Genomic Analysis of a Highly Virulent NDM-1-Producing Escherichia coli ST162 Infecting a Pygmy Sperm Whale (Kogia breviceps) in South America

Carbapenemase-producing Enterobacterales are rapidly spreading and adapting to different environments beyond hospital settings. During COVID-19 lockdown, a carbapenem-resistant NDM-1-positive Escherichia coli isolate (BA01 strain) was recovered from a pygmy sperm whale (Kogia breviceps), which was found stranded on the southern coast of Brazil. BA01 strain belonged to the global sequence type (ST) 162 and carried the bla_NDM–1, besides other medically important antimicrobial resistance genes. Additionally, genes associated with resistance to heavy metals, biocides, and glyphosate were also detected. Halophilic behavior (tolerance to > 10% NaCl) of BA01 strain was confirmed by tolerance tests of NaCl minimal inhibitory concentration, whereas halotolerance associated genes katE and nhaA, which encodes for catalase and Na⁺/H⁺ antiporter cytoplasmic membrane, respectively, were in silico confirmed. Phylogenomics clustered BA01 with poultry- and human-associated ST162 lineages circulating in European and Asian countries. Important virulence genes, including the astA (a gene encoding an enterotoxin associated with human and animal infections) were detected, whereas in vivo experiments using the Galleria mellonella infection model confirmed the virulent behavior of the BA01 strain. WHO critical priority carbapenemase-producing pathogens in coastal water are an emerging threat that deserves the urgent need to assess the role of the aquatic environment in its global epidemiology.

Rapid Increase of Oral Bacteria in Nasopharyngeal Microbiota After Antibiotic Treatment in Children With Invasive Pneumococcal Disease

Introduction

Antibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae. Despite the obvious benefits of antibiotics, little is known about their possible side effects on children’s nasopharyngeal microbiota. In other ecological niches, antibiotics have been described to perturb the balanced microbiota with short- and long-term effects on children’s health. The present study aims to evaluate and compare the nasopharyngeal microbiota of children with IPD and different degree of antibiotic exposure.

Methods

We investigated differences in nasopharyngeal microbiota of two groups of children <18 years with IPD: children not exposed to antibiotics before sample collection (n=27) compared to children previously exposed (n=54). Epidemiological/clinical data were collected from subjects, and microbiota was characterized by Illumina sequencing of V3-V4 amplicons of the 16S rRNA gene.

Results

Main epidemiological/clinical factors were similar across groups. Antibiotic-exposed patients were treated during a median of 4 days (IQR: 3–6) with at least one beta-lactam (100.0%). Higher bacterial richness and diversity were found in the group exposed to antibiotics. Different streptococcal amplicon sequence variants (ASVs) were differentially abundant across groups: antibiotic use was associated to lower relative abundances of Streptococcus ASV2 and Streptococcus ASV11 (phylogenetically close to S. pneumoniae), and higher relative abundances of Streptococcus ASV3 and Streptococcus ASV12 (phylogenetically close to viridans group streptococci). ASVs assigned to typical bacteria from the oral cavity, including Veillonella, Alloprevotella, Porphyromonas, Granulicatella, or Capnocytophaga, were associated to the antibiotic-exposed group. Common nosocomial genera such as Staphylococcus, Acinetobacter, and Pseudomonas were also enriched in the group exposed to antibiotics.

Conclusion

Our results point toward a reduction of S. pneumoniae abundance on the nasopharynx of children with IPD after antibiotic treatment and a short-term repopulation of this altered niche by oral and nosocomial bacteria. Future research studies will have to evaluate the clinical implications of these findings and if these populations would benefit from the probiotic/prebiotic administration or even from the improvement on oral hygiene practices frequently neglected among hospitalized children.

Environmental Recovery of Nosocomial Bacteria in a Companion Animal Shelter Before and After Infection Control Procedures

While the effects of cleaning and disinfection practices on the reduction of environmental nosocomial bacteria are well-established in human and large animal veterinary hospitals, how animal movements within animal health care facilities influence environmental bacterial recovery is poorly understood. During three consecutive weeks, 155 electrostatic wipes were collected from the environment pre- and post-cleaning only or following disinfection from seven target locations within an animal shelter. All samples were cultured, and isolates were identified using a matrix-assisted laser desorption ionization-time of flight mass spectrometry. Social network analysis of animal movements during the sampling period was performed to estimate the level of connectivity of the seven target locations. The relationship between bacterial levels and connectivity estimates of the target locations were investigated using a negative binomial regression model with a random effect of sampling areas. Overall, our results indicate a significant reduction in the total bacterial contamination with disinfection when compared to cleaning only [Coefficient (Coef.) = -1.72, 95% Confidence Interval (CI) = -3.09, -0.34, P = 0.015]. Higher total bacterial contamination was significantly more likely in sampled areas with less animal movement connectivity (Coef. = -0.32, 95% CI = -0.49, -0.15, P ≤ 0.001). Pseudomonas aeruginosa and ampicillin resistant Enterobacteriaceae (Escherichia coli, Enterobacter spp. and Klebsiella spp.) were present in the animal holdings and in the shelters' veterinary clinic environment at all sampling times. Our findings demonstrate that cleaning followed by disinfection practices are effective at reducing environmental bacterial levels. Areas with less animal connectivity are more likely to have a higher bacterial contamination. These areas could represent environmental reservoirs for bacterial infection and should be targeted with effective cleaning and disinfection protocols.

Impacts of Wet Market Modernization Levels and Hygiene Practices on the Microbiome and Microbial Safety of Wooden Cutting Boards in Hong Kong

Accessing food through wet markets is a common global daily occurrence, where fresh meat can be purchased to support an urbanizing world population. Similar to the wet markets in many other metropolitan cities in Asia, Hong Kong wet markets vary and are characterized by differing hygiene routines and access to essential modern technologies. The lack of risk assessments of food contact surfaces in these markets has led to substantial gaps in food safety knowledge and information that could help improve and maintain public health. Microbial profiling analyses were conducted on cutting boards that had been used to process pork, poultry, and seafood at 11 different wet markets. The markets differed in hygiene protocols and access to modern facilities. Irrespective of whether wet markets have access of modern infrastructure, the hygiene practices were largely found to be inefficient based on the prevalence of bacterial species typically associated with foodborne pathogens such as Campylobacter fetus, Clostridium perfringens, Staphylococcus aureus, and Vibrio parahaemolyticus; indicator organisms such as Escherichia coli; as well as nonfoodborne pathogenic bacterial species potentially associated with nosocomial infections, such as Klebsiella pneumoniae and Enterobacter cloacae. Other Vibrio species, V. parahaemolyticus and V. vulnificus, typically associated with contaminated raw or undercooked seafood with the potential to cause illness in humans, were also found on wooden cutting boards. This study indicated that the hygienic practices used in Hong Kong wet markets are not sufficient for preventing the establishment of spoilage or pathogenic organisms. This study serves as a basis to review current hygiene practices in wet markets and provides a framework to reassess existing safety protocols.

Study on the In Vitro Activity of Five Disinfectants against Nosocomial Bacteria

Nosocomial infections cause significant morbidity and mortality worldwide, and the pathogenic organisms responsible for such infections can develop resistance to antimicrobial agents. Understanding the activity of disinfectants against clinical and environmental bacterial isolates is therefore crucial. We analysed the in vitro activity of five antimicrobial products (phenolic compounds, didecyldimethylammonium chloride (DDAC), sodium hypochlorite, isopropanol + ammonium compounds (IACs), hydrogen peroxide) against 187 bacterial strains comprising clinical isolates, as well as 30 environmental isolates of Pseudomonas aeruginosa from hospital water samples. Disk diffusion assays were employed to assess antimicrobial activity. Hydrogen peroxide was significantly more active (p < 0.0001) than the other disinfectants against all P. aeruginosa, Klebsiella pneumoniae, Enterococcus faecalis and Staphylococcus aureus strains. It was also the only disinfectant with activity against both clinical and environmental strains of P. aeruginosa. DDAC and IAC-based disinfectants were ineffective against Gram-negative strains, but showed significant activity (particularly IACs, p < 0.0001) against the Gram-positive strains. Compared with IACs, DDAC was significantly more active on E. faecalis and less active on S. aureus (p < 0.0001). Sodium hypochlorite and phenol compounds, by contrast, were inactive against all bacterial strains. The development of disinfection procedures that are effective against all microorganisms is essential for limiting the spread of nosocomial infections.

Zooanthroponotic Transmission of Drug-Resistant Pseudomonas aeruginosa, Brazil

We recovered VIM-2 carbapenemase-producing Pseudomonas aeruginosa isolates from an infected dog, its owner, and the domestic environment. Genomic investigation revealed household transmission of the high-risk hospital clone sequence type 233 in the human–animal–environment interface. Results suggest zooanthroponotic transmission of VIM-2–producing P. aeruginosa in the household following the patient's hospital discharge.

Antibiotic activity of the antioxidant drink effective Microorganism-X (EM-X) extracts against common nosocomial pathogens: an in vitro study

EM-X is a mixed consortium of beneficial microorganisms of natural occurrence (lactic bacteria, yeast and photosynthetic bacteria). The aim of this study is to evaluate the antimicrobial activity in-vitro of EM-X to the principal pathogens isolated in clinical settings and to understand if it could be a suitable adjuvant to synthetic antibiotics. According the World Health Organization we performed antimicrobial assays to the main pathogens usually found in hospital wards. After antimicrobial testing, EM-X has been shown to be most effective at a concentration of 40 mg/ml four time concentrated than the commercial original solution (10 mg/ml). The EM-X antimicrobial action, although effective against bacteria, has proved to be ineffective against the candida genus. This active range of concentration (mg/ml) may prove a very weak action of EM, but further investigations will be done to separate the active substances form the inactive ones in this complex mixture.