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Chen H, Huang Q, Wu W, Wang Z, Wang W, Liu Y, Ruan F, He C, Li J, Liu J, Wu G. Assessment and clinical utility of metagenomic next-generation sequencing for suspected lower respiratory tract infections. Eur J Med Res 2024; 29:213. [PMID: 38561853 PMCID: PMC10983704 DOI: 10.1186/s40001-024-01806-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES This study aims to compare the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) to traditional diagnostic methods in patients with lower respiratory tract infections (LRTIs), elucidate the etiological spectrum of these infections, and explore the impact of mNGS on guiding antimicrobial therapy. METHODS We retrospectively analyzed data from 128 patients admitted to the Respiratory Department of Anqing 116 Hospital between July 2022 and July 2023. All patients had undergone both mNGS and conventional microbiological techniques (CMT) for LRTI diagnosis. We assessed the diagnostic performance of these methods and examined the influence of mNGS on antimicrobial decision-making. RESULTS Overall, mNGS demonstrated superior sensitivity (96.8%) and accuracy (96.8%) compared to CMT. For Mycobacterium tuberculosis detection, the accuracy and sensitivity of mNGS was 88.8% and 77.6%, which was lower than the 94.7% sensitivity of the T-spot test and the 79.6% sensitivity of CMT. In fungal pathogen detection, mNGS showed excellent sensitivity (90.5%), specificity (86.7%), and accuracy (88.0%). Bacteria were the predominant pathogens detected (75.34%), with Mycobacterium tuberculosis (41.74%), Streptococcus pneumoniae (21.74%), and Haemophilus influenzae (16.52%) being most prevalent. Bacterial infections were most common (62.10%), followed by fungal and mixed infections (17.74%). Of the 118 patients whose treatment regimens were adjusted based on mNGS results, 102 (86.5%) improved, 7 (5.9%) did not respond favorably, and follow-up was lost for 9 patients (7.6%). CONCLUSIONS mNGS offers rapid and precise pathogen detection for patients with suspected LRTIs and shows considerable promise in diagnosing Mycobacterium tuberculosis and fungal infections. By broadening the pathogen spectrum and identifying polymicrobial infections, mNGS can significantly inform and refine antibiotic therapy.
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Affiliation(s)
- Huan Chen
- Department of Respiratory and Critical Care Medicine, Anqing 116th Hospital, No.150 Shuangjing Street, Yingjiang District, Anqing, 246004, Anhui, China.
| | - Qiong Huang
- Department of Respiratory and Critical Care Medicine, Anqing 116th Hospital, No.150 Shuangjing Street, Yingjiang District, Anqing, 246004, Anhui, China
| | - Weiwei Wu
- Dinfectome Inc., 128 Huakang Road, Jiangbei New District, Nanjing, 210000, Jiangsu, China
| | - Zhiguo Wang
- Department of Respiratory and Critical Care Medicine, Anqing 116th Hospital, No.150 Shuangjing Street, Yingjiang District, Anqing, 246004, Anhui, China
| | - Wei Wang
- Department of Respiratory and Critical Care Medicine, Anqing 116th Hospital, No.150 Shuangjing Street, Yingjiang District, Anqing, 246004, Anhui, China
| | - Yigen Liu
- Department of Respiratory and Critical Care Medicine, Anqing 116th Hospital, No.150 Shuangjing Street, Yingjiang District, Anqing, 246004, Anhui, China
| | - Fangfang Ruan
- Department of Respiratory and Critical Care Medicine, Anqing 116th Hospital, No.150 Shuangjing Street, Yingjiang District, Anqing, 246004, Anhui, China
| | - Chengzhen He
- Department of Respiratory and Critical Care Medicine, Anqing 116th Hospital, No.150 Shuangjing Street, Yingjiang District, Anqing, 246004, Anhui, China
| | - Jing Li
- Dinfectome Inc., 128 Huakang Road, Jiangbei New District, Nanjing, 210000, Jiangsu, China
| | - Jia Liu
- Dinfectome Inc., 128 Huakang Road, Jiangbei New District, Nanjing, 210000, Jiangsu, China
| | - Guocheng Wu
- Department of Respiratory and Critical Care Medicine, Anqing 116th Hospital, No.150 Shuangjing Street, Yingjiang District, Anqing, 246004, Anhui, China
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Al-Shahrani GS, Belali TM. Frequency of drug-resistant bacterial isolates among pregnant women with UTI in maternity and children's hospital, Bisha, Saudi Arabia. Sci Rep 2024; 14:7397. [PMID: 38548851 PMCID: PMC10978862 DOI: 10.1038/s41598-024-58275-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/27/2024] [Indexed: 04/01/2024] Open
Abstract
Urinary tract infections (UTIs) are one of the most prevalent bacterial infections affecting humans, with a higher incidence among women. Pregnant women are at an increased risk of developing UTIs, which can have detrimental consequences for both the mother and fetus. UTIs can be caused by various bacteria, and the prevalence of drug-resistant UTIs in maternity and children's hospitals is a cause for concern due to the potential for severe complications if left untreated. The primary objective of the current study was to determine the distribution of UTI-causing bacteria and investigate the antibiotic sensitivity patterns of isolated cultures obtained from pregnant women with UTIs at the Maternity and Children's Hospital, Bisha, Saudi Arabia. This cross-sectional study was conducted from October 2021 to October 2023, involving the analysis of urine samples collected from 321 participants who acquired UTIs during pregnancy. Using biochemical tests and standard cultures, the urine samples were examined for pathogenic bacteria and their anti-microbial sensitivity patterns. The study analyzed susceptibility results according to the Clinical Laboratory Standards Institute guidelines (M100, 28th Edition, 2018). Bacterial strains demonstrating resistance to three or more antibiotics were classified as multidrug-resistant (MDR). This study revealed the distribution of UTI-causing bacteria to be as follows: Escherichia coli, 57.01%; Klebsiella pneumoniae, 24.61%; Pseudomonas aeruginosa, 4.36%; Proteus mirabilis and Enterobacter cloacae, 3.74%; Streptococcus agalactiae, 3.11%; Enterococcus faecalis, 2.18%; and Staphylococcus aureus, 1.24%. Antimicrobial susceptibility testing varied among gram-positive and gram-negative bacteria. Gentamicin demonstrated the highest sensitivity among both gram-positive and gram-negative bacteria; piperacillin-tazobactam was the second most effective drug against gram-negative bacteria. The bacterial isolates showed varying susceptibility to different antibiotics, with Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa being mainly sensitive to gentamicin, piperacillin-tazobactam, and ciprofloxacin, respectively. The strategies for reducing the risk of UTIs need to be improved to limit the spread of MDR bacteria. These strategies may include promoting hygienic practices and administering appropriate antibiotics to prevent the emergence and spread of drug-resistant bacteria. Further research is required to monitor the trends in antibiotic resistance among UTI-causing bacteria and develop effective strategies for managing this public health menace.
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Affiliation(s)
- Ghady S Al-Shahrani
- Faculty of Applied Medical Sciences, University of Bisha, 255, Al Nakhil, 67714, Bisha, Saudi Arabia
| | - Tareg M Belali
- Faculty of Applied Medical Sciences, University of Bisha, 255, Al Nakhil, 67714, Bisha, Saudi Arabia.
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Kebede W, Abebe G, De Boeck I, Gudina EK, Cauwenberghs E, Lebeer S, Van Rie A. Bacterial pathogens in Xpert MTB/RIF Ultra-negative sputum samples of patients with presumptive tuberculosis in a high TB burden setting: a 16S rRNA analysis. Microbiol Spectr 2024; 12:e0293123. [PMID: 38189296 PMCID: PMC10845949 DOI: 10.1128/spectrum.02931-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
In patients with presumptive tuberculosis (TB) in whom the diagnosis of TB was excluded, understanding the bacterial etiology of lower respiratory tract infections (LRTIs) is important for optimal patient management. A secondary analysis was performed on a cohort of 250 hospitalized patients with symptoms of TB. Bacterial DNA was extracted from sputum samples for Illumina 16S rRNA sequencing to identify bacterial species based on amplicon sequence variant level. The bacterial pathogen most likely to be responsible for the patients' LRTI could only be identified in a minority (6.0%, 13/215) of cases based on 16S rRNA amplicon sequencing: Mycoplasma pneumoniae (n = 7), Bordetella pertussis (n = 2), Acinetobacter baumanii (n = 2), and Pseudomonas aeruginosa (n = 2). Other putative pathogens were present in similar proportions of Xpert Ultra-positive and Xpert Ultra-negative sputum samples. The presence of Streptococcus (pseudo)pneumoniae appeared to increase the odds of radiological abnormalities (aOR 2.5, 95% CI 1.12-6.16) and the presence of S. (pseudo)pneumoniae (aOR 5.31, 95% CI 1.29-26.6) and Moraxella catarrhalis/nonliquefaciens (aOR 12.1, 95% CI 2.67-72.8) increased the odds of 6-month mortality, suggesting that these pathogens might have clinical relevance. M. pneumoniae, B. pertussis, and A. baumanii appeared to be the possible causes of TB-like symptoms. S. (pseudo)pneumoniae and M. catarrhalis/nonliquefaciens also appeared of clinical relevance based on 16S rRNA amplicon sequencing. Further research using tools with higher discriminatory power than 16S rRNA sequencing is required to develop optimal diagnostic and treatment strategies for this population.IMPORTANCEThe objective of this study was to identify possible bacterial lower respiratory tract infection (LRTI) pathogens in hospitalized patients who were initially suspected to have TB but later tested negative using the Xpert Ultra test. Although 16S rRNA was able to identify some less common or difficult-to-culture pathogens such as Mycoplasma pneumoniae and Bordetella pertussis, one of the main findings of the study is that, in contrast to what we had hypothesized, 16S rRNA is not a method that can be used to assist in the management of patients with presumptive TB having a negative Xpert Ultra test. Even though this could be considered a negative finding, we believe it is an important finding to report as it highlights the need for further research using different approaches.
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Affiliation(s)
- Wakjira Kebede
- Department of Epidemiology and Social Medicine, Faculty of Medicine and Health sciences, University of Antwerp, Antwerp, Belgium
- Mycobacteriology Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Science, Jimma University, Jimma, Ethiopia
| | - Gemeda Abebe
- Mycobacteriology Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Science, Jimma University, Jimma, Ethiopia
| | - Ilke De Boeck
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Esayas Kebede Gudina
- Department of Internal Medicine, Jimma University Medical Center, Jimma University, Jimma, Ethiopia
| | - Eline Cauwenberghs
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Annelies Van Rie
- Department of Epidemiology and Social Medicine, Faculty of Medicine and Health sciences, University of Antwerp, Antwerp, Belgium
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Jin J, Li C, He Y, Pan J, Zhu J, Tang J. Real world drug treatment models for pregnancy complicated with urinary tract infection in China from 2018 to 2022: a cross-section analysis. Front Pharmacol 2024; 15:1349121. [PMID: 38348394 PMCID: PMC10859756 DOI: 10.3389/fphar.2024.1349121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Objective: Urinary tract infection (UTI) is common in pregnant women. The selection of anti-infection plans during pregnancy must take into account the dual factors of patient pregnancy status and urinary tract infection anti-infection treatment, as well as the efficacy, cost, risk, and potential adverse reactions associated with each method applied to individual patients. Consequently, there are numerous drugs from which to choose; presently, there is no unified conclusion regarding the choice of drug therapy, and there is a lack of long-term drug treatment for UTI during pregnancy. Our objective is to investigate the actual drug treatment patterns of UTI patients during pregnancy in China over the past 5 years, with a particular emphasis on the trend and rationality of antibiotic use in these patients over the past 5 years. Method: We conducted a cross-sectional analysis of data from a China Medical Association-supervised hospital prescription analysis cooperation initiative. From January 2018 to December 2022, the information is extracted from prescriptions/medical orders of patients with UTI during pregnancy. Using a primary anatomical therapeutic chemistry (ATC) classification code and the US Food and Drug Administration (FDA) classification, we quantified the frequency of drug use and drug types. We also calculated the prevalence of the most frequently prescribed antibacterial medications and assessed the efficacy of anti-infection plans based on drug labels and guidelines. Results: Among the 563 patients included in this research, Chengdu (36.59%), Guangzhou (27.72%), and Shanghai (8.70%) were the top three cities. Over the course of 5 years, the average age was 29.60% ± 6.59 years, with approximately 60.21% of women between the ages of 25 and 34. Each patient's primary anti-infection medications were statistically analyzed. Cephalosporins (403, 71.58%), enzyme inhibitors (66, 11.72%), and penicillins (34, 6.04%) were the first few categories, followed by the most commonly used cephalosporins. Cefuroxime, ceftriaxone, and cefdinib, rounded out the top five. Cefoxitin and cefaclor. According to the 5-year change in dosage, cephalosporins have always ranked first. Three of the top five most expensive drugs are cephalosporins, carbapenems, and enzyme inhibitors. Teicoplanin, tigecycline, nifurtel, linezolid, and quinolones ranked among the top five in terms of per-patient drug costs for patients receiving comprehensive treatment drugs. Conclusion: In the 5 years of research, the average age of patients who visit a doctor has not increased substantially, but the opportunity cost of female fertility has increased, which has severely impeded the fulfillment of fertility desires. The selection of medications is generally reasonable, and the dosage of the first-line cephalosporins recommended by the guidelines is relatively high in this study. The dosage of furantoin and fosfomycin, which are more prevalent in urinary tract infections, is however relatively low. In addition, some expensive pharmaceuticals may increase patients' financial burden. On the premise of meeting clinical needs, future research will focus on how to further improve the level of rational drug use in outpatient clinics, attain economical, safe, and effective drug use, and thus reduce the economic burden on patients.
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Affiliation(s)
| | | | | | - Jiaqian Pan
- Department of Pharmacy, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - JiaLei Zhu
- Department of Pharmacy, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jing Tang
- Department of Pharmacy, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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Yohannes H, Belachew T, Assefa M, Getaneh E, Zeray H, Kegne A, Angawu S, Belay G, Biset S, Tigabu A. Pathogenic bacteria recovered from Gene X-pert tuberculosis-negative adult patients in Gondar, Northwest Ethiopia. BMC Pulm Med 2023; 23:197. [PMID: 37280538 DOI: 10.1186/s12890-023-02500-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/30/2023] [Indexed: 06/08/2023] Open
Abstract
INTRODUCTION Lower respiratory tract infections (LRTIs) caused by drug-resistant pathogenic bacteria is a major problem in developing countries including Ethiopia. Therefore, this study aimed to determine the pathogenic bacteria and their antimicrobial susceptibility patterns among Gene X-pert tuberculosis-negative adult patients with clinically suspected LRTIs at the University of Gondar Comprehensive Specialized Referral Hospital, Gondar, Northwest Ethiopia. METHODS This institutional-based cross-sectional study was conducted from February 01 to March 15, 2020. Socio-demographic data were collected by using a structured questionnaire. A total of 254 sputum specimens were collected from Gene X-pert tuberculosis-negative patients. Bacterial recovery was performed using blood, chocolate, and MacConkey agar plates. Bacterial isolates were identified based on Gram staining, colony characteristics, and biochemical reactions. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method. Methicillin resistance of S. aureus was confirmed using cefoxitin (30 µg). Descriptive statistics were calculated for each variable and results are shown in tables and figures. RESULTS In this study, the overall sputum culture positivity rate was 145/254 (57.1%). Gram-negative bacteria 111 (64.9%) were predominant compared to Gram-positive bacteria 60 (35.1%). Of the 145 culture-positive cases, 26 (14.8%) had poly-bacterial infections. S. aureus 40 (66.7%) was the predominant Gram-positive bacterium whereas K. pneumoniae 33 (29.7%), was the most isolated Gram-negative bacterium. Bacterial species, such as S. aureus were sensitive to ciprofloxacin 38/40 (95.0%), gentamicin 37/40 (92.5%), cefoxitin 36/40 (90.0%), and clindamycin 34/40 (85.0%). The proportion of Methicillin-resistant S. aureus was low, 4(10.0%). S. pneumoniae was sensitive to chloramphenicol 8/9 (88.9%) and resistant to ciprofloxacin 6/9 (66.7%). K pneumoniae, P. aeruginosa, E. coli, Serratia species, and H. influenzae also demonstrated high levels of resistance to ampicillin at rates of 21/33 (63.6%), 8/8 (100.0%), 15/17 (88.2%), 7/10 (70.0%), and 6/6 (100.0%), respectively. CONCLUSION This study revealed a higher burden of Gram-negative and Gram-positive pathogenic bacterial agents, which is responsible for LRTs. Therefore, routine sputum culture identification and antibiotic susceptibility testing should be performed in Gene X-pert tuberculosis-negative patients.
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Affiliation(s)
- Hana Yohannes
- Department of Immunology and Molecular biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Teshome Belachew
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Muluneh Assefa
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
| | - Eden Getaneh
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Haymanot Zeray
- University of Gondar Comprehensive Specialized Referral Hospital, University of Gondar, Gondar, Ethiopia
| | - Asamirew Kegne
- University of Gondar Comprehensive Specialized Referral Hospital, University of Gondar, Gondar, Ethiopia
| | - Samre Angawu
- University of Gondar Comprehensive Specialized Referral Hospital, University of Gondar, Gondar, Ethiopia
| | - Gizeaddis Belay
- University of Gondar Comprehensive Specialized Referral Hospital, University of Gondar, Gondar, Ethiopia
| | - Sirak Biset
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Abiye Tigabu
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Fakunle AG, Jafta N, Smit LAM, Naidoo RN. Indoor bacterial and fungal aerosols as predictors of lower respiratory tract infections among under-five children in Ibadan, Nigeria. BMC Pulm Med 2022; 22:471. [PMID: 36494686 PMCID: PMC9733100 DOI: 10.1186/s12890-022-02271-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study aimed to investigate the association between exposure to diverse indoor microbial aerosols and lower respiratory tract infections (LRTI) among children aged 1 to 59 months in Ibadan, Nigeria. METHODS One hundred and seventy-eight (178) hospital-based LRTI cases among under-five children were matched for age (± 3 months), sex and geographical location with 180 community-based controls (under-five children without LRTI). Following consent from caregivers of eligible participants, a child's health questionnaire, clinical proforma and standardized home-walkthrough checklist were used to collect data. Participant homes were visited and sampled for indoor microbial exposures using active sampling approach by Anderson sampler. Indoor microbial count (IMC), total bacterial count (TBC), and total fungal count (TFC) were estimated and dichotomized into high (> median) and low (≤ median) exposures. Alpha diversity measures including richness (R), Shannon (H) and Simpson (D) indices were also estimated. Conditional logistic regression models were used to test association between exposure to indoor microbial aerosols and LRTI risk among under-five children. RESULTS Significantly higher bacterial and fungal diversities were found in homes of cases (R = 3.00; H = 1.04; D = 2.67 and R = 2.56; H = 0.82; D = 2.33) than homes of controls (R = 2.00; H = 0.64; D = 1.80 and R = 1.89; H = 0.55; D = 1.88) p < 0.001, respectively. In the multivariate models, higher categories of exposure to IMC (aOR = 2.67, 95% CI 1.44-4.97), TBC (aOR = 2.51, 95% CI 1.36-4.65), TFC (aOR = 2.75, 95% CI 1.54-4.89), bacterial diversity (aOR = 1.87, 95% CI 1.08-3.24) and fungal diversity (aOR = 3.00, 95% CI 1.55-5.79) were independently associated with LRTI risk among under-five children. CONCLUSIONS This study suggests an increased risk of LRTI when children under the age of five years are exposed to high levels of indoor microbial aerosols.
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Affiliation(s)
- Adekunle Gregory Fakunle
- Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban, 4041, South Africa.
- Department of Public Health, College of Health Sciences, Osun State University, Osogbo, Osun State, Nigeria.
| | - Nkosana Jafta
- Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban, 4041, South Africa
| | - Lidwien A M Smit
- Institute for Risk Assessment (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Rajen N Naidoo
- Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban, 4041, South Africa.
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Ojha SC, Chen K, Yuan Y, Ahmed S, Malik AA, Nisha M, Sheng YJ, Sun C, Wu G, Deng CL. Clinical relevance of molecular testing methods in the diagnosis and guidance of therapy in patients with staphylococcal empyema: a systematic review and meta-analysis. Front Cell Infect Microbiol 2022; 12:758833. [PMID: 35967859 PMCID: PMC9372472 DOI: 10.3389/fcimb.2022.758833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 07/05/2022] [Indexed: 12/14/2022] Open
Abstract
Background Efficient detection tools for determining staphylococcal pleural infection are critical for its eradication. The objective of this meta-analysis was to assess the diagnostic utility of nucleic acid amplification tests (NAAT) in suspected empyema cases to identify staphylococcal strains and avoid unnecessary empiric methicillin-resistant Staphylococcus aureus (MRSA) therapy. Methods From inception to July 24, 2021, relevant records were retrieved from PubMed, Embase, Scopus, Web of Science, and the Cochrane Library. The quality of studies was determined using the QUADAS-2 tool. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and hierarchical summary receiver operating characteristic (HSROC) curve for NAAT's diagnostic performance were evaluated using an HSROC model. Results Eight studies comprising 424 samples evaluated NAAT accuracy for Staphylococcus aureus (SA) identification, while four studies comprising 317 samples evaluated methicillin-resistant Staphylococcus aureus (MRSA) identification. The pooled NAAT summary estimates for detection of both SA (sensitivity: 0.35 (95% CI 0.19-0.55), specificity: 0.95 (95% CI 0.92-0.97), PLR: 7.92 (95% CI 4.98-12.59), NLR: 0.44 (95% CI 0.14-1.46), and DOR: 24.0 (95% CI 6.59-87.61) ) and MRSA (sensitivity: 0.45 (95% CI 0.15-0.78), specificity: 0.93 (95% CI 0.89-0.95), PLR: 10.06 (95% CI 1.49-67.69), NLR: 0.69 (95% CI 0.41-1.15), and DOR: 27.18 (95% CI 2.97-248.6) ) were comparable. The I2 statistical scores for MRSA and SA identification sensitivity were 13.7% and 74.9%, respectively, indicating mild to substantial heterogeneity. PCR was frequently used among NAA tests, and its diagnostic accuracy coincided well with the overall summary estimates. A meta-regression and subgroup analysis of country, setting, study design, patient selection, and sample condition could not explain the heterogeneity (meta-regression P = 0.66, P = 0.46, P = 0.98, P = 0.68, and P = 0.79, respectively) in diagnostic effectiveness. Conclusions Our study suggested that the diagnostic accuracy of NAA tests is currently inadequate to substitute culture as a principal screening test. NAAT could be used in conjunction with microbiological culture due to the advantage of faster results and in situations where culture tests are not doable.
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Affiliation(s)
- Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
| | - Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
| | - Yue Yuan
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Sarfraz Ahmed
- Department of Basic Sciences, University of Veterinary and Animal Sciences Lahore, Narowal, Pakistan
| | - Aijaz Ahmad Malik
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Mehru Nisha
- Investigative Biomedical Science Research Cluster, Institute of Medical Science Technology, Universiti Kuala Lumpur, Kajang, Selangor, Malaysia
| | - Yun-Jian Sheng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
| | - Changfeng Sun
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
| | - Gang Wu
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
| | - Cun-Liang Deng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Molecular detection and clinical characteristics of bacterial and viral main etiological agents causing respiratory tract infections in Tehran, Iran. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Accuracy of Molecular Amplification Assays for Diagnosis of Staphylococcal Pneumonia: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:e0300320. [PMID: 33568465 DOI: 10.1128/jcm.03003-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rapid and accurate identification of staphylococcal pneumonia is crucial for effective antimicrobial stewardship. We performed a meta-analysis to evaluate the diagnostic value of nucleic acid amplification tests (NAAT) from lower respiratory tract (LRT) samples from suspected pneumonia patients to avoid superfluous empirical methicillin-resistant Staphylococcus aureus (MRSA) treatment. PubMed, Scopus, Embase, Web of Science, and the Cochrane Library Database were searched from inception to 2 September 2020. Data analysis was carried out using a bivariate random-effects model to estimate pooled sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR). Of 1,808 citations, 24 publications comprising 32 data sets met our inclusion criteria. Twenty-two studies (n = 4,630) assessed the accuracy of the NAAT for methicillin-sensitive S. aureus (MSSA) detection, while 10 studies (n = 2,996) demonstrated the accuracy of the NAAT for MRSA detection. The pooled NAAT sensitivity and specificity (with 95% confidence interval [CI]) for all MSSA detection were higher (sensitivity of 0.91 [95% CI, 0.89 to 0.94], specificity of 0.94 [95% CI, 0.94 to 0.95]) than those of MRSA (sensitivity of 0.75 [95% CI, 0.69 to 0.80], specificity of 0.88 [95% CI, 0.86 to 0.89]) in lower respiratory tract (LRT) samples. NAAT pooled sensitivities differed marginally among different LRT samples, including sputum, endotracheal aspirate (ETA), and bronchoalveolar lavage (BAL) fluid. Noticeably, NAAT pooled specificity against microbiological culture was consistently ≥88% across various types of LRT samples. A meta-regression and subgroup analysis of study design, sample condition, and patient selection method could not explain the heterogeneity (P > 0.05) in the diagnostic efficiency. This meta-analysis has demonstrated that the NAAT can be applied as the preferred initial test for timely diagnosis of staphylococcal pneumonia in LRT samples for successful antimicrobial therapy.
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Lower Respiratory Tract Pathogens and Their Antimicrobial Susceptibility Pattern: A 5-Year Study. Antibiotics (Basel) 2021; 10:antibiotics10070851. [PMID: 34356772 PMCID: PMC8300710 DOI: 10.3390/antibiotics10070851] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 12/11/2022] Open
Abstract
Lower respiratory tract infections (LRTIs) are the most common infections in humans. It is estimated that 2.74 million deaths worldwide occur each year due to LRTIs. The aim of the study was to determine the frequency and antibiotic susceptibility pattern of microorganisms isolated from respiratory samples of patients with LRTIs. Between January 2015 and December 2019, a total of 7038 sputum and bronchoaspirate samples from suspected LRTI patients were collected. Among them, 2753 samples (39.1%) showed significant microbial growth on culture media. The LRTI rate was higher in patients with male gender (67.1%) and with age between 40–59 years (48.6%). The microorganism identification and antibiotic susceptibility testing were performed with Vitek 2. Out of 4278 isolates species, 3102 (72.5%) were Gram-negative bacteria, 1048 (24.5%) were Gram-positive bacteria, and 128 (3.0%) were Candida spp. Major microorganisms isolated were Acinetobacter baumannii (18.6%), Staphylococcus aureus (15.2%), Pseudomonas aeruginosa (14.2%), and Klebsiella pneumoniae (10.9%). In antimicrobial susceptibility testing, Staphylococcus aureus isolates were mostly resistant to Penicillin G (84.1%) and Oxacillin (48.1%), whereas they demonstrated maximum sensitivity to Tigecycline (100%) and Linezolid (99.5%). Among Gram-negative isolates, Acinetobacter baumannii showed maximum sensitivity to Colistin but was resistant to other antibiotics (95–99%). Klebsiella pneumoniae isolates were mostly resistant to Cefotaxime (72.7%) and sensitive to Gentamicin (54.3%), and Pseudomonas aeruginosa was resistant to Ciprofloxacin (40.3%) and sensitive to Amikacin (85.9%). Gram-negative bacteria represented the species most commonly isolated. A high rate of antimicrobial resistance was observed in this study. In conclusion, the correct identification of causative microorganisms and their susceptibility patterns to antibiotics is crucial for choosing targeted and effective antibiotic therapy in LRTIs, and to prevent the emergence of multidrug-resistant bacteria.
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Ngwa CH, Doungtsop BCK, Bihnwi R, Ngo NV, Yang NM. Burden of vaccine-preventable diseases, trends in vaccine coverage and current challenges in the implementation of the expanded program on immunization: A situation analysis of Cameroon. Hum Vaccin Immunother 2021; 18:1939620. [PMID: 34197271 PMCID: PMC8920166 DOI: 10.1080/21645515.2021.1939620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The discovery and development of vaccines remain one of the major successes of global health with millions of lives saved every year through routine vaccination. Although vaccines provide a safe and cost-effective solution to vaccine-preventable diseases (VPDs), VPDs are still a serious public health problem in most parts of the world, especially in sub-Saharan Africa (SSA) and Asia. In this review, we discuss the burden of VPDs and vaccine coverage several decades after the introduction of the Expanded Program on Immunization (EPI) in Cameroon. We also discuss how different factors affect the implementation of the EPI, highlighting context-specific factors such as the ongoing civil conflict in Cameroon, and the presence of other infectious diseases like COVID-19.
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Affiliation(s)
- Che Henry Ngwa
- School of Public Health and Community Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Languages and Literature, Lund University, Lund, Sweden
| | | | | | - Ngo Valery Ngo
- School of Public Health and Community Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Niendum Mediatrice Yang
- School of Public Health and Community Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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12
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Lim HJ, Kang ER, Park MY, Kim BK, Kim MJ, Jung S, Roh KH, Sung N, Yang JH, Lee MW, Lee SH, Yang YJ. Development of a multiplex real-time PCR assay for the simultaneous detection of four bacterial pathogens causing pneumonia. PLoS One 2021; 16:e0253402. [PMID: 34138947 PMCID: PMC8211157 DOI: 10.1371/journal.pone.0253402] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
Classification of clinical symptoms and diagnostic microbiology are essential to effectively employ antimicrobial therapy for lower respiratory tract infections (LRTIs) in a timely manner. Empirical antibiotic treatment without microbial identification hinders the selective use of narrow-spectrum antibiotics and effective patient treatment. Thus, the development of rapid and accurate diagnostic procedures that can be readily adopted by the clinic is necessary to minimize non-essential or excessive use of antibiotics and accelerate patient recovery from LRTI-induced damage. We developed and validated a multiplex real-time polymerase chain reaction (mRT-PCR) assay with good analytical performance and high specificity to simultaneously detect four bacterial pathogens causing pneumonia: Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Moraxella catarrhalis. The analytical performance of mRT-PCR against target pathogens was evaluated by the limit of detection (LOD), specificity, and repeatability. Two hundred and ten clinical specimens from pneumonia patients were processed using an automatic nucleic acid extraction system for the “respiratory bacteria four” (RB4) mRT-PCR assay, and the results were directly compared to references from bacterial culture and/or Sanger sequencing. The RB4 mRT-PCR assay detected all target pathogens from sputum specimens with a coefficient of variation ranging from 0.29 to 1.71 and conservative LOD of DNA corresponding to 5 × 102 copies/reaction. The concordance of the assay with reference-positive specimens was 100%, and additional bacterial infections were detected from reference-negative specimens. Overall, the RB4 mRT-PCR assay showed a more rapid turnaround time and higher performance that those of reference assays. The RB4 mRT-PCR assay is a high-throughput and reliable tool that assists decision-making assessment and outperforms other standard methods. This tool supports patient management by considerably reducing the inappropriate use of antibiotics.
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Affiliation(s)
- Ho Jae Lim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Integrative Biological Sciences, Chosun University, Gwangju, Republic of Korea
| | - Eun-Rim Kang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Young Park
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Bo Kyung Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Jin Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Sunkyung Jung
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Kyoung Ho Roh
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Gyeonggi, Republic of Korea
| | - Nackmoon Sung
- Clinical Research Institute, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, United States of America
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS) and Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si, Republic of Korea
| | - Sun-Hwa Lee
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Yong-Jin Yang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- * E-mail:
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13
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Shao C, Wang W, Liu S, Zhang Z, Jiang M, Zhang F. Molecular Epidemiology and Drug Resistant Mechanism of Carbapenem-Resistant Klebsiella pneumoniae in Elderly Patients With Lower Respiratory Tract Infection. Front Public Health 2021; 9:669173. [PMID: 34095072 PMCID: PMC8172620 DOI: 10.3389/fpubh.2021.669173] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
Infection by carbapenem-resistant Klebsiella pneumoniae (CRKp) hampers the treatment of elderly patients with lower respiratory tract infection (LRTI); however, relevant data with respect to the characteristics of CRKp in elderly patients with LRTIs are limited. In the present study, K. pneumoniae isolated from elderly patients with LRTIs was collected and identified by VITEK-MS. VITEK 2 compact was used for drug sensitivity test to screen CRKps, and broth dilution method was used for drug sensitivity of tigecycline and colistin. The resistance genes, virulence genes, and serotypes of CRKps were detected via polymerase chain reaction. The homology of CRKps was analyzed via PFGE and MLST. Moreover, plasmid conjugation experiment was carried out to determine the transferability of carbapenem resistance. PCR-based replicon typing (PBRT) and S1 nuclease-PFGE were conducted for plasmid profiling. From January 2019 to August 2019, 258 elderly patients with LRTIs caused by K. pneumoniae were observed; of these, 31 (12.02%) infections were caused by CRKp strains. Majority of the patients were admitted to the intensive care unit and neurosurgery wards. Intracranial hemorrhage and pneumonia were the most common underlying diseases. Furthermore, 29 patients infected by CRKp had been exposed to various antimicrobial drugs before the positive culture. All isolates exhibited high resistance to β-lactam antibiotics. The predominant carbapenem resistance gene was blaKPC−2, and CRKps carrying blaKPC−2 were all ST11 type. Two blaNDM−5 carrying isolates were assigned to ST307 and ST1562, respectively. Conjugative assays revealed that plasmids harboring blaNDM−5 gene were self-transmissible. Plasmid analysis suggested that two blaNDM−5 were located on a ~45 kb IncX3 type plasmid. The high incidence of CRKp in elderly patients with LRTIs indicates the urgent need for further surveillance and strict infection control measures.
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Affiliation(s)
- Chunhong Shao
- Clinical Laboratory of Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong, China
| | - Wei Wang
- Intensive Care Department of Taian City Central Hospital, Shandong, China
| | - Shuang Liu
- Hematology Department of Taian City Central Hospital, Shandong, China
| | - Zhijun Zhang
- Clinical Laboratory of Taian City Central Hospital, Shandong, China
| | - Meijie Jiang
- Clinical Laboratory of Taian City Central Hospital, Shandong, China
| | - Fusen Zhang
- Intensive Care Department of Taian City Central Hospital, Shandong, China
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Gebre AB, Begashaw TA, Ormago MD. Bacterial profile and drug susceptibility among adult patients with community acquired lower respiratory tract infection at tertiary hospital, Southern Ethiopia. BMC Infect Dis 2021; 21:440. [PMID: 33985445 PMCID: PMC8120775 DOI: 10.1186/s12879-021-06151-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 05/06/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Lower respiratory tract infection is a global problem accounting over 50 million deaths annually. Here, we determined the bacterial profile and antimicrobial susceptibility pattern of lower respiratory tract infections among adult patients attending at Tertiary Hospital, Southern Ethiopia. METHODS A cross sectional study was conducted among adult patients with lower respiratory infection at the medical outpatient department of the Hospital. A sputum sample was collected and processed for bacterial culture and antimicrobial susceptibility test. Semi structured questionnaires were used to collect data. SPSS version 22 software was used for statistical analysis and a p value of < 0.05 was considered as statistically significant. RESULTS Out of 406 sputum samples of participants 136(33.5%) were culture positive for 142 bacterial isolates. Klebsiella pneumoniae 36(25.4%) was the predominant isolate followed by Pseudomonas species 25(17.6%). Gram-negative bacteria were sensitive to cefepime (86.0%) and ciprofloxacin (77.8%) antibiotics while gram-positive (76.5%) to clindamycin. CONCLUSION Community acquired lower respiratory tract Infection was highly prevalent in the study area and the isolates showed resistant to common antibiotics such as ampicillin, augmentin, ceftazidime and tetracycline. Therefore, culture and susceptibility test is vital for appropriate management of lower respiratory tract infection in the study area.
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Affiliation(s)
| | | | - Moges Desta Ormago
- Hawassa University College of Medicine and Health Science, Hawassa, Ethiopia.
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Dessie T, Jemal M, Maru M, Tiruneh M. Multiresistant Bacterial Pathogens Causing Bacterial Pneumonia and Analyses of Potential Risk Factors from Northeast Ethiopia. Int J Microbiol 2021; 2021:6680343. [PMID: 33763137 PMCID: PMC7964111 DOI: 10.1155/2021/6680343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Pneumonia is the most common cause of morbidity and mortality in developing countries, mostly caused by different species of bacterial pathogens. Hence, patient management needs awareness of the pathogens and antimicrobial susceptibility testing (AST). This study was aimed to assess the type of bacterial isolates and their antimicrobial susceptibility patterns among pneumonia suspected patients at Dessie Referral Hospital, Northeast Ethiopia. Potential risk factors were also assessed to apply preventive measures accordingly. MATERIALS AND METHODS A cross-sectional study design was employed among pneumonia suspected patients from February to April 2020 at Dessie Referral Hospital. Sociodemographic characteristics and associated risk factors were collected using a pretested questionnaire, and clinical data were extracted by reviewing medical records. Sputum specimens were collected and inoculated into chocolate agar, blood agar, mannitol salt agar, and MacConkey agar which are then incubated at 35°C or 37°C for 24-48 hours. Bacterial species were identified based on Gram stain, colony characteristics, and biochemical techniques. The data were entered in to Epi-Info version 7.1.5 and analyzed with SPSS software version 20. p value <0.05 at 95% CI was considered as statistically significant. RESULTS A total of 406 sputum specimens were collected and cultured, among which 157 (38.7%) were positive for different bacterial pathogens. The predominant pathogens were Klebsiella pneumoniae (28.0%), Streptococcus pneumoniae (24.8%), Staphylococcus aureus (18.5%), and Pseudomonas aeruginosa (14.0%). Majority of the isolates exhibited resistance to ampicillin with 81.5% followed by penicillin with 75.9% and amoxicillin-clavulanate with 61.2%. Multivariable logistic regression showed a significant association of culture positivity with older age (AOR = 2.43, CI: 1.12-5.28, p value = 0.025), cigarette smoking (AOR = 4.67, CI: 2.39-9.20, p value <0.001), and alcohol use (AOR = 5.58, CI: 3.14-9.92, p value <0.001). Resistance to ampicillin and penicillin was associated with repeated prescription and use. CONCLUSIONS This study found high prevalence of bacterial pneumonia in the study area, and high rate of bacterial resistance was observed in ampicillin, penicillin, and amoxicillin-clavulanate. Repeated prescriptions and use of antimicrobials were significantly independent factors of bacterial resistance. Therefore, patient management needs identification of bacteria by routine culture with antimicrobial susceptibility testing.
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Affiliation(s)
- Tewodros Dessie
- Amhara Public Health Institute, Dessie Branch, P.O. Box 686, Dessie, Ethiopia
| | - Mohabaw Jemal
- University of Gondar, College of Medicine and Health Sciences, School of Biomedical and Laboratory Sciences, Department of Medical Microbiology, P.O. Box 196, Gondar, Ethiopia
| | - Minwuyelet Maru
- Amhara Public Health Institute, Dessie Branch, P.O. Box 686, Dessie, Ethiopia
| | - Moges Tiruneh
- University of Gondar, College of Medicine and Health Sciences, School of Biomedical and Laboratory Sciences, Department of Medical Microbiology, P.O. Box 196, Gondar, Ethiopia
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