International Journal of Microbiology
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Acceptance rate10%
Submission to final decision139 days
Acceptance to publication16 days
CiteScore6.500
Journal Citation Indicator0.570
Impact Factor3.4

Absence of Tuberculosis-Causing Mycobacteria from Slaughtered Livestock Tissues and Environmental Samples, Gauteng Province, South Africa

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International Journal of Microbiology publishes papers on microorganisms and their interaction with hosts and the environment. The journal covers all microbes, including bacteria, fungi, viruses, archaea, and protozoa.

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Chief Editor, Professor Urakawa, is currently based at Florida Gulf Coast University as Professor of Marine and Ecological Sciences and has a background in Environmental Microbiology and Microbial Ecology.

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Research Article

Detection of Pathogenic Serogroups and Virulence Genes in Listeria monocytogenes Strains Isolated from Beef and Beef Products Retailed in Gauteng Province, South Africa, Using Phenotypic and Polymerase Chain Reaction (PCR)-Based Methods

South Africa recently (2017-18) experienced the largest outbreak of human listeriosis in the world caused by L. monocytogenes following the consumption of “polony,” a ready-to-eat meat product. Most (59%) cases originated from Gauteng province, South Africa. As a follow-up study to the outbreak, we used standard bacteriological and molecular methods to determine the prevalence of pathogenic and virulent serogroups of L. monocytogenes in various beef and beef products retailed in Gauteng province, South Africa. The overall prevalence of Listeria spp. was 28% (112/400), comprising Listeria monocytogenes (9.3%), Listeria innocua (16.3%), and Listeria welshimeri (2.5%) (). It is crucial to have detected that the region (), type of product (), and temperature at storage () significantly affected the occurrence of L. monocytogenes in beef products. It is alarming that pathogenic serogroups 4b-4d-4e (51.4%) and 1/2a-3a (43.2%) were detected among the isolates of L. monocytogenes. Importantly, they were all carriers of seven virulence-associated genes (hlyA, inlB, plcA, iap, inlA, inlC, and inlJ). Our study also demonstrated that 16.7% of “polony” samples investigated were contaminated with L. monocytogenes. Considering that pathogenic and virulent L. monocytogenes contaminated beef and beef products retailed in South Africa, the food safety risk posed to consumers remains and cannot be ignored. Therefore, it is imperative to reduce the contamination of these products with L. monocytogenes during beef production, processing, and retailing to avoid future outbreaks of human listeriosis in the country.

Research Article

Mycobacterium tuberculosis Lineage Distribution Using Whole-Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin-Resistant Isolates from West Java, Indonesia

Tuberculosis (TB) is caused by Mycobacterium tuberculosis infection. Indonesia is ranked second in the world for TB cases. New anti-TB drugs from groups A and B, such as bedaquiline, clofazimine, and linezolid, have been shown to be effective in curing drug resistance in TB patients, and Indonesia is already using these drugs to treat patients. However, studies comparing the TB strain types with anti-TB resistance profiles are still relevant to understanding the prevalent strains in the country and their phenotypic characteristics. This study aimed to determine the association between the TB lineage distribution using whole-genome sequencing and bedaquiline, clofazimine, and linezolid phenotypic profile resistance among M. tuberculosisrifampicin-resistant isolates from West Java. M. tuberculosis isolates stock of the Department of Microbiology, Faculty of Medicine, Universitas Indonesia, was tested against bedaquiline, clofazimine, and linezolid using a mycobacteria growth indicator tube liquid culture. All isolates were tested for M. tuberculosis and rifampicin resistance using Xpert MTB/RIF. The DNA genome of M. tuberculosis was freshly extracted from a Löwenstein–Jensen medium culture and then sequenced. The isolates showed phenotypically resistance to bedaquiline, clofazimine, and linezolid at 5%, 0%, and 0%, respectively. We identified gene mutations on phenotypically bedaquiline-resistant strains (2/3), and other mutations also found in phenotypically drug-sensitive strains. Mykrobe analysis showed that most (88.33%) of the isolates could be classified as rifampicin-resistant TB. Using Mykrobe and TB-Profiler to determine the lineage distribution, the isolates were found to belong to lineage 4 (Euro-American; 48.33%), lineage 2 (East Asian/Beijing; 46.67%), and lineage 1 (Indo-Oceanic; 5%). This work underlines the requirement to increase the representation of genotype-phenotype TB data while also highlighting the importance and efficacy of WGS in predicting medication resistance and inferring disease transmission.

Research Article

Biofilm Formation, Pyocyanin Production, and Antibiotic Resistance Profile of Pseudomonas aeruginosa Isolates from Wounds

Pseudomonas aeruginosa is one of the most frequently resistant and dangerous bacteria isolated from infected wounds of patients. This study aimed to determine the prevalence of P. aeruginosa from infected wounds of patients in the Dschang District Hospital to evaluate their antibiotic susceptibility profiles and their ability to swarm and swim and correlate pyocyanin production with biofilm formation. Wound swab samples were collected and the identification of P. aeruginosa was performed using microbiological and biochemical tests. Their antimicrobial susceptibility was determined by the broth microdilution method. Swarming and swimming were determined by measuring the diameters of motility in semisolid/low-viscosity media. Furthermore, pyocyanin production and biofilm formation were evaluated spectrophotometrically using a microtiter plate. The prevalence of P. aeruginosa from infected wounds in our study population was 26%. All P. aeruginosa isolates were resistant to streptomycin and paromomycin, and the frequency of multidrug resistance (MDR) was 65.8%. All P. aeruginosa isolates showed the ability to produce biofilm and pyocyanin. Out of the 37 isolates screened, 19 including the reference strains (51.4%) were strong biofilm producers. A significant positive correlation was observed among biofilm formation, pyocyanin production, and the antibiotic resistance profile of the isolates. Findings from this study suggest that infected wounds could act as a reservoir for MDR and virulent P. aeruginosa. The presence of strong biofilm producers of P. aeruginosa in infected wounds is a serious public health concern. Therefore, surveillance programs to monitor and control MDR P. aeruginosa in these patients are required to prevent their dissemination in hospital settings.

Research Article

Phenotypic and Genotypic Characterization of Extended Spectrum Beta-Lactamase-Producing Clinical Isolates of Escherichia coli and Klebsiella pneumoniae in Two Kenyan Facilities: A National Referral and a Level Five Hospital

Background. The emergence of antimicrobial resistance (AMR) and multidrug resistance (MDR) among Escherichia coli and Klebsiella pneumoniae, especially through the production of extended spectrum β-lactamases (ESBLs), limits therapeutic options and poses a significant public health threat. Objective. The aim of this study was to assess the phenotypic and genetic determinants of antimicrobial resistance of ESBL-producing Escherichia coli and Klebsiella pneumoniae isolates from patient samples in two Kenyan Hospitals. Methods. We collected 138 E. coli and 127 K. pneumoniae isolates from various clinical specimens at the two health facilities from January 2020 to February 2021. The isolates’ ESBL production and antibiotic susceptibility were phenotypically confirmed using a standard procedure. Molecular analysis was done through conventional polymerase chain reaction (PCR) with appropriate primers for gadA, rpoB, blaTEM, blaSHV, blaOXA, blaCTX-M-group-1, blaCTX-M-group-2, blaCTX-M-group-9, and blaCTX-M-group-8/25 genes, sequencing and BLASTn analysis. Results. Most E. coli (82.6%) and K. pneumoniae (92.9%) isolates were ESBL producers, with the highest resistance was against ceftriaxone (69.6% among E. coli and 91.3% among K. pneumoniae) and amoxicillin/clavulanic acid (70.9% among K. pneumoniae). The frequency of MDR was 39.9% among E. coli and 13.4% among K. pneumoniae isolates. The commonest MDR phenotypes among the E. coli isolates were CRO-FEP-AZM-LVX and CRO-AZM-LVX, while the FOX-CRO-AMC-MI-TGC-FM, FOX-CRO-FEP-AMC-TZP-AZM-LVX-MI and CRO-AMC-TZP-AZM-MI were the most frequent among K. pneumoniae isolates. Notably, the FOX-CRO-FEP-AMC-TZP-AZM-LVX-MI phenotype was observed in ESBL-positive and ESBL-negative K. pneumoniae isolates. The most frequent ESBL genes were blaTEM (42%), blaSHV (40.6%), and blaOXA (36.2%) among E. coli, and blaTEM (89%), blaSHV (82.7%), blaOXA (76.4%), and blaCTX-M-group-1 (72.5%) were most frequent ESBL genes among K. pneumoniae isolates. The blaSHV and blaOXA and blaTEM genotypes were predominantly associated with FOX-CRO-FEP-MEM and CRO-FEP multidrug resistance (MDR) and CRO antimicrobial resistance (AMR) phenotypes, among E. coli isolates from Embu Level V (16.7%) and Kenyatta National Hospital (7.0%), respectively. Conclusions. The high proportion of ESBL-producing E. coli and K. pneumoniae isolates increases the utilization of last-resort antibiotics, jeopardizing antimicrobial chemotherapy. Furthermore, the antimicrobial resistance patterns exhibited towards extended-spectrum cephalosporins, beta-lactam/beta-lactamase inhibitor combinations, fluoroquinolones, and macrolides show the risk of co-resistance associated with ESBL-producing isolates responsible for MDR. Hence, there is a need for regular surveillance and implementation of infection prevention and control strategies and antimicrobial stewardship programs.

Research Article

Metagenomic Characterization of Poultry Cloacal and Oropharyngeal Swabs in Kenya Reveals Bacterial Pathogens and Their Antimicrobial Resistance Genes

Poultry enteric bacterial diseases are of significant economic importance because they are responsible for production losses due to weight loss, increased morbidity and mortality, and increased cost of production arising from poor feed conversion and treatment. This cross-sectional purposive study characterized enteric bacterial pathogens in poultry from selected agroclimatic regions in Kenya and investigated their antimicrobial resistance gene profiles. Cloacal (n = 563) and oropharyngeal (n = 394) swabs were collected and pooled into 16 and 14 samples, respectively, to characterize bacterial pathogens and their antimicrobial resistance gene profiles. We report that Proteobacteria, Chlamydiae, and Firmicutes are the most dominant phyla present in both cloacal and oropharyngeal swabs of the six poultry species studied, indicating the colonization of the poultry gut by many pathogenic bacteria. Using KEGG and COG databases, some pathways related to metabolism, genetic information, and cellular processing were detected. We also report the abundance of antimicrobial resistance genes that confer resistance to β-lactamases, aminoglycosides, and tetracycline in most of the poultry analyzed, raising concern about the dangers associated with continuous and inappropriate use of these antibiotics in poultry production. The antimicrobial resistance gene data generated in this study provides a valuable indicator of the use of antimicrobials in poultry in Kenya. The information generated is essential for managing bacterial diseases, especially in backyard poultry raised under scavenging conditions.

Research Article

Antibiotic Resistance Profile of E. coli Isolates from Lettuce, Poultry Manure, Irrigation Water, and Soil in Kumasi, Ghana

Inputs such as irrigation water and poultry manure used in lettuce cultivation have been found to be associated with antibiotic-resistant pathogens. The study assessed the antibiotic resistance profile of Escherichia coli isolated from lettuce, poultry manure, irrigation water, and soil in Kumasi. One hundred and fifty-six samples of lettuce, irrigation water, soil, and manure were collected from three farms over a seven-week cultivation period (seedlings to harvest stage). E. coli were enumerated using standard methods. 98% of the samples were positive for E. coli. Geometric means for lettuce, irrigation water, and soil ranged from 2.0 × 105 to 1.67 × 107 MPN/100 ml while that of manure ranged from 2.0 × 105 to 1.31 × 107 MPN/100 ml. Generally, the microbial load of all parameters on all farms across the weeks was significant and exceeded World Health Organization (WHO) and International Commission on Microbiological Specifications for Foods (ICMSF) standard recommendations for food. Using the Kirby Bauer method, antibiotic sensitivity testing was performed against 225 biochemically confirmed E. coli with twelve antibiotics. Relatively high resistance was recorded for some members of the beta-lactam class: meropenem: 94.2%, ampicillin: 91.9%, cefuroxime: 95.1%, ceftriaxone: 94.7%, and cefotaxime: 94.2%. Eighty of the isolates were screened for extended spectrum beta lactamase (ESBL) production using cefotaxime (CTX) and cefotaxime/clavulanic acid (CTX/CLA) discs and three showed positive: one each from poultry manure, irrigation water, and soil. Polymerase chain reaction (PCR) confirmed the presence of blaCTX-M gene. The occurrence of antibiotic-resistant E. coli in vegetables and their production environment is alarming and poses serious health threats to the general public. The presence of blaCTX-M gene in E. coli from a vegetable production site recorded for the first time in Ghana requires enforcement by regulatory bodies on the inappropriate use of antibiotics in the country.

International Journal of Microbiology
 Journal metrics
See full report
Acceptance rate10%
Submission to final decision139 days
Acceptance to publication16 days
CiteScore6.500
Journal Citation Indicator0.570
Impact Factor3.4
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