Salmonella enterica serovar Oranienburg outbreak in a veterinary medical teaching hospital with evidence of nosocomial and on-farm transmission

Detection of Salmonella spp. in pooled environmental samples from an equine veterinary hospital using a novel point-of-care PCR assay

The objective of this study was to evaluate a point-of-care (POC) PCR assay for the detection of Salmonella spp. in pooled environmental samples collected at an equine veterinary hospital. A total of 945 environmental samples were collected from high-risk areas, including ICU and isolation stalls, high-traffic areas, treatment rooms, and surgical suites. The environmental samples were collected using drag swabs placed in selenite broth and individually incubated at 35 °C for 20 h. Following the incubation period, 1 mL of up to 10 individual environmental samples were pooled together. Each pool was processed for nucleic acid purification, followed by qPCR analysis for Salmonella spp., as well as direct testing using the POC PCR assay. PCR analyses were performed in a masked fashion, i.e., qPCR and POC PCR assay results remained unknown. Follow-up testing by qPCR and POC PCR for individual environmental samples was performed when a positive pool was detected. A total of 135 pools ranging from 6 to 10 samples per pool were tested. Results showed 100 % agreement between qPCR and POC PCR, with 118 and 17 pools testing PCR-negative and -positive, respectively. Testing of individual environmental samples from the 17 PCR-positive pools identified the same Salmonella spp. positive individual environmental samples by both qPCR and POC PCR. The strategy of pooling environmental samples for the PCR testing of Salmonella spp. has shown promise in monitoring high-risk areas in equine veterinary hospitals. The Salmonella spp. POC PCR assay showed excellent agreement with qPCR, further improving compliance by reducing the turn-around time to 24 h from sample collection to analysis.

Bridging Classical Methodologies in Salmonella Investigation with Modern Technologies: A Comprehensive Review

Advancements in genomics and machine learning have significantly enhanced the study of Salmonella epidemiology. Whole-genome sequencing has revolutionized bacterial genomics, allowing for detailed analysis of genetic variation and aiding in outbreak investigations and source tracking. Short-read sequencing technologies, such as those provided by Illumina, have been instrumental in generating draft genomes that facilitate serotyping and the detection of antimicrobial resistance. Long-read sequencing technologies, including those from Pacific Biosciences and Oxford Nanopore Technologies, offer the potential for more complete genome assemblies and better insights into genetic diversity. In addition to these sequencing approaches, machine learning techniques like decision trees and random forests provide powerful tools for pattern recognition and predictive modeling. Importantly, the study of bacteriophages, which interact with Salmonella, offers additional layers of understanding. Phages can impact Salmonella population dynamics and evolution, and their integration into Salmonella genomics research holds promise for novel insights into pathogen control and epidemiology. This review revisits the history of Salmonella and its pathogenesis and highlights the integration of these modern methodologies in advancing our understanding of Salmonella.

Retrospective study on the occurrence of Salmonella serotypes in veterinary specimens of Atlantic Canada (2012-2021)

AIM

This study aimed to summarize the frequency and the antimicrobial susceptibility profiles of the Salmonella serotypes identified from the specimens of companion animals, livestock, avian, wildlife and exotic species within Atlantic Canada.

MATERIALS AND METHODS

The retrospective electronic laboratory data of microbiological analyses of a selected subset of samples from 03 January 2012 to 29 December 2021 submitted from various animal species were retrieved. The frequency of Salmonella serotypes identified, and their antimicrobial susceptibility results obtained using the disk diffusion or broth method were analysed. The test results were interpreted according to the Clinical and Laboratory Standards Institute standard. The Salmonella serotypes were identified by slide agglutination (Kauffman-White-Le-Minor Scheme) and/or the Whole Genome Sequencing for the Salmonella in silico Serovar Typing Resource-based identification.

RESULTS

Of the cases included in this study, 4.6% (n = 154) had at least one Salmonella isolate, corresponding to 55 different serovars. Salmonella isolation was highest from exotic animal species (n = 40, 1.20%), followed by porcine (n = 26, 0.78%), and canine (n = 23, 0.69%). Salmonella subsp. enterica serovar Typhimurium was predominant among exotic mammals, porcine and caprine samples, whereas S. Enteritidis was mostly identified in bovine and canine samples. S. Typhimurium of porcine origin was frequently resistant (>70.0%) to ampicillin. In contrast, S. Typhimurium isolates from porcine and caprine samples were susceptible (>70.0%) to florfenicol. S. Oranienburg from equine samples was susceptible to chloramphenicol, but frequently resistant (>90.0%) to azithromycin. In avian samples, S. Copenhagen was susceptible (>90.0%) to florfenicol, whereas Muenchen was frequently resistant (>90.0%) to florfenicol. S. subsp. diarizonae serovar IIIb:61:k:1,5 of ovine origin was resistant (50.0% isolates) to sulfadimethoxine. No significant changes were observed in the antibiotic resistance profiles across the study years.

CONCLUSIONS

This report provides data for surveillance studies, distribution of Salmonella serotypes and their antimicrobial resistance among veterinary specimens of Atlantic Canada.

Bacterial Contamination and Antimicrobial Resistance in Two-Spotted (Gryllus bimaculatus) and House (Acheta domesticus) Cricket Rearing and Harvesting Processes

Food safety for cricket production is a crucial factor in producing edible crickets with safety for consumers and sustainability for two-spotted (Gryllus bimaculatus) as well as house (Acheta domesticus) cricket production. This study was conducted by simultaneously rearing two cricket species, comprising two-spotted crickets (G. bimaculatus) and house crickets (A. domesticus). A total of 16 rearing crates were used for the present study, which were allocated into 8 rearing crates for each studied cricket species, including paper egg cartons. Cricket eggs were incubated in the rearing crates. Once the crickets hatched, tap water and powdered feed were provided ad libitum throughout the experiment. At the end of this study (35 and 42 days for the two-spotted and house crickets, respectively), all crickets were harvested, rinsed in tap water, and boiled in water for 5 min. During the rearing and harvesting processes, samples were collected from various potential contamination points for bacteria, including E. coli and Salmonella spp. There were samples of the initial input (feed, drinking water, and staff hands), rearing environment (water pipe, crate wall, living cartons, frass, and cricket surface), and harvesting crickets (harvested, washed, and boiled crickets), with a 2-week sampling interval, except for the last round of sampling for the two-spotted crickets. Subsequently, all samples were submitted to isolate and identify contaminated bacteria. The samples from the last round of sampling for both kinds of crickets were submitted to quantify the level of contamination for E. coli and Salmonella spp., including antimicrobial resistance by the disk diffusion method for the positive isolate. The results showed that bacterial contamination was found in the rearing of both cricket species, primarily involving Klebsiella spp. and Enterobacter spp., mainly found in prepared drinking water and the water pipes of drinking water supply equipment, which are potential sources of contamination with cricket frass. E. coli was found in 4.8% and 4.3% of the two-spotted and house crickets, respectively, while no presence of Salmonella spp. was detected in any submitted samples. The quantification of E. coli and Salmonella spp. indicated E. coli contamination near the water pipe and the frass of two-spotted crickets, but Salmonella spp. was undetectable in both two-spotted and house crickets. The antimicrobial resistance of isolated E. coli mainly involved penicillin G, amoxicillin, ampicillin, erythromycin, lincomycin, and tiamulin. Thus, good farm management with proper sanitation practices (such as cleaning and keeping the environment dry), as well as boiling crickets during the harvesting process, may help ensure the safety of edible cricket production.

Ciprofloxacin-resistant ST198 Salmonella Kentucky in a hospitalized American black bear (Ursus americanus), with evidence of subsequent nosocomial transmission

Global emergence of ciprofloxacin-resistant ST198 Salmonella Kentucky poses an important public health threat. While conducting Salmonella surveillance among wildlife patients admitted to our veterinary medical teaching hospital in central New York, we isolated multidrug-resistant (MDR) ST198 Salmonella Kentucky from an American black bear (Ursus americanus) in September 2020. The isolate was phenotypically resistant to numerous antimicrobial agents, including ceftriaxone and ciprofloxacin, and several antimicrobial resistance genes and mutational resistance determinants were detected. Between April and July 2021, the same strain of MDR ST198 Salmonella Kentucky was also isolated from seven other wildlife patients and multiple hospital environmental locations, suggesting nosocomial transmission. Ciprofloxacin resistance is conferred by triple point mutations in the quinolone resistance-determining regions (QRDRs), a genotypic profile indicative of Clade ST198.2. To our knowledge, this is the first report of this ciprofloxacin-resistant clade being identified in animals or animal products in the United States. Timely resolution of the outbreak was achieved following efforts to further enhance environmental disinfection protocols and biosecurity measures at the hospital, with no known cases or positive environmental samples after July 2021.

Antimicrobial susceptibility of Salmonella and Escherichia coli from equids sampled in the NAHMS 2015-16 equine study and association of management factors with resistance

Several studies have investigated antimicrobial resistance (AMR) in Salmonella spp. and Escherichia coli isolated from hospitalized horses, but studies conducted on community-based populations of equids are limited. The factors associated with AMR in these bacteria in the general horse population are not well understood. The primary objective of our study was to estimate the prevalence of Salmonella and describe antimicrobial susceptibility of Salmonella and E. coli from equids across the United States. The second objective was to identify associations between health management and biosecurity practices and AMR. Fecal samples submitted from 1357 equids on 199 operations were tested for Salmonella, identifying 27 positive samples with 29 isolates belonging to 18 serotypes. Fecal sample and operation-level prevalence of Salmonella was 2.0% (27/1357) and 7.0% (14/199), respectively. Most (25/29) isolates were pan-susceptible while four isolates exhibited resistance, three of which were multidrug resistant. Of the 721 samples cultured for E. coli, 85% (613/721) were positive. Eighty-six percent of the E. coli isolates recovered were pan-susceptible (529/612). Ten isolates were intermediate to one antimicrobial drug and susceptible to all others. Seventy-three E. coli isolates (11.9%, SE=1.3) were resistant to one or more antimicrobials, corresponding to a 33.0% (64/194) operation-level prevalence. Resistance to sulfonamide drugs was most common with 63 isolates (10.3%) resistant to sulfisoxazole, 57 of which (9.3%) were resistant to trimethoprim-sulfamethoxazole. MDR in E. coli was rare (1.8%, SE=0.5). Univariate and multivariable regression were used to evaluate associations between health management and biosecurity questionnaire items and AMR in E. coli. The outcome modeled was resistance to any of the 14 tested antimicrobials. Depending on the operation type, operations with greater than 20 resident equids were significantly associated with resistance. In addition, performance operations were significantly associated with resistance when compared to farm/ranch operations. Operations with feed containers that prevent fecal contamination and those that had treated any equids for illness or injury were associated with a lower AMR. The study results suggest that equids in the general population appear to pose low risk of shedding antimicrobial resistant strains of Salmonella and E. coli, and therefore low transmission potential to other equids, animals, humans, or the environment. However, it is prudent to practice good hand hygiene to prevent spread of Salmonella as well as AMR, and to protect both animal and human health. Despite study limitations, potential management factors that may influence prevalence and prevent spread of AMR shed by equids were identified.

Antimicrobial prescribing and antimicrobial resistance surveillance in equine practice

BACKGROUND

Antimicrobial resistance (AMR) is an increasingly serious threat to human and animal health, therefore responsible use of antimicrobials in equine practice is vital. There is a need to have accurate, up to date data on antimicrobial prescribing in equine practice in the UK.

OBJECTIVES

To characterise current antimicrobial prescribing practices by equine veterinarians and to describe surveillance, audit processes and identification of AMR.

STUDY DESIGN

Online cross-sectional, questionnaire-based survey.

METHODS

An online questionnaire targeting veterinarians who treat horses in the UK and Europe was distributed. The questionnaire collected data on participants' country of origin, practice policies, prescribing practices including use of high priority critical antimicrobials. Four common clinical case-based scenarios were included to further explore prescribing practice. Responses were compared using both descriptive statistics and multivariable logistic regression models.

RESULTS

Questionnaires were completed by 264 veterinarians from Europe (n=33/264) and the UK (n=231/264); 87% respondents worked only with horses and 67% worked at premises with hospitalisation facilities. Approximately half of respondents (54.4%) had a written antimicrobial use or stewardship policy within their practice. Over half of respondents did not perform any environmental surveillance (54.2%), audit of clinical infections (53.1%) or audit of infection control (57.1%). Potentiated sulphonamides were cited as the most used antimicrobial, although 44% reported using enrofloxacin in the last year and 66% used 3^rd or 4^th generation cephalosporins. Prophylactic antimicrobials before clean surgery were frequently/always prescribed by 48% respondents and 24% respondents frequently/always prescribed antimicrobials post-operatively in clean surgery.

MAIN LIMITATIONS

Potential selection bias of respondents, given individuals volunteered to take part in the survey.

CONCLUSIONS

Compared to a previous similar study conducted in 2009, overall antimicrobial usage appeared to be declining in clinical scenarios and a greater proportion of practices now have stewardship policies. However, the use of high priority critical antimicrobials is still relatively common in equine practice in the UK and Europe.

Widespread Environmental Presence of Multidrug-Resistant Salmonella in an Equine Veterinary Hospital That Received Local and International Horses

Salmonella enterica is a highly infectious microorganism responsible for many outbreaks reported in equine hospitals. Outbreaks are characterized by high morbidity and mortality rates, nosocomial transmission to other patients, zoonotic transmission to hospital personnel, and even closure of facilities. In this study, 545 samples (environmental and hospitalized patients) were collected monthly during a 1-year period from human and animal contact surfaces in an equine hospital that received local and international horses. A total of 22 Salmonella isolates were obtained from human contact surfaces (e.g., offices and pharmacy) and animal contact surfaces (e.g., stalls, surgery room, and waterers), and one isolate from a horse. Molecular serotyping revealed 18 isolates as Salmonella Typhimurium and three as Salmonella Infantis. Nineteen isolates were resistant to at least one antimicrobial class, and only two isolates were susceptible to all antimicrobials tested. In addition, we identified nine multidrug-resistant (MDR) isolates in S. Typhimurium, which displayed resistance to up to eight antimicrobials (i.e., amoxicillin/clavulanate, ampicillin, ciprofloxacin, chloramphenicol, streptomycin, gentamicin, trimethoprim/sulfamethoxazole, and tetracycline). Pulsed-field gel electrophoresis (PFGE) revealed the presence of three PFGE patterns permanently present in the environment of the hospital during our study. The persistent environmental presence of MDR Salmonella isolates, along with the fact that local and international horses are attended in this hospital, highlights the importance of improving biosecurity programs to prevent disease in horses and the hospital personnel and also for the global dissemination and acquisition of MDR Salmonella.

FasTag: Automatic text classification of unstructured medical narratives

Unstructured clinical narratives are continuously being recorded as part of delivery of care in electronic health records, and dedicated tagging staff spend considerable effort manually assigning clinical codes for billing purposes. Despite these efforts, however, label availability and accuracy are both suboptimal. In this retrospective study, we aimed to automate the assignment of top-level International Classification of Diseases version 9 (ICD-9) codes to clinical records from human and veterinary data stores using minimal manual labor and feature curation. Automating top-level annotations could in turn enable rapid cohort identification, especially in a veterinary setting. To this end, we trained long short-term memory (LSTM) recurrent neural networks (RNNs) on 52,722 human and 89,591 veterinary records. We investigated the accuracy of both separate-domain and combined-domain models and probed model portability. We established relevant baseline classification performances by training Decision Trees (DT) and Random Forests (RF). We also investigated whether transforming the data using MetaMap Lite, a clinical natural language processing tool, affected classification performance. We showed that the LSTM-RNNs accurately classify veterinary and human text narratives into top-level categories with an average weighted macro F1 score of 0.74 and 0.68 respectively. In the "neoplasia" category, the model trained on veterinary data had a high validation accuracy in veterinary data and moderate accuracy in human data, with F1 scores of 0.91 and 0.70 respectively. Our LSTM method scored slightly higher than that of the DT and RF models. The use of LSTM-RNN models represents a scalable structure that could prove useful in cohort identification for comparative oncology studies. Digitization of human and veterinary health information will continue to be a reality, particularly in the form of unstructured narratives. Our approach is a step forward for these two domains to learn from and inform one another.

Embracing Diversity: Differences in Virulence Mechanisms, Disease Severity, and Host Adaptations Contribute to the Success of Nontyphoidal Salmonella as a Foodborne Pathogen

Not all Salmonella enterica serovars cause the same disease. S. enterica represents an incredibly diverse species comprising >2,600 unique serovars. While some S. enterica serovars are host-restricted, others infect a wide range of hosts. The diseases that nontyphoidal Salmonella (NTS) serovars cause vary considerably, with some serovars being significantly more likely to cause invasive disease in humans than others. Furthermore, while genomic analyses have advanced our understanding of the genetic diversity of these serovars, they have not been able to fully account for the observed clinical differences. One overarching challenge is that much of what is known about Salmonella's general biology and virulence strategies is concluded from studies examining a select few serovars, especially serovar Typhimurium. As targeted control strategies have been implemented to control select serovars, an increasing number of foodborne outbreaks involving serovars that are less frequently associated with human clinical illness are being detected. Harnessing what is known about the diversity of NTS serovars represents an important factor in achieving the ultimate goal of reducing salmonellosis-associated morbidity and mortality worldwide. In this review we summarize the current understanding of the differences and similarities among NTS serovars, highlighting the virulence mechanisms, genetic differences, and sources that characterize S. enterica diversity and contribute to its success as a foodborne pathogen.

Resistance to Carbapenems in Non-Typhoidal Salmonella enterica Serovars from Humans, Animals and Food

Non-typhoidal serovars of Salmonella enterica (NTS) are a leading cause of food-borne disease in animals and humans worldwide. Like other zoonotic bacteria, NTS have the potential to act as reservoirs and vehicles for the transmission of antimicrobial drug resistance in different settings. Of particular concern is the resistance to critical "last resort" antimicrobials, such as carbapenems. In contrast to other Enterobacteriaceae (e.g., Klebsiella pneumoniae, Escherichia coli, and Enterobacter, which are major nosocomial pathogens affecting debilitated and immunocompromised patients), carbapenem resistance is still very rare in NTS. Nevertheless, it has already been detected in isolates recovered from humans, companion animals, livestock, wild animals, and food. Five carbapenemases with major clinical importance-namely KPC (Klebsiella pneumoniae carbapenemase) (class A), IMP (imipenemase), NDM (New Delhi metallo-β-lactamase), VIM (Verona integron-encoded metallo-β-lactamase) (class B), and OXA-48 (oxacillinase, class D)-have been reported in NTS. Carbapenem resistance due to the production of extended spectrum- or AmpC β-lactamases combined with porin loss has also been detected in NTS. Horizontal gene transfer of carbapenemase-encoding genes (which are frequently located on self-transferable plasmids), together with co- and cross-selective adaptations, could have been involved in the development of carbapenem resistance by NTS. Once acquired by a zoonotic bacterium, resistance can be transmitted from humans to animals and from animals to humans through the food chain. Continuous surveillance of resistance to these "last resort" antibiotics is required to establish possible links between reservoirs and to limit the bidirectional transfer of the encoding genes between S. enterica and other commensal or pathogenic bacteria.

Detection of Salmonella spp. in veterinary samples by combining selective enrichment and real-time PCR

Rapid screening for enteric bacterial pathogens in clinical environments is essential for biosecurity. Salmonella found in veterinary hospitals, particularly Salmonella enterica serovar Dublin, can pose unique challenges for culture and testing because of its poor growth. Multiple Salmonella serovars including Dublin are emerging threats to public health given increasing prevalence and antimicrobial resistance. We adapted an automated food testing method to veterinary samples and evaluated the performance of the method in a variety of matrices including environmental samples ( n = 81), tissues ( n = 52), feces ( n = 148), and feed ( n = 29). A commercial kit was chosen as the basis for this approach in view of extensive performance characterizations published by multiple independent organizations. A workflow was established for efficiently and accurately testing veterinary matrices and environmental samples by use of real-time PCR after selective enrichment in Rappaport-Vassiliadis soya (RVS) medium. Using this method, the detection limit for S. Dublin improved by 100-fold over subculture on selective agars (eosin-methylene blue, brilliant green, and xylose-lysine-deoxycholate). Overall, the procedure was effective in detecting Salmonella spp. and provided next-day results.

A survey of methods used for antimicrobial susceptibility testing in veterinary diagnostic laboratories in the United States

Antimicrobial resistance is a serious threat to animal and human health worldwide, requiring a collaborative, holistic approach. The U.S. Government has developed a national strategy to address antimicrobial resistance, with one component being to monitor antimicrobial resistance in agricultural settings. We developed a survey to collect information about antimicrobial susceptibility testing (AST) from the veterinary diagnostic laboratory community in the United States, assessing current practices and technologies and determining how AST information is shared. Of the 132 surveys administered, 52 (39%) were returned. Overall, responding laboratories conducted susceptibility tests on 98,788 bacterial isolates in 2014, with Escherichia coli being the most common pathogen tested across all animal species. The 2 most common AST methods employed were the disk diffusion method (71%) and the Sensititre platform broth microdilution system (59%). Laboratories primarily used the Clinical Laboratory Standards Institute (CLSI) VET-01 standard (69%) and the automatically calculated interpretations provided by the commercial AST systems (61%) for interpreting their AST data. Only 22% of laboratories published AST data on a periodic basis, usually via annual reports published on the laboratory's website or through peer-reviewed journals for specific pathogens. Our results confirm that disk diffusion and broth microdilution remain the standard AST methods employed by U.S. veterinary diagnostic laboratories, and that CLSI standards are commonly used for interpreting AST results. This information will help determine the most efficient standardized methodology for future surveillance. Furthermore, the current infrastructure within laboratories, once harmonized, will help provide a mechanism for conducting national surveillance programs.

Vigilance for Salmonella in Feedstuffs Available in Costa Rica: Prevalence, Serotyping and Tetracycline Resistance of Isolates Obtained from 2009 to 2014

Relevant epidemiological information is provided in this report for Salmonella based on data obtained from a Costa Rican surveillance program for animal feeds. In addition to prevalence, a description in terms of serotypes and tetracycline (TET) resistance of the isolates is included. A total of 1725 feed and feed ingredients samples were analyzed during 2009 and 2014, from which 110 Salmonella strains were recovered (76 from poultry, 23 from meat and bone meal [MBM], 3 from pet foods, and 8 from other feed). Retrieved isolates were serotyped and tested for minimum inhibitory concentration (MIC) against TET. Salmonella strains were found mainly from poultry feed (different growth stages, n = 76/110; 69.1%) and MBM (n = 23/109; 21.1%). The rest of the isolates were recovered from feather meal, pet food, fish meal (n = 3/110; 2.3% each) and swine feed (n = 1/110; 0.9%). From the different serotypes recovered (n = 21), the most common were Salmonella Give (n = 18; 13.8%) and Salmonella Rissen (n = 6; 4.6%) for MBM and Salmonella Havana (n = 14; 10.8%), Salmonella Rissen, Salmonella Soerenga, and Salmonella Schwarzengrund (n = 8; 6.2% each) in poultry feed. Recovered strains were regarded to be sensitive or have an intermediate resistance to TET as evidenced by their MIC50 and MIC90 concentrations of 4 and 8 μg/mL for MBM and poultry feed, respectively. Compound feed and MBM samples exhibited strains characterized by 86.8 and 88.9% of the isolates classified (according to CLSI, 2015 ) as sensitive, 7.7 and 3.7% as intermediate, and 5.5% (with >256 μg/mL as the highest concentration) and 7.4% (with 64 μg/mL as the highest concentration) as resistant to TET, respectively. Salmonella serovars Anatum and Havana exhibited the highest resistance profile >256 and 128 μg/mL, respectively. Hence, MBM and poultry feed seem to be a target of interest if Salmonella incidence is to be controlled. Serotypes recovered have in the past demonstrated pathogenic capability; therefore, hereafter a stricter surveillance program may be in order.