Endotracheal tube microbiome in hospitalized patients defined largely by hospital environment.

BACKGROUND: Studies of the respiratory tract microbiome primarily focus on airway and lung microbial diversity, but it is still unclear how these microbial communities may be affected by intubation and long periods in intensive care units (ICU), an aspect that today could aid in the understanding of COVID19 progression and disease severity. This study aimed to explore and characterize the endotracheal tube (ETT) microbiome by analyzing ETT-associated microbial communities. METHODS: This descriptive study was carried out on adult patients subjected to invasive mechanical ventilation from 2 to 21 days. ETT samples were obtained from 115 patients from ICU units in two hospitals. Bacteria isolated from endotracheal tubes belonging to the ESKAPE group were analyzed for biofilm formation using crystal violet quantification. Microbial profiles were obtained using Illumina sequencing of 16S rRNA gene. RESULTS: The ETT microbiome was mainly composed by the phyla Proteobacteria, Firmicutes and Bacteroidetes. Microbiome composition correlated with the ICU in which patients were hospitalized, while intubation time and diagnosis of ventilator-associated pneumonia (VAP) did not show any significant association. CONCLUSION: These results suggest that the ICU environment, or medical practices, could be a key to microbial colonization and have a direct influence on the ETT microbiomes of patients that require mechanical ventilation.

Genomic Diversity of Burkholderia pseudomallei Isolates, Colombia.

We report an analysis of the genomic diversity of isolates of Burkholderia pseudomallei, the cause of melioidosis, recovered in Colombia from routine surveillance during 2016-2017. B. pseudomallei appears genetically diverse, suggesting it is well established and has spread across the region.

Case Report: Gestational Melioidosis through Perinatal Transmission.

Burkholderia pseudomallei is an emerging pathogen in the Americas. Cases of mother-to-child transmission of B. pseudomallei are rare and probably occur by placental or perinatal infection. We report the first case of native gestational and neonatal melioidosis in the Western hemisphere. The isolated strains in the mother and newborn were confirmed by whole-genome sequencing and identified as a novel sequence type ST1748. The comparison of both genomes revealed a nucleotide similarity of 100%. Melioidosis should be considered within the differential diagnosis of febrile illness or pneumonia in pregnant women and newborns from endemic areas of the Americas.

Melioidosis is in the Americas: A Call to Action for Diagnosing and Treating the Disease.

Melioidosis, a disease caused by the pathogen Burkholderia pseudomallei, is a significant underreported endemic disease found in tropical countries worldwide. Recent studies have demonstrated that human melioidosis cases have been increasingly recognized in the Americas. Therefore, the first Scientific Reunion of Melioidosis in the Americas was organized in Colombia, with the participation of health authorities of 11 Latin American countries and the United States. This report summarizes the topics reviewed during the meeting, including how to identify human infections and properly diagnose them, with the goal of increasing recognition of the disease in the Americas.

Klebsiella pneumoniae yfiRNB operon affects biofilm formation, polysaccharide production and drug susceptibility.

Klebsiella pneumoniae is an opportunistic pathogen important in hospital-acquired infections, which are complicated by the rise of drug-resistant strains and the capacity of cells to adhere to surfaces and form biofilms. In this work, we carried out an analysis of the genes in the K. pneumoniae yfiRNB operon, previously implicated in biofilm formation. The results indicated that in addition to the previously reported effect on type 3 fimbriae expression, this operon also affected biofilm formation due to changes in cellulose as part of the extracellular matrix. Deletion of yfiR resulted in enhanced biofilm formation and an altered colony phenotype indicative of cellulose overproduction when grown on solid indicator media. Extraction of polysaccharides and treatment with cellulase were consistent with the presence of cellulose in biofilms. The enhanced cellulose production did not, however, correlate with virulence as assessed using a Caenorhabditis elegans assay. In addition, cells bearing mutations in genes of the yfiRNB operon varied with respect to the WT control in terms of susceptibility to the antibiotics amikacin, ciprofloxacin, imipenem and meropenem. These results indicated that the yfiRNB operon is implicated in the production of exopolysaccharides that alter cell surface characteristics and the capacity to form biofilms--a phenotype that does not necessarily correlate with properties related with survival, such as resistance to antibiotics.

Comparative analysis of diguanylate cyclase and phosphodiesterase genes in Klebsiella pneumoniae.

BACKGROUND: Klebsiella pneumoniae can be found in environmental habitats as well as in hospital settings where it is commonly associated with nosocomial infections. One of the factors that contribute to virulence is its capacity to form biofilms on diverse biotic and abiotic surfaces. The second messenger Bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) is a ubiquitous signal in bacteria that controls biofilm formation as well as several other cellular processes. The cellular levels of this messenger are controlled by c-di-GMP synthesis and degradation catalyzed by diguanylate cyclase (DGC) and phophodiesterase (PDE) enzymes, respectively. Many bacteria contain multiple copies of these proteins with diverse organizational structure that highlight the complex regulatory mechanisms of this signaling network. This work was undertaken to identify DGCs and PDEs and analyze the domain structure of these proteins in K. pneumoniae. RESULTS: A search for conserved GGDEF and EAL domains in three sequenced K. pneumoniae genomes showed that there were multiple copies of GGDEF and EAL containing proteins. Both single domain and hybrid GGDEF proteins were identified: 21 in K. pneumoniae Kp342, 18 in K. pneumoniae MGH 78578 and 17 in K. pneumoniae NTUH-K2044. The majority had only the GGDEF domain, most with the GGEEF motif, and hybrid proteins containing both GGDEF and EAL domains were also found. The I site for allosteric control was identified only in single GGDEF domain proteins and not in hybrid proteins. EAL-only proteins, containing either intact or degenerate domains, were also identified: 15 in Kp342, 15 in MGH 78578 and 10 in NTUH-K2044. Several input sensory domains and transmembrane segments were identified, which together indicate complex regulatory circuits that in many cases can be membrane associated. CONCLUSIONS: The comparative analysis of proteins containing GGDEF/EAL domains in K. pneumoniae showed that most copies were shared among the three strains and that some were unique to a particular strain. The multiplicity of these proteins and the diversity of structural characteristics suggest that the c-di-GMP network in this enteric bacterium is highly complex and reflects the importance of having diverse mechanisms to control cellular processes in environments as diverse as soils or plants and clinical settings.

[Helicobacter pylori genotypes in non atrophic gastritis are different of the found in peptic ulcer, premalignant lesions and gastric cancer in Colombia]. / Los genotipos de Helicobacter pylori en gastritis no atrófica difieren de los encontrados en úlcera péptica, lesiones premalignas y cáncer gástrico en Colombia.

BACKGROUND: Helicobacter pylori is recognized as an etiologic agent of several gastric diseases. Bacterial genotypes have been related to clinical outcome in several populations. AIM: To compare cagA, vacA and iceA genotypes of Colombian isolates from patients with several gastrointestinal diseases, including gastric cancer. MATERIAL AND METHODS: We used polymerase chain reactions to amplify vacA, cagA and iceA genes of 137 H pylori isolates coming from 26 patients with gastric cancer (GC), 34 with peptic ulcer (PU), 19 with intestinal metaplasia (IM), 23 with atrophic gastritis (AG) and 35 with non atrophic gastritis (NAG). RESULTS: vacA s1-m1, cagA+, iceA+ were the most frequently found genotypes. vacA s1 and m1 subtypes were found in 92 (67%) and 82 (60%) cases respectively. Sixty three percent were cagA+ and 85% were iceA+. There was a lower prevalence of s1 allele in cases of NAG (43%), compared with GC, PU and IM (81%, 77% and 81% prevalence, respectively, p < 0.01). Isolates from NAG also showed a low frequency of vacA m1 subtype (40%) compared with GC or IM (81% and 84% respectively, p < 0.01). The prevalence of cagA+ strains was significantly higher in GC patients (80%) than in NAG patients (51.4%, p < 0.01). No differences in the frequency of vacA s1a, s1b and iceA subtypes, were observed. CONCLUSIONS: A lower frequency of cytotoxic H pylori genotypes such as cagA and vacA s1m1 and a higher frequency of non cytotoxic genotypes, was observed in patients with NAG, when compared to patients with GC or PU. These results suggest that even in Colombia, vacA and cagA could be used as markers of increased virulence.

Los genotipos de helicobacter pylori en gastritis no atrófica difieren de los encontrados en úlcera péptica, lesiones premalignas y cáncer gástrico en Colombia / Helicobacter pylori genotypes in non atrophic gastritis, peptic ulcer disease, premalignant lesions and gastric cancer in Colombia

Background: Helicobacter pylori is recognized as an etiologic agent of several gastric diseases. Bacterial genotypes have been related to clinical outcome in several populations. Aim: To compare cagA, vacA and iceA genotypes of Colombian isolates from patients with several gastrointestinal diseases, including gastric cancer. Material and methods: We used polymerase chain reactions to amplify vacA, cagA and iceA genes of 137 H pylori isolates coming from 26 patients with gastric cancer (GC), 34 with peptic ulcer (PU), 19 with intestinal metaplasia (IM), 23 with atrophic gastritis (AG) and 35 with non atrophic gastritis (NAG). Results: vacA s1-m1, cagA+, iceA+ were the most frequently found genotypes. vacA s1 and m1 subtypes were found in 92 (67 percent) and 82 (60 percent) cases respectively. Sixty three percent were cagA+ and 85 percent were iceA+. There was a lower prevalence of s1 allele in cases of NAG (43 percent), compared with GC, PU and IM (81 percent, 77 percent and 81 percent prevalence, respectively, p <0.01). Isolates from NAG also showed a low frequency of vacA m1 subtype (40 percent) compared with GC or IM (81 percent and 84 percent respectively, p <0.01). The prevalence of cagA+ strains was significantly higher in GC patients (80 percent) than in NAG patients (51.4 percent, p <0.01). No differences in the frequency of vacA s1a, s1b and iceA subtypes, were observed. Conclusions: A lower frequency of cytotoxic H pylori genotypes such as cagA and vacA s1m1 and a higher frequency of non cytotoxic genotypes, was observed in patients with NAG, when compared to patients with GC or PU. These results suggest that even in Colombia, vacA and cagA could be used as markers of increased virulence