Genetic resistance factors and antimicrobial resistance phenotypes in methicillin- resistant Staphylococcus aureus isolates of animals and humans

To describe the prevalence of positive bacterial culture and associated bacterial species in 45 dogs with surgically managed cholelithiasis. Medical records of dogs from a multicenter small-animal specialty surgical private practice treated surgically for cholelithiasis from January 1, 2010, through December 31, 2020, were evaluated. For this descriptive observational study, medical records were retrospectively reviewed to identify dogs with culture and susceptibility testing. Dogs were included if they had an extrahepatic biliary surgery for a diagnosis of cholelithiasis and results of culture and susceptibility testing. Prior antimicrobial use, specific surgical procedure performed, bacterial culture type and source, organisms isolated, and antimicrobial resistance phenotypes were evaluated. Prevalences of positive culture and antimicrobial phenotypes were recorded. 45 dogs met inclusion criteria. Twenty-four of 45 dogs (53%) had a positive bacterial culture. Seven of 24 positive cultures (29%) were polymicrobial. The most common bacterial isolates were Escherichia coli and Enterococcus spp. Seven of 32 isolates (22%) were considered multidrug-resistant organisms (MDROs). Prior antimicrobial use was not significantly associated with the presence of a positive culture result, a culture including an MDRO, or an isolate being classified as an MDRO. Nearly half of dogs undergoing surgery for cholelithiasis had positive biliary cultures. Nearly a fourth of detected bacterial isolates were classified as MDROs. Perioperative antimicrobial use may be indicated in dogs with surgically managed cholelithiasis. Previous antimicrobial use does not appear to be associated with the presence of multidrug resistance.

Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States

BackgroundMulti-drug-resistant organisms (MDROs) in gram-negative bacteria have caused a global epidemic, especially the bacterial resistance to carbapenem agents. Plasmid is the common vehicle for carrying antimicrobial resistance genes (ARGs), and the transmission of plasmids is also one of the important reasons for the emergence of MDROs. Different incompatibility group plasmid replicons are highly correlated with the acquisition, dissemination, and evolution of resistance genes. Based on this, the study aims to identify relevant characteristics of various plasmids and provide a theoretical foundation for clinical anti-infection treatment.Methods330 gram-negative strains with different antimicrobial phenotypes from a tertiary hospital in Henan Province were included in this study to clarify the difference in incompatibility group plasmid replicons. Additionally, we combined the information from the PLSDB database to elaborate on the potential association between different plasmid replicons and ARGs. The VITEK mass spectrometer was used for species identification, and the VITEK-compact 2 automatic microbial system was used for the antimicrobial susceptibility test (AST). PCR-based replicon typing (PBRT) detected the plasmid profiles, and thirty-three different plasmid replicons were determined. All the carbapenem-resistant organisms (CROs) were tested for the carbapenemase genes.Results21 plasmid replicon types were detected in this experiment, with the highest prevalence of IncFII, IncFIB, IncR, and IncFIA. Notably, the detection rate of IncX3 plasmids in CROs is higher, which is different in strains with other antimicrobial phenotypes. The number of plasmid replicons they carried increased with the strain resistance increase. Enterobacterales took a higher number of plasmid replicons than other gram-negative bacteria. The same strain tends to have more than one plasmid replicon type. IncF-type plasmids tend to be associated with MDROs. Combined with PLSDB database analysis, IncFII and IncX3 are critical platforms for taking blaKPC−2 and blaNDM.ConclusionsMDROs tend to carry more complex plasmid replicons compared with non-MDROs. The plasmid replicons that are predominantly prevalent and associated with ARGs differ in various species. The wide distribution of IncF-type plasmids and their close association with MDROs should deserve our attention. Further investigation into the critical role of plasmids in the carriage, evolution, and transmission of ARGs is needed.

Pseudomonas aeruginosa is a significant nosocomial pathogen with increasing antibiotic resistance worldwide. Understanding local resistance patterns is crucial for effective antimicrobial stewardship. This study aimed to determine the antibiotic resistance patterns and Multiple Antibiotic Resistance (MAR) index of Pseudomonas aeruginosa isolates from various clinical specimens at University of Calabar Teaching Hospital, Nigeria. One hundred clinical samples, including wound swabs (20), ear swabs (20), eye swabs (20), stool (20) and urine (20), were processed using standard microbiological techniques and inoculated onto cetrimide agar. Antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method, and MAR indices were calculated for all isolates. Ethical approval was obtained from the University of Calabar Teaching Hospital Ethics Committee. Fifty Pseudomonas aeruginosa isolates were obtained from wound swabs (20), ear swabs (14), eye swabs (9), stool (4), and urine (3). All isolates (100%) showed resistance to nalidixic acid, with high resistance to augmentin (90%) and pefloxacin (72%). Gentamicin showed moderate effectiveness with 60% sensitivity, while ofloxacin demonstrated 50% sensitivity and ciprofloxacin 40% sensitivity. The mean MAR index was 0.72, with all isolates exceeding the 0.2 threshold, indicating widespread multidrug resistance. Our findings reveal concerning levels of multidrug resistance among Pseudomonas aeruginosa isolates from University of Calabar Teaching Hospital. Resistance to commonly used antibiotics, including gentamicin, poses serious clinical challenges. The high MAR indices underscore the urgent need for enhanced infection control measures and antimicrobial stewardship programs.

We examined antimicrobial resistance (AR) phenotypes among commensal Escherichia coli isolated from fecal matter of humans and swine housed in a semi-closed and uniquely integrated multi-site farrow-to-plate operation. Aggregate cohorts of humans consisted of (1) "control" groups of consumers, (2) groups of swine workers, and (3) groups of slaughter-plant workers. Analyses of cross-sectional AR data from 472 human and 376 swine isolates are presented. AR phenotypes among these isolates were compared by (1) host species, (2) facility location, (3) facility type, (4) housing (human) or production (swine) cohort, and (5) sample collection period and time of day. There were significant (p < 0.05) differences in isolates among host-species with swine uniformly at greater risk for (1) AR to four specific antimicrobials (kanamycin, streptomycin, sulfamethoxazole, tetracycline), and (2) multiple resistance phenotypes (p < 0.0001). Facility type and unit location were more often associated with AR differences among swine isolates than among human isolates. Swine production group was significantly associated with AR prevalence (p < 0.05) for nine antimicrobials; in general, purchased boars, suckling piglets, weaned piglets, and lactating sows were at higher risk of AR. There was no significant (p > 0.05) association of human occupational/consumer cohort with AR prevalence. Several unique AR phenotypes were detected in each of the human- and swine-intake groups. These data establish baseline characteristics for an on-going 3-year longitudinal study designed to further characterize AR phenotype and genotype in this population. Host-, facility-, and cohort-specific data demonstrate that sufficient prevalence differences exist to permit the future quantification of AR transmission, should it occur. Based on these cross-sectional data, occupational exposure to either swine-rearing or swine-slaughter facilities does not appear to be associated with the prevalence of phenotypic resistance among the commensal fecal E. coli isolated from this integrated system.

High diversity of coagulase negative staphylococci species in wild boars, with low antimicrobial resistance rates but detection of relevant resistance genes

Evaluation of multiple antibiotic resistance (MAR) index and Doxycycline susceptibility of Acinetobacter species among inpatients

Antimicrobial phenotypes and molecular basis in clinical strains of Clostridium difficile

Coagulase-negative staphylococci (CoNS) are increasingly associated with nosocomial infections, especially among the immunocompromised and those with invasive medical devices, posing a significant concern. We report on clinical multidrug-resistant CoNS from the uMgungundlovu District, KwaZulu-Natal Province, South Africa, as emerging pathogens. One hundred and thirty presumptive CoNS were obtained from blood cultures. Culture, biochemical tests, and the Staphaurex™ Latex Agglutination Test were used for the initial identification of CoNS isolates; confirmation and speciation were undertaken by the VITEK 2 system. Susceptibilities of isolates against a panel of 20 antibiotics were determined using the Kirby-Bauer disk diffusion method, and the multiple antibiotic resistance (MAR) indices of the isolates were determined. The polymerase chain reaction (PCR) was used to amplify the mecA gene to confirm methicillin resistance. Overall, 89/130 presumptive CoNS isolates were confirmed as CoNS by the VITEK 2 system. Of these, 68 (76.4%) isolates were putatively methicillin-resistant by the phenotypic cefoxitin screen test and 63 (92.6%) were mecA positive. Staphylococcus epidermidis (19.1%), S. hominis ssp. hominis (15.7%), and S. haemolyticus (16.9%) were the most common CoNS species. Isolates showed high percentage resistance against penicillin (100.0%), erythromycin (74.2%), and azithromycin (74.2%) while displaying high susceptibilities to linezolid (95.5%), gentamicin (95.5%), and tigecycline (94.4%). Multidrug resistance (MDR) was observed in 76.4% of isolates. MAR index calculation revealed 71.9% of isolates with MAR index >0.2 and 20.2% >0.5. Isolates with the highest MAR indices (0.7 and 0.8) were recovered from the neonatal intensive care unit. Fifty-one MDR antibiograms were observed. The high prevalence of methicillin resistance and multidrug resistance in several species of CoNS necessitates surveillance of this emerging pathogen, currently considered a contaminant of microbial cultures.

Indoor air quality (IAQ) is vital to environmental health, especially in high-density living spaces like university hostels. This study assessed the microbiological air quality in male and female hostels at Wellspring University, Benin City. Air sampling was conducted in eight hostels using the settle plate method. Four rooms per hostel were randomly selected, and nutrient agar and MacConkey agar plates were exposed for 10 minutes to collect airborne microorganisms. Colonies were subcultured, and isolates identified through standard biochemical and microscopic techniques. Additional IAQ parameters such as particulate matter (PM2.5 and PM10), total volatile organic compounds (TVOCs), humidity, and temperature were also monitored. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method on Mueller-Hinton agar, and multiple antibiotic resistance (MAR) indices were calculated. M4 and F2 hostels recorded the highest bacterial load (78 CFU/m³), while F3 hostel had the lowest (1 CFU/m³). Staphylococcus aureus (27.39%) was the most prevalent isolate, followed by Escherichia coli (22.82%), Pseudomonas aeruginosa (20.12%), Enterococcus faecalis (17.66%), and Bacillus subtilis (12.01%). S. aureus was resistant to ofloxacin, while B. subtilis showed resistance to 5 of 12 antibiotics. MAR indices indicated high-risk levels for most isolates except S. aureus. Air quality monitoring revealed that PM2.5, PM10, and TVOC levels in M1–M4 hostels exceeded WHO limits, while temperature and humidity were slightly above recommended values. The study highlights significant microbial and air quality differences between male and female hostels, underscoring the need for improved hygiene and ventilation strategies in shared accommodations.

BackgroundTyphoid fever, an infective bacterial disease, is capable of causing fatal systemic infection in humans, and in an era of antimicrobial resistance, it has become of public health importance. This study aimed to investigate the laboratory diagnosis of Salmonella bloodstream infection, its serotype, antimicrobial resistance pattern, and seasonal variation at a tertiary care children’s hospital.MethodsWe undertook a retrospective, cross-sectional study by reviewing hospital-based laboratory records of patients whose blood culture samples were submitted from the outpatient department to the laboratory of a tertiary care children’s hospital in Kathmandu, Nepal, from January 2017 to January 2019.ResultsAmong the total blood culture samples obtained (n = 39,771), bacterial isolates (n = 1,055, 2.65%) belonged either to the Genus Enterobacteriaceae or Genus Acinetobacter. Altogether (n = 91, 8.63%), isolates were positive for Salmonella spp., which were further identified as Salmonella enterica subsp. enterica ser. Typhi (n = 79, 7.49%), Salmonella enterica subsp. enterica ser. Paratyphi A (n = 11, 1.04%), and Salmonella enterica subsp. enterica ser. Paratyphi B (n = 1, 0.1%). The median age of patients was 6 years (IQR: 4–9), with male and female patients constituting (n = 53, 58.24%; OR, 1.0; 95% CI, 0.60–1.67) and (n = 38, 41.76%; OR, 0.98; 95% CI, 0.49–2.05) cases, respectively. The disease was observed throughout the year, with a high prevalence toward the spring season (March–May). An antibiogram showed resistance more toward nalidixic acid with S. Typhi, comprising half the isolates (n = 52, 65.82%; p = 0.11). Resistance toward β-lactams with β-lactamase inhibitors (amoxicillin/clavulanate; 1.27%) was seen in a single isolate of S. Typhi. The multidrug resistance pattern was not pronounced. The multiple antibiotic resistance (MAR) index was in the range between 0.14 and 0.22 in S. Typhi and 0.22 and 0.23 in S. Paratyphi.ConclusionSalmonella Typhi was the predominant ser. Infection was common among children between 1 and 5 years of age, showing male predominance and with the spring season contributing to a fairly higher number of cases. Antimicrobial susceptibility testing of S. Typhi showed more resistance toward nalidixic acid, with only a single isolate resistant to β-lactamase inhibitors (amoxicillin/clavulanate). Alarming multidrug resistance patterns were not observed. The MAR index in this study indicates the importance of the judicious use of antimicrobials and hospital infection prevention and control practices.

Phenotypic and genotypic methods for the detection of antimicrobial resistance (AMR) in Shigella sonnei in England and Wales were compared and evaluated. WGS data from 341 isolates of S. sonnei isolated between June 2015 and January 2016 were mapped to genes known to be associated with phenotypic AMR. Antimicrobial susceptibility testing was performed on all viable isolates (n = 335). Fifteen of 335 isolates had a discrepancy between phenotypic and genotypic testing for 1 of the 10 antimicrobial classes tested, equating to 15 (0.45%) discordant results out of a possible 3350 isolate/antimicrobial combinations. All 15 mismatched results were genotypically resistant but phenotypically susceptible. Eleven of the 15 discrepancies were observed in streptomycin resistance profiles. The most common resistance profile was trimethoprim, sulphonamides, tetracyclines and streptomycin, occurring in 97 (28.4%) isolates. Resistances to ciprofloxacin and the third-generation cephalosporins, not detected in England and Wales prior to 2002, were identified in 18.2% and 12% of isolates, respectively. Three hundred and four (89.1%) isolates were MDR. There was no significant association between any of the AMR determinants tested and recent foreign travel in male or female cases. The number of isolates of S. sonnei harbouring blaTEM-1 and ermB/mphA was significantly higher in men who reported no recent travel outside the UK. The use of WGS for routine public health surveillance is a reliable method for rapid detection of emerging AMR in isolates of S. sonnei.

Antimicrobial resistance in large clostridial toxin-negative, binary toxin-positive Clostridium difficile ribotypes

The spread of antibiotic-resistant microorganisms in the environment is recognized widely as an important public health issue, with concerns about future ability to treat infectious diseases. The main risk to public health is that the resistance genes are transferred from environmental bacteria to human pathogens. Safe water is one of the most important needs in public health in the twenty first century. Radiation sensitivity (D10) is defined as the radiation dose (kGy) required to reduce the number of that microorganism by 10-fold. The aim of this paper is to determine the association between multiple antibiotic resistance and radiation sensitivity (D10).Four hundred and sixty four (464) water samples were collected for assessment. E. coli isolation and identification were done using API 20E, and a PCR based DNA STRIP technology that allows simultaneous detection of virulence genes and confirmation of E. coli isolates. Antibiotic susceptibility testing was also conducted using the Kirby-bauer method. Radiation sensitivity was done using a cobalt 60 source. Sixty-three percent (63%) of the multidrug resistant E. coli strains recorded a multiple antibiotic resistance (MAR) index value of >0.2. The mean radiation sensitivity (D10) of the E. coli isolates is 0.33±0.11 kGy. The study confirmed a high prevalence of multiple antibiotic resistances in E. coli isolates. Lastly, there is no association between multiple antibiotic resistant indexes and radiation sensitivity (D10) of antibiotic resistant E. coli. Keywords : Antibiotics, Escherichia coli, water-borne, multi drug resistant radiation, Sensitivity.

Several items containing residual antimicrobial agents are disposed of in dumpsites, placing a pressure on the microbial flora and a potential for development of resistance in these microorganisms. Multidrug resistancepatterns and multiple antibiotic resistance index of Salmonella spp. isolated from waste dumps in Zaria Metropolis were thus assayed in this study using one hundred and twelve (112) soil samples collected from four waste dumpsites located in Sabon-Gari, Samaru, Tudun-Wada and Zaria City. Salmonella spp. were isolated by culture methods on selective media and characterized using a series of biochemical tests. The isolates were confirmed using microgen identification kits. Results were statistically analysed using percentages. The antibiotic resistance patterns were determined, using the disc-diffusion method. Ten antibiotics belonging to eight different classes, namely B-lactams, aminoglycosides, tetracycline, cephalosporins, fluoroquinolone, Nitrofurantoins, sulphonamides, and phenicols were tested. The result of the study revealed that 57.2% of the isolates exhibited multidrug resistance (MDR) taken as resistance to four or more antibiotics tested. On the other hand, all the isolates showed 100% susceptibility to Chloramphenicol (30μg) and Gentamicin (30μg) while 76.2% had Multiple Antibiotic Resistance (MAR) Index of 0.2 and above. The isolates showing resistance to the highest number of antibiotics were obtained from refuse dumpsites in Zaria City while an isolate from Sabon-Gari was found to be resistant to six antibiotics. These results could be indicative of possible disposal of these drug residues in the waste dump locations making them hot spots for development of resistance.Keywords: Salmonella spp., Waste Dumps, Resistance Pattern, MAR Index, Zaria Metropolis.