Genotypic and antimicrobial resistance characterizations of Cronobacter sakazakii isolated from powdered milk infant formula: A comparison between domestic and imported products

Clinical Profile and Antibiotic Susceptibility Patterns of Cronobacter sakazakii in the Northern Region of Oman

Background

Cronobacter sakazakii is an opportunistic pathogen that mostly affects neonates, infants, and elderly people with weakened immune systems. No study has reported the frequency and antibiotic susceptibility patterns of C. sakazakii from Oman, and thus this study was conducted to fill this gap in the literature.

Materials and Methods

This single-center retrospective study included C. sakazakii isolates identified from different clinical samples of patients treated at Sohar Hospital, Oman, between January 2017 and December 2023. Bacterial identification and antibiotic susceptibility testing were done using the VITEK II automated microbiological system in accordance with the Clinical Laboratory Standards Institute (CLSI) guidelines.

Results

A total of 185 C. sakazakii isolates were included, most commonly from patients aged >60 years (42.7%) and <1 year (11.4%). C. sakazakii strains had high susceptibility (>80%) to most of the tested antibiotics; however, for beta-lactam antibiotics, it ranged from 0% to 50%. Approximately 26.5% of the strains were multidrug resistant. Independent risk factors for increased frequency of multidrug-resistant strains were urinary catheterization (P = 0.002), surgery (P = 0.021), previous antibiotic therapy (P = 0.047), and critical care unit admission (P = 0.048). About one-fifth of the patients experienced life-threatening C. sakazakii infections such as septicemia (15%) and pneumonia (4.7%). All deaths due to septicemia occurred in the >60 years (n = 12) and <1 year (n = 4) age groups.

Conclusions

Cronobacter sakazakii isolates from the North Batinah region of Oman were most frequently isolated from elderly and infant patients and had high antibiotic susceptibility; however, the significant resistance against beta-lactams suggests their low effectiveness. The high number of multidrug-resistant strains coupled with the independent risk factors suggests the need for following stricter antibiotic stewardship protocols and infection control practices.

Prevalence of Foodborne Bacterial Pathogens and Antibiotic Resistance Genes in Sweets from Local Markets in Iran

BACKGROUND

This study aimed to investigate the prevalences of some important antibiotic-resistance genes (ARGs) and foodborne bacterial pathogens in sweet samples collected from local markets in Iran.

METHODS

Forty sweet samples were collected. Foodborne pathogens and ARGs were detected in the sweet samples by conventional and multiplex PCR assays using species-specific primers.

RESULTS

Staphylococcus aureus, Cronobacter sakazakii, Shigella spp., Campylobacter jejuni, and Campylobacter coli were detected and identified in 47.5%, 20%, 45%, 5%, and 30% of the sweet samples, respectively. We found S. aureus and Shigella spp. were the most prevalent bacterial pathogens. S. aureus was found to be the most frequent pathogenic bacteria profiled in these samples. We also found a significant correlation between the presence of C. coli and Cr. sakazakii. We detected the blaSHV resistance gene in 97.5% of the sweet samples; however, blaTEM was detected in only one sample (2.5%).

CONCLUSIONS

Regarding these results, we suggest preventive strategies such as implementing automation of food processing; monitoring the personal hygiene and health of food handlers, and testing regularly for antibiotic resistance in raw materials and products.

Predominance of Multidrug Resistant Escherichia coli of Environmental Phylotype in Different Environments of Dhaka, Bangladesh

Considering the ecological diversity of E. coli, the main aim of this study was to determine the prevalence, phylogroup diversity, and antimicrobial susceptibility of E. coli isolated from 383 different clinical and environmental sources. In total, varied prevalence was observed of the 197 confirmed E. coli that were isolated (human-100%, animal-67.5%, prawn-49.23%, soil-30.58%, and water-27.88%). Of these isolates, 70 (36%) were multidrug-resistant (MDR). MDR E. coli was significantly associated with their sources (χ² = 29.853, p = 0.001). Humans (51.67%) and animals (51.85%) carried more MDR E. coli than other environments. The eae gene indicative of recent fecal contamination was not detected in any isolate, indicating that these E. coli isolates could be present in these environments for a long time and became naturalized. Phylogroup B1 (48.22%) was the predominant group, being present in all hosts analyzed and with the commensal E. coli group A (26.9%) representing the second predominant group. According to chi-square analysis, phylogroup B1 was significantly associated with E. coli from humans (p = 0.024), soil (p < 0.001) and prawn samples (p < 0.001). Human samples were significantly associated with phylogroup B1 (p = 0.024), D (p < 0.001), and F (p = 0.016) of E. coli strains, whereas phylogroup A (p < 0.001), C (p < 0.001), and E (p = 0.015) were associated with animal samples. Correspondence analysis results also indicated the association of these phylogroups with their hosts/sources. The findings of this study exhibited a non-random distribution of phylogenetic groups, though the diversity index was highest for human E. coli phylogroups.

Identification, Typing and Drug Resistance of Cronobacter spp. in Powdered Infant Formula and Processing Environment

Cronobacter spp. is a food-borne pathogenic microorganism that can cause serious diseases such as meningitis, sepsis, and necrotizing colitis in infants and young children. Powdered infant formula (PIF) is one of the main contamination routes, in which the processing environment is an important source of pollution. In this investigation, 35 Cronobacter strains isolated from PIF and its processing environment were identified and typed by 16S rRNA sequencing and multilocus sequence typing (MLST) technology. A total of 35 sequence types were obtained, and three new sequence types were isolated for the first time. The antibiotic resistance was analyzed, showing that all isolates were resistant to erythromycin but sensitive to ciprofloxacin. Multi-drug resistant strains accounted for 68.57% of the total, among which Cronobacter strains with the strongest drug resistance reached 13 multiple drug resistance. Combined with transcriptomics, 77 differentially expressed genes related to drug resistance were identified. The metabolic pathways were deeply excavated, and under the stimulation of antibiotic conditions, Cronobacter strains can activate the multidrug efflux system by regulating the expression of chemotaxis-related genes, thus, secreting more drug efflux proteins to enhance drug resistance. The study of drug resistance of Cronobacter and its mechanism has important public health significance for the rational selection of existing antibacterial drugs, the development of new antibacterial drugs to reduce the occurrence of bacterial resistance, and the control and treatment of infections caused by Cronobacter.

Molecular Mechanisms of Shigella Pathogenesis; Recent Advances

Shigella species are the main cause of bacillary diarrhoea or shigellosis in humans. These organisms are the inhabitants of the human intestinal tract; however, they are one of the main concerns in public health in both developed and developing countries. In this study, we reviewed and summarised the previous studies and recent advances in molecular mechanisms of pathogenesis of Shigella Dysenteriae and non-Dysenteriae species. Regarding the molecular mechanisms of pathogenesis and the presence of virulence factor encoding genes in Shigella strains, species of this bacteria are categorised into Dysenteriae and non-Dysenteriae clinical groups. Shigella species uses attachment, invasion, intracellular motility, toxin secretion and host cell interruption mechanisms, causing mild diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome diseases in humans through the expression of effector delivery systems, protein effectors, toxins, host cell immune system evasion and iron uptake genes. The investigation of these genes and molecular mechanisms can help us to develop and design new methods to detect and differentiate these organisms in food and clinical samples and determine appropriate strategies to prevent and treat the intestinal and extraintestinal infections caused by these enteric pathogens.

Phylogenetic analysis and antibiotic resistance of Shigella sonnei isolates

Shigellosis is one of the most important gastric infections caused by different species of Shigella and has been regarded as a serious threat to public health. Lineage/sublineage profile of S. sonnei is strongly associated with the antibiotic resistance and population structure of this pathogen. In this study, we determined the phylogeny and antibiotic resistance profiles of S. sonnei strains, isolated from 1246 stool and 580 food samples, using multiplex PCR-HRMA genotyping and Kirby-Bauer disk diffusion methods, respectively. A total of 64 S. sonnei strains were isolated (13 food and 51 clinical isolates). Multiplex PCR-HMR assay was able to differentiate the lineages II and III, and sublineages IIIb and IIIc strains successfully considering the definite melting curves and temperatures. Lineage I and sublineage IIIa strain were not isolated in this study. We also demonstrated that most of the S. sonnei strains isolated from both food and clinical samples clustered within the lineage III and sublineage IIIc. Resistance against trimethoprim-sulfamethoxazole, tetracycline, chloramphenicol and streptomycin antibiotics were the most prevalent phenotypes among the S. sonnei lineage III and sublineage IIIc strains.

Antibiotic Resistance and Molecular Characterization of Cronobacter sakazakii Strains Isolated from Powdered Infant Formula Milk

BACKGROUND

Cronobacter sakazakii is a new emerging foodborne bacterial pathogen associated with severe lethal diseases such as meningitis, necrotizing enterocolitis, and septicemia in infants and neonates. Powdered infant formula milk (PIFM) has been recognized as one of the main transmission vehicles and contaminated sources of this pathogen. This study aimed to investigate the prevalence rate, genotypic and phenotypic antibiotic resistance profile, and clonal relatedness of C. sakazakii strains isolated from 364 PIFM samples collected from Tehran city, Iran.

METHODS

Culture-based methods, Kirby-Bauer disk diffusion antibiotic resistance testing, conventional Polymerase Chain Reaction (PCR), and Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR) assays were used in this study to detect and characterize the C. sakazakii isolates.

RESULTS

We isolated 25 C. sakazakii strains from PIFM samples (6.86%). The isolates were highly resistant to amoxicillin-clavulanic acid, amoxicillin, ampicillin, cefoxitin, cefepime, erythromycin, ceftriaxone, ciprofloxacin, and chloramphenicol and susceptible to gentamicin, tetracycline, norfloxacin, and azithromycin antibiotics. The blaCTX-M-1 gene was detected in 96% of the isolates. The isolates were categorized into eight distinct clonal types using the ERIC-PCR method, showing a high genetic diversity among the isolates. However, there was a significant correlation between the genotypic and phenotypic antibiotic resistance properties of the isolates.

CONCLUSIONS

Novel microbial surveillance systems for detecting multi-drug-resistant C. sakazakii are required to control the contamination of this foodborne pathogen in infant foods.

Prevalence, Antibiotic Resistance, Toxin-Typing and Genotyping of Clostridium perfringens in Raw Beef Meats Obtained from Qazvin City, Iran

Background: Clostridium perfringens is one of the highest prevailing spore-forming foodborne pathogens, which is widely distributed and causes severe disease and outbreaks in humans and animals. Raw meat and poultry are the main vehicles of this pathogen. In this study, we investigated the prevalence, antibiotic resistance pattern, toxin-encoding genes and genetic diversity of C. perfringens isolates from raw whole and minced meat samples purchased from local markets in Qazvin city, Iran (the source of beef cattle production was also located in Qazvin city, Iran). Methods: We used conventional culture-based and Kirby–Bauer disk diffusion and conventional and arbitrary primer PCR methods. Results: A total of 18 C. perfringens strains were isolated from 133 raw meat samples (13.53%). Up to 44.4 and 55.5% of these isolates were detected in raw minced and whole meat samples, respectively. We found that 72.2, 66.6, 61.1, 37.8 and 33.3% of the C. perfringens isolates were resistant to ampicillin, tetracycline, amoxicillin, ciprofloxacin and chloramphenicol antibiotics, respectively. Multidrug resistance was found in 38% of the isolates. Among the four main toxin genes evaluated, the Cpa gene was detected in all isolates, and 61.1% of the isolates were mostly recognized as type A C. perfringens. High levels of genetic diversity were observed among the isolates, and they were classified into five distinct groups. Conclusions: The isolates from whole meat samples were more resistant to antibiotics. However, toxin genes were more detected in the isolates from minced meat samples. Our findings suggest that contamination of raw meat products with multidrug resistant C. perfringens could be regarded as one of the concerning pathogens in these products. Comprehensive monitoring of C. perfringens isolates is strongly recommended.

Genetic diversity and antibiotic resistance of Shigella spp. isolates from food products

The emergence of multidrug-resistant Shigella is a significant threat to global public health. Limited studies have investigated the incidence, antimicrobial susceptibility, and genetic diversity of Shigella isolated from food products. Conventional culture-based, serologic, molecular, disk diffusion, PCR, and RAPD-PCR methods were used to determine the prevalence rate, phenotypic and genotypic antibiotic resistance profile, and genetic diversity of the Shigella isolates from food samples including vegetable salad, ground meat, and raw cow's milk (405 samples). The prevalence rate of Shigella in food samples was 4.44%. The incidence of S. sonnei (3.7%) was higher than that of S. flexneri (0.74%). S. dysenteriae and S. boydii were not detected in food samples examined. Also, no Shigella were recovered from raw cow's milk. This study showed that the Shigella isolates were resistant to sulfamethoxazole/trimethoprim (83.3%), amoxicillin (66.6%), streptomycin (66.6%), tetracycline (61.1%), ampicillin (50%), amoxicillin-clavulanic acid (50%), azithromycin (50%), and chloramphenicol (50%) and completely sensitive to cefoxitin, cefepime, amikacin, and gentamicin. All Shigella isolates were multidrug-resistant. We detected bla SHV resistance gene in all isolates; however, no isolate harbored bla TEM gene. RAPD-PCR categorized the Shigella isolates into five main clusters. The highest antibiotic resistance was observed in the isolates of cluster R4. The finding of this study also indicated an association between antimicrobial resistance profiles and genotyping properties of the isolates. Novel food monitoring systems, including surveillance of multidrug-resistant foodborne pathogens, especially in developing countries, are required to control the foodborne diseases.

Prevalence, Phylogroups and Antimicrobial Susceptibility of Escherichia coli Isolates from Food Products

The emergence of multi-drug resistant E. coli is an important matter of increasing considerable concern to global public health. The aim of this study was to investigate the incidence, antibiotic resistance pattern and phylogroups of E. coli isolates obtained from raw milk, vegetable salad and ground meat samples collected from Qazvin Province (Iran). Culture-based techniques, Kirby-Bauer disk diffusion susceptibility testing and PCR assays were used to determine the incidence rate, antimicrobial resistance pattern and phylogenetic groups of the E. coli isolates. The E. coli isolates were highly resistant to amoxicillin (79.1%), trimethoprim-sulfamethoxazole (70.8%), amoxicillin-clavulanic acid (62.5%), tetracycline (54.1%), chloramphenicol (54.1%), nitrofurantoin (54.1%), ampicillin (45.8%), streptomycin (45.8%), and kanamycin (33.3%); and completely susceptible to norfloxacin and azithromycin and 70.8% of the isolates were multi-drug resistant. Most E. coli isolates (46%) belonged to phylogroup A. Novel, practical, efficient food safety control and surveillance systems of multi-drug resistant foodborne pathogens are required to control the foodborne pathogen contamination.

Invited review: Stress resistance of Cronobacter spp. affecting control of its growth during food production

Members of the Cronobacter genus include food-borne pathogens that can cause infections in infants, with a mortality rate as high as 40 to 80%. The high fatality rate of Cronobacter and its isolation from numerous types of food, especially from powdered infant formula, demonstrate the serious nature of this organism. The source tracking of Cronobacter spp. and the analysis of high-frequency species from different sources are helpful for a more targeted control. Furthermore, the persistence during food processing and storage may be attributed to strong resistance of Cronobacter spp. to environment stresses such as heat, pH, and desiccation. There are many factors that support the survival of Cronobacter spp. in harsh environments, such as some genes, regulatory systems, and biofilms. Advanced detection technology is helpful for the strict monitoring of Cronobacter spp. In addition to the traditional heat treatment, many new control techniques have been developed, and the ability to control Cronobacter spp. has been demonstrated. The control of this bacteria is required not only during manufacture, but also through the selection of packaging methods to reduce postprocessing contamination. At the same time, the effect of inactivation methods on product quality and safety must be considered. This review considers the advances in our understanding of environmental stress response in Cronobacter spp. with special emphasis on its implications in food processing.

Genomic Landscape and Phenotypic Assessment of Cronobacter sakazakii Isolated From Raw Material, Environment, and Production Facilities in Powdered Infant Formula Factories in China

Cronobacter is a foodborne pathogen associated with severe infections and high mortality in neonates. The bacterium may also cause gastroenteritis, septicemia, and urinary tract and wound infectious in adults. A total of 15 Cronobacter isolates collected from 617 raw materials and environment samples from Powdered Infant Formula manufacturing factories during 2016 in Shaanxi, China, were analyzed for antimicrobial susceptibilities, species identification, biofilm formation, and whole-genome sequencing. The results showed that all 15 isolates were Cronobacter sakazakii, while the antimicrobial susceptibility test showed that all 15 C. sakazakii were pan susceptible. Most isolates were able to produce a weak biofilm, and two isolates from soil samples produced a strong biofilm formation. All isolates were classified into seven STs including ST4, ST40, ST64, ST93, ST148, ST256, and ST494, with ST64 (4/15, 26.7%) being dominant, and most were clinically related. The isolates harbored at least 11 virulence genes and two plasmids, with one isolate being positive for all virulence genes. Phylogenetic and ANI analysis showed strong clustering by sequence types and isolates from different sources or regions with a similar genomic background. The fact that isolates were obtained from raw materials and environment samples of PIF facilities shared a close phylogeny with one another suggests that cross-contamination events may have occurred between the processing room and external environments, which may give rise to a recurring risk of a continuous contamination during production.