Transparent deep learning to identify autism spectrum disorders (ASD) in EHR using clinical notes.

OBJECTIVE: Machine learning (ML) is increasingly employed to diagnose medical conditions, with algorithms trained to assign a single label using a black-box approach. We created an ML approach using deep learning that generates outcomes that are transparent and in line with clinical, diagnostic rules. We demonstrate our approach for autism spectrum disorders (ASD), a neurodevelopmental condition with increasing prevalence. METHODS: We use unstructured data from the Centers for Disease Control and Prevention (CDC) surveillance records labeled by a CDC-trained clinician with ASD A1-3 and B1-4 criterion labels per sentence and with ASD cases labels per record using Diagnostic and Statistical Manual of Mental Disorders (DSM5) rules. One rule-based and three deep ML algorithms and six ensembles were compared and evaluated using a test set with 6773 sentences (N = 35 cases) set aside in advance. Criterion and case labeling were evaluated for each ML algorithm and ensemble. Case labeling outcomes were compared also with seven traditional tests. RESULTS: Performance for criterion labeling was highest for the hybrid BiLSTM ML model. The best case labeling was achieved by an ensemble of two BiLSTM ML models using a majority vote. It achieved 100% precision (or PPV), 83% recall (or sensitivity), 100% specificity, 91% accuracy, and 0.91 F-measure. A comparison with existing diagnostic tests shows that our best ensemble was more accurate overall. CONCLUSIONS: Transparent ML is achievable even with small datasets. By focusing on intermediate steps, deep ML can provide transparent decisions. By leveraging data redundancies, ML errors at the intermediate level have a low impact on final outcomes.

Antimicrobial Resistance Profiles and Molecular Characteristics of Salmonella enterica Serovar Agona Isolated from Food-Producing Animals During 2010-2020 in South Korea.

Multidrug-resistant (MDR) Salmonella enterica serovar Agona infections affect public health globally. This investigation aimed to ascertain the antimicrobial resistance profiles and molecular characteristics of Salmonella Agona isolates obtained from food-producing animals. A total of 209 Salmonella Agona isolates were recovered from mostly chickens (139 isolates), pigs (56 isolates), cattle (11 isolates), and ducks (3 isolates) between 2010 and 2020 in South Korea. In addition, these Salmonella Agona isolates were obtained from 25 slaughterhouses nationwide. Furthermore, this serotype suddenly increased in chickens in 2020. Salmonella Agona from chickens showed high resistance (69-83%) to ampicillin, streptomycin, tetracycline, trimethoprim/sulfamethoxazole, and chloramphenicol. Moreover, chicken/duck isolates (83.1%) showed significantly higher levels of MDR than cattle/pig isolates (1.5%). For molecular analysis by pulsed-field gel electrophoresis, infrared spectroscopy biotyping, and multilocus sequence typing in combination, a total of 23 types were observed. Especially two major types, P1-III-2-13 and P1-IV-2-13, comprised 59.3% of the total isolates spreading in most farms. Moreover, Salmonella Agona sequence type (ST)13 was predominant (96.7%) among three different STs (ST13, ST11, and ST292) widely detected in chickens (94.3%) in most farms located nationwide. Taken together, MDR Salmonella Agona in chickens might pose a potential risk to public health through direct contact or the food chain.

Initial experience with the enhanced recovery after surgery (ERAS) protocols in gynecologic surgery at an urban academic tertiary medical center.

Background: The enhanced recovery after surgery (ERAS) protocols have been consistently associated with improved patient experience and surgical outcomes. Despite the release of ERAS Society guidelines specific to gynecologic oncology, the adoption of ERAS in gynecology on global level has been disappointingly low and some centers have shown minimal improvement in clinical outcomes after adopting ERAS. The aim of this study is to describe the development and early experience of ERAS protocols in gynecologic surgery at an urban academic tertiary medical center. Methods: This was an observational prospective cohort study. The target patient population included those with low comorbidities who were scheduled to undergo various types of gynecologic surgeries for both benign and malignant diseases between October 2020 and February 2021. Two attending surgeons implemented the protocols for their patients (ERAS cohort) while three attending surgeons maintained the conventional perioperative care for their patients (non-ERAS cohort). Baseline characteristics, surgical outcomes and patients' answers to a 12-question survey were compared. A case-matched comparative analysis was also performed between the ERAS cohort and the historical non-ERAS cohort (those who received the same types of surgical procedures from the two ERAS attending surgeons prior to the implementation of the protocols). Results: A total of 244 patients were evaluated (122 in the ERAS cohort vs. 122 in the non-ERAS cohort). The number of vials of opioid analgesia used during the first two postoperative days was significantly lower whereas the use of nonsteroidal anti-inflammatory drugs (NSAIDs) and acetaminophen was more frequent in the ERAS cohort group. The patients in the ERAS group reported less postoperative pain, feelings of hunger and thirst, and greater amount of exercise postoperatively. These benefits of the ERAS cohort were more pronounced in the patients who underwent laparotomic surgeries than those who underwent laparoscopic surgeries. The case-matched comparative analysis also showed similar results. The length of hospital stay did not differ between those who underwent the ERAS protocols and those who did not. Conclusions: The results of the study demonstrated the safety, clinical feasibility and benefits of the ERAS protocols for patients undergoing gynecologic surgeries for both benign and malignant indications.

Antibiotic Resistance Profiles and Molecular Characteristics of blaCMY-2-Carrying Salmonella enterica Serovar Albany Isolated from Chickens During 2013-2020 in South Korea.

The production of ß-lactamase by nontyphoidal Salmonella has become a public health issue throughout the world. In this study, we aimed to investigate the antimicrobial resistance profiles and molecular characteristics of ß-lactamase-producing Salmonella enterica serovar Albany isolates. A total of 434 Salmonella Albany were obtained from feces and carcasses of healthy and diseased food-producing animals [cattle (n = 2), pigs (n = 3), chickens (n = 391), and ducks (n = 38)] during 2013-2020. Among the 434 Salmonella Albany isolates, 3.7% showed resistance to cefoxitin, and all the cefoxitin-resistant isolates were obtained from chickens. Moreover, Salmonella Albany isolates demonstrated high resistance to nalidixic acid (99.3%), trimethoprim/sulfamethoxazole (97.9%), ampicillin (86.6%), chloramphenicol (86.6%), and tetracycline (85.7%), as well as higher rates of multidrug resistance were detected in cefoxitin-resistant isolates compared to cefoxitin-susceptible isolates. All cefoxitin-resistant isolates harbored CMY-2-type ß-lactamase and belonged to seven different pulsotypes, with type IV-b (43.75%) and IV-a (25%) making up the majority. In addition, genes encoding cefoxitin resistant of all blaCMY-2-harboring Salmonella Albany isolates were horizontally transmitted to a recipient Escherichia coli J53 by conjugation. Furthermore, 93.75% (15/16) of conjugative plasmids harboring blaCMY-2 genes belong to ST12/CC12-IncI1. Genetic characteristics of transmitted blaCMY-2 genes were associated with ISEcp1, which can play an essential role in the effective mobilization and expression of these genes. Salmonella Albany containing blaCMY-2 in chickens can potentially be transferred to humans. Therefore, it is necessary to restrict antibiotic use and conduct continuous monitoring and analysis of resistant bacteria in the poultry industry.

Prevalence and Characterization of Extended-Spectrum ß-Lactamase-Producing Escherichia coli Isolated from Dogs and Cats in South Korea.

Overall, 836 Escherichia coli isolates (695 isolates from dogs and 141 from cats) were recovered from the diarrhea, skin/ear, urine, and genitals of dogs and cats between 2018 and 2019. Cefovecin and enrofloxacin resistance were noted in 17.1% and 21.2% of E. coli isolates, respectively. The cefovecin and enrofloxacin resistance rates were higher in dog isolates (18.1% and 22.9%) compared with the rates in cat isolates (12.1%, 12.8%). Interestingly, resistance to both antimicrobials was noted in 10.8% (90/836) of the isolates, predominantly in isolates from dogs. blaCTX-M-14, blaCTX-M-15, and blaCMY-2 were the most frequent extended-spectrum ß-lactamase/plasmid-mediated AmpC ß-lactamase (ESBL/AmpC)- gene types. The co-existence of blaCTX-M andblaCMY-2 was noted in six E. coli isolates from dogs. Sequencing analysis demonstrated that S83L and D87N in gyrA and S80I in parC were the most frequent point mutations in the quinolone resistance-determining regions of the cefovecin and enrofloxacin-resistant isolates. A total of 11 isolates from dogs carried the plasmid-mediated quinolone resistance genes (six aac(6')-Ib-cr, four qnrS, and one qnrB), while only two cat isolates carried the qnrS gene. Multilocus sequence typing of the cefovecin and enrofloxacin-resistant isolates revealed that sequence type (ST)131 E. coli carrying blaCTX-M-14 and blaCTX-M-15 genes and ST405 E. coli carrying blaCMY-2 gene were predominant among the isolated E. coli strains. The majority of the ESBL/AmpC-producing isolates displayed diverse pulsed-field gel electrophoresis profiles. This study demonstrated that third-generation cephalosporin- and fluoroquinolone-resistant E. coli were widely distributed in companion animals. The detection of the pandemic ST131 clone carrying blaCTX-M-14/15 in companion animals presented a public health threat.

Antimicrobial Resistance Profiles and Molecular Characteristics of Extended-Spectrum ß-Lactamase-Producing Escherichia coli Isolated from Healthy Cattle and Pigs in Korea.

Antimicrobial-resistant bacteria isolated from food animals pose a major health threat to the public on this planet. This study aimed to determine the susceptibility profiles of Escherichia coli isolated from cattle and pig fecal samples and investigate the molecular characteristics of extended-spectrum ß-lactamase (ESBL)-producing E. coli using gene identification, conjugation, and Southern blot approach. Overall 293 E. coli were recovered from cattle (120 isolates) and pigs (173 isolates) in 7 provinces of Korea during 2017-2018. Ampicillin, chloramphenicol, streptomycin, and sulfisoxazole resistance rates were the highest in pigs' isolates (>60%, p ≤ 0.001) compared to that in cattle (3-39%). Multidrug resistance (MDR) was higher in pig isolates (73%) than in cattle (31%), and the MDR profile usually includes streptomycin, sulfisoxazole, and tetracycline. Resistance to critically important antimicrobials such as ceftiofur, colistin, and ciprofloxacin was higher in weaners than those from finishers in pigs. The qnrS gene was detected in 13% of the pig isolates. Eight isolates from pigs and one isolate from cattle were identified as ESBL-producers and ESBL genes belonged to blaCTX-M-55 (n = 4), blaCTX-M-14 (n = 3), and blaCTX-M-65 (n = 2). Notably, the blaCTX-M-65 and qnrS1 genes were found to be carried together in an identical plasmid (IncHI2) in two isolates from finisher pigs. The blaCTX-M-carrying isolates belonged to phylogenetic groups B1 (n = 4), B2 (n = 2), A (n = 2), and D (n = 1). The blaCTX-M genes and non-ß-lactam resistance traits were transferred to the E. coli J53 recipient from seven blaCTX-M-positive strains isolated from pigs. The blaCTX-M genes belonged to the IncI1α, IncFII, and IncHI2 plasmids and are also associated with the ISEcp1, IS26, IS903, and orf477 elements. These findings suggested the possibility of blaCTX-M-carrying E. coli transmission to humans through direct contact with cattle and pigs or contamination of food products.

Antibiotic Resistance Profiles and Molecular Characteristics of blaCTX-M-15-Carrying Salmonella enterica Serovar Enteritidis Isolates from Healthy and Diseased Chickens in Korea.

Extended-spectrum ß-lactamase (ESBL)-producing Salmonella enterica serovar Enteritidis has emerged as a public health concern. The main objectives of this study were therefore to determine the antimicrobial susceptibility profiles of Salmonella Enteritidis and to investigate the molecular characteristics of identified ESBL-producing isolates. In the study, 237 Salmonella Enteritidis isolates (232 isolates from chickens, 4 from cattle, and 1 from a pig) were recovered from carcasses and fecal samples of healthy and diseased food animals between 2010 and 2017. Ceftiofur resistance was noted only in chicken isolates (43%, 102/237), with the highest in healthy chickens and their carcasses (48.3%, 83/172) compared with that in diseased chickens (31.7%, 19/60). All of the ceftiofur-resistant isolates exhibited resistance to multiple antimicrobials. Indeed, a relatively higher percentage of ceftiofur-resistant isolates demonstrated resistance to the tested aminoglycosides and tetracycline compared with the ceftiofur-susceptible strains. In this study, blaCTX-M-15 was the only ESBL gene detected in all of the ceftiofur-resistant isolates. The blaCTX-M-15-carrying isolates belonged to 11 different pulsotypes. The blaCTX-M-15 gene was transferred from 20.6% (21/102) of the blaCTX-M-15-harboring isolates to a recipient Escherichia coli J53. The coexistence of IncHI2/ST2 and IncFIIs/ST1 plasmids was noted in the majority (81.8%, 18/22) of the transconjugants. E. coli J53 transconjugants carrying blaCTX-M-15 gene showed distinct genetic environments, predominantly ISEcp1-blaCTX-M-15-orf477 (15/21, 71.4%). This study demonstrated that healthy chickens and their carcasses act as reservoirs of blaCTX-M-15-carrying Salmonella Enteritidis that can potentially be transmitted to humans.

Bacterial Prevalence in Skin, Urine, Diarrheal Stool, and Respiratory Samples from Dogs.

The emergence of bacterial infections in companion animals is a growing concern as humans can also be infected through the transmission of pathogenic bacteria. Because there have been few studies conducted on companion animals, the extent and significance of prevalence in veterinary practices remain unknown. This is the first nationwide surveillance report aimed at elucidating the prevalence pattern and associated infections of isolated bacteria from dogs in Korea. Bacterial isolates were collected from seven different laboratories participating in the Korean Veterinary Antimicrobial Resistance Monitoring System from 2018 to 2019. The samples were obtained from the diarrheal stool, skin/ear, urine, and respiratory samples of veterinary hospital-visited dogs. Isolation and identification of bacterial species was carried out using a bacterial culture approach and then confirmed with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF) and polymerase chain reaction (PCR). Out of 3135 isolates in dogs, 1085, 1761, 171, and 118 were extracted from diarrheal stool, skin/ear, urine, and respiratory samples, respectively. The overall prevalence of bacteria was higher among two age groups (1-5 and 6-10 years) with a 66.5 percent prevalence. This study showed that Escherichia coli was the most prevalent species among isolated bacterial species of diarrheal and urine origin, whereas Staphylococcus pseudintermedius was the most prevalent among skin and respiratory sample isolates. The data on the prevalence of bacteria for each dog specimen could provide basic information to estimate the extent of bacterial infection and antimicrobial resistance development and to guide veterinarians in therapeutic decisions in clinical practices throughout Korea.

Prevalence of Bacterial Species in Skin, Urine, Diarrheal Stool, and Respiratory Samples in Cats.

Bacterial infections are a significant cause of illness and death in different animals. However, these bacterial infections could be a source of human disease or illness if these pathogenic bacteria are present in companion animals. This study aimed to investigate the prevalence of pathogenic bacteria associated with different site infections in cats in the Republic of Korea. For this purpose, samples were collected from the skin/ear, urine, respiratory, and diarrheal stool origins of cats obtained between 2018 and 2019 from seven different laboratories and centers participating in the Korean Veterinary Antimicrobial Resistance Monitoring System. These samples were subjected to analysis for the identification and isolation of associated bacterial species using a bacterial culture approach. A total of 609 isolates were identified in four different cat samples. Among them, 267, 184, 57, and 101 were extracted from diarrheal stool, skin, urine, and respiratory samples, respectively. The findings of this study showed that Escherichia coli was the most prevalent species among isolated bacterial species of diarrheal stool and urine origin. Staphylococcus felis and Pasteurella multocida were most prevalent in the skin and respiratory tract, respectively. However, there was no significant difference in bacterial distribution among the different age groups in all samples. This is the first nationwide surveillance report that associates bacterial prevalence with their site of origin and helps in the prevention of bacterial infections in cats. Moreover, the pattern of bacterial prevalence could provide sufficient guidance for the selection of empirical antimicrobial therapy against infections in cats.

Antimicrobial Resistance in Escherichia coli Isolates from Healthy Food Animals in South Korea, 2010-2020.

Antimicrobial-resistant bacteria in food animals pose a major public health threat worldwide. In this study, we aimed to assess the antimicrobial resistance profiles and resistance trends of commensal Escherichia coli isolated from the feces of healthy cattle, pigs, and chickens in South Korea during 2010 and 2020. A total of 7237 E. coli isolates (2733 cattle, 2542 pig, and 1962 chicken isolates) were tested for susceptibility towards 12 antimicrobials. About 48%, 90%, and 97% of cattle, pig, and chicken isolates, respectively, were resistant to one or more antimicrobial agents. Cattle isolates presented low resistance (<15%) to most of the tested antimicrobials. In contrast, chicken and pig isolates demonstrated a relatively high (>45%) resistance rate to ampicillin, chloramphenicol, streptomycin, and tetracycline. We observed high ciprofloxacin and nalidixic acid resistance rates in chicken (76.1% and 88.6%, respectively), isolates in pig (12.7% and 26.7%, respectively) and cattle (2.7% and 8.2%, respectively) isolates. Notably, a very small proportion of isolates (<5%) from cattle, chickens, and pigs demonstrated resistance to amoxicillin/clavulanic acid, cefoxitin, and colistin. We identified ceftiofur resistance in a small proportion of chicken (8.8%), pig (3.7%), and cattle (0.7%) isolates. We noted an increasing but fluctuating trend of ampicillin, amoxicillin/clavulanic acid, ceftiofur, cefoxitin, chloramphenicol, ciprofloxacin, and streptomycin resistance in pig isolates. Similarly, the ampicillin, ceftiofur, and chloramphenicol resistance rates were increased but fluctuated through time in chicken isolates. Overall, 56% of the isolates showed multidrug-resistant (MDR). The proportion of MDR isolates was low in cattle (17.1%); however, this proportion was high in chickens (87.1%) and pigs (73.7%). Most of the resistance patterns included streptomycin and tetracycline in pigs and cattle, and ciprofloxacin and nalidixic acid in chickens. In conclusion, this study showed high resistance of commensal E. coli isolated from major food animals in Korea to commonly used antimicrobials including critically important antimicrobials. These bacteria could not only be a resistance reservoir but also could have potential to spread this resistance through gene transfer to pathogenic bacteria. Thus, the high prevalence of antimicrobial resistance in food animals highlights the urgent need for measures to restrict and ensure the prudent use of antimicrobials in Korea.

Imipenem Resistance Mediated by blaOXA-913 Gene in Pseudomonas aeruginosa.

Treatment of infectious diseases caused by carbapenem-resistant Pseudomonas aeruginosa is becoming a greater challenge. This study aimed to identify the imipenem resistance mechanism in P. aeruginosa isolated from a dog. Minimum Inhibitory Concentration (MIC) was determined by the broth microdilution method according to the Clinical and Laboratory Standards Institute recommendations. We performed polymerase chain reaction and whole-genome sequencing to detect carbapenem resistance genes. Genomic DNA of P. aeruginosa K19PSE24 was sequenced via the combined analysis of 20-kb PacBio SMRTbell and PacBio RS II. Peptide-Peptide Nucleic Acid conjugates (P-PNAs) targeting the translation initiation region of blaOXA-913 were synthesized. The isolate (K19PSE24) was resistant to imipenem and piperacillin/tazobactam yet was susceptible to most of the tested antimicrobials. Whole-genome sequencing revealed that the K19PSE24 genome comprised a single contig amounting to 6,815,777 base pairs, with 65 tRNA and 12 rRNA genes. K19PSE24 belonged to sequence type 313 and carried the genes aph(3)-IIb, fosA, catB7, crpP, and blaOXA-913 (an allele deposited in GenBank but not described in the literature). K19PSE24 also carried genes encoding for virulence factors (exoenzyme T, exotoxin A, and elastase B) that are associated with adhesion, invasion, and tissue lysis. Nevertheless, we did not detect any of the previously reported carbapenem resistance genes. This is the first report of the blaOXA-913 gene in imipenem-resistant P. aeruginosa in the literature. Notably, no viable colonies were found after co-treatment with imipenem (2 µg/mL) and either of the P-PNAs (12.5 µM or 25 µM). The imipenem resistance in K19PSE24 was primarily due to blaOXA-913 gene carriage.

Antimicrobial Resistance Profiles and Macrolide Resistance Mechanisms of Campylobacter coli Isolated from Pigs and Chickens.

We identified 1218 Campylobacter coli isolates from fecal and carcass samples of pigs (n = 643) and chickens (n = 575) between 2010 and 2018. About 99% of the isolates were resistant to at least one antimicrobial agent. The isolates exhibited high resistance rates (>75%) to ciprofloxacin, nalidixic acid, and tetracycline. Azithromycin and erythromycin resistance rates were the highest in isolates from pigs (39.7% and 39.2%, respectively) compared to those of chickens (15.8% and 16.3%, respectively). Additionally, a low-to-moderate proportion of the isolates were resistant to florfenicol, gentamicin, clindamycin, and telithromycin. Multidrug resistance (MDR) was found in 83.1% of the isolates, and profiles of MDR usually included ciprofloxacin, nalidixic acid, and tetracycline. We found point mutation (A2075G) in domain V of the 23S rRNA gene in the majority of erythromycin-resistant isolates. Multilocus sequence typing of 137 erythromycin-resistant C. coli isolates revealed 37 previously reported sequence types (STs) and 8 novel STs. M192I, A103VI, and G74A substitutions were frequently noted in the ribosomal proteins L4 or L22. Further, we identified a considerable proportion (>90%) of erythromycin-resistant isolates carrying virulence factor genes: flaA, cadF, ceuE, and VirB. The prudent use of antimicrobials and regular microbiological investigation in food animals will be vital in limiting the public health hazards of C. coli in Korea.

Nationwide Surveillance on Antimicrobial Resistance Profiles of Enterococcus faecium and Enterococcus faecalis Isolated from Healthy Food Animals in South Korea, 2010 to 2019.

Intestinal commensal bacteria are considered good indicators for monitoring antimicrobial resistance. We investigated the antimicrobial resistance profiles and resistance trends of Enterococcus faecium and Enterococcus faecalis isolated from food animals in Korea between 2010 and 2019. E. faecium and E. faecalis, isolated from chickens and pigs, respectively, presented a relatively high resistance rate to most of the tested antimicrobials. We observed high ciprofloxacin (67.9%), tetracycline (61.7%), erythromycin (59.5%), and tylosin (53.0%) resistance in E. faecium isolated from chickens. Similarly, more than half of the E. faecalis isolates from pigs and chickens were resistant to erythromycin, tetracycline and tylosin. Notably, we observed ampicillin, daptomycin, tigecycline and linezolid resistance in a relatively small proportion of enterococcal isolates. Additionally, the enterococcal strains exhibited an increasing but fluctuating resistance trend (p < 0.05) to some of the tested antimicrobials including daptomycin and/or linezolid. E. faecalis showed higher Multidrug resistance (MDR) rates than E. faecium in cattle (19.7% vs. 8.6%, respectively) and pigs (63.6% vs. 15.6%, respectively), whereas a comparable MDR rate (≈60.0%) was noted in E. faecium and E. faecalis isolated from chickens. Collectively, the presence of antimicrobial-resistant Enterococcus in food animals poses a potential risk to public health.

Nationwide Surveillance on Antimicrobial Resistance Profiles of Staphylococcus aureus Isolated from Major Food Animal Carcasses in South Korea During 2010-2018.

Contamination of meat with antimicrobial-resistant bacteria represents a major public health threat worldwide. In this study, we determined the antimicrobial resistance profiles and resistance trends of Staphylococcus aureus isolated from major food animal carcasses (408 cattle, 1196 pig, and 1312 chicken carcass isolates) in Korea from 2010 to 2018. Approximately 75%, 92%, and 77% of cattle, pig, and chicken carcass isolates, respectively, were resistant to at least one antimicrobial agent. Resistance to penicillin (62.1%) was the highest, followed by resistance to tetracycline (42.1%) and erythromycin (28.2%). About 30% of pig and chicken isolates were resistant to ciprofloxacin. We observed linezolid resistance only in pig isolates (2.3%). However, all S. aureus isolates were sensitive to rifampin and vancomycin. We noted an increasing but fluctuating trend of kanamycin and penicillin resistance in cattle isolates. Similarly, the chloramphenicol, ciprofloxacin, tetracycline, and trimethoprim resistance rates were increased but fluctuated through time in pig isolates. Methicillin-resistant S. aureus (MRSA) accounted for 5%, 8%, and 9% of the cattle, pig, and chicken isolates, respectively. The MRSA strains exhibited significantly high resistance rates to most of the tested antimicrobials, including ciprofloxacin, erythromycin, and tetracycline compared with methicillin-susceptible S. aureus (MSSA) strains. Notably, a relatively high percentage of MRSA strains (5.2%) recovered from pig carcasses were resistant to linezolid compared with MSSA strains (2.1%). In addition, almost 37% of the isolates were multi-drug resistant. S. aureus isolates recovered from major food animal carcasses in Korea exhibited resistance to clinically important antimicrobials, posing a public health risk.

Mobile Colistin Resistance Gene mcr-1 Detected on an IncI2 Plasmid in Salmonella Typhimurium Sequence Type 19 from a Healthy Pig in South Korea.

Colistin is considered the last resort for the treatment of multi-drug resistant Gram-negative bacterial infections. We studied colistin resistance and the mcr-1 gene carriage in Salmonella isolates recovered from food animals in South Korea between 2010 and 2018. Colistin resistance was found in 277 isolates, predominantly in Salmonella Enteritidis (57.1%) and Salmonella Gallinarum (41.9%). However, the mcr-1 gene was identified in only one colistin-resistant Salmonella Typhimurium (MIC = 16 µg/mL) isolated from a healthy pig. The mcr-1 carrying isolate presented additional resistance to multiple antimicrobials. The strain belonged to sequence type (ST)19 and carried various virulence factor genes that are associated with adhesion and invasion of Salmonella into intestinal epithelial cells, as well as its survival in macrophages. The mcr-1 gene was identified on an IncI2 plasmid and it was also transferred to the E. coli J53 recipient strain. The mcr-1-carrying plasmid (pK18JST013) in this study was closely related to that previously reported in S. Indiana (pCFSA664-3) from chicken in China. This is the first report of mcr-1 carrying S. Typhimurium in South Korea. The finding indicates the importance of regular screening for the presence of the mcr-1 gene in S. Typhimurium in food animals to prevent the spread to humans.

Short communication: First detection of Panton-Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus ST30 in raw milk taken from dairy cows with mastitis in South Korea.

We identified 199 Staphylococcus aureus isolates from quarter milk samples of 1,289 dairy cattle between 2014 and 2018. About 66% of the isolates were resistant to at least 1 antimicrobial agent; the highest rate of resistance was to penicillin, followed by resistance to ampicillin, erythromycin, and sulfadimethoxine. We obtained 30 methicillin-resistant S. aureus (MRSA) strains from 6 farms in 3 provinces. The MRSA strains exhibited a significantly higher resistance rate to most of the tested antimicrobials than the oxacillin-susceptible strains. The MRSA strains represented 5 genotypes: ST72-t324-SCCmec IV (n = 14), ST30-t1752-SCCmec IV (n = 8), ST188-t189-SCCmec NT (n = 6), ST188-t2284-SCCmec NT (n = 1), and NT-NT-SCCmec IV (n = 1). One of the ST188 MRSA strains represented a novel staphylococcal protein A (spa) type (t2284). In addition, 7 of the 8 ST30 MRSA strains were Panton-Valentine leukocidin (PVL)-positive and carried various staphylococcal enterotoxin encoding genes. This is the first report of PVL-positive ST30 MRSA-t1752-SCCmec IV from bovine mastitis in Korea. All of ST72-t324-SCCmec IV MRSA strains carried staphylococcal enterotoxin and leukotoxin encoding genes. They were also sensitive to most of the tested non-ß-lactam antimicrobials. In contrast, ST188-t189 MRSA strains were resistant to multiple antimicrobials and predominantly carried the leukotoxin encoding gene. Taken together, these findings may indicate that dairy cows could be a major source for spreading MRSA strains, and contaminated milk could be a vehicle for transmission. Suitable hygienic measures should be established in dairy farms and processing plants to limit the likelihood of introducing MRSA into the food chain.

Resistance profiling and molecular characterization of Staphylococcus aureus isolated from goats in Korea.

Staphylococcus aureus is among the most common zoonotic pathogens that cause foodborne illnesses worldwide. The main objectives of the current study were therefore to determine the antimicrobial susceptibility profiles of S. aureus isolated from goats in Korea and to investigate the molecular characteristics of identified methicillin-resistant S. aureus (MRSA). In the study, 481 S. aureus isolates (431 from the nasal cavity and 50 from carcass) were recovered from 1146 carcasses and nasal swabs between July 2018 and January 2019. Approximately 82% and 72.6% of nasal and carcass isolates, respectively, were resistant to at least one antimicrobial agent, with the highest rate of resistance to penicillin, followed by resistance to chloramphenicol and tetracycline. Relatively small proportions of the isolates were resistant to cefoxitin, clindamycin, and erythromycin. However, all S. aureus isolates were sensitive to linezolid, rifampin, and vancomycin. Six MRSA isolates were obtained, three each from the nasal cavity and carcass. MRSA isolates were of two sequence types (ST) (ST72 and ST398), three spa types (t664, t324, and t571), and two SCCmec types (IV and V). The ST72 MRSA isolates had identical PFGE profiles. In addition, ST72 MRSA-SCCmec IV isolates carried at least six staphylococcal leukotoxin- and enterotoxin-encoding genes (lukED, seg, sei, sem, sen, seo, and seq). The remaining ST398 isolate carried only the lukED gene and was additionally resistant to eight non-ß-lactam antibiotics. To the best of our knowledge, this is the first report of MRSA from goats in Korea. There is a possibility of transmission of MRSA from goat to human or contamination of food products. Therefore, regular microbiological investigation in goats, farms, and slaughterhouses is critical to determine the existence of virulent and multi-drug resistant (MDR) S. aureus and to implement preventive strategies.

First Report of an Escherichia coli Strain Carrying the Colistin Resistance Determinant mcr-1 from a Dog in South Korea.

We studied the presence of the mobile colistin resistance gene mcr-1 in Escherichia coli isolates recovered from fecal and urine samples of companion animals, that were collected from South Korea in 2018 and 2019. The mcr-1 gene was detected in one colistin-resistant E. coli isolated from a diarrheic dog. The isolate exhibited additional resistance to multiple antimicrobials, including fluoroquinolones and third-generation cephalosporins. The mcr-1 carrying isolate belonged to ST160. The pulsed-field gel electrophoresis pattern of our strain differed from those ST160 E. coli strains previously identified from chickens in Korea. The mcr-1 gene was identified in the IncI2 plasmid. It was also transferred to E. coli J53 recipient strain, with a conjugation efficiency of 2.8 × 10-4. Average nucleotide identity analysis demonstrated that the mcr-1-carrying plasmid in this study was closely related to those from patients in Korea. To the best of our knowledge, this is the first report of mcr-1 carrying E. coli from a companion animal in South Korea. Our findings support One Health approach is necessary to prevent the dissemination of this high-risk gene.

Emergence of cfr-Mediated Linezolid Resistance in Staphylococcus aureus Isolated from Pig Carcasses.

Altogether, 2547 Staphylococcus aureus isolated from cattle (n = 382), pig (n = 1077), and chicken carcasses (n = 1088) during 2010-2017 were investigated for linezolid resistance and were further characterized using molecular methods. We identified linezolid resistance in only 2.3% of pig carcass isolates. The linezolid-resistant (LR) isolates presented resistance to multiple antimicrobials, including chloramphenicol, clindamycin, and tiamulin. Molecular investigation exhibited no mutations in the 23S ribosomal RNA. Nevertheless, we found mutations in ribosomal proteins rplC (G121A) and rplD (C353T) in one and seven LR strains, respectively. All the LR isolates carried the multi-resistance gene cfr, and six of them co-carried the mecA gene. Additionally, all the LR isolates co-carried the phenicol exporter gene, fexA, and presented a high level of chloramphenicol resistance. LR S. aureus isolates represented 10 genotypes, including major genotypes ST433-t318, ST541-t034, ST5-t002, and ST9-t337. Staphylococcal enterotoxin and leukotoxin-encoding genes, alone or in combination, were detected in 68% of LR isolates. Isolates from different farms presented identical or different pulsed-field gel electrophoresis patterns. Collectively, toxigenic and LR S. aureus strains pose a crisis for public health. This study is the first to describe the mechanism of linezolid resistance in S. aureus isolated from food animal products in Korea.

Nationwide surveillance on serotype distribution and antimicrobial resistance profiles of non-typhoidal Salmonella serovars isolated from food-producing animals in South Korea.

Food-producing animals are considered a leading source of human Salmonella infections in Korea. However, there is a lack of comprehensive and up-to-date data regarding the diversity and resistance profiles of Salmonella serotypes in these animals. Therefore, this study aimed to determine the distribution and antimicrobial resistance profiles of Salmonella serotypes isolated from cattle, pigs, and chickens in Korea between 2010 and 2018. A total of 3018 Salmonella isolates were obtained from 16 laboratories/centers participating in the Korean Veterinary Antimicrobial Resistance Monitoring System. Salmonella serotypes were identified from the following isolates: 179 cattle (17 serotypes), 959 pig (45 serotypes), and 1880 chicken (64 serotypes). The most frequent serotypes in cattle (Typhimurium, Salmonella 4,[5],12:i:-, and Schwarzengrund), pigs (Typhimurium, Rissen, and S. 4,[5],12:i:-), and chickens (Enteritidis, Albany, Virchow, and Montevideo) accounted for more than 50% of the total serotypes in the respective animal species. To the best of our knowledge, Salmonella 4,[5],12:i:- has not been identified in cattle in Korea to date. More than 80% of the isolates demonstrated resistance to at least one antimicrobial agent. Multidrug-resistance was found in almost half of the serotypes; the highest proportion in cattle (59.2%), followed by pigs (53.4%), and chickens (45.7%). Significant proportions of the serotypes were resistant to ampicillin, streptomycin, and tetracycline. Ceftiofur and ciprofloxacin resistance rates were the highest in Salmonella isolated from chickens (17.1% and 4.1%, respectively) and cattle (10.1% and 3.9%, respectively) compared to that in pigs. Among the frequent serotypes, Albany demonstrated the highest resistance rate (>90%) to five different antimicrobials. Alarmingly, some Salmonella serotypes that are frequently associated with human infections demonstrated a trend of increasing resistance to critically important antibiotics, including 3rd generation cephalosporins and quinolones. Collectively, the presence of antibiotic-resistant Salmonella in food-producing animals poses a potential risk to public health.