Patterns and predictors of antimicrobial resistance among Staphylococcus spp. from canine clinical cases presented at a veterinary academic hospital in South Africa

Not just in man's best friend: A review of Staphylococcus pseudintermedius host range and human zoonosis

Staphylococcus pseudintermedius is one species in the commensal staphylococcal population in dogs. While it is commonly carried on healthy companion dogs it is also an opportunistic pathogen associated with a range of skin, ear, wound and other infections. While adapted to dogs, it is not restricted to them, and we have reviewed its host range, including increasing reports of human colonisation and infections. Despite its association with pet dogs, S. pseudintermedius is found widely in animals, covering companion, livestock and free-living species of birds and mammals. Human infections, typically in immunocompromised individuals, are increasingly being recognised, in part due to improved diagnosis. Colonisation, infection, and antimicrobial resistance, including frequent multidrug resistance, among S. pseudintermedius isolates represent important One Health challenges.

A Retrospective Descriptive Study of Staphylococcus Species Isolated from Canine Specimens Submitted to a Diagnostic Laboratory in South Africa, 2012-2017

There is a scarcity of published studies on the occurrence of Staphylococcus spp. Among dogs in South Africa. The objective of the study was to characterise the Staphylococcus spp. Isolated from dog samples submitted to a veterinary diagnostic laboratory in South Africa in terms of time, place, and person. This study utilised a dataset of 1627 positive Staphylococcus isolates obtained from a veterinary diagnostic laboratory in South Africa from 2012 to 2017. Out of the 1627 confirmed isolates, 10 different species of Staphylococcus were identified. Among these, 92.0% were classified as coagulase-positive staphylococci (CoPS), 6.0% were coagulase-negative staphylococci (CoNS), and 3.0% were coagulase-variable. Male dogs contributed just over half (53.2%) of the Staphylococcus isolates, while female dogs contributed the remaining 46.8%. The largest proportion of isolates (23.2%) were obtained from dogs aged ≥ 9 years, with the highest number of isolates originating from KwaZulu-Natal Province (45.0%) and the least from Northern Cape Province (0.1%). Out of the total samples included in the records, the majority (46.0%) were skin specimens. The number of Staphylococcus isolates recorded showed limited variation between the seasons (24.3% in autumn, 26.3% in winter, 26.0% in spring, and 24.0% in summer). This study highlighted the diversity of Staphylococcus spp. isolated from dogs, and the burden of staphylococcal carriage among dogs in South Africa. Further research is required to examine the factors that contribute to the observed discrepancies in the proportions of Staphylococcus spp. between the provinces.

Risk Factors, Genetic Diversity, and Antimicrobial Resistance of Staphylococcus spp. Isolates in Dogs Admitted to an Intensive Care Unit of a Veterinary Hospital

Intensive Care Units (ICU) usually provide an excellent environment for the selection of pathogens associated with hospital-acquired infections (HAI), leading to increased mortality and hospitalization costs. Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a major cause of HAI in dogs worldwide, but the risk factors and dynamics of colonization by MRSP are largely unknown. This study aimed to evaluate the risk factors associated with the acquisition of MRSP in dogs admitted to an ICU, and to report the antimicrobial resistance profiles and genetic relatedness of MRSP isolates. Sterile swabs from the nostril, axilla, and rectum were collected daily during the hospitalization of 54 dogs. Samples were subjected to Mannitol Salt Agar, and colonies were identified by MALDI-ToF, polymerase chain reaction (PCR), and sequencing of the rpoB gene. Antimicrobial susceptibility testing and PCR detection of mecA were performed. Staphylococcus spp. was isolated from 94% of the dogs, and the most frequently isolated species was S. pseudintermedius (88.2%). Carriage of multidrug resistant (MDR) staphylococci was observed in 64.4% of the dogs, and approximately 39% had methicillin-resistant Staphylococcus sp. (MRS), of which 21.6% had MRSP and 1.9% had methicillin-resistant S. aureus (MRSA). The acquisition of MRSP during ICU hospitalization was associated with sex (female), age (>7 years), and dogs that had previously been treated with antimicrobials. Animals colonized by MRSP resistant to ≥9 antimicrobial classes had longer hospital stays than those colonized by other MRS strains. Among the 13 MRSP isolates that were subjected to whole-genome sequencing, ten were classified as ST71. A single nucleotide polymorphism (SNP) analysis revealed three clones, including one that was detected in infected dogs outside the ICU. This study indicates novel risk factors associated with colonization by MRSP. The detection of the same MRSP clone causing HAI outside the ICU reinforces the need for improved infection prevention and control practices at veterinary hospitals in general and at the ICU in particular.

Dog Owners’ Attitude toward Veterinary Antibiotic Use and Antibiotic Resistance with a Focus on Canine Diarrhea Management

An ad hoc questionnaire was designed in order to investigate AMR knowledge amongst Italian dog owners, owner expectations concerning pharmacological treatment of canine AD, and client attitudes towards and compliance with alternative strategies to antimicrobial administration. A total of 250 questionnaires were returned. Most of respondents were female, aged 36–70 and workers. More than a half of participants owned one dog with mixed breed, with Labrador retriever, golden retriever, dachshund, and border collie being the most represented breeds. On average, each dog was treated with an oral antibiotic 1.044 times per year. Intestinal diseases were among the main reasons (19%) for antibiotic prescription. Oral antibiotic courses without veterinary consultation (21%) and anticipated termination of the therapy (17.1%) were less common than reported elsewhere. The majority of respondents knew the meaning of AMR with a significant inverse association between the level of education and the tendency to administer antimicrobials without consulting a clinician (p = 0.004). Most of the owners expected a rapid recovery of clinical signs after a first episode of AD and accepted natural dietary supplementation for treating the condition. Ninety-five percent of the respondents believed that public funding should be spent to study AMR. Even though an acceptable degree of AMR awareness emerged, we feel that further efforts should be made to increase public AMR knowledge and to stimulate proactive measures to fight the phenomenon. On the other hand, the development of guidelines for the treatment of uncomplicated canine AD would help clinicians to rationalize antimicrobial use.

A retrospective study of cases of canine demodicosis submitted to a commercial diagnostic laboratory servicing the United Kingdom and Ireland (2017-2018) part 2; Aerobic culture and antimicrobial susceptibility results

Clinical diagnostic reports from 508 cases of canine demodicosis diagnosed either by histological or skin scraping analysis from a United Kingdom Accreditation Service (UKAS) accredited veterinary diagnostic laboratory servicing the United Kingdom (UK) and Ireland were evaluated. Of the 508 cases, 284 had skin swabs submitted for culture on the same day the skin biopsy and/or skin scraping were obtained. Dogs with juvenile-onset (JO) demodicosis represented 57.4% of these cases, whilst adult-onset (AO) cases comprised 42.6%. The data revealed that overgrowth of pathogenic bacteria was more common in AO demodicosis cases (75.2%) in comparison to the JO cases (57%). Adult-onset cases also had increased involvement of bacteria belonging to multiple genera and/or yeast (28.9%) in comparison to JO cases (18.4%). Pruritus was significantly associated with an overgrowth of Staphylococcus pseudintermedius (p < 0.001). Resistance to one or more antimicrobial classes was noted in S. pseudintermedius isolates from 56.3% of JO cases with 10.3% of these cases being classified as Multi-Drug Resistant (MDR). Similarly, 51.9% of S. pseudintermedius isolates from the AO cases were noted to be resistant to one or more antimicrobial class with 8.6% of these cases being considered MDR. Cephalosporins were the most frequently administered antimicrobial class noted in submission histories, followed by the penicillin and fluoroquinolone classes. Whilst our findings reveal a high prevalence of concurrent overgrowth of pathogenic bacteria warranting therapeutic intervention in canine demodicosis, the presence of resistance within isolates highlights the need for prudent selection and targeted use of antimicrobial therapy that encompass the key principles of antimicrobial stewardship.

Epidemiology and antimicrobial resistance of staphylococci other than Staphylococcus aureus from domestic animals and livestock in Africa: a systematic review

Introduction

Staphylococci other than Staphylococcus aureus (SOSA) in animals are becoming more pathogenic and antibiotic resistant and can potentially disseminate to humans. However, there is little synthesized information regarding SOSA from animals in Africa. This systematic review provides a comprehensive overview of the epidemiology and antimicrobial resistance of SOSA in companion animals (pets) and livestock in Africa.

Method

This systematic review (PROSPERO-CRD42021252303) was conducted according to the PRISMA guidelines, and 75 eligible studies from 13 countries were identified until August 2022. Three electronic databases (Pubmed, Scopus and Web of Science) were employed.

Results

The frequently isolated SOSA were S. epidermidis, S. intermedius, S. pseudintermedius, S. xylosus, S. chromogenes, S. hyicus, M. sciuri, S. hominis, and S. haemolyticus. Thirty (40%) studies performed antibiotic susceptibility testing (AST). Penicillin (58%) and tetracycline (28%) resistance were most common across all SOSA with high rates of resistance to aminoglycosides, fluoroquinolones, and macrolides in some species. Resistance to last-resort antibiotics such as linezolid and fusidic acid were also reported. Limited data on strain typing and molecular resistance mechanisms precluded analysis of the clonal diversity of SOSA on the continent.

Conclusion

The findings of this review indicate that research on livestock-associated SOSA in Africa is lacking in some regions such as Central and Western Africa, furthermore, research on companion animals and more advanced methods for identification and strain typing of SOSA need to be encouraged.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier: CRD42021252303.

Artificial Intelligence Models for Zoonotic Pathogens: A Survey

Zoonotic diseases or zoonoses are infections due to the natural transmission of pathogens between species (animals and humans). More than 70% of emerging infectious diseases are attributed to animal origin. Artificial Intelligence (AI) models have been used for studying zoonotic pathogens and the factors that contribute to their spread. The aim of this literature survey is to synthesize and analyze machine learning, and deep learning approaches applied to study zoonotic diseases to understand predictive models to help researchers identify the risk factors, and develop mitigation strategies. Based on our survey findings, machine learning and deep learning are commonly used for the prediction of both foodborne and zoonotic pathogens as well as the factors associated with the presence of the pathogens.

Patterns of antimicrobial, multidrug and methicillin resistance among Staphylococcus spp. isolated from canine specimens submitted to a diagnostic laboratory in Tennessee, USA: a descriptive study

Background

Multidrug- and methicillin-resistant staphylococci are both veterinary and public health concerns due to their zoonotic potential. Therefore, the objective of this study was to investigate patterns of antimicrobial, multidrug, and methicillin resistance among four Staphylococcus spp. commonly isolated from canine clinical specimens submitted to the Clinical Bacteriology Laboratory at the University of Tennessee College of Veterinary Medicine (UTCVM).

Methods

Results of antimicrobial susceptibility testing and mecA polymerase chain reaction (PCR) for isolates of four common Staphylococcus spp. isolates were obtained from the Bacteriology Laboratory at the UTCVM between 01/01/2006 and 12/31/2017. Cochran-Armitage trend test was used to assess temporal trends of antimicrobial resistance (AMR), multidrug resistance (MDR), and methicillin resistance. Kappa test of agreement was used to assess agreement between the results of PCR and disk diffusion tests.

Results

Most of the 7805 isolates were S. pseudintermedius (6453 isolates), followed by S. coagulans (860), S. aureus (330), and S. schleiferi (162). Among S. pseudintermedius isolates, 45.5% were MDR, and 30.8% were methicillin-resistant (MRSP). There was a significant temporal increase in MRSP (p = 0.017). Chloramphenicol resistance increased among both MRSP and methicillin-susceptible (MSSP) isolates (p <  0.0001). Among S. aureus isolates, 40.9% were MDR, 37.4% were methicillin-resistant (MRSA), and the proportion of MRSA isolates increased significantly (p = 0.0480) over time. There was an increasing temporal trend in the proportion of MDR isolates among MSSP (p = 0.0022), but a decrease among MRSP (p <  0.0001) and MRSA (p = 0.0298). S. schleiferi had the highest percentage (56.9%) of methicillin-resistant isolates. Oxacillin disk diffusion was superior to cefoxitin for the detection of mecA-mediated resistance and had almost perfect agreement with mecA PCR assay for S. pseudintermedius (95.4% agreement, kappa (κ) = 0.904; p <  0.0001), S. coagulans (95.6%, κ = 0.913; p <  0.0001) and S. schleiferi (97.7%, κ = 0.945; p <  0.0001). However, cefoxitin disk diffusion was superior to oxacillin disk diffusion and had almost perfect agreement with mecA PCR assay for S. aureus (95.3%, κ = 0.834; p <  0.0001).

Conclusions

The levels of resistance and increasing temporal trends are concerning. These findings have implications for treatment decisions and public health due to the zoonotic potential of staphylococci. Continued surveillance and use of antibiograms to guide clinical decisions will be critical.

Prevalence and Patterns of Antimicrobial Resistance among Escherichia coli and Staphylococcus spp. in a Veterinary University Hospital

The occurrence of antimicrobial resistance in commensal strains of Escherichia coli and Staphylococcus spp. was investigated in 320 samples collected from patients and the environment of a veterinary university hospital-specifically, the consultation area (CA) and intensive care unit (ICU). E. coli was isolated in 70/160 samples (44%), while Staphylococcus spp. were isolated in 110/160 (69%) samples. The occurrence of multidrug-resistant (MDR) isolates from CA and ICU admission were similar for E. coli (1/12 (8%) versus 4/27 (15%), respectively) and Staphylococcus spp. (10/19 (53%) versus 26/50 (52%), respectively). MDR E. coli isolates increased significantly at hospital discharge (18/31; 58%; p = 0.008). Antimicrobial treatment administered during hospitalization was a risk factor for carriage of MDR E. coli (OR, 23.9; 95% CI: 1.18-484.19; p = 0.04) and MDR Staphylococcus spp. (OR, 19.5; 95% CI 1.30-292.76; p = 0.02), respectively. The odds ratio for MDR E. coli was 41.4 (95% CI 2.13-806.03; p = 0.01), if the administration of fluoroquinolones was evaluated. The mecA gene was detected in 19/24 (79%) coagulase-positive Staphylococcus spp. isolates resistant to oxacillin. High rates of MDR Staphylococcus spp. were reported. Hospitalization in the ICU and antimicrobial treatment were risk factors for colonization by MDR commensal bacteria.

Evaluation of the Resistance Profile of Bacteria Obtained From Infected Sites of Dogs in a Veterinary Teaching Hospital in Brazil: A Retrospective Study

The aim of this study was to evaluate the prevalence and antimicrobial resistance profile of bacterial species isolated from infected sites of canines. All samples were collected from canine patients who received clinical or surgical care at the veterinary teaching hospital between March 2016 and November 2017. The samples were analyzed in a private pathology laboratory. A descriptive analysis of 295 antimicrobial susceptibility test reports was performed. Staphylococcus spp. (104/295 [35.25%]), Escherichia coli (100/295 [33.90%]), Proteus spp. (44/295 [14.92%]), Pseudomonas spp. (25/295 [8.47%]), and Klebsiella spp. (20/295 [6.78%]) were more frequently isolated, and a high incidence of multidrug resistance was observed (69,83% [206/295]). Methicillin-resistant Staphylococcus spp. accounted for 33% (33/100) of the Staphylococcus strains. Enterobacteriaceae cefotaxime resistance constituted 22.82 ± 4.49% and Enterobacteriaceae imipenem resistance constituted 5% (1/20) for Klebsiella spp., 5% (5/100) for E coli, and 6.82% (3/44) for Proteus spp. Pseudomonas spp. strains accounted for 8% (2/25) of imipenem resistance and 45.45% (10/22) of polymyxin B resistance. Our findings revealed a high rate of multidrug-resistant bacteria involvement in the infectious process of dogs. From the perspective of the One Health scenario, our results showed alarming data, given the high risk of resistant-strain dissemination between animals, owners, and healthcare professionals. There is an urgent need for strategies to control and prevent the evolution of new multidrug-resistant bacteria in veterinary hospitals. It is also crucial to understand and emphasize the role of veterinary professionals in this public health battle.

Occurrence and Predictors of Bacterial Respiratory Tract Infections and Antimicrobial Resistance Among Isolates From Dogs Presented With Lower Respiratory Tract Infections at a Referral Veterinary Hospital in South Africa

Background: Respiratory tract infections (RTIs) associated with Pasteurella multocida, Bordetella bronchiseptica, Streptococci, Staphylococci, and Pseudomonas species have been reported in dogs. The objective of this study was to investigate the occurrence and predictors of bacterial RTIs and antimicrobial resistance among samples from dogs with lower RTIs at a referral veterinary teaching hospital in South Africa.

Methods: Records of 157 dogs with lower RTIs presented to the veterinary teaching hospital between 2007 and 2013 were included in the study. Crude and factor-specific proportions of RTIs and antimicrobial resistance by breed, season, year, sex, age category, and specimen type were computed. Chi-square or Fisher's exact tests were used to compare proportions of RTIs and antimicrobial resistant isolates across categorical variables. Associations between breed, season, year, sex, age, specimen, and odds of RTIs or multidrug resistance were assessed using Generalized Estimating Equations.

Results: There was only one sample per clinical case and bacterial RTIs were observed in 53.5% of the samples tested. Pasteurella species (23.5%) were more common than other species. Almost all (99.5%) isolates were resistant to at least one antimicrobial, while 64.7% were multidrug resistant (MDR). Additionally, 17.0% and 3.3% showed evidence of extensive drug resistance (XDR) and pan-drug resistance (PDR), respectively. The majority of MDR isolates were resistant to penicillin-G (90.9%), lincomycin (100%), tylosine (75.8%), lincospectin (73.7%), ampicillin (72.5%), and kanamycin (68.4%). None of the investigated predictors had significant association with RTIs or antimicrobial resistance.

Conclusion:Pasturella species were the most common causes of RTIs. The high levels of MDR and the presence of both XDR and PDR isolates raise the question of the effectiveness of the current antimicrobial therapy used in patients with RTIs in referral hospitals. Given the high level of resistance observed in this study, it is advisable that the choice of antimicrobials for treatment of RTIs be based on antibiograms. This will ensure use of the most efficacious antimicrobials and will minimize treatment failures among cases presented with RTIs.

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant

This study explores the prevalence, emission, and reduction of five ARGs (sulI, tetA, mphB, qnrD, and mcr-1) and integron (intI) through a distributed swine wastewater purification facility and the effluent-receiving environment. Typical metal resistance genes (MRGs), pathogenic bacterial indicators, the bacterial community, and wastewater properties were also explored to determine their effects on the fates of ARGs. Results indicated that the purification process could hardly effectively remove ARGs' prevalence. 3.1 × 10⁴ -7.1 × 10⁸  copies/L were present after purification, and 4%-57% of them persisted in the subsequent creek and adjacent soil. 16S rRNA sequencing suggested that the discharge of wastewater significantly changed the bacterial community in receiving creek and soil. Molecular ecological networks analysis detected the wide co-occurrence among ARGs, MRGs, and PBGs, which could further facilitate the propagation of antibiotic resistance. ARG incidence and specific bacterial genera were closely correlated, suggesting an extensive hosting relationship. Redundancy analyses showed wastewater organics and nutrients showed positive correlation to most ARGs' abundance, but negatively correlated to their relative abundance. PRACTITIONER POINTS: Fate of five ARGs and intI was studied in a swine wastewater treatment system. The treatment process could not effectively reduce ARGs' abundance. ARGs and pathogens in wastewater were transferred to the receiving creek and soil. The network analysis found wide co-occurrence among ARGs, metal resistance genes, and pathogens. Wastewater nutrients positively correlated to ARG's abundance but negatively correlated to their relative abundance.

Geographic distribution of staphylococcus spp. infections and antimicrobial resistance among dogs from Gauteng Province presented at a veterinary teaching hospital in South Africa

The objective of this study was to investigate spatial patterns of staphylococcal infections and resistance patterns of clinical isolates among dogs from Gauteng province in South Africa. Data from records of 1497 dog clinical samples submitted to a veterinary teaching hospital between 2007 and 2012 were used in the study. Spatial empirical Bayesian smoothed risk maps were used to investigate spatial patterns of staphylococcal infections, antimicrobial resistance (AMR), and multidrug resistance (MDR). Moran's I and spatial scan statistics were used to investigate spatial clusters at municipal and town spatial scales. Significant clusters of staphylococcal infections were identified at both the municipal (Relative Risk [RR] = 1.71, p = 0.003) and town (RR = 1.65, p = 0.039) scales. However, significant clusters of AMR (p = 0.003) and MDR (p = 0.007) were observed only at the town scale. Future larger studies will need to investigate local determinants of geographical distribution of the clusters so as to guide targeted control efforts.

Temporal trends and predictors of antimicrobial resistance among Staphylococcus spp. isolated from canine specimens submitted to a diagnostic laboratory

Background

Resistance to commonly used antimicrobials is a growing concern in both human and veterinary medicine. Understanding the temporal changes in the burden of the problem and identifying its determinants is important for guiding control efforts. Therefore, the objective of this study was to investigate temporal patterns and predictors of antimicrobial resistance among Staphylococcus spp. isolated from canine specimens submitted to the University of Kentucky Veterinary Diagnostic Laboratory (UKVDL) between 1993 and 2009.

Methods

Retrospective data of 4,972 Staphylococcus isolates assessed for antimicrobial susceptibility using the disk diffusion method at the UKVDL between 1993 and 2009 were included in the study. Temporal trends were assessed for each antimicrobial using the Cochran-Armitage trend test. Logistic regression models were used to investigate predictors of antimicrobial resistance (AMR) and multidrug resistance (MDR).

Results

A total of 68.2% (3,388/4,972) Staphylococcus isolates were S. intermedius group (SIG), 18.2% (907/4,972) were coagulase-negative staphylococci (CoNS), 7.6% (375/4,972) were S. aureus, 5.8% (290/4,972) were S. hyicus, and S. schleiferi subsp. coagulans comprised 0.2% (12/4,972) of the isolates. The overall percentage of AMR and MDR were 77.2% and 25.6%, respectively. The highest levels of AMR were seen in CoNS (81.3%; 737/907), S. aureus (80.5%; 302/375), and SIG (77.6%; 2,629/3388). The lowest levels of AMR were observed in S. hyicus (57.9%; 168/290) and S. schleiferi subsp. coagulans (33.3%; 4/12). Overall, AMR and MDR showed significant (p<0.001) decreasing temporal trends. Significant temporal trends (both increasing and decreasing) were observed among 12 of the 16 antimicrobials covering 6 of the 9 drug classes assessed. Thus, significant increasing temporal trends in resistance were observed to β-lactams (p<0.001) (oxacillin, amoxicillin-clavulanate, cephalothin, and penicillin (p = 0.024)), aminoglycosides (p<0.001) (gentamicin, and neomycin), bacitracin (p<0.001), and enrofloxacin (p<0.001). In contrast, sulfonamide (p<0.001) (sulfadiazin) and tetracycline (p = 0.010) resistant isolates showed significant decreasing temporal trends in AMR. Staphylococcus spp., geographic region, and specimen source were significant predictors of both AMR and MDR.

Conclusions

Although not unexpected nor alarming, the high levels of AMR to a number of antimicrobial agents and the increasing temporal trends are concerning. Therefore, continued monitoring of AMR among Staphylococcus spp. is warranted. Future studies will need to identify local factors responsible for the observed geographic differences in risk of both AMR and MDR.