Metabolic immaturity of newborns and breast milk bile acid metabolites are the central determinants of heightened neonatal vulnerability to norovirus diarrhea.

Noroviruses are the leading global cause of acute gastroenteritis, responsible for 685 million annual cases. While all age groups are susceptible to noroviruses, children are vulnerable to more severe infections than adults, underscored by 200 million pediatric cases and up to 200,000 deaths in children annually. Understanding the basis for the increased vulnerability of young hosts is critical to developing effective treatments. The pathogenic outcome of any enteric virus infection is governed by a complex interplay between the virus, intestinal microbiota, and host immune factors. A central mediator in these complex relationships are host- and microbiota-derived metabolites. Noroviruses bind a specific class of metabolites, bile acids, which are produced by the host and then modified by commensal bacterial enzymes. Paradoxically, bile acids can have both proviral and antiviral roles during norovirus infections. Considering these opposing effects, the microbiota-regulated balance of the bile acid pool may be a key determinant of the pathogenic outcome of a norovirus infection. The bile acid pool in newborns is unique due to immaturity of host metabolic pathways and developing gut microbiota, which could underlie the vulnerability of these hosts to severe norovirus infections. Supporting this concept, we demonstrate herein that microbiota and their bile acid metabolites protect from severe norovirus diarrhea whereas host-derived bile acids promote disease. Remarkably, we also report that maternal bile acid metabolism determines neonatal susceptibility to norovirus diarrhea during breastfeeding by delivering proviral bile acids to the newborn. Finally, directed targeting of maternal and neonatal bile acid metabolism can protect the neonatal host from norovirus disease. Altogether, these data support the conclusion that metabolic immaturity in newborns and ingestion of proviral maternal metabolites in breast milk are the central determinants of heightened neonatal vulnerability to norovirus disease.

The molecular epidemiology and antimicrobial resistance of Staphylococcus pseudintermedius canine clinical isolates submitted to a veterinary diagnostic laboratory in South Africa.

Staphylococcus pseudintermedius is an important cause of clinical infections in small-animal-veterinary medicine. Evolutionary changes of strains using multilocus sequence typing (MLST) have been observed among S. pseudintermedius in European countries and the United States. However, there are limited or no studies on the detection of methicillin resistant Staphylococcus pseudintermedius (MRSP) and predominating MLST strains in South Africa. Therefore, this study aimed to determine the molecular epidemiology of S. pseudintermedius in South Africa. Twenty-six, non-duplicate, clinical isolates from dogs were obtained as convenience samples from four provinces in South Africa. The Kirby Bauer disk diffusion test was used to determine antimicrobial susceptibility. We used Resfinder and the Comprehensive Antibiotic Resistance Database (CARD) to detect antimicrobial resistance genes. Virulence genes were identified using the virulence factor database and Basic Local Alignment Search Tool (BLASTN) on Geneious prime. geoBURST analysis was used to study relationships between MLST. Finally, the maximum likelihood phylogeny was determined using Randomized Axelerated Maximum Likelihood (RAxML). Twenty-three isolates were confirmed as S. pseudintermedius of which 14 were MRSP. In addition to ß-lactam antimicrobials, MRSP isolates were resistant to tetracycline (85.7%), doxycycline (92.8%), kanamycin (92.8%), and gentamicin (85.7%). The isolates harbored antimicrobial resistance genes (tetM, ermB, drfG, cat, aac(6')-Ie-aph(2")-Ia, ant(6)-Ia, and aph(3')-III) and virulence genes (AdsA, geh, icaA, and lip). MLST analysis showed that ST2228, ST2229, ST2230, ST2231, ST2232, ST2318, ST2326 and ST2327 are unique sequence types in South Africa. Whereas, previously reported major STs including ST45, ST71, ST181, ST551 and ST496 were also detected. The geoBURST and phylogenetic analysis suggests that the isolates in South Africa are likely genetically related to isolates identified in other countries. Highly resistant MRSP strains (ST496, ST71, and ST45) were reported that could present challenges in the treatment of canine infections in South Africa. Hence, we have gained a better understanding of the epidemiology of MRSP in the African continent, the genes involved in resistance and virulence factors associated with these organisms.

Temporal changes in antibiotic resistance and population structure of methicillin-resistant Staphylococcus pseudintermedius between 2010 and 2021 in the United States.

The aim of this study was to perform a phenotypic and molecular epidemiological survey to determine temporal changes in the antimicrobial resistance and population structure of methicillin-resistant Staphylococcus pseudintermedius (MRSP) in the United States. Samples from 200 S. pseudintermedius isolates were obtained from veterinary diagnostic facilities located in geographic regions sampled approximately ten years ago and compared to samples obtained in 2021. Kirby-Bauer disk diffusion was used to determine antimicrobial susceptibility. geoBURST analysis and MrBayes were used to infer relationships of isolates using MLST data. Almost all MRSP isolates (98%) in 2021 were multidrug-resistant with 21% of these isolates resistant to more than 16 antimicrobials. In 2010, 190 S. pseudintermedius isolates were collected and 141 of them were MRSP. From 2010-2021 there was a significant increase in resistance observed to all antibiotics tested except cephalothin and sulfonamides. Whereas ten years previously multilocus sequence types (ST) ST68 (35.7%), ST71 (10%), and ST84 (17.4%) predominated, these strains have been supplanted by other STs, notably ST45 (n = 14), ST155 (n = 9), ST181 (n = 13), ST496 (n = 9) and ST551 (n = 9). The newly prevalent STs are distantly related to ST68, ST71 and ST84 and most likely do not share any recent common ancestors. The population structure of MRSP is far more elastic than expected with new, highly resistant strains replacing the ones that predominated in the United States a decade ago. Antibiotic use may play a role in selection; however, the strains that were replaced were also multidrug-resistant and other factors are likely involved.

Complete Genome Sequences of 11 Staphylococcus pseudintermedius Isolates from Dogs in the United States.

We report here the genome sequences of 11 canine Staphylococcus pseudintermedius isolates from New York, New Hampshire, California, Pennsylvania, and Kansas. The sequencing information will enable spatial phylogenetic comparisons of staphylococcal species and other related species and will help in better understanding their virulence potential.

Species identification and cow risks of non-aureus staphylococci from South African dairy herds.

Detailed information on specific species of non-aureus staphylococci (NAS) has become a necessity for effective udder health control programs in South Africa. The main objective of this preliminary study was to identify the different NAS species and strains present in dairy herds in South Africa using a cost-effective method. A further objective was to investigate the effects of cow risk factors and farming systems on the NAS isolates identified. A total of 214 NAS, isolated from milk collected from 17 South African dairy herds, were identified using three diagnostic tests (API Staph test, MALDI-TOF and 16s rRNA). There was a good observed agreement between the MALDI-TOF and 16S rRNA sequencing (92.2%) and a poor observed agreement between the MALDI-TOF and API Staph (25.7%). The genetic relatedness within species was investigated in 128 of these isolates using random polymorphic amplified deoxyribonucleic acid (DNA) (RAPD), verified by multilocus sequence typing (MLST), and phylogenetic analysis and cow risk factors were investigated on species level. The main NAS species isolated were Staphylococcus chromogenes (75.2%), Staphylococcus epidermidis (9.4%) and Staphylococcus haemolyticus (8.9%). The RAPD test identified 34 Staphylococcus chromogenes, 13 Staphylococcus epidermidis and nine Staphylococcus haemolyticus strains, indicating genetic diversity amongst strains and herds. The presence of NAS intramammary infections was found to be significantly related to the farming systems, composite cow milk somatic cell count (SCC), parity and days in milk (DIM). Significantly more NAS were isolated from primiparous and from older cows. This knowledge could assist with the management of NAS on dairy farms.

Antimicrobial resistance patterns and biofilm formation of coagulase-negative Staphylococcus species isolated from subclinical mastitis cow milk samples submitted to the Onderstepoort Milk Laboratory.

BACKGROUND: Increased prevalence of antimicrobial resistance, treatment failure, and financial losses have been reported in dairy cows with coagulase-negative Staphylococcus (CoNS) clinical mastitis, however, studies on CoNS infections are limited in South Africa. Therefore, the objectives of this study were to investigate the antimicrobial resistance patterns and biofilm formation in CoNS isolated from cow milk samples submitted to the Onderstepoort Milk Laboratory. RESULTS: A total of 142 confirmed CoNS isolates were used for this study. Biofilm formation was identified in 18% of CoNS tested. Staphylococcus chromogenes (11%) had the highest proportion of biofilm formation followed by S. haemolyticus (4.0%), S. epidermidis, S. hominis, S. xylosus, and S. simulans with 1% respectively. Ninety percent (90%) of CoNS were resistant to at least one antimicrobial (AMR) and 51% were multidrug-resistant (MDR). Resistance among CoNS was the highest to ampicillin (90%) and penicillin (89%), few isolates resistant to cefoxitin and vancomycin, 9% respectively. Similarly, MDR-S. haemolyticus (44%), MDR-S. epidermidis (65%), and MDR-S. chromogenes (52%) were mainly resistant to penicillins. The most common resistance patterns observed were resistance to penicillin-ampicillin (16%) and penicillin-ampicillin-erythromycin (10%). Only 42% of biofilm positive CoNS were MDR. CONCLUSION: The majority of CoNS in this study were resistance to penicillins. In addition, most isolates were ß-lactam resistant and MDR. Biofilm formation among the CoNS in this study was uncommon and there was no significant difference in the proportion of MDR-CoNS based on the ability to form a biofilm.

Antimicrobial resistance among Escherichia coli isolates from dogs presented with urinary tract infections at a veterinary teaching hospital in South Africa.

BACKGROUND: This study investigated the burden and predictors of canine E. coli urinary tract infections (UTI) and antimicrobial resistance among dogs presented at a veterinary teaching hospital in South Africa, 2007-2012. METHODS: The Cochran-Armitage trend test was used to investigate temporal trends while logistic regression models were used to investigate predictors (age, sex, breed, year) of E. coli infections and antimicrobial resistance (AMR). RESULTS: A total of 22.3% (168/755) of the urinary specimens tested positive for E. coli. A significant (p = 0.0004) decreasing temporal trend in the percentage of E. coli positive isolates was observed over the study period. There were high levels of AMR to penicillin-G (99%), clindamycin (100%), tylosine (95%), cephalothin (84%) but relatively low levels of resistance to enrofloxacin (16%), orbifloxacin (21%). Almost all (98%, 164/167) the isolates exhibited multidrug resistance (MDR), while only 11% (19/167) and 2% (4/167) exhibited extensive drug resistance (XDR) and pan-drug resistance (PDR), respectively. CONCLUSIONS: Although, the risk of E. coli UTI declined during the study period, the risk of AMR increased. The high levels of AMR and MDR as well as the presence of XDR and PDR is concerning as these have the potential of affecting prognosis of UTI treatments.