Risk factors for colonization with extended-spectrum cephalosporin-resistant and carbapenem-resistant Enterobacterales among hospitalized patients in Guatemala: An Antibiotic Resistance in Communities and Hospitals (ARCH) study.

Objectives: The spread of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) and carbapenem-resistant Enterobacterales (CRE) has resulted in increased morbidity, mortality, and health care costs worldwide. To identify the factors associated with ESCrE and CRE colonization within hospitals, we enrolled hospitalized patients at a regional hospital located in Guatemala. Methods: Stool samples were collected from randomly selected patients using a cross-sectional study design (March-September, 2021), and samples were tested for the presence of ESCrE and CRE. Hospital-based and household variables were examined for associations with ESCrE and CRE colonization using lasso regression models, clustered by ward (n = 21). Results: A total of 641 patients were enrolled, of whom complete data sets were available for 593. Colonization with ESCrE (72.3%, n = 429/593) was negatively associated with carbapenem administration (odds ratio [OR] 0.21, 95% confidence interval [CI] 0.11-0.42) and positively associated with ceftriaxone administration (OR 1.61, 95% CI 1.02-2.53), as was reported hospital admission within 30 days of the current hospitalization (OR 2.84, 95% CI 1.19-6.80). Colonization with CRE (34.6%, n = 205 of 593) was associated with carbapenem administration (OR 2.62, 95% CI 1.39-4.97), reported previous hospital admission within 30 days of current hospitalization (OR 2.58, 95% CI 1.17-5.72), hospitalization in wards with more patients (OR 1.05, 95% CI 1.02-1.08), hospitalization for ≥4 days (OR 3.07, 95% CI 1.72-5.46), and intubation (OR 2.51, 95% CI 1.13-5.59). No household-based variables were associated with ESCrE or CRE colonization in hospitalized patients. Conclusion: The hospital-based risk factors identified in this study are similar to what has been reported for risk of health care-associated infections, consistent with colonization being driven by hospital settings rather than community factors. This also suggests that colonization with ESCrE and CRE could be a useful metric to evaluate the efficacy of infection and prevention control programs in clinics and hospitals.

Colonization With Antibiotic-Resistant Bacteria in a Hospital and Associated Communities in Guatemala: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study.

BACKGROUND: We estimated the prevalence of colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) and carbapenem-resistant Enterobacterales (CRE) from a hospital and associated communities in western Guatemala. METHODS: Randomly selected infants, children, and adults (<1, 1-17, and ≥18 years, respectively) were enrolled from the hospital (n = 641) during the coronavirus disease 2019 (COVID-19) pandemic, March to September 2021. Community participants were enrolled using a 3-stage cluster design between November 2019 and March 2020 (phase 1, n = 381) and between July 2020 and May 2021 (phase 2, with COVID-19 pandemic restrictions, n = 538). Stool samples were streaked onto selective chromogenic agar, and a Vitek 2 instrument was used to verify ESCrE or CRE classification. Prevalence estimates were weighted to account for sampling design. RESULTS: The prevalence of colonization with ESCrE and CRE was higher among hospital patients compared to community participants (ESCrE: 67% vs 46%, P < .01; CRE: 37% vs 1%, P < .01). Hospital ESCrE colonization was higher for adults (72%) compared with children (65%) and infants (60%) (P < .05). Colonization was higher for adults (50%) than children (40%) in the community (P < .05). There was no difference in ESCrE colonization between phase 1 and 2 (45% and 47%, respectively, P > .05), although reported use of antibiotics among households declined (23% and 7%, respectively, P < .001). CONCLUSIONS: While hospitals remain foci for ESCrE and CRE colonization, consistent with the need for infection control programs, community prevalence of ESCrE in this study was high, potentially adding to colonization pressure and transmission in healthcare settings. Better understanding of transmission dynamics and age-related factors is needed.

Mycoplasma hyorhinis infection in early cases of mycoplasmal pneumonia in swine and evaluation of diagnostic assays / Infecção por Mycoplasma hyorhinis em casos precoces de pneumonia micoplásmica em suínos e comparação entre técnicas diagnósticas

Mycoplasmal pneumonia is an important disease in the pig industry. Due to the controversial role of Mycoplasma hyorhinis in this disease, confirmation of the presence of this bacterium and the identification of its roles in respiratory disease remain major challenges. The objectives of this study were to evaluate the presence of M. hyorhinis in early cases of mycoplasmal pneumonia and to determine the usefulness of fluorescent in situ hybridization (FISH) for the diagnosis of respiratory mycoplasmosis in naturally infected pigs. Ninety M. hyopneumoniae and/or M. hyorhinis-infected lung tissue samples based on diagnostic mosaic (DM) were used. The average age of the animals was 116 and 57 days (P<0.01) for groups 1 (positive-M. hyopneumoniae only) and 2 (positive-M. hyorhinis only), respectively. These findings suggest that development of lesions caused by M. hyorhinis occurs earlier than for M. hyopneumoniae. Using the DM as the gold standard, the sensitivity and specificity of FISH for M. hyopneumoniae were 75 and 100%, respectively, and were 40 and 73.3% for the immunohistochemistry (IHC). The sensitivity and specificity of FISH for M. hyorhinis were 76.7 and 100%, respectively. These findings demonstrate that FISH can be a useful tool for diagnosing mycoplasmosis. Viral antigens (PCV2 or influenza A) were detected in 53.3% (16/30) of the samples in group 2 (M. hyorhinis-PCR positive) and 13.3% (4/30) of the samples in group 1 (M. hyopneumoniae-PCR positive). This finding indicates that the association of M. hyorhinis and viral infection in nursery pigs likely starts due to a viral immunosuppressive condition.(AU)

A pneumonia micoplásmica causada por bactérias do gênero Mycoplasma é uma enfermidade de grande importância para indústria suinícola, sendo ainda controverso o papel desempenhado por Mycoplasma hyorhinis nessa doença. A confirmação da presença dessas bactérias bem como a identificação de seus papéis em doenças respiratórias continua sendo um grande desafio. Os objetivos desse estudo foram comparar diferentes técnicas, em especial a de hibridização fluorescente in situ (FISH), para diagnóstico de micoplasmoses respiratória em suínos naturalmente infectados e avaliar a presença do M. hyorhinis em casos precoces de pneumonia micoplásmica. Foram utilizadas 90 amostras de tecido pulmonar infectado para cada um ou ambos os agentes (M. hyopneumoniae e M. hyorhinis) determinados pelo mosaico de diagnóstico (sinais clínicos, lesões macroscópicas e microscópicas e pela PCR). No grupo de animais positivos pela PCR apenas para M. hyorhinis (Grupo 2) a média da idade foi de 57,32 dias e no grupo apenas positivo para M. hyopneumoniae (Grupo 1) a média foi de 116,31 dias (P<0,01). Estes achados sugerem que a colonização e o aparecimento de lesões causadas pelo M. hyorhinis seja mais precoce do que aquelas causadas pelo M. hyopneumoniae. As alterações microscópicas foram estatisticamente (P<0,01) mais intensas no grupo 1 do que no grupo 2. Usando o mosaico de diagnóstico como padrão ouro, a sensibilidade e especificidade na FISH para M. hyopneumoniae foi de 75 e 100%, respectivamente, e 40 e 73,3%, na imuno-histoquímica. A sensibilidade e especificidade da FISH para M. hyorhinis foi de 76,7 e 100%. Esses valores demonstram que a FISH pode ser uma ferramenta útil para diagnóstico de micoplasmoses. Foi detectada a presença de agentes virais (PCV2 ou influenza) em 53,3% das amostras do grupo 2 (M. hyorhinis) e em 13,3% das amostras do grupo 1 (M. hyopneumoniae).(AU)

Mycoplasma hyopneumoniae genetic variability within a swine operation.

The objective of our study was to characterize the Mycoplasma hyopneumoniae genetic diversity within a swine operation comingling weaned pigs. Bronchial swabs and tracheal aspirates were collected from 3 nursery-to-finish farms. During the finishing production stages, samples were obtained from mortalities and from live coughing pigs in rooms where mortality was not observed. A total of 105 samples were examined by a M. hyopneumoniae real-time polymerase chain reaction and subjected to genetic typing using a multilocus variable number tandem repeat analysis (MLVA) assay. The MLVA was used to identify genetic variants based on the number of repeats in 2 variable number tandem repeats loci, namely P97 and P146, thought to mediate adherence of M. hyopneumoniae to swine cilia. Four distinguishable M. hyopneumoniae variants were identified: MVLA variants 9-15, 11-21, 9-21, and 7-15. Variant 9-15 was the most prevalent, observed in 79% of rooms, and detected on all 3 farms. Variant 11-21 was present in 37% of the rooms on 2 of the 3 farms. Only one 9-21 variant was identified in 1 farm, and all samples of variant 7-15 were recovered from another farm. Based on the low prevalence and limited geographic distribution of the last 2 variants, it is hypothesized that they might be the result of in-situ recombination. All variants detected in this investigation appeared to belong to 3 clusters. Overall, a limited number of variants and clusters were identified in a system that comingles pigs from different sources, suggesting limited M. hyopneumoniae genetic variation within commercial swine production environments.

Genotyping of Mycoplasma hyorhinis using multiple-locus variable number tandem repeat analysis.

Mycoplasma hyorhinis (M. hyorhinis) has re-emerged as an important swine pathogen in recent years causing significant economic losses in post weaning pigs. Genetic variability of M. hyorhinis has been described based on different molecular methods that have limited resolution and reproducibility. The present study was undertaken to develop a molecular epidemiological typing tool for M. hyorhinis based on multiple loci of variable number of tandem repeats in its genome, termed MLVA. The typing method was designed on the basis of the number of repeats in two hypothetical proteins, MHR_0152 and MHR_0298. A total of 205 samples were analyzed, including field isolates, clinical specimens, and a reference strain. Analysis of the combination of the 2 loci revealed 16 MLVA types in 165 of the 205 samples. In the remaining forty samples only one locus could be amplified. The most frequent types obtained from the set of samples were 8-4 (36.9%), 8-3 (11.5%), 7-4 (11.5%), 9-4 (10.9%) and 10-4 (9.3%). The Simpson's diversity index for the assay was D=0.814 when the 165 samples were taken into account. No clustering was observed based on the geographical location, sample type, or year of isolation or sampling. The MLVA assay developed in this investigation showed to be a reproducible and portable assay which could be easily performed and transferred to other laboratories. The use of this technique will assist in epidemiological investigations and can be used to improve the understanding the molecular biology of M. hyorhinis variants.

Genotype distribution of Mycoplasma hyopneumoniae in swine herds from different geographical regions.

Genetic heterogeneity of Mycoplasma hyopneumoniae in pigs has been reported, however there has been limited reproducibility on the molecular methods employed so far. The aim of this study was to modify and standardize a high-resolution multiple locus variable number tandem repeat analysis (MLVA), to investigate the genetic variability of M. hyopneumoniae circulating in the United States of America (USA), Brazil, Mexico and Spain. The MLVA was standardized on the basis of the number of tandem repeats in two Mycoplasma adhesins, P97 and P146, which are proteins involved in the adherence of the pathogen to cilia. A total of 355 samples obtained from the four countries were analyzed. The Simpson's diversity index for the assay was D=0.976 when samples from all countries were combined. A large number of MLVA types (n=139) were identified, suggesting that multiple M. hyopneumoniae variants are circulating in swine. The locus P97 had 17 different types with 2-18 repeats. The P146 locus showed higher heterogeneity, with 34 different types, ranging from 7 to 48 repeats. MLVA types that presented more than 30 repeats in P146 were found in Spain and Brazil, while shorter repeats were observed in the USA and Mexico. This simplified MLVA method proved to be an efficient tool for typing M. hyopneumoniae with a high degree of stability, repeatability, and discriminatory power. In conclusion, M. hyopneumoniae showed a high variable number tandem repeat heterogeneity and this assay can be applied in molecular epidemiology investigations within farms and productions systems.