Molecular detection of Enteropathogens from diarrheic stool of HIV positive patients in Gondar, Ethiopia

High prevalence of multidrug resistant and extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolated from urinary tract infections in the West region, Cameroon

BACKGROUND

Antimicrobial resistance remains a worldwide health problem with serious societal and economical repercussions. Multidrug resistant and Extended-Spectrum β-Lactamase producing-Enterobacterales (ESBL-E) are pathogens of critical public health priority that urgently require the research and development of new drugs. This study aims to determine the prevalence and characterize the genes conferring resistance to β-lactams among Escherichia coli and Klebsiella pneumoniae isolated from patients with urinary tract infections (UTIs) in the West region, Cameroon.

METHODS

A cross-sectional study was conducted among two healthcare facilities during a four-month period from February to May, 2023. All mid-stream urine samples were collected from UTIs patients. The Escherichia coli and K. pneumoniae strains were identified using Enterosystem 18R kit following the manufacturer's instructions. The antimicrobial susceptibility test (AST) was performed using the Kirby-Bauer disk diffusion method. The screening of ESBL production was done using ESBL ChromAgar medium combined with the double-disk synergy test (DDT). Antimicrobial resistance genes were detected using polymerase chain methods. The data analysis was performed using Excel 2016 and IBM SPSS version 20.

RESULTS

A total of 215 urine samples were collected and analyzed during the study period. A 31.62% (68/215) prevalence of Enterobacterales was detected with prevalence of 79.41% (54/68) and 14.70% (10/68) for Escherichia coli and Klebsiella pneumoniae respectively. The overall prevalence of ESBL-Enterobacterales was 64.70% (44/68). About 82% (36/44) of isolates were MDR and high resistance level was observed for amoxicillin + clavulanic acid and ceftazidime. The resistance genes detected were blaCTX-M, and blaTEM respectively.

CONCLUSION

The findings of this study highlight the high burden of MDR and ESBL-E. coli and K. pneumoniae isolates from UTIs. The study emphasizes the necessity of routine screening and monitoring of antimicrobial resistance in healthcare facilities and community settings. It is therefore crucial to implement antimicrobial stewardship programs in the country and infection prevention and control (IPC) measures in hospital settings.

Acute Viral Gastrointestinal (GI) Infections in the Tropics-A Role for Cartridge-Based Multiplex PCR Panels?

Acute gastroenteritis (AGE) contributes to increased morbidity and mortality worldwide. In particular, children in resource-poor settings suffer from frequent episodes of diarrhea. A variety of pathogens, including bacteria, viruses, fungi, and protozoa, can cause AGE. Common viruses associated with AGE are norovirus, rotavirus, astrovirus, adenovirus, and sapovirus. Due to their similar clinical presentation, AGE pathogens cannot be distinguished on clinical grounds rendering the etiological diagnosis challenging. However, reliable diagnosis is essential for individual and public health reasons, e.g., to limit transmission, for appropriate antibiotic use, prognostic appreciation, and vaccination programs. Therefore, high-quality data derived by accurate diagnostics are important to improve global health. In Western industrialized countries, diagnosis relies on microbiological testing, including culture methods, microscopy, immunochromatography, and single-target molecular methods. Recently, multiplex PCR or syndromic panels have been introduced, which simultaneously analyze for multiple pathogens in a very short time. A further technological advancement is cartridge-based syndromic panels, which allow for near patient/point-of-care testing independently from a laboratory. In resource-poor tropical regions, however, laboratory diagnosis is rarely established, and there are little routine laboratory data on the epidemiology of viral AGE pathogens. Limiting factors for the implementation of syndromic panels are high costs, sophisticated equipment, and the need for trained personnel. In addition, pilot studies have shown a large number of viral (co-)detections among healthy controls, thus further challenging their clinical utilization. Hence, there are little evidence-based data on the impact of multiplex syndromic panels from resource-limited regions. Here, we aim to provide a brief overview of what is known about the use of syndromic panels for virus-associated AGE in tropical regions and to address future challenges.

Multicentric Evaluation of SeeGene Allplex Real-Time PCR Assays Targeting 28 Bacterial, Microsporidal and Parasitic Nucleic Acid Sequences in Human Stool Samples

Prior to the implementation of new diagnostic techniques, a thorough evaluation is mandatory in order to ensure diagnostic reliability. If positive samples are scarcely available, however, such evaluations can be difficult to perform. Here, we evaluated four SeeGene Allplex real-time PCR assays amplifying a total of 28 bacteria, microsporidal and parasitic nucleic acid sequence targets in human stool samples in a multicentric approach. In the assessments with strongly positive samples, sensitivity values ranging between 13% and 100% were recorded for bacteria, between 0% and 100% for protozoa and between 7% and 100% for helminths and microsporidia; for the weakly positive samples, the recorded sensitivity values for bacteria ranged from 0% to 100%; for protozoa, from 0% to 40%; and for helminths and microsporidia, from 0% to 53%. For bacteria, the recorded specificity was in the range between 87% and 100%, while a specificity of 100% was recorded for all assessed PCRs targeting parasites and microsporidia. The intra- and inter-assay variations were generally low. Specifically for some helminth species, the sensitivity could be drastically increased by applying manual nucleic acid extraction instead of the manufacturer-recommended automatic procedure, while such effects were less obvious for the bacteria and protozoa. In summary, the testing with the chosen positive control samples showed varying degrees of discordance between the evaluated Allplex assays and the applied in-house reference assays associated with higher cycle threshold values in the Allplex assays, suggesting that samples with very low pathogen densities might be missed. As the targeted species can occur as harmless colonizers in the gut of individuals in high-endemicity settings as well, future studies should aim at assessing the clinical relevance of the latter hint.

Association between Blastocystis sp. infection and immunocompromised patients: a systematic review and meta-analysis

The significance of opportunistic infections in immunocompromised patients and the enigmatic pathogenicity of Blastocystis directed us to conduct the first global systematic review and meta-analysis on Blastocystis prevalence, odds ratios (ORs), and subtypes distribution in various immunocompromised patients (HIV/AIDS, cancer and hemodialysis patients, as well as transplant recipients). The systematic searching procedure was done in Web of Science, PubMed, Scopus, and Google Scholar databases for relevant published literature until November 11, 2020. Random-effects model was utilized to calculate the weighted estimates and 95% confidence intervals (95% CIs). The computed pooled prevalence of Blastocystis inferred from 118 papers (128 datasets) on immunocompromised patients was 10.3% (95% CI: 8.7-12.2%), with 16.1% (95% CI: 11.3-22.2%), 12.5% (95% CI: 8.5-18%), 8.4% (95 % CI: 6.6-10.6%), and 6% (95% CI: 2.6-13.3%) for hemodialysis patients, cancer patients, HIV/AIDS patients, and transplant recipients, respectively. Based on 50 case-control studies (54 datasets), the highest ORs were associated with cancer [2.81 (95% CI: 1.24-6.38, P = 0.013)] and hemodialysis patients [2.78 (95% CI: 1.19-6.48, P = 0.018)]. The most frequent subtype being found in immunocompromised patients was ST3 [41.7% (95% CI: 31.4-52.7%)], followed by ST1 [31.7% (95% CI: 23.2-41.8%)] and ST2 [23.1% (95% CI: 14.8-34.1%)]. Also, the weighted frequency of Blastocystis in various subgroups (publication year, WHO regions, geographical distribution, continents, and country income) was analyzed separately. In total, the results of the present meta-analysis highlighted that one's immunodeficiency status is probably associated with an increased Blastocystis infection, underpinning strict preventive measures to be taken.

Cryptosporidium infection among people living with HIV/AIDS in Ethiopia: a systematic review and meta-analysis

Studies on the prevalence of Cryptosporidium infection in People Living with HIV/AIDS (PLWHA) are inconsistent and heterogeneous. Therefore, this systematic review with meta-analysis was performed to assess the burden of the infection relative to the proportion of CD4 + T cell count among PLWHA in Ethiopia. Articles published before 15 May 2019, have been retrieved for this systematic review using five databases; PubMed, Scopus, Web of Science, Google Scholar and ProQuest, supplemented by the search for gray literature. The overall pooled prevalence and pooled Odds Ratio (OR) with their 95% Confidence Intervals (CI) were estimated using STATA 14 statistical Software. Of the 255 studies retrieved, 31 were considered for the final analysis. As many as 8,645 Ethiopians infected with HIV were included in the final quantitative synthesis. The overall pooled prevalence estimate of Cryptosporidium infection among PLWHA in Ethiopia was 11% (95%CI: 0.09-0.13). HIV-infected people with low CD4 + T cell count (CD4 < 200 cells/mm3) were 13.07 times more likely to become infected with Cryptosporidium than those with high CD4 + T cell count (CD4 > 500 cells/mm3) (OR: 13.07 (95%CI: 6.38-26.75). Cryptosporidium infection in PLWHA in Ethiopia showed decreasing patterns in 2001-2010, 2011-2014, and in 2015-2019, 14.6% (95%CI: 0.076-0.217), 12.71% (95%CI: 0.086-0.167) and 6.7% (95%CI: 0.044-0.090), respectively (p < 0.001). Though the pattern of Cryptosporidium infection in HIV-infected Ethiopians showed a declining trend; it remains a considerable problem that requires improvement in routine screening for Cryptosporidium in HIV-infected people, particularly with poor or declining CD4 + T cell count.

Norovirus Infections and Disease in Lower-MiddleandLow-Income Countries, 1997⁻2018

Noroviruses are a major cause of viral gastroenteritis. The burden of the norovirus in low-resource settings is not well-established due to limited data. This study reviews the norovirus prevalence, epidemiology, and genotype diversity in lower-middle-income countries (LMIC) and in low-income countries (LIC). PubMed was searched up to 14 January 2019 for norovirus studies from all LIC and LMIC (World Bank Classification). Studies that tested gastroenteritis cases and/or asymptomatic controls for norovirus by reverse transcription-polymerase chain reaction (RT-PCR) were included. Sixty-four studies, the majority on children <5 years of age, were identified, and 14% (95% confidence interval; CI 14–15, 5158/36,288) of the gastroenteritis patients and 8% (95% CI 7–9, 423/5310) of healthy controls tested positive for norovirus. In LMIC, norovirus was detected in 15% (95% CI 15–16) of cases and 8% (95% CI 8–10) of healthy controls. In LIC, 11% (95% CI 10–12) of symptomatic cases and 9% (95% CI 8–10) of asymptomatic controls were norovirus positive. Norovirus genogroup II predominated overall. GII.4 was the predominant genotype in all settings, followed by GII.3 and GII.6. The most prevalent GI strain was GI.3. Norovirus causes a significant amount of gastroenteritis in low-resource countries, albeit with high levels of asymptomatic infection in LIC and a high prevalence of coinfections.