Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) for Identification of Bacterial Isolates From Horses

Diagnosis of bacteria from the CMNR group in farm animals

The CMNR group comprises bacteria of the genera Corynebacterium, Mycobacterium, Nocardia, and Rhodococcus and share cell wall and DNA content characteristics. Many pathogenic CMNR bacteria cause diseases such as mastitis, lymphadenitis, and pneumonia in farmed animals, which cause economic losses for breeders and represent a threat to public health. Traditional diagnosis in CMNR involves isolating target bacteria on general or selective media and conducting metabolic analyses with the assistance of laboratory biochemical identification systems. Advanced mass spectrometry may also support diagnosing these bacteria in the clinic's daily routine despite some challenges, such as the need for isolated bacteria. In difficult identification among some CMNR members, molecular methods using polymerase chain reaction (PCR) emerge as reliable options for correct specification that is sometimes achieved directly from clinical samples such as tracheobronchial aspirates and feces. On the other hand, immunological diagnostics such as the skin test or Enzyme-Linked Immunosorbent Assay (ELISA) for Mycobacterium tuberculosis yield promising results in subclinical infections with no bacterial growth involved. In this review, we present the methods most commonly used to diagnose pathogenic CMNR bacteria and discuss their advantages and limitations, as well as challenges and perspectives on adopting new technologies in diagnostics.

Bacterial and fungal isolates from 107 cases of ulcerative keratitis in Japanese Thoroughbred racehorses (2017-2021)

Infectious ulcerative keratitis is a common disease in racehorses. To improve treatment outcomes, this study aimed to assess the antimicrobial susceptibilities of bacterial and fungal isolates obtained from the cornea of Japanese Thoroughbred racehorses with equine infectious ulcerative keratitis. Bacterial and fungal cultures were performed for 166 corneal swabs from 107 cases. A disc diffusion test and minimum inhibitory concentration test were also performed to assess antimicrobial susceptibility of the bacterial and fungal isolates, respectively. Bacterial and/or fungal isolates were obtained from 85.0% (91/107) of the cases. Staphylococcus was primarily isolated from bacterial isolates, including methicillin-resistant Staphylococcus aureus (MRSA), Aerococcus, Streptococcus, Acinetobacter, and Pseudomonas. Aspergillus was primarily isolated from filamentous fungi, and Debaryomyces species was primarily identified in yeast-like fungi. Ofloxacin resistance was observed in 100% (12/12), 15.9% (7/44), and 25.0% (3/12) of MRSA, Staphylococcus, and Streptococcus isolates, respectively. The prevalence of quinolone-resistant Staphylococci and Streptococci has increased in the past two decades. All Aspergillus isolates were susceptible to voriconazole, whereas other filamentous fungi, including Fusarium, were less susceptible to voriconazole. Further studies are required to determine effective treatments for antimicrobial-resistant isolates.

Antimicrobial Resistance and Extended-Spectrum Beta-Lactamase Genes in Enterobacterales, Pseudomonas and Acinetobacter Isolates from the Uterus of Healthy Mares

Antibiotic-resistant bacteria are a growing concern for human and animal health. The objective of this study was to determine the antimicrobial resistance and extended-spectrum beta-lactamase genes in Enterobacterales, Pseudomonas spp. and Acinetobacter spp. isolates from the uterus of healthy mares. For this purpose, 21 mares were swabbed for samples, which were later seeded on blood agar and MacConkey agar. The isolates were identified using MALDI-TOF and the antimicrobial susceptibility test was performed using the Kirby-Bauer technique. To characterize the resistance genes, a polymerase chain reaction (PCR) scheme was performed. Of the isolates identified as Gram-negative, 68.8% were Enterobacterales, represented by E. coli, Enterobacter cloacae, Citrobacter spp., and Klebsiella pneumoniae; 28.1% belonged to the genus Acinetobacter spp.; and 3.1% to Pseudomonas aeruginosa. A 9.3% of the isolates were multidrug-resistant (MDR), presenting resistance to antibiotics from three different classes, while 18.8% presented resistance to two or more classes of different antibiotics. The diversity of three genes that code for ESBL (blaTEM, blaCTX-M and blaSHV) was detected in 12.5% of the strains. The most frequent was blaSHV, while blaTEM and blaCTX-M were present in Citrobacter spp. and Klebsiella pneumoniae. These results are an alarm call for veterinarians and their environment and suggest taking measures to prevent the spread of these microorganisms.

Comparing the Efficacy of MALDI-TOF MS and Sequencing-Based Identification Techniques (Sanger and NGS) to Monitor the Microbial Community of Irrigation Water

In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world's rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water.

Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in veterinary medicine: Recent advances (2019-present)

Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a valuable laboratory tool for rapid diagnostics, research, and exploration in veterinary medicine. While instrument acquisition costs are high for the technology, cost per sample is very low, the method requires minimal sample preparation, and analysis is easily conducted by end-users requiring minimal training. Matrix-assisted laser desorption ionization-time-of-flight MS has found widespread application for the rapid identification of microorganisms, diagnosis of dermatophytes and parasites, protein/lipid profiling, molecular diagnostics, and the technique demonstrates significant promise for 2D chemical mapping of tissue sections collected postmortem. In this review, an overview of the MALDI-TOF technique will be reported and manuscripts outlining current uses of the technology for veterinary science since 2019 will be summarized. The article concludes by discussing gaps in knowledge and areas of future growth.

Equine blood cultures: Can we do better?

Blood culture is considered the gold standard test for documenting bacteraemia in patients with suspected bacterial sepsis in veterinary and human medicine. However, blood culture often fails to yield bacterial growth even though the clinical picture is strongly suggestive of bacterial sepsis, or contaminating organisms can overgrow the true pathogen, making accurate diagnosis and appropriate management of this life-threatening condition very challenging. Methodology for collecting blood cultures in equine medicine, and even in human hospitals, is not standardised, and many variables can affect the yield and type of microorganisms cultured. Microbiological culture techniques used in the laboratory and specific sample collection techniques, including volume of blood collected, aseptic technique utilised, and the site, timing and frequency of sample collection, all have substantial impact on the accuracy of blood culture results. In addition, patient-specific factors such as husbandry factors, the anatomical site of the primary infection, and changing microflora in different geographic locations, also can impact blood cultures. Thus, blood cultures obtained in practice may not always accurately define the presence or absence of, or specific organisms causing, bacteraemia in horses and foals with suspected sepsis. Erroneous blood culture results can lead to inappropriate antimicrobial use, which can result in poor outcomes for individual patients and contribute to the development of antimicrobial resistance in the patient's microflora and the environmental microcosm. This review summarises current indications and methodology, and specific factors that may be optimised, for equine blood culture, with particular focus on available literature from neonatal foals with suspected bacterial sepsis. To standardise and optimise blood culture techniques in horses and foals, future research in this area should be aimed at determining the optimal volume of blood that should be collected for culture, and the ideal site, timing, and frequency of sample collection.

Isolation and Identification of Staphylococcus Species Obtained from Healthy Companion Animals and Humans

The close contact between people and their pets has generated the exchange of skin microbiota, accompanied by bacteria that present resistance to antibiotics. Staphylococcus spp., opportunistic pathogens present in the skin and mucosa of mammals, have had their importance recognized in human and veterinary medicine. The objectives of this study were to identify Staphylococcus spp. present in isolates from the nostrils of healthy humans, dogs and cats as well as to determine their phenotype of resistance to methicillin. Strain identification was performed by MALDI-TOF mass spectrometry and antimicrobial susceptibility was determined using a disk diffusion assay for 12 antibiotics. Sixty humans (veterinary and technicians), sixty dogs and sixty cats were sampled; of them, 61.6%, 56.6% and 46.6%, respectively, carried Staphylococcus spp. in their nostrils, and only two people carried two different species of Staphylococcus in the only anatomical site sampled. A methicillin-resistant phenotype was present in 48.7% of the humans, 26.5% of the dogs and 57.1% of the cats, and sampled. These results demonstrate the presence of Staphylococcus spp. strains resistant to methicillin in personnel who work in contact with animals, as well as in dogs and cats that entered the same hospital or veterinary clinic, which alerts us to the potential transfer of these strains to or between people, dogs and/or cats.

First Case Report of Aspergillary Rhinopharyngitis in a Foal From Chile

We present the first case of rhinopharyngitis due to Aspergillus fumigatus in a purebred Chilean horse. Clinically, manifested mucopurulent discharge from both nostrils, inflammation of the nasal, ocular, and ear mucosa; associated with decay and hyporexia. Based on the clinical signs and analysis of the mycological and molecular transtracheal aspirate sample, the present case was diagnosed as Aspergillus fumigatus rhinopharyngitis. After the antifungal susceptibility test, oral itraconazole treatment was maintained for 45 days, showing no clinical sign.

High prevalence of Mycoplasma equirhinis in Thoroughbred horses with respiratory symptoms in autumn 2018

Mycoplasma species are often isolated from horses with respiratory symptoms; however, the pathogenicity of Mycoplasma is still unclear. In autumn of 2018, we encountered an increase in cases with respiratory symptoms, mainly coughing, in a group of Thoroughbred racehorses in Japan. We examined tracheal wash samples obtained from 40 of those cases. Bacteria and viruses that commonly cause respiratory symptoms were investigated, and anaerobes were detected in only 5 cases and Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) was detected in only 1 case of 40 cases with loop-mediated isothermal amplification assay. S. zooepidemicus and Streptococcus pneumoniae were isolated at a bacterial count of higher than 1.0 × 10⁴ CFU/ml from 5 and 2 cases of 28 cases cultured, respectively. None of the viruses investigated was detected in 40 cases. Mycoplasma equirhinis (M. equirhinis) was isolated from 40.0% (16/40) of the cases, which was higher than previously reported isolation rates. The rate of M. equirhinis isolation in the cases from 2018 was significantly higher than the isolation rates in the other horses: clinical cases with respiratory symptoms in 2019-2020 (13.6%, 3/22) and healthy horses (13.5%, 5/37) in Japan. In this study, the isolation rate of M. equirhinis from horse group with cough symptoms in 2018 was high and no other common etiological agents were detected. The pathogenesis of M. equirhinis is still unclear, however, M. equirhinis might have been associated with respiratory symptoms in the Thoroughbred horse cases in 2018.

Construction and Application of an In-House Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Database Specific to Bacteria From Horses

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is used for identification of bacterial species isolated from horses. However, because of insufficiencies in the reference database, some bacterial species isolated from horses are difficult to identify with MALDI-TOF MS, and enriching the databases is expected to enhance the accuracy of MALDI-TOF MS identification. Here we created an in-house database including 271 bacterial isolates from horses. Furthermore, we used an enhanced database (our in-house database plus a commercially provided database) to examine 91 newly obtained isolates that could not be identified with MALDI-TOF MS using the commercially provided database. The enhanced database could identify 15 of those 91 isolates to the species level; including streptococcus (3/19), Gram-positive rod (4/17), Gram-negative rod (8/17) isolates. The enhanced database increased the average identification score of the 91 isolates (1.64-1.76). The in-house database increased the number of isolates that MALDI-TOF MS could identify to the species level and contributed to more accurate identification of bacterial isolates from horses.

Pathogenicity and drug resistance of animal streptococci responsible for human infections

Bacteria of the genus Streptococcus, earlier considered typically animal, currently have also been causing infections in humans. It is necessary to make clinicians aware of the emergence of new species that may cause the development of human diseases. There is an increasing frequency of isolation of streptococci such as S. suis, S. dysgalactiae, S. iniae and S. equi from people. Isolation of Streptococcus bovis/Streptococcus equinus complex bacteria has also been reported. The streptococcal species described in this review are gaining new properties and virulence factors by which they can thrive in new environments. It shows the potential of these bacteria to changes in the genome and the settlement of new hosts. Information is presented on clinical cases that concern streptococcus species belonging to the groups Bovis, Pyogenic and Suis. We also present the antibiotic resistance profiles of these bacteria. The emerging resistance to β-lactams has been reported. In this review, the classification, clinical characteristics and antibiotic resistance of groups and species of streptococci considered as animal pathogens are summarized.