Gut microbiota transfer evidence from mother to newborn.

Early life microbiota is a risk factor for future diseases. The main purpose of this study was to investigate the transfer of gut microbiota from mother to newborn. A biological sample was collected from the anal mucosa of the pregnant women before delivery and from the newborns between 24 and 48 h after delivery, as it was not possible to collect a meconium sample at that time. The microbiome of the samples was analyzed by sequencing the hypervariable regions V3-V4 of the 16S gene. To determine the likelihood of microbiota transfer from mother to newborn and examine the relationship with the mode of delivery, we utilized Fisher's exact test and odds ratio. A weighted transfer ratio was employed as a comprehensive measure of transfer. A total of 5767 ASVs were identified in newborn samples (n = 30) and 7253 in maternal samples (n = 30). In the analysis of transfer correlated with the mode of delivery, we observed significant ASVs (p < 0.05). Vaginal delivery showed a positive probability of transfer (OR = 2.184 and WTR = 1.852). We found a negative correlation (OR < 1) between the abundance of maternal ASVs and the likelihood of microbiota transfer to the newborn in both delivery modes. The relationship was inversely proportional for both cesarean section (log10 = - 0.2229) and vaginal delivery (log10 = - 0.1083), with statistical significance observed only for cesarean section (p = 0.0083).  Conclusion: In our sample, the maternal gut microbiome was found to be associated with the infant gut microbiome, indicating evidence of ASV-specific transfer from the maternal microbiome to newborns. What is Known: • There is a relationship of early-life microbiota composition with future health outcomes. What is New: • This was the first study to evaluate maternal gut microbiota transfer to newborns in Brazil.

High rate of Clostridioides difficile colonization in patients admitted to intensive care: A prospective cohort study.

Here, we evaluated the frequency of C. difficile colonization and its impact on clinical outcomes in patients admitted to intensive care units in Brazil. From ninety-two patients screened 16 (17.3%) were colonized by C. difficile. Colonized patients had higher Simplified Acute Physiology Score III (SAPS III), however there was no association between C. difficile colonization with diarrhea or mortality. The C. difficile strains sequenced belonged to clade 1 and presented high vancomycin-resistant rates.

Molecular identification of Mycobacterium spp. isolated from Brazilian wild boars.

Wild boars (Sus scrofa) are susceptible to mycobacterial infections, including tuberculous and non-tuberculous mycobacteria. Recently, Mycobacterium spp. infections were described in Brazilian wild boars, which can act as bacterial reservoirs. Here, we aim to characterize 15 Mycobacterium spp. isolates from Brazilian wild boars' tissues through partial sequencing of the heat shock protein 65 (hsp65) gene and phylogenetic analysis. The isolates were classified as M. tuberculosis (33.3%), M. colombiense (33.3%), M. avium subsp. hominissuis (13.3%), M. parmense (13.3%) and M. mantenii (6.66%). The isolates classified as M. tuberculosis were confirmed as variant bovis by PCR. At phylogenetic analysis some isolates formed separated clades, indicating genetic variability. Different Mycobacterium species were recovered from wild boars circulating in Brazil, including mycobacteria associated to zoonotic infections, such as M. tuberculosis. In addition, this is the first report in Brazilian wild boars on M. mantenii and M. parmense detection, two recently described pathogenic mycobacteria. However, the isolates' genetic diversity-i.e. identities lower than 100% when compared to reference sequences-suggests that other genotyping tools would allow a deeper characterization. Nonetheless, the reported data contributes to the knowledge on mycobacterial infections in wild boars from Brazil.

Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalisation rate, February 2021, Rio Grande do Sul, Southern Brazil.

The emergence of SARS-CoV-2 P.1 lineage coincided with a surge in hospitalisations in the North region of Brazil. In the South region's Rio Grande do Sul state, severe COVID-19 case numbers rose 3.8 fold in February 2021. During that month, at a COVID-19 referral hospital in this state, whole-genome sequencing of a subset of cases' specimens (n = 27) revealed P.1 lineage SARS-CoV-2 in most (n = 24). Findings raise concerns regarding a possible association between lineage P.1 and rapid case and hospitalisation increases.

Susceptibility evaluation of novel beta-lactam/beta-lactamase inhibitor combinations against carbapenem-resistant Klebsiella pneumoniae from bloodstream infections in hospitalized patients in Brazil.

Novel beta-lactams/beta-lactamase inhibitors (BIBLI) combinations are commercially available and they have been used for treating carbapenem-resistant Klebsiella pneumoniae (CRKP) infections. Continuous surveillance of susceptibility profile and resistance mechanisms identification are necessary to monitor the evolution of resistance as these agents are used. The purpose of this study was to evaluate susceptibility rates to ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam in CRKP isolates from patients with bloodstream infection screened for a randomized clinical trial in Brazil. Minimum inhibitory concentration (MIC) was determined by gradient diffusion strip method for meropenem, ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam. Carbapenemase genes were detected by multiplex qPCR. KPC-producing isolates showing resistance to any BLBLI and NDM-producing isolates showing susceptibility to any BLBLI were further submitted to whole genome sequencing. From a total of 69 CRKP isolates, 39 were positive for blaKPC, 19 for blaNDM and 11 for blaKPC and blaNDM. KPC-producing isolates demonstrated susceptibility rates above 94% for all BLBLI. Two isolates with resistance to meropenem/vaborbactam showed a Gly and Asp duplication at OmpK36 protein and truncated ompK35 genes. All NDM-producing isolates, including KPC and NDM coproducers, demonstrated susceptibility rates for ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam of 0%, 9.1 to 21.1% and 9.1 to 26.3%, respectively. Five NDM-producing isolates that presented susceptibility to BLBLI also demonstrated alterations in porins. This study demonstrated that, although high susceptibility rates to the BLBLI were found, KPC-2 isolates can also demonstrate resistance due to porin mutations. Additionally, NDM-1 isolates can demonstrate susceptibility in vitro to the BLBLI.

First report of carbapenem-resistant Acinetobacter nosocomialis isolates harboring ISAba1-blaOXA-23 genes in Latin America.

In recent years, different resistance genes have been found in Acinetobacter spp., especially in the species A. baumannii. We describe two isolates of carbapenem-resistant A. nosocomialis harboring ISAba1-blaOXA-23 and blaOXA-51 found in patients from the city of Porto Alegre, southern Brazil. To the best of the authors' knowledge, this is the first report of carbapenem-resistant A. nosocomialis in Latin America.

Hetero- and adaptive resistance to polymyxin B in OXA-23-producing carbapenem-resistant Acinetobacter baumannii isolates.

BACKGROUND: Resistance rates to polymyxin B in surveillance studies have been very low despite its increasing use worldwide as the last resort therapy for multidrug-resistant Gram-negative bacilli. However, two other resistance phenotypes, hetero- and adaptive resistance, have been reported to polymyxin. We aimed to investigate the presence of polymyxin B hetero- and adaptive resistance and evaluate its stability in carbapenem-resistant Acinetobacter baumannii (CRAB) clinical isolates. METHODS: CRAB isolates were recovered from hospitalized patients at three Brazilian hospitals. Hetero-resistance was determined by population analysis profile (PAP). Adaptive resistance was evaluated after serial daily passages of isolates in Luria-Bertani broth containing increasing polymyxin B concentrations. MICs of polymyxin B of colonies growing at the highest polymyxin B concentration were further determined after daily sub-cultured in antibiotic-free medium and after storage at -80°C, in some selected isolates. RESULTS: Eighty OXA-23-producing CRAB isolates were typed resulting in 15 distinct clones. Twenty-nine randomly selected isolates (at least one from each clone) were selected for hetero- resistance evaluation: 26 (90%) presented growth of subpopulations with higher polymyxin B MIC than the original one in PAP. No isolate has grown at polymyxin B concentrations higher than 2 mg/L. Polymyxin B MICs of subpopulations remained higher than the original population after daily passages on antibiotic-free medium but returned to the same or similar levels after storage. Twenty-two of the 29 isolates (at least one from each clone) were evaluated for adaptive resistance: 12 (55%) presented growth in plates containing 64 mg/L of polymyxin B. Polymyxin B MICs decreased after daily passages on antibiotic-free medium and returned to the same levels after storage. CONCLUSIONS: The presence of subpopulations with higher polymyxin B MIC was extremely common and high-level adaptive resistance was very frequent in CRAB isolates.

Evaluation of Aztreonam and Ceftazidime/Avibactam Synergism against Klebsiella pneumoniae by MALDI-TOF MS.

INTRODUCTION: Resistance to carbapenems due to the co-production of NDM and ESBL or NDM and KPC is increasing. Therefore, combined therapy with aztreonam (ATM) plus ceftazidime/avibactam (CZA) has been recommended. Then, it is necessary to develop and evaluate fast and simple methods to determine synergism in vitro in microbiology laboratories. OBJECTIVE: To develop a method to determine the synergism of ATM and CZA by MALDI-TOF MS (SynMALDI). METHOD: Klebsiella pneumoniae (n = 22) isolates with blaNDM and/or blaKPC genes were tested. The time-kill curve assay was performed for four isolates (three positives for blaNDM and blaKPC and one positive for blaNDM only). For SynMALDI, each isolate was incubated for 3 h in 4 tubes containing brain-heart infusion broth with the following: (1) no antibiotic; (2) ATM at 64 mg/L; (3) CZA at 10/4 mg/L; and (4) ATM at 64 mg/L plus CZA at 10/4 mg/L. After incubation, the bacterial protein extract was analyzed by MALDI-TOF MS, and the relative growth (RG) was determined for each isolate, considering intensities of the peaks of the bacterium incubated with antibiotic (tubes 2, 3, and 4) to the same bacterium incubated without antibiotic (tube 1), as follows: RG = IntensityWith antibiotic/IntensityWithout antibiotic. The combination was determined as synergistic when there was an RG decrease of 0.3 in the antibiotic combination in relation to the RG of the most active antibiotic alone. RESULTS: The combination of ATM plus CZA proved to be synergic by time-kill curve assay. All isolates tested with the SynMALDI method also presented synergism. CONCLUSIONS: Detection of synergism for ATM plus CZA combination can be determined by MALDI-TOF MS, providing fast results in order to improve patient treatment.

Whole-genome sequencing-based characterization of Streptomyces sp. 6(4): focus on natural product.

We have sequenced the whole genome of Streptomyces sp. 6(4) isolated from tomato roots that presents antifungal activity against phytopathogenic fungi, mainly Bipolaris sorokiniana. The genome has almost 7 Mb and 3368 hypothetical proteins that were analysed and characterized in Uniprot with the emphasis on biological compounds. Multilocus sequence typing (MLST) analyses were performed in an effort to characterize and identify this isolate, resulting in a new sequence type (ST), classified as ST64. Phenetic and phylogenetic trees were constructed to investigate Streptomyces sp. 6(4) evolution and sequence similarity, and the isolate is a strain closer to Streptomyces prasinus and Streptomyces viridosporus . It is known that the genus Streptomyces possess huge metabolic capacity with the presence of cryptic genes. These genes are usually present in clusters, which are responsible for the production of diverse natural products, mainly antibiotics. In addition, 6(4) showed 11 biosynthetic gene clusters through antiSMASH, including 3 polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) type clusters.

Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil.

The SARS-CoV-2 P.1 lineage emerged in Amazonas (AM), North Brazil and its evolution has been dynamically reported associated with increased transmissibility and/or immune evasion. Here, we evaluated the lineages circulating in 29 cities in Rio Grande do Sul (RS), Southern Brazil between March 2020 and May 2021 and investigated the genetic events associated with the emergence of the P.1. A total of 202 oro/nasopharyngeal SARS-CoV-2 specimens from patients during routine hospital care were submitted to whole-genome sequencing. Phylogenetic and Bayesian Evolutionary Analyses of the P.1 lineage were carried out to determine the relationship between sequences from RS and AM and dated their common ancestor and origin. One hundred six (53%) sequences were assigned as P.1 and most carried the 22 lineage-defining mutations. All the P.1 sequences included other important mutations, such as P314L and R203K/G204R, and revealed a high genetic diversity in the phylogenetic tree. The time-scaled inference suggests that the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM, but the origin of some sequences from RS is unknown. Further, the common ancestor of sequences from RS is dated to mid-June/July 2020, earlier than those previously reported from AM. Our results demonstrate that there is a high degree of genetic diversity among P.1 sequences, which suggests a continuous evolution and community spread of the virus. Although the first P.1 outbreak was reported in AM, the lineage was associated with multiple introductory events and had already been circulating in Southern Brazil prior to November 2020. IMPORTANCE The SARS-CoV-2 P.1 lineage is associated with increased transmissibility and/or immune evasion and presents a dynamic evolution in Brazil. The significance of our research relies in the fact that we evaluated the SARS-CoV-2 lineages circulating in Southern Brazil between March 2020 and May 2021. This evaluation allowed us to detect the genetic events associated with the emergence of the P.1 and its sublineages. This study is important because we were able to establish that the common ancestor of P.1 sequences from Rio Grande do Sul, Southern Brazil, is dated of mid-June/July 2020, earlier than the P.1 sequences previously reported from Amazonas (AM) state. Noteworthy, the high degree of genetic diversity among P.1 sequences found in this study suggests a continuous evolution and community spread of the virus. Moreover, the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM.

Evaluation of Clinical Course of Gamma (P.1) Variant of Concern versus Lineages in Hospitalized Patients with COVID-19 in a Reference Center in Brazil.

The SARS-CoV-2 variant of concern (VOC) gamma (P.1) has increased transmissibility and resulted in elevated hospitalization and mortality rates in Brazil. We investigated the clinical course of COVID-19 caused by gamma and non-VOCs at a reference hospital in Brazil in a retrospective cohort study with nonelderly hospitalized patients from two periods, before and after the emergence of gamma. Cohort 1 included patients from both periods whose samples would be eligible for whole-genome sequencing (WGS). Cohort 2 was composed of randomly selected patients from Cohort 1 whose samples were submitted to WGS. A total of 433 patients composed Cohort 1: 259 from the first and 174 from the second period. Baseline characteristics were similar, except for a higher incidence of severe distress respiratory syndrome at admission in patients from the second period. Patients from the second period had significantly higher incidence rates of advanced respiratory support (adjusted hazard ratio [aHR]: 2.04; 95% confidence interval [CI], 1.60-2.59), invasive ventilatory support (aHR: 2.72; 95% CI: 2.05-3.62), and 28-day mortality from the onset of symptoms (aHR: 2.62; 95% CI: 1.46-4.72). A total of 86 (43 gamma and 43 non-gamma) patients composed Cohort 2. Patients with confirmed gamma VOC infections had higher advanced ventilatory support and mortality rates than non-gamma-infected patients. Our study suggests that non-elderly patients hospitalized for COVID-19 in the second period (used as a proxy of gamma infection) had a more severe clinical course. This might have contributed to higher hospitalization and death rates observed in the second wave in Brazil.

The occurrence of antimicrobial residues and antimicrobial resistance genes in urban drinking water and sewage in Southern Brazil.

Antimicrobial resistance (AMR) is currently discussed as an important issue worldwide, and the presence of antimicrobial residues (ARs) and antimicrobial resistance genes (ARGs) in the environment, especially in the water sources, is a challenge for public health. This study was conducted to evaluate the occurrence and diversity of AR and ARG in water sources from an urban center, in Southern Brazil. A total of thirty-two water samples from drinking water treatment plants (24) and sewage systems (8) were collected during two annual samplings, winter and summer. The PCR was performed by 18 ARGs, and the detection of 47 ARs was performed by LC-MS/MS. All sewage samples presented carbapenemases, ESBL, and mcr-1 genes as well as quinolones and sulfamethoxazole residues. In drinking water, we just detected blaTEM and tetB genes and doxycycline residues in samples before treatment. This study provides data about AR and ARG in drinking water and sewage systems showing that these sources are important reservoirs of both. The limited effectiveness of wastewater treatment processes to remove mainly AR demonstrates the need to implement better protocols of disinfection, in order to limit the spread of AMR in the environment.

Identification of pesticides in water samples by solid-phase extraction and liquid chromatography-electrospray ionization mass spectrometry.

The Contaminants of Emerging Concern (CECs), including pesticides, have been a trending topic and Brazil is the country with the highest usage of pesticides worldwide. This study aimed to measure the presence of pesticide residues in the water from different sources in the city of Porto Alegre. We analyzed 55 samples from drinking water treatment plants, public water sites, and sewage treatment plants from winter 2018 to summer 2020 by solid-phase extraction and high-performance liquid chromatography-electrospray ionization mass spectrometry. Among 184 pesticides evaluated, 107 matched validation criteria (linearity, trueness, accuracy, repeatability, reproducibility) and 15 of them were detected in different water samples, including seven insecticides, five antifungals, and three herbicides, with a wide range of toxicity levels and noticeable seasonal differences. For the worst-case scenario evaluation, 20 out of 22 (90.9%) samples exceeded the Risk Quotient of 1. The sum of pesticide concentrations exceeded 100 ng L-1 in 66.7% of samples in February 19 and in 75% of samples in February 20 and the total pesticide concentration has reached the worrisome mark of 1615 and 954.96 ng L-1 respectively. Therefore, our results make evident the need to promote public policies to achieve better water quality monitoring. PRACTITIONER POINTS: Among 184 pesticides evaluated, 107 matched validation criteria (linearity, trueness, accuracy, repeatability, reproducibility). A total of 55 different water samples were analyzed, and 15 pesticides were detected and five quantified. For the worst-case scenario evaluation, 20 out of 21 samples exceeded the Risk Quotient of 1 on Feb/20. The pesticide concentrations sum exceeded 100 ng L-1 in 66.7% of samples on February 19 and in 75% of samples on February 20. It is mandatory to improve water monitoring to guide the development of public policies concerning its quality.

From the Approach to the Concept: One Health in Latin America-Experiences and Perspectives in Brazil, Chile, and Colombia.

Professionals throughout the world have been working to assess the interdisciplinary interaction and interdependence between health and wellbeing in a constantly changing environment. The One Health concept was developed to encourage sustainable collaborative partnerships and to promote optimal health for people, animals, plants, the environment, and the whole planet. The dissemination of scientific discoveries and policies, by working directly with diverse communities, has been one of the main goals for Global One Health. The One Health concept has also been referred or related to as "One Medicine, One Medicine-One Health, One World-One Health, EcoHealth," and Planetary Health," depending on each fundamental view and approach. In Latin America, despite the concept still being discussed among health professionals and educators, several One Health initiatives have been used daily for more than decades. One Health action has been applied especially in rural and underserved urban areas where low socioeconomic status, lack of health professionals, and scarcity of medical resources may require professionals to work together. Local communities from diverse social and economic statuses, including indigenous populations have been working with institutions and social organizations for many years, accomplishing results through grassroots movements. These "bottom-up" socio-community approaches have also been tools for the prevention and control of diseases, such practice has preceded the One Health concepts in Latin American countries. It is strongly believed that collaborative, multidisciplinary, political, and economic initiatives with prosocial focus may become investments toward obtaining significant results in the face of global, economic and health challenges; working for a healthier world with inclusivity, equity, and equality. In this study, it is briefly presented how the One Health approach has been initiated and developed in Latin America, highlighting the events and actions taken in Brazil, Chile, and Colombia.

High Levels of Resistance to Cephalosporins Associated with the Presence of Extended-Spectrum and AmpC ß-Lactamases in Escherichia coli from Broilers in Southern Brazil.

The clinical importance of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has increased steadily over the years. The presence of the blaTEM, blaSHV, and blaCTX-M genes in the environment has been recently recognized as an important issue in the dissemination of resistance to cephalosporins. Food animals are considered important vectors for transfer of ESBL genes from the environment to humans. The objective of this study was to characterize the ESBL genes (blaTEM, blaSHV, and blaCTX-M types) that were most prevalent among 343 ceftazidime-resistant E. coli isolates (17 batches from 12 different farms) obtained from cloacal swabs of broiler chicken in southern Brazil. The blaSHV, blaCTX-M, blaTEM, blaIMP-type, blaVIM-type, blaNDM-1, blaKPC-type, blaGES-type, blaOXA-48, and mcr-1 genes were evaluated by polymerase chain reaction. A total of 27 (7.9%) E. coli isolates were positive for ESBL genes as follows: 24 for blaCTX-M (23 blaCTX-M-2 Group and 1 blaCTX-M-8) and 3 for blaSHV (2 blaSHV-2a and 1 blaSHV-18). A random sample of 32 ceftazidime/cefotaxime-resistant isolates that were negative for ESBL genes were evaluated for the presence of blaCMY-2 and 24 (75%) tested positive. We detected the blaCMY-2 gene in isolates from all farms. All isolates positive for ESBL or blaCMY-2 are considered multidrug resistant (resistant to at least three antibiotic classes). Our results suggest that broiler chickens are an important reservoir of blaCMY-2 and ESBL genes, including blaSHV-2a, described for the first time in animals originating from Brazil in this study, and blaSHV-18, which has never been described in Brazil before. This fact highlights the importance of controlling the use of antibiotics in animal production to reduce environmental sources of resistance genes.

Synergy of polymyxin B, tigecycline and meropenem against carbapenem-resistant Enterobacter cloacae complex isolates.

Here, we evaluated the combinations of antibiotics polymyxin B (PMB), tigecycline (TGC) and meropenem (MEM) by time-kill curves (TKC) against carbapenem-resistant Enterobacter cloacae isolates. Combination of PMB/TGC and PMB/MEM showed promising results in sub-inhibitory concentration of PMB indicating the possibility of reducing the dose of PMB used in the treatment.

Rapid tools to gain insights into the interaction dynamics of new 8-hydroxyquinolines with few fungal lines.

The combination of tools such as time-kill assay with subsequent application of mathematical modeling can clarify the potential of new antimicrobial compounds, since minimal inhibitory concentration (MIC) value does not provide a very detailed characterization of antimicrobial activity. Recently, our group has reported that the 8-hydroxy-5-quinolinesulfonic acid presents relevant antifungal activity. However, its intrinsic acidity could lead to an ionization process, decreasing fungal cell permeability. To overcome this potential problem and enhance activity, the purpose of this study was to synthesize and evaluate a novel series of hybrids between the 8-hydroxyquinoline core and sulfonamide and to prove their potential using broth microdilution method, obtaining the pharmacodynamic parameters of the most active derivatives combining time-kill studies and mathematical modeling and evaluating their toxicity. Compound 5a was the most potent, being active against all the fungal species tested, with low toxicity in normal cells. 5a and 5b have presented important antibacterial activity against Staphylococcus aureus strain. The EC50 values obtained by combination of time-kill studies with mathematical model were similar to those of MIC, which confirms the potential of compounds. In addition, these derivatives are non-irritant molecules with the absence of topical toxicity. Finally, 5a and 5b are promising candidates for treatment of dermatomycosis and candidiasis.

Acquisition of the mcr-1 gene by a high-risk clone of KPC-2-producing Klebsiella pneumoniae ST437/CC258, Brazil.

We identified one clinical isolate of K. pneumoniae harboring the mcr 1 (plasmid of IncX4 family) and blaKPC-2 (plasmid of IncFIB family) genes in southern Brazil. These findings highlight that K. pneumoniae isolates carrying both mcr-1 and blaKPC-2 may emergence as a serious threat to antimicrobial therapy.