Molecular Epidemiology of Acinetobacter calcoaceticus-Acinetobacter baumannii Complex Isolated From Children at the Hospital Infantil de México Federico Gómez

Molecular epidemiology of carbapenemase encoding genes in A. baumannii-calcoaceticus complex infections in children: a systematic review

Background

Acinetobacter baumannii-calcoaeticus complex is the leader pathogen for the World Health Organization's list due to the escalating prevalence of multidrug-resistant strains. Insights into the molecular characterization of carbapenemase genes in A. baumannii-calcoaceticus complex infections among children are scarce. To address this gap, we conducted a systematic review to describe the molecular epidemiology of the carbapenemase genes in A. baumannii-calcoaceticus complex infections in the pediatric population.

Methods

Adhering to the PRISMA 2020 guidelines for reporting systematic reviews, we conducted a review of in chore bibliographic databases published in English and Spanish, between January 2020 and December 2022. All studies conducted in patients ≤6 years with molecular characterization of carbapenemase-encoding genes in A. baumannii-calcoaceticus infections were included.

Results

In total, 1129 cases were reviewed, with an overall carbapenem-resistance rate of 60.3%. A. baumannii-calcoaceticus was isolated from blood cultures in 66.6% of cases. Regionally, the Eastern Mediterranean exhibited the highest prevalence of carbapenem resistance (88.3%). Regarding the carbapenemase genes, blaKPC displayed an overall prevalence of 1.2%, while class B blaNDM had a prevalence of 10.9%. Class D blaOXA-23-like reported a prevalence of 64%, blaOXA-48 and blaOXA-40 had a prevalence of 33% and 18.1%, respectively. Notably, the Americas region showed a prevalence of blaOXA-23-like at 91.6%.

Conclusion

Our work highlights the high prevalence of carbapenem-resistant A. baumannii-calcoaceticus and class D carbapenemase genes in children. Of note the distribution of different carbapenemase genes reveals considerable variations across WHO regions. To enhance epidemiological understanding, further extensive studies in children are imperative.

Antimicrobial resistance genes harbored in invasive Acinetobacter calcoaceticus-baumannii complex isolated from Korean children during the pre-COVID-19 pandemic periods, 2015-2020

Background

Acinetobacter baumannii (AB) has emerged as one of the most challenging pathogens worldwide, causing invasive infections in the critically ill patients due to their ability to rapidly acquire resistance to antibiotics. This study aimed to analyze antibiotic resistance genes harbored in AB and non-baumannii Acinetobacter calcoaceticus-baumannii (NB-ACB) complex causing invasive diseases in Korean children.

Methods

ACB complexes isolated from sterile body fluid of children in three referral hospitals were prospectively collected. Colistin susceptibility was additionally tested via broth microdilution. Whole genome sequencing was performed and antibiotic resistance genes were analyzed.

Results

During January 2015 to December 2020, a total of 67 ACB complexes were isolated from sterile body fluid of children in three referral hospitals. The median age of the patients was 0.6 (interquartile range, 0.1-7.2) years old. Among all the isolates, 73.1% (n=49) were confirmed as AB and others as NB-ACB complex by whole genome sequencing. Among the AB isolates, only 22.4% susceptible to carbapenem. In particular, all clonal complex (CC) 92 AB (n=33) showed multi-drug resistance, whereas 31.3% in non-CC92 AB (n=16) (P<0.001). NB-ACB showed 100% susceptibility to all classes of antibiotics except 3rd generation cephalosporin (72.2%). The main mechanism of carbapenem resistance in AB was the bla oxa23 gene with ISAba1 insertion sequence upstream. Presence of pmr gene and/or mutation of lpxA/C gene were not correlated with the phenotype of colistin resistance of ACB. All AB and NB-ACB isolates carried the abe and ade multidrug efflux pumps.

Conclusions

In conclusion, monitoring and research for resistome in ACB complex is needed to identify and manage drug-resistant AB, particularly CC92 AB carrying the bla oxa23 gene.

Detection of florfenicol resistance in opportunistic Acinetobacter spp. infections in rural Thailand

Florfenicol (Ff) is an antimicrobial agent belonging to the class amphenicol used for the treatment of bacterial infections in livestock, poultry, and aquaculture (animal farming). It inhibits protein synthesis. Ff is an analog of chloramphenicol, an amphenicol compound on the WHO essential medicine list that is used for the treatment of human infections. Due to the extensive usage of Ff in animal farming, zoonotic pathogens have developed resistance to this antimicrobial agent. There are numerous reports of resistance genes from organisms infecting or colonizing animals found in human pathogens, suggesting a possible exchange of genetic materials. One of these genes is floR, a gene that encodes for an efflux pump that removes Ff from bacterial cells, conferring resistance against amphenicol, and is often associated with mobile genetic elements and other resistant determinants. In this study, we analyzed bacterial isolates recovered in rural Thailand from patients and environmental samples collected for disease monitoring. Whole genome sequencing was carried out for all the samples collected. Speciation and genome annotation was performed revealing the presence of the floR gene in the bacterial genome. The minimum inhibitory concentration (MIC) was determined for Ff and chloramphenicol. Chromosomal and phylogenetic analyses were performed to investigate the acquisition pattern of the floR gene. The presence of a conserved floR gene in unrelated Acinetobacter spp. isolated from human bacterial infections and environmental samples was observed, suggesting multiple and independent inter-species genetic exchange of drug-resistant determinants. The floR was found to be in the variable region containing various mobile genetic elements and other antibiotic resistance determinants; however, no evidence of HGT could be found. The floR gene identified in this study is chromosomal for all isolates. The study highlights a plausible impact of antimicrobials used in veterinary settings on human health. Ff shares cross-resistance with chloramphenicol, which is still in use in several countries. Furthermore, by selecting for floR-resistance genes, we may be selecting for and facilitating the zoonotic and reverse zoonotic exchange of other flanking resistance markers between human and animal pathogens or commensals with detrimental public health consequences.

Case Report: Molecular Characterization of Bloodstream Infections due to Carbapenem-Resistant Acinetobacter baumannii: A Pediatric Case Series

Acinetobacter baumannii poses a significant threat to public health due to the high rate of multidrug-resistant strains. However, information on the molecular characterization of carbapenem-resistant Acinetobacter baumannii (CRAB) bloodstream infections in children is scarce. This study aimed to describe the molecular characterization of carbapenem-resistant A. baumannii infections in children from a hospital in Mexico. A retrospective study was conducted during the period 2017-2022. Clinical and demographic data were collected from the clinical records. Mass spectrometry was used for the identification of the strains. To confirm A. baumannii strains, a polymerase chain reaction (PCR) method was applied using a gyrB sequence. The carbapenemase-encoding resistance genes were detected by PCR. Six cases of CRAB were documented, including five in neonates. The median intensive care unit stay was 20 days, and all cases had an invasive medical device. Half of the patients had at least one medical condition. A high prevalence of coresistance was observed in most of the antibiotic groups. Three of the six strains coharbored carbapenemase genes: blaOXA-51, blaOXA-24, and blaIMP. Mortality was reported in two neonate patients. The present study shows a high rate of coharboring blaOXA-51, blaOXA-24, and blaIMP-1, which has a direct impact on therapeutic decisions. Implementation of antimicrobial stewardship programs is urgent to stop the spread of this microorganism.

Genome sequence of a tigecycline-resistant Acinetobacter seifertii recovered in human bloodstream infection in China

OBJECTIVES

The phylogenetic characteristics of Acinetobacter seifertii clinical strain are not well-studied. Here, we reported one tigecycline-resistant ST1612Pasteur A. seifertii isolated from bloodstream infections (BSI) in China.

METHODS

Antimicrobial susceptibility tests were conducted via broth microdilution. Whole-genome sequencing (WGS) was performed and annotation was conducted using rapid annotations subsystems technology (RAST) server. Multilocus sequence typing (MLST), capsular polysaccharide (KL), and lipoolygosaccharide (OCL) were analysed using PubMLST and Kaptive. Resistance genes, virulence factors, and comparative genomics analysis were performed. Cloning, mutations of efflux pump-related genes, and expression level were further investigated.

RESULTS

The draft genome sequence of A. seifertii ASTCM strain is made up of 109 contigs with a total length of 4,074,640 bp. Based on the RAST results, 3923 genes that belonged to 310 subsystems were annotated. Acinetobacter seifertii ASTCM was ST1612Pasteur with KL26 and OCL4, respectively. It was resistant to gentamicin and tigecycline. ASTCM harboured tet(39), sul2, and msr(E)-mph(E), and one amino acid mutation in Tet(39) (T175A) was further identified. Nevertheless, the signal mutation failed to contribute to susceptibility change of tigecycline. Of note, several amino acid substitutions were identified in AdeRS, AdeN, AdeL, and Trm, which could lead to overexpression of adeB, adeG, and adeJ efflux pump genes and further possibly lead to tigecycline resistance. Phylogenetic analysis showed that a huge diversity was observed among A. seifertii strains based on 27-52,193 SNPs difference.

CONCLUSION

In summary, we reported a tigecycline-resistant ST1612Pasteur A. seifertii in China. Early detection is recommended to prevent their further spread in clinical settings.

Prevalence of Carbapenem Resistance Genes among Acinetobacter baumannii Isolated from a Teaching Hospital in Taiwan

The problem of antibiotic-resistant strains has become a global public issue; antibiotic resistance not only limits the choice of treatments but also increases morbidity, mortality and treatment costs. The multi-drug resistant Acinetobacter baumannii is occurring simultaneously in hospitals and has become a major public health issue worldwide. Although many medical units have begun to control the use of antibiotics and paid attention to the issue of drug resistance, understanding the transmission pathways of clinical drug-resistant bacteria and drug-resistant mechanisms can be effective in real-time control and prevent the outbreak of antibiotic-resistant pathogens. In this study, a total of 154 isolates of Acinetobacter baumannii obtained from Chia-Yi Christian Hospital in Taiwan were collected for specific resistance genotyping analysis. Ten genes related to drug resistance, including blaOXA-51-like, blaOXA-23-like, blaOXA-58-like, blaOXA-24-like, blaOXA-143-like, tnpA, ISAba1, blaPER-1, blaNDM and blaADC, and the repetitive element (ERIC2) were selected for genotyping analysis. The results revealed that 135 A. baumannii isolates (87.6%) carried the blaOXA-51-like gene, 4.5% of the isolates harbored the blaOXA-23-like gene, and 3.2% of the isolates carried the blaOXA-58-like gene. However, neither the blaOXA-24-like nor blaOXA-143-like genes were detected in the isolates. Analysis of ESBL-producing strains revealed that blaNDM was not found in the test strains, but 38.3% of the test isolates carried blaPER-1. In addition, blaADC, tnpA and ISAba1genes were found in 64.9%, 74% and 93% of the isolates, respectively. Among the carbapenem-resistant strains of A. baumannii, 68% of the isolates presenting a higher antibiotic resistance carried both tnpA and ISAba1 genes. Analysis of the relationship between their phenotypes (antibiotic resistant and biofilm formation) and genotypes (antibiotic-resistant genes and biofilm-related genes) studied indicated that the bap, ompA, ISAba1and blaOXA-51 genes influenced biofilm formation and antibiotic resistance patterns based on the statistical results of a hierarchical clustering dendrogram. The analysis of the antibiotic-resistant mechanism provides valuable information for the screening, identification, diagnosis, treatment and control of clinical antibiotic-resistant pathogens, and is an important reference pointer to prevent strains from producing resistance.

Alterations in gene expression of recA and umuDC in antibiotic-resistant Acinetobacter baumannii

Acinetobacter baumannii is a critical pathogen with an efficient SOS (Save Our Ship) system that plays a significant role in antibiotic resistance. This prospective descriptive study aimed to investigate the association between expression levels of recA and umuDC genes, which are critical in SOS pathways, and antibiotic resistance in A. baumannii. We analyzed 78 clinical isolates and 31 ecological isolates using the Vitek-2 system for bacterial identification and antibiotic susceptibility testing and confirmed molecular identification of A. baumannii by conventional PCR of blaOXA-51 and blaOXA-23. Quantitative real-time polymerase chain reaction was used to determine gene expression levels of recA and umuDC. The results showed that in 25 clinical strains, 14/25 strains showed upregulation of recA, 7/25 strains exhibited upregulation of both umuDC and recA, and 1/25 strains showed upregulation of umuDC. Of these, 16/25 clinical strains were extensively resistant to antibiotics, except for colistin, and showed upregulation of recA and/or umuDC gene expression levels. In 6 ecological strains, recA showed upregulation in 3/6 strains, while both recA and umuDC were upregulated in 1/6 strain. In conclusion, high expression levels of recA and/or umuDC genes in A. baumannii complex and A. baumannii strains may contribute to increasing resistance to a wide range of antibiotics and may result in the initiation of an extensively drug-resistant (XDR) phenotype.

The Molecular Detection of Class B and Class D Carbapenemases in Clinical Strains of Acinetobacter calcoaceticus-baumannii Complex: The High Burden of Antibiotic Resistance and the Co-Existence of Carbapenemase Genes

The emergence of carbapenem-resistant Acinetobacter calcoaceticus-baumannii complex (CRACB) in clinical environments is a significant global concern. These critical pathogens have shown resistance to a broad spectrum of antibacterial drugs, including carbapenems, mostly due to the acquisition of various β-lactamase genes. Clinical samples (n = 1985) were collected aseptically from multiple sources and grown on blood and MacConkey agar. Isolates and antimicrobial susceptibility were confirmed with the VITEK-2 system. The modified Hodge test confirmed the CRACB phenotype, and specific PCR primers were used for the molecular identification of bla_OXA and bla_NDM genes. Of the 1985 samples, 1250 (62.9%) were culture-positive and 200 (43.9%) were CRACB isolates. Of these isolates, 35.4% were recovered from pus samples and 23.5% from tracheal secretions obtained from patients in intensive care units (49.3%) and medical wards (20.2%). An antibiogram indicated that 100% of the CRACB isolates were resistant to β-lactam antibiotics and β-lactam inhibitors, 86.5% to ciprofloxacin, and 83.5% to amikacin, while the most effective antibiotics were tigecycline and colistin. The CRACB isolates displayed resistance to eight different AWaRe classes of antibiotics. All isolates exhibited the bla_OXA-51 gene, while bla_OXA-23 was present in 94.5%, bla_VIM in 37%, and bla_NDM in 14% of the isolates. The bla_OXA-51, bla_OXA-23, and bla_OXA-24 genes co-existed in 13 (6.5%) isolates. CRACB isolates with co-existing bla_OXA-23, bla_OXA-24, bla_NDM, bla_OXA-51 and bla_VIM genes were highly prevalent in clinical samples from Pakistan. CRACB strains were highly critical pathogens and presented resistance to virtually all antibacterial drugs, except tigecycline and colistin.

Profiling Antibiotic Resistance in Acinetobacter calcoaceticus

Background: Acinetobacter spp. have emerged as troublesome pathogens due to their multi-drug resistance. The majority of the work to date has focused on the antibiotic resistance profile of Acinetobacter baumannii. Although A. calcoaceticus strains are isolated in the hospital setting, limited information is available on these closely related species. Methods & Results: The computational analysis of antibiotic resistance genes in 1441 Acinetobacter genomes revealed that A. calcoaceticus harbored a similar repertoire of multi-drug efflux pump and beta-lactam resistance genes as A. baumannii, leading us to speculate that A. calcoaceticus would have a similar antibiotic resistance profile to A. baumannii. To profile the resistance patterns of A. calcoaceticus, strains were examined by Kirby−Bauer disk diffusion and phenotypic microarrays. We found that Acinetobacter strains were moderately to highly resistant to certain antibiotics within fluoroquinolones, aminoglycosides, tetracyclines, and other antibiotic classes. These data indicate that A. calcoaceticus has a similar antibiotic resistance profile as A. baumannii ATCC 19606. We also identified that all Acinetobacter species were sensitive to 5-fluoroorotic acid, novobiocin, and benzethonium chloride. Conclusion: Collectively, these data provide new insights into the antibiotic resistance in A. calcoaceticus and identify several antibiotics that could be beneficial in treating Acinetobacter infections.

First exploratory study of bacterial pathogens and endosymbionts in head lice from a Mayan community in southern Mexico

Lice represent one of the most neglected group of vectors worldwide, particularly in Latin America. Records of bacterial agents related to head lice are non-existent in this region of the continent. Many of these communities often do not have adequate access to public services and/or health protection. The normalization of this condition prevents them from manifesting discomfort, such as bites and itching, which further aggravates the situation, as they can be vectors of important diseases. For this reason, the aim of this work was to identify the richness of bacterial pathogens (Acinetobacter, Bartonella, and Rickettsia) and endosymbionts (Wolbachia) in head lice of paediatric patients from the indigenous municipality of Hoctun, Yucatan, Mexico. DNA extraction was performed using the QIAamp DNA Mini Kit. For the detection of bacterial pathogens, fragments of the gltA, rpoB, and 16S rDNA genes were amplified. For the detection of Wolbachia, the wsp gene was amplified. Of the 28 lice analysed, the presence of two genera of bacterial pathogens was detected Acinetobacter (42.9% = 12/28) and Bartonella (7.14% = 2/28). We also detected the endosymbiont Wolbachia (71.42% = 20/28). Our results showed that DNA from three bacteria species (Acinetobacter baumannii, Bartonella quintana, and Wolbachia pipientis) was present with frequencies ranging from 3.57% to 71.42%. This work represents the first exploratory study of the diversity of agents associated with head lice (Pediculus humanus capitis) in Mexico and Latin America. Due to the findings generated in the present study, it is important to perform surveillance of head lice populations to identify the degree of spread of these pathogens and their impact on populations in the region.

Acinetobacter calcoaceticus is Well Adapted to Withstand Intestinal Stressors and Modulate the Gut Epithelium

Background: The gastrointestinal tract has been speculated to serve as a reservoir for Acinetobacter, however little is known about the ecological fitness of Acinetobacter strains in the gut. Likewise, not much is known about the ability of Acinetobacter to consume dietary, or host derived nutrients or their capacity to modulate host gene expression. Given the increasing prevalence of Acinetobacter in the clinical setting, we sought to characterize how A. calcoaceticus responds to gut-related stressors and identify potential microbe-host interactions. Materials and Methods: To accomplish these aims, we grew clinical isolates and commercially available strains of A. calcoaceticus in minimal media with different levels of pH, osmolarity, ethanol and hydrogen peroxide. Utilization of nutrients was examined using Biolog phenotypic microarrays. To examine the interactions of A. calcoaceticus with the host, inverted murine organoids where the apical membrane is exposed to bacteria, were incubated with live A. calcoaceticus, and gene expression was examined by qPCR. Results: All strains grew modestly at pH 6, 5 and 4; indicating that these strains could tolerate passage through the gastrointestinal tract. All strains had robust growth in 0.1 and 0.5 M NaCl concentrations which mirror the small intestine, but differences were observed between strains in response to 1 M NaCl. Additionally, all strains tolerated up to 5% ethanol and 0.1% hydrogen peroxide. Biolog phenotypic microarrays revealed that A. calcoaceticus strains could use a range of nutrient sources, including monosaccharides, disaccharides, polymers, glycosides, acids, and amino acids. Interestingly, the commercially available A. calcoaceticus strains and one clinical isolate stimulated the pro-inflammatory cytokines Tnf, Kc, and Mcp-1 while all strains suppressed Muc13 and Muc2. Conclusion: Collectively, these data demonstrate that A. calcoaceticus is well adapted to dealing with environmental stressors of the gastrointestinal system. This data also points to the potential for Acinetobacter to influence the gut epithelium.

Molecular Epidemiology of Multidrug-Resistant Uropathogenic Escherichia coli O25b Strains Associated with Complicated Urinary Tract Infection in Children

Background: Uropathogenic Escherichia coli (UPEC) has increased the incidence of urinary tract infection (UTI). It is the cause of more than 80% of community-acquired cystitis cases and more than 70% of uncomplicated acute pyelonephritis cases. Aim: The present study describes the molecular epidemiology of UPEC O25b clinical strains based on their resistance profiles, virulence genes, and genetic diversity. Methods: Resistance profiles were identified using the Kirby–Bauer method, including the phenotypic production of extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs). The UPEC serogroups, phylogenetic groups, virulence genes, and integrons were determined via multiplex PCR. Genetic diversity was established using pulsed-field gel electrophoresis (PFGE), and sequence type (ST) was determined via multilocus sequence typing (MLST). Results: UPEC strains (n = 126) from hospitalized children with complicated UTIs (cUTIs) were identified as O25b, of which 41.27% were multidrug resistant (MDR) and 15.87% were extensively drug resistant (XDR). The O25b strains harbored the fimH (95.23%), csgA (91.26%), papGII (80.95%), chuA (95.23%), iutD (88.09%), satA (84.92%), and intl1 (47.61%) genes. Moreover, 64.28% were producers of ESBLs and had high genetic diversity. ST131 (63.63%) was associated primarily with phylogenetic group B2, and ST69 (100%) was associated primarily with phylogenetic group D. Conclusion: UPEC O25b/ST131 harbors a wide genetic diversity of virulence and resistance genes, which contribute to cUTIs in pediatrics.

Complete Genome Sequence of Acinetobacter pittii BHS4, Isolated from Air-Conditioning Condensate in Hong Kong

Acinetobacter pittii is widespread in the environment, and the Acinetobacter calcoaceticus-baumannii complex, to which it belongs, is a major cause of hospital-acquired pneumonia and bacteremia. A. pitti BHS4 was isolated from an air-conditioning unit in Hong Kong and its complete genome sequence (3,901,980 bp; GC content, 38.79%) established through hybrid assembly.

Identification and Antifungal Susceptibility Analysis of Stephanoascus ciferrii Complex Species Isolated From Patients With Chronic Suppurative Otitis Media

Background

Stephanoascus ciferrii is a heterothallic ascomycetous yeast-like fungus. Recently, the concept of S. ciferrii complex has been proposed and it consists of S. ciferrii, Candida allociferrii, and Candida mucifera. We aimed to identify 32 strains of S. ciferrii complex isolated from patients with chronic suppurative otitis media (CSOM) at the species level and analyze the morphology and antifungal susceptibility profiles of the three species.

Method

The sequencing of the internal transcribed spacer (ITS) region and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) were used to identify S. ciferrii complex species. The SARAMIS software was used for cluster analysis of the mass spectra. All the strains were cultured on Sabouraud dextrose agar (SDA) and CHROM plates for 7 days. In the meantime, colonies of the 32 strains went through Gram staining. The Sensititre YeastOne YO10 colorimetric panel was used for the antifungal susceptibility analysis.

Results

There were 10 strains of C. allociferrii (31.25%), six strains of C. mucifera (18.75%), and 16 strains of S. ciferrii (50%) in the 32 strains of S. ciferrii complex according to the sequencing of the ITS region. MALDI-TOF MS could identify S. ciferrii but showed no results for C. allociferrii and C. mucifera. The cluster analysis of the mass spectra by SARAMIS indicated that the MALDI-TOF MS could distinguish the three species. The morphology characteristics of the three species were similar. As for antifungal susceptibility, S. ciferrii and C. mucifera tended to have high fluconazole MICs compared with C. allociferrii. C. mucifera and C. allociferrii had relatively low flucytosine MICs while S. ciferrii owned high flucytosine MICs. Besides, C. mucifera tended to have a higher MIC value than S. ciferrii for amphotericin B and C. allociferrii for anidulafungin, micafungin, and caspofungin.

Conclusion

The antifungal susceptibility profiles of the three species of S. ciferrii complex had their own characteristics. Besides, more mass spectra of C. allociferrii and C. mucifera are needed to construct the reference database for S. ciferrii complex species, enabling MALDI-TOF MS to identify S. ciferrii complex at species level.