.58%, respectively. 26.92% of the organisms are resistant to all three antibiotics. 50.4% of Klebsiella spp. and Escherichia coli were ESBL producers. Gram-negative organisms showed 11.63% resistance to β-lactam/β-lactamase inhibitor combination, and 22.22% of gram-negative organisms are resistant to carbapenems. 50% of the Staphylococcus spp. were methicillin resistant, but all were sensitive to vancomycin. Conclusion. The surge in the number of gram-negative infections emphasizes the need for broad-spectrum empirical therapy targeting the same. Rate of resistance of the isolated gram-negative organisms to the routinely used empirical therapy is alarming. Prudent use of antibiotics, based on culture reports wherever possible, is of utmost importance to save the lives of infected patients and prevent further development of antibiotic resistance.

Evaluation of resistant profiles and detection of antimicrobial-resistant genes of bacterial pathogens in the nonclinical milieu is imperative to assess the probable risk of dissemination of resistant genes in the environment. This paper sought to identify antibiotic-resistant genes in Pseudomonas aeruginosa from nonclinical sources in Mthatha, Eastern Cape, and evaluate its public health implications. Samples collected from abattoir wastewater and aquatic environment were processed by membrane filtration and cultured on CHROMagarTM Pseudomonas medium. Species identification was performed by autoSCAN-4 (Dade Behring Inc., IL). Molecular characterization of the isolates was confirmed using real-time polymerase chain reaction (rPCR) and selected isolates were further screened for the possibility of harboring antimicrobial resistance genes. Fifty-one Pseudomonas species were recovered from abattoir wastewater and surface water samples, out of which thirty-six strains were Pseudomonas aeruginosa (70.6%). The P. aeruginosa isolates demonstrated resistance to aztreonam (86.1%), ceftazidime (63.9%), piperacillin (58.3%), cefepime (55.6%), imipenem (50%), piperacillin/tazobactam (47.2%), meropenem (41.7%), and levofloxacin (30.6%). Twenty out of thirty-six P. aeruginosa displayed multidrug resistance profiles and were classified as multidrug-resistant (MDR) (55.6%). Most of the bacterial isolates exhibited a high Multiple Antibiotic Resistance (MAR) Index ranging from 0.08 to 0.69 with a mean MAR index of 0.38. In the rPCR analysis of fifteen P. aeruginosa isolates, 14 isolates (93.3%) were detected harboring bla_SHV, six isolates (40%) harbored bla_TEM, and three isolates (20%) harbored bla_CTX-M, being the least occurring ESBL. Results of the current study revealed that P. aeruginosa isolates recovered from nonclinical milieu are resistant to frontline clinically relevant antipseudomonal drugs. This is concerning as it poses a risk to the environment and constitutes a public health threat. Given the public health relevance, the paper recommends monitoring of multidrug-resistant pathogens in effluent environments.

Fresh-produce consumers may be at risk of pathogen infection due to fecal contamination of the agricultural environment. Indicators of fecal contamination may be used as a proxy to evaluate the potential presence of human pathogens, such as norovirus and hepatitis A, on agricultural samples. The objective of this systematic review was to determine whether the presence of human norovirus or hepatitis A was associated with microbial indicators in agricultural samples including fresh produce, equipment surfaces, and hands. Four databases (Embase, PubMed, Web of Science, and Agricola) were systematically searched and fifteen articles met inclusion and exclusion criteria. After data extraction, individual indicator-pathogen relationships were assessed using Cohen’s Kappa coefficient. The level of agreement between norovirus with adenovirus was 0.09 (n = 16, 95% CI −0.05, 0.23), indicating poor agreement using Landis and Koch’s criterion. Similarly, the Kappa coefficient between norovirus with E. coli (κ = 0.04, n = 14, 95% CI −0.05, 0.49) or total coliforms (κ = 0.03, n = 4, 95% CI −0.01, 0.02) was also poor. The level of agreement between hepatitis A with adenovirus (κ = −0.03, n = 3, 95% CI −0.06, 0.01) or fecal coliforms (κ = 0, n = 1, 95% CI 0, 0) was also poor. There were moderate relationships between hepatitis A with E. coli (κ = 0.49, n = 3, 95% CI 0.28, 0.70) and total coliforms (κ = 0.47, n = 2, 95% CI 0.47, 0.47). Based on these limited results, common indicator organisms are not strong predictors of the presence of norovirus and hepatitis A virus in the agricultural environment.

The Sudd wetland is one of the oil-rich regions of South Sudan where environmental pollution resulting from oil extraction activities has been unprecedented. Although phytoremediation is the most feasible technique, its efficacy reduces at high TPH concentration in soil. This has made rhizoremediation the most preferred approach. Rhizoremediation involves use of a combination of phytoremediation and biostimulation. The process is catalyzed by the action of rhizobacteria. Therefore, the objective of this study is to characterize rhizobacteria communities prevalent in phytoremediation species growing in hydrocarbon-contaminated soils biostimulated with cattle manure. The treatments studied were plant species only (T1), plant species and hydrocarbons (T2), plant species and manure (T3), and plant species, manure, and hydrocarbons (T4). The rhizobacteria communities were determined using pyrosequencing of 16S rRNA. In the treatment with phytoremediation species, hydrocarbons 75 g · kg⁻¹soil, and cattle manure 5 g · kg⁻¹soil (T4), there was a significant increase () in rhizobacteria abundance with the highest ASV observed in H. rufa (4980) and the lowest in S. arundinaceum (3955). In the same treatment, bacteria community diversity was high in H. rufa (Chao1, 10310) and the least in S. arundinaceum (Chao 1, 8260) with Proteobacteria, Firmicutes, and Actinobacteria as the dominant phyla. Similarly, in contaminated soil treated with cattle manure, there was a significant increase () in abundance of rhizobacteria genera with Pseudomonas dominating across phytoremediation species. H. rufa was dominated by Bacillus, Fusibacter, and Rhodococcus; G. barbadense was mainly associated with Luteimonas and Mycobacterium, and T. diversifolia was inhabited by Bacillus and Luteimonas. The rhizosphere of O. longistaminata was dominated by Bacillus, Fusibacter, and Luteimonas, while S. arundinaceum was largely inhabited by Sphingomonas. These rhizobacteria genera ought to be applied in the Sudd region for bioremediation.