Healthcare-Associated Infections-Related Bacteriome and Antimicrobial Resistance Profiling: Assessing Contamination Hotspots in a Developing Country Public Hospital

Hospital-built environment colonization by healthcare-associated infections-related bacteria (HAIrB) and the interaction with their occupants have been studied to support more effective tools for HAI control. To investigate HAIrB dynamics and antimicrobial resistance (AMR) profile we carried out a 6-month surveillance program in a developing country public hospital, targeting patients, hospital environment, and healthcare workers, using culture-dependent and culture-independent 16S rRNA gene sequencing methods. The bacterial abundance in both approaches shows that the HAIrB group has important representativeness, with the taxa Enterobacteriaceae, Pseudomonas, Staphylococcus, E. coli, and A. baumannii widely dispersed and abundant over the time at the five different hospital units included in the survey. We observed a high abundance of HAIrB in the patient rectum, hands, and nasal sites. In the healthcare workers, the HAIrB distribution was similar for the hands, protective clothing, and mobile phones. In the hospital environment, the healthcare workers resting areas, bathrooms, and bed equipment presented a wide distribution of HAIrB and AMR, being classified as contamination hotspots. AMR is highest in patients, followed by the environment and healthcare workers. The most frequently detected beta-lactamases genes were, bla_SHV–like, bla_{OXA–23–like}, bla_{OXA–51–like}, bla_KPC–like, bla_CTX–M–1, bla_CTX–M–8, and bla_CTX–M–9 groups. Our results demonstrate that there is a wide spread of antimicrobial resistance due to HAIrB in the hospital environment, circulating among patients and healthcare workers. The contamination hotspots identified proved to be constant over time. In the fight for patient safety, these findings can reorient practices and help to set up new guidelines for HAI control.

Emergence of rmtD1 gene in clinical isolates of Pseudomonas aeruginosa carrying blaKPC and/or blaVIM-2 genes in Brazil

OBJECTIVES

The aim of the present study is to describe clinical aminoglycoside- or carbapenem-resistant Pseudomonas aeruginosa isolates collected between 2018 and 2019 in a hospital in Recife City, Northeastern Brazil. It was done based on phenotypic and molecular markers of antimicrobial resistance, as well as on the clonal diversity of the investigated isolates.

METHODS

Thirty-four carbapenem- and/or aminoglycoside-resistant P. aeruginosa isolates were collected in a hospital in Recife City-PE, Brazil. Their antimicrobial susceptibility profile was identified based on the automated BD Phoenix ™ system. In addition, broth microdilution was performed to determine the MICs of tobramycin and polymyxin B. Eventually, isolates were subjected to PCR and sequencing in order to detect the carbapenemase enzyme (bla_KPC, bla_NDM, bla_VIM, bla_SPM-1, and bla_IMP) and 16S rRNA methylase (armA, rmtB, rmtD, rmtF, and rmtG) genes; ERIC-PCR was conducted for clonal profile determination purposes.

RESULTS

Thirty-four of the 64 isolates evaluated in the present study were selected for complementary molecular phenotypic tests, based on sample inclusion criteria. The bla_KPC and bla_VIM-2 genes were identified in 32.4% (11/34) and 38.2% (13/34) of tested isolates, respectively. The rmtD1 gene was detected in 32.4% (11/34) of analyzed isolates. Eight isolates carried both the bla_KPC and rmtD1 genes, whereas bla_VIM-2 and rmtD1 genes co-occurrence was detected in three strains; one isolate had all bla_KPC, bla_VIM-2, and rmtD1 genes. ERIC-PCR molecular typing has evidenced cross-transmission of three pathogenic clones among patients in the hospital.

CONCLUSIONS

The present study is a pioneer in describing isolates harboring both bla_VIM-2 and rmtD1 genes. Moreover, it emphasizes the need of conducting local molecular epidemiology studies at different time intervals in order to monitor measures adopted to prevent nosocomial infections in different hospital units.

Molecular Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolated from Egyptian Pediatric Cancer Patients Including a Strain with a Rare Gene-Combination of β-Lactamases

PURPOSE

Healthcare-associated infections caused by multi-drug-resistant (MDR) pathogens are a global threat. We aim to assess the clonal relatedness among carbapenemase-producing Klebsiella pneumoniae (CPKP) strains infecting Egyptian pediatric cancer patients.

MATERIALS AND METHODS

Identification and antimicrobial susceptibility testing of 149 Gram-negative isolates obtained from pediatric cancer patients were performed by VITEK 2. Genes encoding carbapenemases and extended-spectrum β-lactamases were detected by PCR and verified by DNA sequencing of representative samples. The transferability of the plasmids harboring bla OXA-48, from representative clinical samples, was evaluated by performing a conjugation experiment followed by PCR and MIC shift determination. Clonal relationships among the bla OXA-48-harboring K. pneumoniae isolates were determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR and pulsed-field gel electrophoresis (PFGE).

RESULTS

Carbapenem resistance was observed in 59% of the isolates. The most prevalent species was K. pneumoniae (45.6%) and 57% of them were isolated from ICU. Fifty-nine % of the K. pneumoniae isolates were carbapenemase-producers and bla OXA-48 was detected in (58%) of them. One isolate co-harbored bla OXA-48, bla NDM-1, and bla IMP-1 genes for the first time in Egypt. PCR and meropenem MIC shift confirmed the success of the transferability of representative plasmids to E. coli K12. ERIC and PFGE identified 93% and 100% of the K. pneumoniae with a similarity coefficient ≥85%, respectively, including strains with indistinguishable patterns, suggesting possible clonal dissemination.

CONCLUSION

Our findings underline the dissemination of diverse clones of MDR CPKP among Egyptian pediatric cancer patients. Hence, routine molecular characterizations followed by strict implementation of infection control measures are crucial to tackling this threat.

High mortality by nosocomial infections caused by carbapenem-resistant P. aeruginosa in a referral hospital in Brazil: facing the perfect storm

Introduction. Carbapenem-resistant Pseudomonas aeruginosa is responsible for increased patient mortality.Gap Statement. Five and 30 day in-hospital all-cause mortality in patients with P. aeruginosa infections were assessed, followed by evaluations concerning potential correlations between the type III secretion system (TTSS) genotype and the production of metallo-β-lactamase (MBL).Methodology. This assessment comprised a retrospective cohort study including consecutive patients with carbapenem-resistant infections hospitalized in Brazil from January 2009 to June 2019. PCR analyses were performed to determine the presence of TTSS-encoding genes and MBL genes.Results. The 30-day and 5-day mortality rates for 262 patients were 36.6 and 17.9 %, respectively. The unadjusted survival probabilities for up to 5 days were 70.55 % for patients presenting exoU-positive isolates and 86 % for those presenting exo-negative isolates. The use of urinary catheters, as well as the presence of comorbidity conditions, secondary bacteremia related to the respiratory tract, were independently associated with death at 5 and 30 days. The exoS gene was detected in 64.8 % of the isolates, the presence of the exoT and exoY genes varied and exoU genes occurred in 19.3 % of the isolates. The exoU genotype was significantly more frequent among multiresistant strains. MBL genes were not detected in 92 % of the isolates.Conclusions. Inappropriate therapy is a crucial factor regarding the worse prognosis among patients with infections caused by multiresistant P. aeruginosa, especially those who died within 5 days of diagnosis, regardless of the genotype associated with TTSS virulence.

The H-NS Regulator Plays a Role in the Stress Induced by Carbapenemase Expression in Acinetobacter baumannii

Carbapenem-resistant A. baumannii (CRAB) is recognized as one of the most threatening Gram-negative bacilli. H-NS is known to play a role in controlling the transcription of a variety of different genes, including those associated with the stress response, persistence, and virulence. In the present work, we uncovered a link between the role of H-NS in the A. baumannii stress response and its relationship with the envelope stress response and resistance to DNA-damaging agents. Overall, we posit a new role of H-NS, showing that H-NS serves to endure envelope stress and could also be a mechanism that alleviates the stress induced by MBL expression in A. baumannii. This could be an evolutionary advantage to further resist the action of carbapenems.

Disruption of the histone-like nucleoid structuring protein (H-NS) was shown to affect the ability of Gram-negative bacteria to regulate genes associated with virulence, persistence, stress response, quorum sensing, biosynthesis pathways, and cell adhesion. Here, we used the expression of metallo-β-lactamases (MBLs), known to elicit envelope stress by the accumulation of toxic precursors in the periplasm, to interrogate the role of H-NS in Acinetobacter baumannii, together with other stressors. Using a multidrug-resistant A. baumannii strain, we observed that H-NS plays a role in alleviating the stress triggered by MBL toxic precursors and counteracts the effect of DNA-damaging agents, supporting its role in stress response.

IMPORTANCE Carbapenem-resistant A. baumannii (CRAB) is recognized as one of the most threatening Gram-negative bacilli. H-NS is known to play a role in controlling the transcription of a variety of different genes, including those associated with the stress response, persistence, and virulence. In the present work, we uncovered a link between the role of H-NS in the A. baumannii stress response and its relationship with the envelope stress response and resistance to DNA-damaging agents. Overall, we posit a new role of H-NS, showing that H-NS serves to endure envelope stress and could also be a mechanism that alleviates the stress induced by MBL expression in A. baumannii. This could be an evolutionary advantage to further resist the action of carbapenems.

Synergistic Effect between Usnic Acid and Polymyxin B against Resistant Clinical Isolates of Pseudomonas aeruginosa

The present study aimed to characterize the susceptibility profile of Pseudomonas aeruginosa and Acinetobacter spp. clinical isolates to polymyxin B in a public hospital in Recife-PE, Brazil, between the years of 2018 and 2019, as well as to search for the presence of the mcr-1 gene and evaluate the interaction between polymyxin B and usnic acid against these isolates. The strains were identified using the BD Phoenix™ automated system and the agar-spot test was used to determine the susceptibility profile to polymyxin B. The minimum inhibitory concentrations (MICs) of usnic acid and polymyxin B were determined through the broth microdilution method according to the Clinical and Laboratory Standards Institute (CLSI). Subsequently, Polymerase Chain Reaction (PCR) was performed to detect the mcr-1 gene in the isolates. The interaction between usnic acid and polymyxin B was evaluated by the Checkerboard assay. Among 34 isolates of P. aeruginosa, 26.5% (9/34) were positive for the polymyxin B agar-spot test, and 11.8% (4/34) presented an intermediate susceptibility (MIC = 4 μg/mL), while 14.7% (5/34) presented antimicrobial resistance with MIC values ranging from 8 to 32 μg/mL. Among 38 isolates of Acinetobacter spp., 13.2% (5/38) were positive for the polymyxin B agar-spot test and all of them were resistant to polymyxin B with a MIC value > 32 μg/mL. The mcr-1 gene was not detected in the clinical isolates. Regarding usnic acid, it presented a moderate antibacterial activity against two P. aeruginosa isolates (MIC = 250 μg/mL) and no activity was detected against the others. A synergistic effect between usnic acid and polymyxin B was observed against three clinical isolates of P. aeruginosa which were resistant to polymyxin B (FICI ≤ 0.5). Therefore, it was possible to observe that usnic acid is a promising candidate to be used in combination with polymyxin B against infections caused by resistant P. aeruginosa.

Profile of Enterobacteria Resistant to Beta-Lactams

A serious emerging problem worldwide is increased antimicrobial resistance. Acquisition of coding genes for evasion methods of antimicrobial drug mechanisms characterizes acquired resistance. This phenomenon has been observed in Enterobacteriaceae family. Treatment for bacterial infections is performed with antibiotics, of which the most used are beta-lactams. The aim of this study was to correlate antimicrobial resistance profiles in Enterobacteriaceae by phenotypic methods and molecular identification of 14 beta-lactamase coding genes. In this study, 70 exclusive isolates from Brazil were used, half of which were collected in veterinary clinics or hospitals Phenotypic methodologies were used and real-time PCR was the molecular methodology used, through the Sybr Green system. Regargding the results found in the tests it was observed that 74.28% were resistant to ampicillin, 62.85% were resistant to amoxicillin associated with clavalunate. The mechanism of resistance that presented the highest expression was ESBL (17.14%). The genes studied that were detected in a greater number of species were blaGIM and blaSIM (66.66% of the samples) and the one that was amplified in a smaller number of samples was blaVIM (16.66%). Therefore, high and worrying levels of antimicrobial resistance have been found in enterobacteria, and a way to minimize the accelerated emergence of their resistance includes developing or improving techniques that generate diagnoses with high efficiency and speed.

Global Survey of Antibiotic Resistance Genes in Air

Despite its emerging significant public health concern, the presence of antibiotic resistance genes (ARGs) in urban air has not received significant attention. Here, we profiled relative abundances (as a fraction, normalized by 16S rRNA gene) of 30 ARG subtypes resistant to seven common classes of antibiotics, which are quinolones, β-lactams, macrolides, tetracyclines, sulfonamides, aminoglycosides, and vancomycins, in ambient total particulate matter (PM) using a novel protocol across 19 world cities. In addition, their longitudinal changes in PM_2.5 samples in Xi'an, China as an example were also studied. Geographically, the ARGs were detected to vary by nearly 100-fold in their abundances, for example, from 0.07 (Bandung, Indonesia) to 5.6 (San Francisco, USA). The β-lactam resistance gene blaTEM was found to be most abundant, seconded by quinolone resistance gene qepA; and their corresponding relative abundances have increased by 178% and 26%, respectively, from 2004 to 2014 in Xi'an. Independent of cities, gene network analysis indicates that airborne ARGs were differentially contributed by bacterial taxa. Results here reveal that urban air is being polluted by ARGs, and different cities are challenged with varying health risks associated with airborne ARG exposure. This work highlights the threat of urban airborne transmission of ARGs and the need of redefining our current air quality standards in terms with public health.