Insights into the global molecular epidemiology of carbapenem non-susceptible clones of Acinetobacter baumannii

Genomic plasticity of extensively drug-resistant and multidrug-resistant Acinetobacter baumannii ST208 isolates from a fatal outbreak

BACKGROUND

The prevalence of multidrug-resistant Acinetobacter baumannii (MDRA) has rapidly increased and is linked to severe nosocomial infections. MDRA outbreaks in a Japanese hospital were analysed using whole-genome sequencing.

METHODS

Antibiotic susceptibility testing was performed on clinical isolates from hospitalised patients before and during the 2009 and 2010 outbreaks. Whole-genome sequencing was conducted to identify acquired antibiotic-resistance genes and genetic mutations.

RESULTS

Clinical A. baumannii isolates were resistant to β-lactams (broad-spectrum cephalosporins and carbapenems), aminoglycosides, chloramphenicol, fosfomycin, fluoroquinolones, tetracyclines, and trimethoprim-sulfamethoxazole. MDRA isolates harboured aac(6')-Ib-cr, abaF, armA, blaADC-30, blaTEM-1, and blaOXA-82, or both blaOXA-66 and blaOXA-23, catB8, mphE, msrE, and tet(B). blaOXA-82 genes were recombinationally multiplied. Quinolone resistance was also associated with gyrA S81L and parC S84L mutations. The MDRA isolates belonged to Oxford sequence type (ST) 208 and Pasteur ST2. Three of the 15 isolates developed an extensively drug-resistant (XDR) phenotype, and two isolates harboured an adeS mutation.

CONCLUSIONS

We identified molecular resistance markers in three XDR and one MDR isolate and provided a genomic description of resistance and virulence, as well as the origins of the isolates. The isolates are closely related to MDRA Oxford ST208 and Pasteur ST2, identified in Asia and Australia. MDRA isolates are of concern in both hospital and community settings in the Western Pacific region.

The fitness connection of antibiotic resistance

More than three decades ago multidrug-resistant (MDR) clones of the pathogens: Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Clostridioides difficile, Enterococcus faecium, Pseudomonas aeruginosa and Acinetobacter baumannii have started to disseminate across wide geographical areas. A characteristic feature of all these MDR lineages is the carriage of some mutations in the quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV which besides conferring resistance to fluoroquinolones are associated with a fitness benefit. Several lines of evidence strongly suggest that extra fitness conferred by these mutations facilitated the dissemination of the international MDR lineages. MDR pathogens require extra energy to cover the fitness cost conferred by the excess antibiotic resistance gene cargo. However, extra energy generated by upgraded metabolic activity was demonstrated to increase the uptake of antibiotics enhancing susceptibility. Accordingly, MDR bacteria need additional positive fitness schemes which, similarly to the QRDR advantage, will not compromise resistance. Some of these, not clone-specific effects are large genomes, the carriage of low-cost plasmids, the transfer of plasmid genes to the chromosome, the application of weak promoters in integrons and various techniques for the economic control of the activity of the integrase enzyme including a highly sophisticated system in A. baumannii. These impacts - among others - will confer a fitness advantage promoting the spread of MDR pathogens. However, even the potential of extra fitness generated by the combined effect of various schemes is not without limit and virulence-related genes or less relevant antibiotic resistance gene cargoes will often be sacrificed to permit the acquisition of high-priority resistance determinants. Accordingly major MDR clone strains are usually less virulent than susceptible isolates. In summary, a fitness approach to the research of antibiotic resistance is very useful since the fitness status of MDR bacteria seem to profoundly impact the capacity to disseminate in the healthcare setting.

Genetic basis of antimicrobial resistance, virulence features and phylogenomics of carbapenem-resistant Acinetobacter baumannii clinical isolates

PURPOSE

The worldwide emergence and clonal spread of carbapenem-resistant Acinetobacter baumannii (CRAB) is of great concern. In the present study, we determined the mechanisms of antimicrobial resistance, virulence gene repertoire and genomic relatedness of CRAB isolates circulating in Serbian hospitals.

METHODS

CRAB isolates were analyzed using whole-genome sequencing (WGS) for the presence of antimicrobial resistance-encoding genes, virulence factors-encoding genes, mobile genetic elements and genomic relatedness. Antimicrobial susceptibility testing was done by disk diffusion and broth microdilution methods.

RESULTS

Eleven isolates exhibited an MDR resistance phenotype, while four of them were XDR. MIC90 for meropenem and imipenem were > 64 µg/mL and 32 µg/mL, respectively. While all CRABs harbored blaOXA-66 variant of blaOXA-51 gene, those assigned to STPas2, STPas636 and STPas492 had blaADC-73,blaADC-74 and blaADC-30 variants, respectively. The following acquired carbapenemases-encoding genes were found: blaOXA-72 (n = 12), blaOXA-23 (n = 3), and blaNDM-1(n = 5), and were mapped to defined mobile genetic elements. MLST analysis assigned the analyzed CRAB isolates to three Pasteur sequence types (STs): STPas2, STPas492, and STPas636. The Majority of strains belonged to International Clone II (ICII) and carried tested virulence-related genes liable for adherence, biofilm formation, iron uptake, heme biosynthesis, zinc utilization, serum resistance, stress adaptation, intracellular survival and toxin activity.

CONCLUSION

WGS elucidated the resistance and virulence profiles of CRABs isolated from clinical samples in Serbian hospitals and genomic relatedness of CRAB isolates from Serbia and globally distributed CRABs.

Characterization and genomic analysis of the highly virulent Acinetobacter baumannii ST1791 strain dominating in Anhui, China

The multidrug-resistant Acinetobacter baumannii clonal complex 92 is spreading worldwide due to its high-frequency gene mutation and recombination, posing a significant threat to global medical and health safety. Between November 2021 and April 2022, a total of 132 clinical A. baumannii isolates were collected from a tertiary hospital in China. Their growth ability and virulence of these isolates were assessed using growth curve analyses and the Galleria mellonella infection model. The genetic characteristics of the isolates were further examined through whole-genome sequencing. ST1791O/ST2P isolates represented the largest proportion of isolates in our collection and exhibited the highest growth rate and strongest virulence among all sequence types (STs) analyzed. Whole-genome sequences from 14,159 clinical isolates were collected from the National Center for Biotechnology Information database, and only nine ST1791O/ST2P isolates were detected. Comparative genomic analysis revealed that ST1791O/ST2P carried 11 unique genes, 5 of which were located within the capsular polysaccharide synthesis (cps) gene cluster. Single nucleotide polymorphisms (SNPs) between ST1791O/ST2P and other isolates were primarily found in the cps gene cluster. Among the other isolates, ST195O/ST2P and ST208O/ST2P exhibited the smallest SNP differences from ST1791O/ST2P, while ST195O/ST2P and ST1486O/ST2P had high homology. The ST1791O/ST2P strain in Anhui, China, displayed significant homology with ST195O/ST2P, ST208O/ST2P, and ST1486O/ST2P isolates. Compared to other isolates in this study, ST1791O/ST2P exhibited strong growth ability and virulence. Therefore, preventing the further spread of ST1791O/ST2P should be a top public health priority.

In the search for new gold metalloantibiotics: In vitro evaluation of Au(III) (C^S)-cyclometallated complexes

A series of (C^S)-cyclometallated Au(III) cationic complexes of general formula [Au(dppta)(dtc)]+, [Au(dppta)(azmtd)]+ and [Au(dppta)(azc)Cl]+ (dppta = N,N-diisopropyl-P,P-diphenylphosphinothioic amide-κ2C,S; dtc = dithiocarbamate-κ2S,S'; azc = azolium-2-dithiocarboxylate-κ1S; azmdt = azol(in)ium-2-(methoxy)methanedithiol-κ2S,S') were synthetized and tested against a panel of bacterial strains belonging to different Gram-positive and Gram-negative species of the ESKAPE group of pathogens. Among the tested compounds, complex 4c had the higher Therapeutic Index (TI) against multidrug resistant strains of S. aureus, S. epidermidis and A. baumannii, showing a more favourable cytotoxicity profile than the reference gold metalloantibiotic Auranofin. © 2024 xxxxxxxx. Hosting by Elsevier B.V. All rights reserved.

Exploiting human immune repertoire transgenic mice for protective monoclonal antibodies against antimicrobial resistant Acinetobacter baumannii

The use of monoclonal antibodies for the control of drug resistant nosocomial bacteria may alleviate a reliance on broad spectrum antimicrobials for treatment of infection. We identify monoclonal antibodies that may prevent infection caused by carbapenem resistant Acinetobacter baumannii. We use human immune repertoire mice (Kymouse platform mice) as a surrogate for human B cell interrogation to establish an unbiased strategy to probe the antibody-accessible target landscape of clinically relevant A. baumannii. After immunisation of the Kymouse platform mice with A. baumannii derived outer membrane vesicles (OMV) we identify 297 antibodies and analyse 26 of these for functional potential. These antibodies target lipooligosaccharide (OCL1), the Oxa-23 protein, and the KL49 capsular polysaccharide. We identify a single monoclonal antibody (mAb1416) recognising KL49 capsular polysaccharide to demonstrate prophylactic in vivo protection against a carbapenem resistant A. baumannii lineage associated with neonatal sepsis mortality in Asia. Our end-to-end approach identifies functional monoclonal antibodies with prophylactic potential against major lineages of drug resistant bacteria accounting for phylogenetic diversity and clinical relevance without existing knowledge of a specific target antigen. Such an approach might be scaled for a additional clinically important bacterial pathogens in the post-antimicrobial era.

Genetic characterization of plasmid-borne blaOXA-58 and blaOXA-72 in Acinetobacter pittii in Shaanxi, China

OBJECTIVES

Acinetobacter pittii has emerged as an opportunistic nosocomial pathogen associated with hospital-acquired infections. The purpose of this study was to investigate the genetic structures of plasmids carrying carbapenemase genes blaOXA-58 and blaOXA-72 in A. pittii strains AR3676 and AR3651 isolated from patients.

METHODS

Antimicrobial susceptibility testing was performed using broth microdilution. Whole-genome sequencing and bioinformatics analysis were performed to characterize the genome of A. pittii AR3676 and AR3651. Conjugation experiments were conducted to evaluate plasmid transferability. Phylogenetic and comparative genomic analysis were performed to explore the characteristics of carbapenem-resistant A. pittii isolates worldwide.

RESULTS

The AR3676 strain showed resistance to imipenem. The 19 700-bp plasmid pAR3676-OXA-58 harboured blaOXA-58 with genetic contexts consisting of a truncated ISAba3-like-blaOXA58-ISAba3. Additionally, the AR3651 strain showed resistance to imipenem and meropenem. The AR3651 genome comprised one 9,837-bp RepA_AB plasmid pAR3651-OXA-72 harbouring blaOXA-72. This blaOXA-72 was flanked by XerC/XerD recombination sites. The conjugation of plasmids pAR3676-OXA-58 and pAR3651-OXA-72 from A. pittii to Acinetobacter baumannii ATCC 17978RIFR failed three independent times. Phylogenetic analysis of A. pittii strains AR3676, AR3651, and a further 504 A. pittii strains collected between 1966 and 2022 from various geographic localities revealed genetic diversity with a heterogeneous distribution of carbapenemase genes.

CONCLUSIONS

A. pittii strains with a plasmid carrying blaOXA-58 or blaOXA-72 may serve as an important reservoir of carbapenemase genes. Carbapenemase genes on a single plasmid may facilitate their dissemination and persistence. Additionally, pdif sites and mobile elements play an important role in the mobilization of resistance genes and plasmid evolution.

Efficacy of Tamoxifen Metabolites in Combination with Colistin and Tigecycline in Experimental Murine Models of Escherichia coli and Acinetobacter baumannii

This study aimed to evaluate the potential of tamoxifen and N-desmethyltamoxifen metabolites as therapeutic agents against multidrug-resistant Escherichia coli and Acinetobacter baumannii, using a repurposing approach to shorten the time required to obtain a new effective treatment against multidrug-resistant bacterial infections. Characterisation and virulence studies were conducted on E. coli (colistin-susceptible C1-7-LE and colistin-resistant MCR-1+) and A. baumannii (tigecycline-susceptible Ab#9 and tigecycline-resistant Ab#186) strains. The efficacy of the metabolite mix (33.3% each) and N-desmethyltamoxifen in combination with colistimethate sodium (CMS) or tigecycline was evaluated in experimental models in mice. In the pneumonia model, N-desmethyltamoxifen exhibited significant efficacy against Ab#9 and both E. coli strains, especially E. coli MCR-1+ (-2.86 log10 CFU/g lungs, -5.88 log10 CFU/mL blood, and -50% mortality), and against the Ab#186 strain when combined with CMS (-2.27 log10 CFU/g lungs, -2.73 log10 CFU/mL blood, and -40% mortality) or tigecycline (-3.27 log10 CFU/g lungs, -4.95 log10 CFU/mL blood, and -50% mortality). Moreover, the metabolite mix in combination with both antibiotics decreased the bacterial concentrations in the lungs and blood for both A. baumannii strains. In the sepsis model, the significant efficacy of the metabolite mix was restricted to the colistin-susceptible E. coli C1-7-LE strain (-3.32 log10 CFU/g lung, -6.06 log10 CFU/mL blood, and -79% mortality). N-desmethyltamoxifen could be a new therapeutic option in combination with CMS or tigecycline for combating multidrug-resistant GNB, specifically A. baumannii.

Exploring the resistome and virulome in major sequence types of Acinetobacter baumannii genomes: Correlations with genome divergence and sequence types

The increasing global prevalence of antimicrobial resistance in Acinetobacter baumannii has led to concerns regarding the effectiveness of infection treatment. Moreover, the critical role of virulence factor genes in A. baumannii's pathogenesis and its propensity to cause severe disease is of particular importance. Comparative genomics, including multi-locus sequence typing (MLST), enhances our understanding of A. baumannii epidemiology. While there is substantial documentation on A. baumannii, a comprehensive study of the antibiotic-resistant mechanisms and the virulence factors contributing to pathogenesis, and their correlation with Sequence Types (STs) remains incompletely elucidated. In this study, we aim to explore the relationship between antimicrobial resistance genes, virulence factor genes, and STs using genomic data from 223 publicly available A. baumannii strains. The core phylogeny analysis revealed five predominant STs in A. baumannii genomes, linked to their geographical sources of isolation. Furthermore, the resistome and virulome of A. baumannii followed an evolutionary pattern consistent with their pan-genome evolution. Among the major STs, we observed significant variations in resistant genes against "aminoglycoside" and "sulphonamide" antibiotics, highlighting the role of genotypic variations in determining resistance profiles. Furthermore, the presence of virulence factor genes, particularly exotoxin and nutritional / metabolic factor genes, played a crucial role in distinguishing the major STs, suggesting a potential link between genetic makeup and pathogenicity. Understanding these associations can provide valuable insights into A. baumannii's virulence potential and clinical outcomes, enabling the development of effective strategies to combat infections caused by this opportunistic pathogen.

The whole-genome molecular epidemiology of sequential isolates of Acinetobacter baumannii colonizing the rectum of patients in an adult intensive care unit of a tertiary hospital

IMPORTANCE

Acinetobacter baumannii is a multidrug-resistant nosocomial pathogen that colonizes and infects debilitated patients in the ICU. There is very little information on the genomic characteristics of colonizing strains. This information is important to understand the evolution of lineages of A. baumannii that develop resistance while patients receive antibiotic treatment in the ICU. Our study demonstrated different patterns of colonization of the rectum of ICU patients with different STs of A. baumannii while one ST colonized all patients. Some STs carried more antibiotic resistance genes compared to others. However, there was a correlation between ST and a particular resistance gene profile. Our results further elucidate the dynamics of enteric colonization of this opportunistic pathogen.

Molecular Epidemiology of Carbapenem Resistant Klebsiella Pneumoniae in Northern China: Clinical Characteristics, Antimicrobial Resistance, Virulence and Geographic Distribution

Purpose

In this article, we studied in detail 74 Carbapenem Resistant Klebsiella pneumoniae (CRKP) in Shanxi to provide essential insight into development of effective strategies for control of CRKP.

Patients and Methods

From 2018 to 2021, we collected 74 clinical CRKP from 11 hospitals in Shanxi Province. Clinical data were obtained from medical records, and all isolates were subjected to antimicrobial susceptibility testing, multi locus sequence typing, capsular serotypes, resistant gene profiles and virulence gene profiles. The synergistic activity was performed by microdilution checkerboard method.

Results

Our study found differences in the clinical characteristics of CRKP between regions in Shanxi. Sequence type (ST) 11 was the dominant ST in Shanxi; however, the ST types in Shanxi had become more diverse over time and the proportion of STs showed a more balanced distribution with a significant decrease in ST11. NDM was the most common carbapenemase in Shanxi. In addition, the STs, carbapenemases, serotypes and virulence gene distribution varied by region in Shanxi. Moreover, tigecycline in combination with carbapenems and aztreonam had an excellent synergistic effect on CRKP in vitro.

Conclusion

The results of this study provide essential insight into development of effective strategies for control of CRKP in Shanxi.

Epidemiological characteristics of multidrug-resistant Acinetobacter baumannii ST369 in Anhui, China

IMPORTANCE

Acinetobacter baumannii is a major health threat due to its antibiotic resistance and ability to cause nosocomial infections. Epidemiological studies indicated that the majority of globally prevalent ST369 clones originated from China, indicating a significant impact on public health in the country. In this study, we conducted whole-genome sequencing, comparative genomics, and Galleria mellonella infection model on eight A. baumannii ST369 isolates collected from a provincial hospital in China to comprehensively understand the organism. We identified two mutations (G540A and G667D) on the wzc gene that can affect bacterial virulence and viscosity. We confirmed their impact on resistance and virulence. We also investigated the potential involvement of AB46_0125 and AB152_03903 proteins in virulence. This finding provides a theoretical reference for further research on A. baumannii ST369 clinical isolates with similar mutations.

Occurrence of Acinetobacter baumannii genomic resistance islands (AbGRIs) in Acinetobacter baumannii strains belonging to global clone 2 obtained from COVID-19 patients

AIM

The Acinetobacter baumannii genomic resistance islands (AbGRIs), which were characterized in the genome of the global clone 2 (GC2) A. baumannii contain resistance genes. Here, we aimed to determine the occurrence of AbGRIs in GC2 A. baumannii obtained from COVID-19 patients in a referral hospital in Tehran, Iran.

METHODS

A total of 19 carbapenem-resistant A. baumannii (CRAB) isolates belonging to GC2 and sequence type 2 (ST2), including 17 from COVID-19 patients and two from the devices used in the ICU that the COVID-19 patients were admitted, were examined in this study. Antibiotic susceptibility testing was performed by the disk diffusion method. PCR and PCR mapping, followed by sequencing, were performed to characterize the structure of AbGRI resistance islands in the isolates tested.

RESULTS

The AbGRI3 was the most frequent resistance island (RI) detected, present in all the 19 isolates, followed by AbGRI1 (15 isolates; 78.9%) and AbGRI2 (three isolates; 15.8%). Notably, AbGRIs were identified in one of the A. baumannii strains, which was isolated from a medical device used in the ICU where COVID-19 patients were admitted. Furthermore, new structures of AbGRI1 and AbGRI3 resistance islands were found in this study, which was the first report of these structures.

CONCLUSIONS

The present study provided evidence for the circulation of the GC2 A. baumannii strains harboring AbGRI resistance islands in a referral hospital in Tehran, Iran. It was found that resistance to several classes of antibiotics in the isolates collected from COVID-19 patients is associated with the resistance genes located within AbGRIs.

International Clones of High Risk of Acinetobacter Baumannii-Definitions, History, Properties and Perspectives

Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of A. baumannii is driven by several lineages named 'international clones of high risk' (ICs), two of which were first revealed in the 1970s. Epidemiological surveillance is a crucial tool for controlling the spread of this pathogen, which currently increasingly involves whole genome sequencing. However, the assignment of a particular A. baumannii isolate to some IC based on its genomic sequence is not always straightforward and requires some computational skills from researchers, while the definitions found in the literature are sometimes controversial. In this review, we will focus on A. baumannii typing tools suitable for IC determination, provide data to easily determine IC assignment based on MLST sequence type (ST) and intrinsic blaOXA-51-like gene variants, discuss the history and current spread data of nine known ICs, IC1-IC9, and investigate the representation of ICs in public databases. MLST and cgMLST profiles, as well as OXA-51-like presence data are provided for all isolates available in GenBank. The possible emergence of a novel A. baumannii international clone, IC10, will be discussed.

Risk factors and cerebrospinal fluid indexes analysis of intracranial infection by Acinetobacter baumannii after neurosurgery

Background

Intracranial infection by Acinetobacter baumannii (A. baumannii) after neurosurgery has always been a difficult problem for neurosurgeons. This study analyzed risk factors that discriminated A. baumannii from other bacteria causing intracranial infection after neurosurgery. It also examined the differences in the cerebrospinal fluid (CSF) indexes to explore their value in the early diagnosis of intracranial infection by A. baumannii.

Methods

We retrospectively reviewed ten years (January 2011 to May 2021) of postoperative central nervous system (CNS) infections in the First Hospital of China Medical University. According to the pathogen, CNS infections were divided into A. baumannii group and other species of bacteria group. We collected clinical and laboratory information of patients, and statistical analysis was performed with SPSS 26.0. Risk factors were screened by univariate analysis, and independent risk factors were screened by multiple logistic regression analysis. Finally, CSF-Pro, CSF-Glu, CSF-Cl, CSF-monocytes (%), CSF-multinucleated cells (%) levels, and CSF multinucleated cells%/monocytes% in the different groups were analyzed.

Results

A total of 155 patients were included, 62 cases (40%) of intracranial infection by A. baumannii and 93 cases (60%) by other species of bacteria. The analysis showed that indwelling nasogastric tubes (P＜0.001, OR = 4.231), indwelling peripherally inserted central catheters (PICCs) (P = 0.041, OR = 2.765), and CSF drainage obstruction (P = 0.003, OR = 3.765) were independent risk factors for intracranial infection by A. baumannii after neurosurgery. Indwelling ventriculoperitoneal shunt (VPS) was a protective factor (P = 0.033, OR = 0.22). In addition, compared with other bacterial groups, the A. baumannii group had higher CSF-pro and CSF- multinucleated cells (%) levels and lower CSF-Glu and CSF- monocytes (%) levels, and the difference was statistically significant (P < 0.01).

Conclusions

Our results elucidate risk factors and differences in CSF indexes for intracranial infection by A. baumannii after neurosurgery that could be detected and prevented early to reduce mortality.

Acinetobacter baumannii Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt

Acinetobacter baumannii (A. baumannii) is a highly problematic pathogen with an enormous capacity to acquire or upregulate antibiotic drug resistance determinants. The genomic epidemiology and resistome structure of 46 A. baumannii clinical isolates were studied using whole-genome sequencing. The isolates were chosen based on reduced susceptibility to at least three classes of antimicrobial compounds and were initially identified using MALDI-TOF/MS, followed by polymerase chain reaction amplification of bla_OXA-51-like genes. The susceptibility profiles were determined using a broth microdilution assay. Multi-, extensive-, and pan-drug resistance was shown by 34.8%, 63.0%, and 2.2% of the isolates, respectively. These were most susceptible to colistin (95.7%), amikacin, and trimethoprim/sulfamethoxazole (32.6% each), while only 26.1% of isolates were susceptible to tigecycline. In silico multi-locus sequence typing revealed 8 Pasteur and 22 Oxford sequence types (STs) including four novel STs (ST^Oxf 2805, 2806, 2807, and 2808). The majority of the isolates belonged to Global Clone (GC) 2 (76.4%), GC5 (19.6%), GC4 (6.5%), GC9 (4.3%), and GC7 (2.2%) lineages. An extensive resistome potentially conferring resistance to the majority of the tested antimicrobials was identified in silico. Of all known carbapenem resistance genes, bla_OXA-23 was carried by most of the isolates (69.6%), followed by ISAba1-amplified bla_ADC (56.5%), bla_NDM-1 and bla_GES-11 (21.7% each), and bla_GES-35 (2.2%) genes. A significant correlation was found between carbapenem resistance and carO mutations, which were evident in 35 (76.0%) isolates. A lower proportion of carbapenem resistance was noted for strains possessing both bla_OXA-23- and bla_GES-11. Amikacin resistance was most probably mediated by armA, aac(6')-Ib9, and aph(3')-VI, most commonly coexisting in GC2 isolates. No mutations were found in pmrABC or lpxACD operons in the colistin-resistant isolates. Tigecycline resistance was associated with adeS (N268Y) and baeS (A436T) mutations. While the lineage-specific distribution of some genes (e.g., bla_ADC and bla_OXA-51-like alleles) was evident, some resistance genes, such as bla_OXA-23 and sul1, were found in all GCs. The data generated here highlight the contribution of five GCs in A. baumannii infections in Egypt and enable the comprehensive analysis of GC-specific resistomes, thus revealing the dissemination of the carbapenem resistance gene bla_OXA-23 in isolates encompassing all GCs.

Healthcare-Associated Bloodstream Infections Due to Multidrug-Resistant Acinetobacter baumannii in COVID-19 Intensive Care Unit: A Single-Center Retrospective Study

Healthcare-associated infections are an emerging cause of morbidity and mortality in COVID-19 intensive care units (ICUs) worldwide, especially those caused by multidrug-resistant (MDR) pathogens. The objectives of this study were to assess the incidence of bloodstream infections (BSIs) among critically ill COVID-19 patients and to analyze the characteristics of healthcare-associated BSIs due to MDR Acinetobacter baumannii in an COVID-19 ICU. A single-center retrospective study was conducted at a tertiary hospital during a 5-month period. The detection of carbapenemase genes was performed by PCR and genetic relatedness by pulsed-field gel electrophoresis (PFGE) and multilocus-sequence typing. A total of 193 episodes were registered in 176 COVID-19 ICU patients, with an incidence of 25/1000 patient-days at risk. A. baumannii was the most common etiological agent (40.3%), with a resistance to carbapenems of 100%. The blaOXA-23 gene was detected in ST2 isolates while the blaOXA-24 was ST636-specific. PFGE revealed a homogeneous genetic background of the isolates. The clonal spread of OXA-23-positive A. baumannii is responsible for the high prevalence of MDR A. baumannii BSIs in our COVID-19 ICU. Further surveillance of resistance trends and mechanisms is needed along with changes in behavior to improve the implementation of infection control and the rational use of antibiotics.

Clonal evolution and antimicrobial resistance of Acinetobacter baumannii isolates from Korean hospitals over the last decade

The wide-spread of drug-resistant Acinetobacter baumannii is a global health problem. This study investigated the clonal distribution and antimicrobial resistance of 167 A. baumannii isolates from two Korean university hospitals from 2009 to 2019 by analyzing the sequence types (STs), antimicrobial resistance, and resistance determinants of carbapenems and aminoglycosides. Twenty STs, including 16 pre-existing STs and four unassigned STs, were identified in A. baumannii isolates using the Oxford multilocus sequence typing scheme. Two STs, ST191 (n = 77) and ST451 (n = 40), were prevalent, and majority (n = 153) of the isolates belonged to clonal complex 208. The ST191 isolates were detected during the study period, whereas ST451 isolates were detected after 2016. One hundred forty-seven (87%) of 167 A. baumannii isolates were non-susceptible to carbapenems. The ST191 and ST451 isolates exhibited higher resistance to antimicrobial agents than that of the sporadic ST isolates. Interestingly, ST451 isolates exhibited lower susceptibility to minocycline and tigecycline than the other ST isolates. All carbapenem-non-susceptible A. baumannii isolates, except four, carried the ISAbaI-bla_OXA-23 structure. armA was detected in all amikacin-non-susceptible isolates (n = 128) except for one isolate. Five aminoglycoside-modifying enzyme (AME) genes were detected, but their carriage varied between STs; ant(3″)-Ia and aac(6')-Ib were more common in ST191 than in ST451, while aph(3')-Ia was more common in ST451 than in ST191. This study demonstrated the clonal evolution related to antimicrobial resistance in A. baumannii.

Multidrug-resistant Acinetobacter baumannii in healthcare settings in Africa

The emergence of multidrug-resistant Acinetobacter baumannii is a major concern to healthcare providers and facilities in many parts of the world. This bacterial pathogen is commonly implicated in hospital-acquired infections, particularly in critically ill patients admitted to the intensive care unit (ICU). The extensive use of antibiotics, particularly in ICUs, and the lack of proper infection control interventions in many hospitals have led to an increased emergence of multidrug-resistant A. baumannii. Infections due to multidrug-resistant A. baumannii are associated with prolonged hospital stays and high morbidity and mortality, particularly among hospitalized ICU patients. The lack of antibiotic stewardship programmes in many healthcare facilities has exacerbated the burden of A. baumannii infections in many parts of Africa. This review discusses the prevalence and antibiotic-resistance pattern of the multidrug-resistant A. baumannii, and the possible ways to address or minimise its emergence in healthcare settings in Africa.

Molecular tracking of carbapenem-resistant Acinetobacter baumannii clinical isolates: a multicentre study over a 4-year period across eastern China

Introduction. Colonization by carbapenem-resistant Acinetobacter baumannii (CRAB) causes therapeutic and economic problems for critically ill patients.Gap Statement. The analysis of CRAB in China was limited to certain regions.Aims. To investigate the antibiotic susceptibility, molecular characterization and clonal relationship among CRAB isolates from multiple hospitals of eastern China.Methodology. Isolates from 29 tertiary hospitals from September 2015 to September 2018 were recovered. All strains were analysed using antimicrobial susceptibility testing to detect their tolerance. PCR was also used to detect multiple β-lactamase genes. After multilocus sequence typing (MLST) of seven house-keeping genes. eBURST was used to assess clonal complexes and explore evolutionary relationships.Results. All isolates showed resistance to carbapenems, while remaining susceptible to colistin and tigecycline. All isolates were detected with bla _OXA-51 gene by PCR, and 80.1 % harboured the bla _OXA-23 gene. The prevalence of bla_OXA-23 gene was remarkably increased from 50.7 % in 2015 to 90.5 % in 2018. Other genes such as bla _OXA-24, bla _OXA-58, bla _IMP-2/4, bla _VIM-2, bla _SHV, bla _AmpC and bla _TEM were also obtained. While bla _KPC, bla _NDM-1, bla _IMP-4 and bla _SIM-1 were not found in these strains. MLST showed all isolates could be divided into 26 known sequence types (STs) and ten novel STs and 47.2 % isolates belong to ST195 and ST208. eBURST revealed clonal complex 92 as the major clonal complex (98.4 %), which includes 88.5 % (23/26) of known STs and 80 % (8/10) of unknown STs. Phylogenetic analysis also found that almost all CRAB isolates could cluster into one lineage, suggesting an epidemic of this CRAB lineage. This indicated severe nosocomial infections of CRAB in multiple hospitals of eastern China.Conclusion. An outbreak of ST195 and ST208 CRAB-resistant clones with bla _OXA-23 gene might be happening in multiple hospitals in eastern China.

Prevalent Dominant Acinetobacter baumannii ST191/195/208 Strains in Bloodstream Infections Have High Drug Resistance and Mortality

Background

Different sequence types of Acinetobacter baumannii (AB) have their own epidemiological characteristics, drug resistance, and toxicity.

Methods

AB bloodstream infection (BSI) in the First Affiliated Hospital of Medical College of Zhejiang University from January 2012 to December 2017 were classified by multilocus sequence typing. Clinical data of patients were retrospectively analyzed, drug resistance and toxicity were respectively studied by drug sensitivity and complement killing tests.

Results

247 unduplicated AB strains were collected, and ST191/195/208, the main epidemic dominant strain, accounted for 70.9%. Patients with ST191/195/208 on infection had higher white blood cell (10.8 vs 8.9, p = 0.004), neutrophil% (89.5 vs 86.9, p = 0.005), neutrophil count (9.5 vs 7.1, p = 0.021), D-dimer (6.7 vs 3.8, p = 0.000), total bilirubin (27.0 vs 21.5, p = 0.038), pronatriuretic peptide (324 vs 164, p = 0.042), C-reactive protein (82.5 vs 56.3, p = 0.048), clinical pulmonary infection score (CPIS; 7.33 ± 2.30 vs 6.50 ± 2.72, p = 0.045), and acute physiology and chronic health evaluation-II (APACHE-II; 19.620 ± 5.1850 vs 17.648 ± 6.1251, p = 0.011). Patients with ST191/195/208 had more complications, including pulmonary infection (p = 0.041), septic shock (p = 0.009), and multiple organ failure (p = 0.019). Patients with ST191/195/208 had higher 3 day mortality (24.6% vs 13.9%, p = 0.043), 14 day mortality (46.8% vs 26.8%, p = 0.003), and 28 day mortality (55.0% vs 32.4%, p = 0.001). ST191/195/208 strains had higher drug resistance to most antibiotics, and higher survival rate at 90% normal serum concentration (p < 0.001).

Conclusion

ST191/195/208 strains predominate in the hospital and prevails in patients with severe infections with increased multidrug antimicrobial resistance and excessive mortality compared to any other AB stains.

Molecular mechanisms and clonal lineages of colistin-resistant bacteria across the African continent: a scoping review

Colistin (also known as polymyxin E), a polymyxin antibiotic discovered in the late 1940s, has recently reemerged as a last-line treatment option for multidrug-resistant infections. However, in recent years, colistin-resistant pathogenic bacteria have been increasingly reported worldwide. Accordingly, the presented review was undertaken to identify, integrate and synthesize current information regarding the detection and transmission of colistin-resistant bacteria across the African continent, in addition to elucidating their molecular mechanisms of resistance. PubMed, Google Scholar and Science Direct were employed for study identification, screening and extraction. Overall, based on the developed literature review protocol and associated inclusion/exclusion criteria, 80 studies published between 2000 and 2021 were included comprising varying bacterial species and hosts. Numerous mechanisms of colistin resistance were reported, including chromosomal mutation(s) and transferable plasmid-mediated colistin resistance (encoded by mcr genes). Perhaps unexpectedly, mcr-variants have exhibited rapid emergence and spread across most African regions. The genetic variant mcr-1 is predominant in humans, animals and the natural environment, and is primarily carried by IncHI2- type plasmid. The highest number of studies reporting the dissemination of colistin-resistant Gram-negative bacteria were conducted in the North African region.

Molecular epidemiology and carbapenem resistance characteristics of Acinetobacter baumannii causing bloodstream infection from 2009 to 2018 in northwest China

Bloodstream infection (BSI) caused by Acinetobacter baumannii poses a serious threat to health and is correlated with high mortality in patients with hospital-acquired infections, so the molecular epidemiology and antimicrobial resistance characteristics of this pathogen urgently need to be explored. A. baumannii isolates from BSI patients were collected in three tertiary hospitals in northwest China from 2009 to 2018. Antimicrobial susceptibility testing was used to determine the MICs of the A. baumannii isolates. Whole-genome sequencing based on the Illumina platform was performed for molecular epidemiological analyses and acquired resistance gene screening. The efflux pump phenotype was detected by examining the influence of an efflux pump inhibitor. The expression of efflux pump genes was evaluated by RT-PCR. In total, 47 A. baumannii isolates causing BSI were collected and they presented multidrug resistance, including resistance to carbapenems. Clone complex (CC) 92 was the most prevalent with 30 isolates, among which a cluster was observed in the phylogenetic tree based on the core genome multi-locus sequence type, indicating the dissemination of a dominant clone. BSI-related A. baumannii isolates normally harbour multiple resistance determinants, of which oxacillinase genes are most common. Except for the intrinsic bla_OXA-51 family, there are some carbapenem-resistant determinants in these A. baumannii isolates, including bla_OXA-23, which is encoded within the Tn2006, Tn2008 or Tn2009 transposon structures and bla_OXA-72. The transfer of bla_OXA-72 was suggested by XerC/D site-specific recombination. The AdeABC efflux pump system contributed to carbapenem resistance in A. baumannii isolates, as evidenced by the high expression of some of its encoding genes. Both the clone dissemination and carbapenem resistance mediated by oxacillinase or efflux pumps suggest an effective strategy for hospital infection control.

A 12-year epidemiological study of Acinetobacter baumannii from blood culture isolates in a single tertiary-care hospital using polymerase chain reaction (PCR)-based open reading frame typing

Objective

Acinetobacter baumannii is a causative agent of healthcare-associated infections, and the introduction and spread of A. baumannii that has acquired drug resistance within a hospital are serious healthcare problems. We investigated the transition of epidemic clones and the occurrence of outbreaks by molecular epidemiological analysis to understand the long-term behavior of A. baumannii within a single facility.

Methods

A. baumannii isolates collected from blood-culture-positive patients between January 2009 and December 2020 were subjected to PCR-based open reading frame typing (POT) for species identification, clonal typing, and homology searches.

Results

Of the strains isolated from blood cultures, 49 were identified as A. baumannii and analyzed with POT. The POT#1=122 clones had different antimicrobial resistance profiles to the other POT clones, and strains belonging to this clone were dominant during outbreaks of multidrug-resistant Acinetobacter. Although the clonal diversity of A. baumannii decreased and its antimicrobial resistance increased during the outbreaks, clonal diversity and the in-hospital antibiogram improved at the end of the outbreaks. The POT#1=122 clone was not eliminated from the hospital during the study period.

Conclusions

POT is a simple and suitable method for molecular epidemiological monitoring and can show the introduction, outbreak, and subsequent transition of an epidemic clone of A. baumannii.

Genetic Configuration of Genomic Resistance Islands in Acinetobacter baumannii Clinical Isolates From Egypt

In Acinetobacter baumannii (A. baumannii), a wide repertoire of resistance genes is often carried within genomic resistance islands (RIs), particularly in high-risk global clones (GCs). As the first in Egypt, the current study aimed at exploring the diversity and genetic configuration of RIs in the clinical isolates of A. baumannii. For this purpose, draft genomes of 18 isolates were generated by Illumina sequencing. Disk diffusion susceptibility profiling revealed multidrug resistance (MDR) and extensive drug resistance (XDR) phenotypes in 27.7 and 72.2%, respectively. The highest susceptibility was noted for tigecycline (100.0%) followed by colistin (94.4%), for which an MIC₅₀ of 0.25 μg/ml was recorded by the broth microdilution assay. Sequence typing (ST) showed that the majority of the isolates belonged to high-risk global clones (GC1, GC2, and GC9). A novel Oxford sequence type (ST2329) that also formed a novel clonal complex was submitted to the PubMLST database. A novel bla_ADC variant (bla_ADC−258) was also identified in strain M18 (ST85^Pas/1089^Oxf). In addition to a wide array of resistance determinants, whole-genome sequencing (WGS) disclosed at least nine configurations of genomic RIs distributed over 16/18 isolates. GC2 isolates accumulated the largest number of RIs (three RIs/isolate) followed by those that belong to GC1 (two RIs/isolate). In addition to Tn6022 (44.4%), the comM gene was interrupted by AbaR4 (5.5%) and three variants of A. baumanniigenomic resistance island 1(AbGRI)-type RIs (44.4%), including AbaR4b (16.6%) and two novel configurations of AbGRI1-like RIs (22.2%). Three of which (AbaR4, AbaR4b, and AbGRI1-like-2) carried bla_OXA−23 within Tn2006. With less abundance (38.8%), IS26-bound RIs were detected exclusively in GC2 isolates. These included a short version of AbGRI2 (AbGRI2-15) carrying the genes bla_TEM−1 and aphA1 and two variants of AbGRI3 RIs carrying up to seven resistance genes [mphE-msrE-armA-sul1-aadA1-catB8-aacA4]. Confined to GC1 (22.2%), sulfonamide resistance was acquired by an ISAba1 bracketed GIsul2 RI. An additional RI (RI-PER-7) was also identified on a plasmid carried by strain M03. Among others, RI-PER-7 carried the resistance genes armA and bla_PER−7. Here, we provided a closer view of the diversity and genetic organization of RIs carried by a previously unexplored population of A. baumannii.

Origin, Phylogeny, and Transmission of the Epidemic Clone ST208 of Carbapenem-Resistant Acinetobacter baumannii on a Global Scale

Carbapenem-resistant Acinetobacter baumannii (CRAB) is an opportunistic pathogen that has become a global threat. The dissemination of global clone 2 (GC2) CRAB has been well documented. Oxford sequence type (ST) 208 is one of the most prevalent lineages of A. baumannii GC2; however, its evolution and phylogeny are unclear. We collected 45 representative ST208 isolates from 14 cities in China between 1999 and 2018. Moreover, 411 ST208 genome sequences were downloaded from the GenBank database for comparison. The global ST208 phylogeny showed that ST208 might have originated from North America and subsequently evolved into two clades. Notably, the widespread OXA-23-producing ST208 A. baumannii was correlated with the transposon structure and dynamics of replicative transposition, and the Tn2009 tandem structure of five copies of blaOXA-23 and potential circular intermediate of Tn2009 were first detected. Furthermore, 15 Chinese ST208 isolates carried GR25 pABTJ1-like plasmids, which contained blaOXA-23 and have only been found in China in the last decade. In conclusion, our work suggests that replicative transposition contributes to the evolution and transmission of OXA-23-producing ST208 A. baumannii and highlights the new challenges posed by the epidemiological surveillance of globally distributed clonal groups via whole genome sequencing. IMPORTANCE ST208 as one of the most prevalent lineages of CRAB has caused several difficult-to-treat infections and outbreaks around the world. However, few studies have focused on evaluating the genetic background differences of ST208 A. baumannii isolated from very distant geographic regions. A comprehensive genomic analysis of 456 clinical strains of ST208 A. baumannii from a wide temporal and geographic range was performed in this study. Moreover, the mechanisms leading to the horizontal transfer of blaOXA-23 in ST208 A. baumannii are poorly understood. We first describe experimental evidence of the potential circular intermediate of Tn2009, and the Tn2009 tandem structure of five copies of blaOXA-23 was first detected. The interbacterial transfer of genetic elements carrying resistance to last-line antibiotic carbapenems highlights the essential need to enhance epidemiologic surveillance.

InvL, an Invasin-Like Adhesin, Is a Type II Secretion System Substrate Required for Acinetobacter baumannii Uropathogenesis

Acinetobacter baumannii is an opportunistic pathogen of growing concern, as isolates are commonly multidrug resistant. While A. baumannii is most frequently associated with pulmonary infections, a significant proportion of clinical isolates come from urinary sources, highlighting its uropathogenic potential. The type II secretion system (T2SS) of commonly used model Acinetobacter strains is important for virulence in various animal models, but the potential role of the T2SS in urinary tract infection (UTI) remains unknown. Here, we used a catheter-associated UTI (CAUTI) model to demonstrate that a modern urinary isolate, UPAB1, requires the T2SS for full virulence. A proteomic screen to identify putative UPAB1 T2SS effectors revealed an uncharacterized lipoprotein with structural similarity to the intimin-invasin family, which serve as type V secretion system (T5SS) adhesins required for the pathogenesis of several bacteria. This protein, designated InvL, lacked the β-barrel domain associated with T5SSs but was confirmed to require the T2SS for both surface localization and secretion. This makes InvL the first identified T2SS effector belonging to the intimin-invasin family. InvL was confirmed to be an adhesin, as the protein bound to extracellular matrix components and mediated adhesion to urinary tract cell lines in vitro. Additionally, the invL mutant was attenuated in the CAUTI model, indicating a role in Acinetobacter uropathogenesis. Finally, bioinformatic analyses revealed that InvL is present in nearly all clinical isolates belonging to international clone 2, a lineage of significant clinical importance. In all, we conclude that the T2SS substrate InvL is an adhesin required for A. baumannii uropathogenesis. IMPORTANCE While pathogenic Acinetobacter can cause various infections, we recently found that 20% of clinical isolates come from urinary sources. Despite the clinical relevance of Acinetobacter as a uropathogen, few virulence factors involved in urinary tract colonization have been defined. Here, we identify a novel type II secretion system effector, InvL, which is required for full uropathogenesis by a modern urinary isolate. Although InvL has predicted structural similarity to the intimin-invasin family of autotransporter adhesins, InvL is predicted to be anchored to the membrane as a lipoprotein. Similar to other invasin homologs, however, we demonstrate that InvL is a bona fide adhesin capable of binding extracellular matrix components and mediating adhesion to urinary tract cell lines. In all, this work establishes InvL as an adhesin important for Acinetobacter's urinary tract virulence and represents the first report of a type II secretion system effector belonging to the intimin-invasin family.

Differential Binding of Carbapenems with the AdeABC Efflux Pump and Modulation of the Expression of AdeB Linked to Novel Mutations within Two-Component System AdeRS in Carbapenem-Resistant Acinetobacter baumannii

Resistance-nodulation-division-type efflux system AdeABC plays an important role in carbapenem resistance among Acinetobacter baumannii. However, a knowledge gap is observed regarding the role of its regulator AdeRS in carbapenem-resistant A. baumannii (CRAB). This study effectively combines microbiological analysis with an in-silico structural approach to understand the contribution of AdeRS among CRAB (n = 38). Additionally, molecular docking was performed for the first time to study the interaction of FDA-approved carbapenems and pump inhibitor PAβN with the open and closed structure of AdeB at the three binding sites (periplasmic, proximal, distal). It was observed that open conformation of AdeB facilitates the binding of carbapenems and PAβN at entrance and proximal sites compared to the closed conformation. PAβN was found to block carbapenem interacting residues in AdeB, establishing its role as a competitive inhibitor of AdeB substrates. Overexpression of AdeABC was detected by q-RT-PCR among 29% of CRABs, and several mutations within AdeS (GLY186VAL, SER188PHE, GLU121LYS, VAL255ILE) and AdeR (VAL120ILE, ALA136VAL) were detected by sequencing. The sequence and structure-based study of AdeRS was performed to analyze the probable effect of these mutations on regulation of the two-component system (TCS), especially, utilizing its three-dimensional structure. AdeS mutations inhibited the transfer of a phosphate group to AdeR, preventing the binding of AdeR to the intercistronic region, leading to overexpression of AdeABC. The elucidation of the role of mutations in AdeRS improves our understanding of TCS-based regulation. Identification of the key residues of AdeB interacting with carbapenems and PAβN may help in future designing of novel inhibitors.

IMPORTANCE AdeABC is an important efflux pump in A. baumannii that plays a role in resistance toward different antibiotics including the “last resort” antibiotic, carbapenem. This pump is regulated by a two-component system, AdeRS. To understand the binding of carbapenems with AdeABC and pump inhibition by PAβN, we analyzed for the first time the possible atomic level interactions of carbapenems and PAβN with AdeB. In the current study, AdeRS-associated novel mutations in clinical A. baumannii are reported for the first time, and a sequence-structure based in-silico approach was used to interpret their role in AdeABC overexpression, leading to carbapenem resistance. None of the previous studies had undertaken both these aspects simultaneously. This study analyzes the open and closed conformation of AdeB, their binding with carbapenems, and key residues involved in it. This helps in visualizing the plausible atomic level causes of pump inhibition driving the discovery of novel inhibitors.

The Changes in Epidemiology of Imipenem-Resistant Acinetobacter baumannii Bacteremia in a Pediatric Intensive Care Unit for 17 Years

BACKGROUND

Acinetobacter baumannii infections cause high morbidity and mortality in intensive care unit (ICU) patients. However, there are limited data on the changes of long-term epidemiology of imipenem resistance in A. baumannii bacteremia among pediatric ICU (PICU) patients.

METHODS

A retrospective review was performed on patients with A. baumannii bacteremia in PICU of a tertiary teaching hospital from 2000 to 2016. Antimicrobial susceptibility tests, multilocus sequence typing (MLST), and polymerase chain reaction for antimicrobial resistance genes were performed for available isolates.

RESULTS

A. baumannii bacteremia occurred in 27 patients; imipenem-sensitive A. baumannii (ISAB, n = 10, 37%) and imipenem-resistant A. baumannii (IRAB, n = 17, 63%). There was a clear shift in the antibiogram of A. baumannii during the study period. From 2000 to 2003, all isolates were ISAB (n = 6). From 2005 to 2008, both IRAB (n = 5) and ISAB (n = 4) were isolated. However, from 2009, all isolates were IRAB (n = 12). Ten isolates were available for additional test and confirmed as IRAB. MLST analysis showed that among 10 isolates, sequence type 138 was predominant (n = 7). All 10 isolates were positive for OXA-23-like and OXA-51-like carbapenemase. Of 27 bacteremia patients, 11 were male (41%), the median age at bacteremia onset was 5.2 years (range, 0-18.6 years). In 33% (9/27) of patients, A. baumannii was isolated from tracheal aspirate prior to development of bacteremia (median, 8 days; range, 5-124 days). The overall case-fatality rate was 63% (17/27) within 28 days. There was no statistical difference in the case fatality rate between ISAB and IRAB groups (50% vs. 71%; P = 0.422).

CONCLUSION

IRAB bacteremia causes serious threat in patients in PICU. Proactive infection control measures and antimicrobial stewardship are crucial for managing IRAB infection in PICU.

Characterization of carbapenem resistant Acinetobacter baumannii ST540 and Klebsiella pneumoniae ST2237 isolates in a pneumonia case from China

AIMS

This study aimed to characterize the chromosome and plasmid sequences, and determine the transferability of plasmids in carbapenem-resistance Acinetobacter baumannii (A. baumannii) DD520 and Klebsiella pneumoniae (K. pneumoniae) DD521 isolates from the same patient who was co-infected in a hospital in China.

METHODS AND RESULTS

Both isolates DD520 and DD521 exhibited multi-drug resistance phenotype, especially the former isolate which was resistant to 9 classes of antimicrobials including carbapenems, quinolones, penicillins, cephalosporins, tetracyclines, phenicols, fosfomycins, sulfanilamides, and aminoglycosides. Carbapenem resistance genes of bla_OXA-23 and bla_OXA-66 were identified on the chromosome of A. baumannii DD520, and bla_KPC-2 was found in the plasmid pDD521.2 from K. pneumoniae DD521. Phylogenetic analysis revealed that A. baumannii DD520 belonged to the ST540 clone, and K. pneumoniae DD521 belonged to the ST2237 clone. Plasmid analysis suggested that bla_KPC-2 was embedded into plasmid pDD521.2, which might be resulted from IS26- and Tn1721-mediated transposition. Plasmid pDD521.2 carrying bla_KPC-2 successfully transferred from K. pneumoniae DD521 into Escherichia coli C600, and carbapenems resistance also transferred in the conjugation.

CONCLUSIONS

To our knowledge, it was the first report of A. baumannii ST540 and K. pneumoniae ST2237 in the same patient in China. Both these two isolates exhibited resistance to carbapenem, which was likely to be resulted from carbapenem resistance genes bla_OXA-23 -bla_OXA-66 on the chromosome of A. baumannii ST540, and bla_KPC-2 in the plasmid of K. pneumoniae ST2237.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study highlighted that effective measures were urgent to prevent and control the co-infection caused by two or more carbapenem-resistance pathogens in the same patient.

Multidrug-resistant organisms in intensive care units and logistic analysis of risk factors

BACKGROUND

Intensive care unit (ICU) patients are critically ill and have low immunity. They will undergo various trauma medical procedures during diagnosis and treatment. The use of high-dose hormones and broad-spectrum antibiotics will increase the incidence of nosocomial infection in ICU patients. Therefore, it is necessary to explore the causes of nosocomial infection in ICU and provide basis for the prevention and control of nosocomial infection in ICU.

AIM

To explore major pathogens of nosocomial infection in ICUs, methods of detection and drug resistance trends.

METHODS

Risk factors of multidrug-resistant infection were analyzed to provide a basis for clinical rational use of antimicrobial drugs in the ICU. These findings were used to standardize rational use of antimicrobial agents. BD PhoenixTM100 automatic bacterial identification analyzer was used to for cell identification in specimens collected from the ICU between January 2016 and December 2019. Drug sensitivity tests were carried out and drug resistance trends were analyzed using the optical disc diffusion method. Odds ratios and corresponding 95%CI of independent variables were calculated using a logistic regression model. Backward elimination (trend = 0.1) was used as an inclusion criterion for multivariate analysis. All data were analyzed using SPSS version 22.0, and P < 0.05 was considered statistically significant.

RESULTS

We collected 2070 samples from ICU patients between January 2016 and December 2019. Sample types comprised sputum (1139 strains, 55.02%), blood (521 strains, 25.17%), and drainage fluid (117 strains, 5.65%). A total of 1051 strains of major pathogens, including Acinetobacter baumannii, Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), Klebsiella pneumoniae (K. pneumoniae) and Staphylococcus aureus, were detected, with a detection rate of 35.97% (378/1051). Most of these strains were resistant to antibiotics. Detection rate of E. coli was 21.79% (229/1051), and it was generally sensitive to many antimicrobial drugs. Detection rate of P. aeruginosa was 24.74% (260/1051), and showed low sensitivity to most antibiotics. Detection rate of K. pneumoniae was 9.42% (99/1051), which was generally resistant to multiple antimicrobial drugs and resistant forms. K. pneumoniae was resistant to imipenem for approximate 4 years, and showed a 19.9% (19/99) and 20.20% (20/99) rate of meropenem resistance. Logistic analysis showed that mechanical ventilation and ureteral intubation were risk factors for multidrug-resistant bacterial infections.

CONCLUSION

This study showed a high incidence of ICU infections. Mechanical ventilation and urine tube intubation were risk factors for infection with multidrug-resistant bacteria.

Infections Due to Acinetobacter baumannii-calcoaceticus Complex: Escalation of Antimicrobial Resistance and Evolving Treatment Options

Bacteria within the genus Acinetobacter (principally A. baumannii-calcoaceticus complex [ABC]) are gram-negative coccobacilli that most often cause infections in nosocomial settings. Community-acquired infections are rare, but may occur in patients with comorbidities, advanced age, diabetes mellitus, chronic lung or renal disease, malignancy, or impaired immunity. Most common sites of infections include blood stream, skin/soft-tissue/surgical wounds, ventilator-associated pneumonia, orthopaedic or neurosurgical procedures, and urinary tract. Acinetobacter species are intrinsically resistant to multiple antimicrobials, and have a remarkable ability to acquire new resistance determinants via plasmids, transposons, integrons, and resistance islands. Since the 1990s, antimicrobial resistance (AMR) has escalated dramatically among ABC. Global spread of multidrug-resistant (MDR)-ABC strains reflects dissemination of a few clones between hospitals, geographic regions, and continents; excessive antibiotic use amplifies this spread. Many isolates are resistant to all antimicrobials except colistimethate sodium and tetracyclines (minocycline or tigecycline); some infections are untreatable with existing antimicrobial agents. AMR poses a serious threat to effectively treat or prevent ABC infections. Strategies to curtail environmental colonization with MDR-ABC require aggressive infection-control efforts and cohorting of infected patients. Thoughtful antibiotic strategies are essential to limit the spread of MDR-ABC. Optimal therapy will likely require combination antimicrobial therapy with existing antibiotics as well as development of novel antibiotic classes.

The Antimicrobial Peptide Esc(1-21) Synergizes with Colistin in Inhibiting the Growth and in Killing Multidrug Resistant Acinetobacter baumannii Strains

Multidrug-resistant microbial infections and the scarce availability of new antibiotics capable of eradicating them are posing a serious problem to global health security. Among the microorganisms that easily acquire resistance to antibiotics and that are the etiological cause of severe infections, there is Acinetobacter baumannii. Carbapenems are the principal agents used to treat A. baumannii infections. However, when strains develop resistance to this class of antibiotics, colistin is considered one of the last-resort drugs. However, the appearance of resistance to colistin also makes treatment of the Acinetobacter infections very difficult. Antimicrobial peptides (AMP) from the innate immunity hold promise as new alternative antibiotics due to their multiple biological properties. In this study, we characterized the activity and the membrane-perturbing mechanism of bactericidal action of a derivative of a frog-skin AMP, namely Esc(1-21), when used alone or in combination with colistin against multidrug-resistant A. baumannii clinical isolates. We found that the mixture of the two compounds had a synergistic effect in inhibiting the growth and killing of all of the tested strains. When combined at dosages below the minimal inhibitory concentration, the two drugs were also able to slow down the microbial growth and to potentiate the membrane-perturbing effect. To the best of our knowledge, this is the first report showing a synergistic effect between AMPs, i.e., Esc(1-21), and colistin against colistin-resistant A. baumannii clinical isolates, highlighting the potential clinical application of such combinational therapy.

Assessment of In Vitro Cefiderocol Susceptibility and Comparators against an Epidemiologically Diverse Collection of Acinetobacter baumannii Clinical Isolates

Cefiderocol is a catechol-substituted siderophore cephalosporin combining rapid penetration into the periplasmic space with increased stability against β-lactamases. This study provides additional data on the in vitro antimicrobial activity of cefiderocol and commercially available comparators against an epidemiologically diverse collection of Acinetobacter baumannii clinical isolates. Antimicrobial susceptibility was tested using pre-prepared frozen 96-well microtiter plates containing twofold serial dilutions of: cefepime, ceftazidime/avibactam, imipenem/relebactam, ampicillin/sulbactam, meropenem, meropenem/vaborbactam, ciprofloxacin, minocycline, tigecycline, trimethoprim/sulfamethoxazole and colistin using the standard broth microdilution procedure in cation-adjusted Mueller–Hinton broth (CAMHB). For cefiderocol, iron-depleted CAMHB was used. A collection of 113 clinical strains of A. baumannii isolated from Argentina, Azerbaijan, Croatia, Greece, Italy, Morocco, Mozambique, Peru and Spain were included. The most active antimicrobial agents against our collection were colistin and cefiderocol, with 12.38% and 21.23% of non-susceptibility, respectively. A high proportion of multidrug-resistant (76.77%) and carbapenem-resistant (75.28%) A. baumannii isolates remained susceptible to cefiderocol, which was clearly superior to novel β-lactam/β-lactamase inhibitor combinations. Cefiderocol-resistance was higher among carbapenem-resistant isolates and isolates belonging to ST2, but could not be associated with any particular resistance mechanism or clonal lineage. Our data suggest that cefiderocol is a good alternative to treat infections caused by MDR A. baumanni, including carbapenem-resistant strains.

Genomic insights of Acinetobacter baumannii ST374 reveal wide and increasing resistome and virulome

WGS-based surveillance has significantly improved the ability to track global spread and emergence of multidrug-resistant clones of clinically relevant pathogens. In this study, we performed the genomic characterization and comparative analysis of an Acinetobacter baumannii (strain Ac56) belonging to the sequence type ST374, which was isolated for the first time in Brazil, in 1996. Genomic analysis of Ac56 predicted a total of 5373 genes, with 3012 being identical across nine genomes of A. baumannii isolates of ST374 from European, Asian, North and South American countries. GoeBURST analysis grouped ST374 lineages into clonal complex CC3 (international clone IC-III). Resistome analysis of ST374 clone predicted genes associated with resistance to heavy metals and clinically relevant beta-lactams and aminoglycosides antibiotics. In this regard, in two closely related A. baumannii strains, the intrinsic bla_ADC gene was linked to the insertion sequence ISAba1; including the Ac56 strain, where it has been possibly associated with intermediate susceptibility to meropenem. Other four carbapenem-resistant A. baumannii strains carried the ISAba1/bla_OXA-23 gene array, which was associated with the transposon Tn2008 or with Tn2006 in an AbaR4-type resistance island. While most virulence genes were shared for A. baumannii strains of ST374, three isolates from Thailand harbored KL49 capsular loci, previously identified in the hypervirulent A. baumannii LAC-4 strain. Analysis of thirty-four predicted plasmids showed eight major groups, of which GR-6 (LN-1) and GR-2 (LN-2) were prevalent. All strains, including the earliest isolate Ac56 harbored at least one complete prophage, whereas none CRISPR-associated (cas) gene was detected. In summary, genomic data of A. baumannii ST374 reveal a potential of this lineage to become a successful clone.

Deciphering Multidrug-Resistant Acinetobacter baumannii from a Pediatric Cancer Hospital in Egypt

Infection by multidrug-resistant (MDR) Acinetobacter baumannii is one of the major causes of hospital-acquired infections worldwide. The ability of A. baumannii to survive in adverse conditions as well as its extensive antimicrobial resistance make it one of the most difficult to treat pathogens associated with high mortality rates. The aim of this study was to investigate MDR A. baumannii that has spread among pediatric cancer patients in the Children’s Cancer Hospital Egypt 57357. Whole-genome sequencing was used to characterize 31 MDR A. baumannii clinical isolates. Phenotypically, the isolates were MDR, with four isolates showing resistance to the last-resort antibiotic colistin. Multilocus sequence typing showed the presence of eight clonal groups, two of which were previously reported to cause outbreaks in Egypt, and one novel sequence type (ST), Oxf-ST2246. Identification of the circulating plasmids showed the presence of two plasmid lineages in the isolates, strongly governed by sequence type. A large number of antimicrobial genes with a range of resistance mechanisms were detected in the isolates, including β-lactamases and antibiotic efflux pumps. Analysis of insertion sequences (ISs) revealed the presence of ISAba1 and ISAba125 in all the samples, which amplify β-lactamase expression, causing extensive carbapenem resistance. Mutation analysis was used to decipher underlying mutations responsible for colistin resistance and revealed novel mutations in several outer membrane proteins, in addition to previously reported mutations in pmrB. Altogether, understanding the transmissibility of A. baumannii as well as its resistance and virulence mechanisms will help develop novel treatment options for better management of hospital-acquired infections.

IMPORTANCEAcinetobacter baumannii represents a major health threat, in particular among immunocompromised cancer patients. The rise in carbapenem-resistant A. baumannii, and the development of resistance to the last-resort antimicrobial agent colistin, complicates the management of A. baumannii outbreaks and increases mortality rates. Here, we investigate 31 multidrug resistant A. baumannii isolates from pediatric cancer patients in Children’s Cancer Hospital Egypt (CCHE) 57357 via whole-genome sequencing. Multilocus sequence typing (MLST) showed the presence of eight clonal groups including a novel sequence type. In silico detection of antimicrobial-resistant genes and virulence factors revealed a strong correlation between certain virulence genes and mortality as well as several point mutations in outer membrane proteins contributing to colistin resistance. Detection of CRISPR/Cas sequences in the majority of the samples was strongly correlated with the presence of prophage sequences and associated with failure of bacteriophage therapy. Altogether, understanding the genetic makeup of circulating A. baumannii is essential for better management of outbreaks.

Genomic Characterization of Extensively Drug-Resistant NDM-Producing Acinetobacter baumannii Clinical Isolates With the Emergence of Novel bla ADC-257

Acinetobacter baumannii has become a major challenge to clinicians worldwide due to its high epidemic potential and acquisition of antimicrobial resistance. This work aimed at investigating antimicrobial resistance determinants and their context in four extensively drug-resistant (XDR) NDM-producing A. baumannii clinical isolates collected between July and October 2020 from Kasr Al-Ainy Hospital, Cairo, Egypt. A total of 20 A. baumannii were collected and screened for acquired carbapenemases (bla_NDM, bla_VIM and bla_IMP) using PCR. Four NDM producer A. baumannii isolates were identified and selected for whole-genome sequencing, in silico multilocus sequence typing, and resistome analysis. Antimicrobial susceptibility profiles were determined using disk diffusion and broth microdilution tests. All bla_NDM-positive A. baumannii isolates were XDR. Three isolates belonged to high-risk international clones (IC), namely, IC2 corresponding to ST570^Pas/1701^Oxf (M20) and IC9 corresponding to ST85^Pas/ST1089^Oxf (M02 and M11). For the first time, we report bla_NDM-1 gene on the chromosome of an A. baumannii strain that belongs to sequence type ST164^Pas/ST1418^Oxf. Together with AphA6, bla_NDM-1 was bracketed by two copies of ISAba14 in ST85^Pas isolates possibly facilitating co-transfer of amikacin and carbapenem resistance. A novel bla_ADC allele (bla_ADC-257) with an upstream ISAba1 element was identified in M19 (ST/CC164^Pas and ST1418^Oxf/CC234^Oxf). bla_ADC genes harbored by M02 and M11 were uniquely interrupted by IS1008. Tn2006-associated bla_OXA-23 was carried by M20. bla_OXA-94 genes were preceded by ISAba1 element in M02 and M11. AbGRI3 was carried by M20 hosting the resistance genes aph(3`)-Ia, aac(6`)-Ib`, catB8, ant(3``)-Ia, sul1, armA, msr(E), and mph(E). Nonsynonymous mutations were identified in the quinolone resistance determining regions (gyrA and parC) of all isolates. Resistance to colistin in M19 was accompanied by missense mutations in lpxACD and pmrABC genes. The current study provided an insight into the genomic background of XDR phenotype in A. baumannii recovered from patients in Egypt. WGS revealed strong association between resistance genes and diverse mobile genetic elements with novel insertion sites and genetic organizations.

Activity of imipenem/relebactam on Klebsiella pneumoniae with different mechanisms of imipenem non-susceptibility

Background and Objectives:

Imipenem/relebactam (IMP/R) is a newly FDA approved β-lactam/β-lactamase inhibitor combination. Relebactam ability to restore IMP activity could differ according to the cause of imipenem non-susceptibility. Therefore, we investigated the in-vitro activity of IMP/R against Klebsiella pneumoniae with different mechanisms of imipenem non-susceptibility.

Materials and Methods:

Imipenem-nonsusceptible (IMP-NS) K. pneumoniae isolates were collected and characterized for β-lactamase encoding genes by multiplex PCR. For IMP-NS carbapenemase-negative isolates, study of Ompk35 & Ompk36 gene expression was performed by reverse transcription-PCR while efflux pump activity was studied by minimum inhibitory concentration (MIC) reduction assay using efflux pump inhibitor. Susceptibility testing of K. pneumoniae to IMP and IMP/R were achieved by broth microdilution (BMD) method.

Results:

During the study period, 140 isolates of IMP-NS K. pneumoniae were collected. BMD method showed that relebactam restored IMP susceptibility in 100%, 60% and 49% of isolates that only harbor AmpC, extended spectrum beta lactamase (ESBL) and carbapenemases, respectively. IMP/R was most potent against all bla _KPC and 50% of bla _OXA-48 _producing isolates. No demonstrable activity of IMP/R against K. pneumoniae harboring metallo-β-lactamases (MBLs). Out of 18 isolates with IMP non-suceptibility due to porins loss with overproduction of ESBL and/or AmpC, 14 (77.7%) isolates were IMP/R susceptible. IMP/R showed no activity against isolates with only efflux pump hyperactivity.

Conclusion:

Relebactam could restore IPM activity in KPC or AmpC-producing IMP/NS K. pneumoniae but with no activity against MBL⁻ producing isolates. Relebactam activity against isolates harbouring-bla _OXA-48 or with altered Ompk35 & Ompk36 gene expression and efflux pump hyperactivity need further studies. Therefore, using IMP/R antibiotic in the treatment of infections caused by IMP/NS K. pneumoniae should be based on its molecular profile of IMP resistance to optimize the utility of IMP/R.

Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii isolated from three major hospitals in Jordan

BACKGROUND

In the last decade, incidences of carbapenem-resistant Acinetobacter baumannii have been increasingly reported worldwide. Consequently, A. baumannii was included in the World Health Organization's new list of critical pathogens, for which new drugs are desperately needed. The objective of this research was to study the molecular epidemiology and antimicrobial susceptibility of clinical carbapenem-resistant A. baumannii isolated from Jordanian hospitals.

METHODS

A total of 78 A. baumannii and 8 Acinetobacter spp. isolates were collected from three major hospitals in Jordan during 2018. Disc diffusion and microdilution methods were used to test their susceptibility against 19 antimicrobial agents. Multilocus sequence typing (MLST) was performed using the Pasteur scheme, followed by eBURST analysis for all isolates. PCR was used to detect β-lactam resistance genes, bla_OXA-23-like , bla_OXA-51-like , and bla_NDM-1 .

RESULTS

Of the 86 tested isolates, 78 (90.6%) exhibited resistance to carbapenems, whereas no resistance was recorded to tigecycline or polymyxins. Based on the resistance profiles, 10.4% and 84.8% of isolates were classified into multidrug resistant (MDR) or extensively drug resistant (XDR), respectively. The most prevalent carbapenems resistance genes amongst isolates were bla_OXA-51-Like (89.5%), followed by bla_OXA-23-Like (88.3%) and bla_NDM-1 (10.4%). MLST revealed the presence of 19 sequence types (STs), belonging to eight different international complexes. The most commonly detected clonal complex (CC) was CC2, representing 64% of all typed isolates.

CONCLUSIONS

This is the first study to report the clonal diversity of A. baumannii isolates in Jordan. A high incidence of carbapenem resistance was detected in the isolates investigated. In addition, our findings provided evidence for the widespread of bla_OXA-23-like harbouring carbapenem-resistant A. baumannii and belonging to CC2. The number of XDR isolates identified in this study is alarming. Thus, periodic surveillance and molecular epidemiological studies of resistance factors are important to improve treatment outcomes and prevent the spread of A. baumannii infections.

An Outbreak of tet(X6)-Carrying Tigecycline-Resistant Acinetobacter baumannii Isolates with a New Capsular Type at a Hospital in Taiwan

Dissemination of multidrug-resistant, particularly tigecycline-resistant, Acinetobacter baumannii is of critical importance, as tigecycline is considered a last-line antibiotic. Acquisition of tet(X), a tigecycline-inactivating enzyme mostly found in strains of animal origin, imparts tigecycline resistance to A. baumannii. Herein, we investigated the presence of tet(X) variants among 228 tigecycline-non-susceptible A. baumannii isolates from patients at a Taiwanese hospital via polymerase chain reaction using a newly designed universal primer pair. Seven strains (3%) carrying tet(X)-like genes were subjected to whole genome sequencing, revealing high DNA identity. Phylogenetic analysis based on the PFGE profile clustered the seven strains in a clade, which were thus considered outbreak strains. These strains, which were found to co-harbor the chromosome-encoded tet(X6) and the plasmid-encoded bla_OXA-72 genes, showed a distinct genotype with an uncommon sequence type (Oxford ST793/Pasteur ST723) and a new capsular type (KL129). In conclusion, we identified an outbreak clone co-carrying tet(X6) and bla_OXA-72 among a group of clinical A. baumannii isolates in Taiwan. To the best of our knowledge, this is the first description of tet(X6) in humans and the first report of a tet(X)-like gene in Taiwan. These findings identify the risk for the spread of tet(X6)-carrying tigecycline- and carbapenem-resistant A. baumannii in human healthcare settings.

Whole-Genome Sequencing Elucidates the Epidemiology of Multidrug-Resistant Acinetobacter baumannii in an Intensive Care Unit

The nosocomial pathogen Acinetobacter baumannii is a frequent cause of healthcare-acquired infections, particularly in critically ill patients, and is of serious concern due to its potential for acquired multidrug resistance. Whole-genome sequencing (WGS) is increasingly used to obtain a high-resolution view of relationships between isolates, which helps in controlling healthcare-acquired infections. Here, we conducted a retrospective study to identify epidemic situations and assess the percentage of transmission in intensive care units (ICUs). Multidrug-resistant A. baumannii (MDR-AB) were continuously isolated from the lower respiratory tract of different patients (at the first isolation in our ICU). We performed WGS, pulsed-field gel electrophoresis (PFGE), and multilocus-sequence typing (MLST) analyses to elucidate bacterial relatedness and to compare the performance of conventional methods with WGS for typing MDR-AB. From June 2017 to August 2018, A. baumannii complex strains were detected in 124 of 796 patients during their ICU stays, 103 of which were MDR-AB. Then we subjected 70 available MDR-AB strains to typing with WGS, PFGE, and MLST. Among the 70 A. baumannii isolates, 38 (54.29%) were isolated at admission, and 32(45.71%) were acquisition isolates. MLST identified 12 unique sequence types, a novel ST (ST2367) was founded. PFGE revealed 16 different pulsotypes. Finally, 38 genotypes and 23 transmissions were identified by WGS. Transmission was the main mode of MDR-AB acquisition in our ICU. Our results demonstrated that WGS was a discriminatory technique for epidemiological healthcare-infection studies. The technique should greatly benefit the identification of epidemic situations and controlling transmission events in the near future.

Mechanical ventilation-associated pneumonia caused by Acinetobacter baumannii in Northeast China region: analysis of genotype and drug resistance of bacteria and patients' clinical features over 7 years

Objective

To investigate the clinical features and outcomes of patients with mechanical ventilation-associated pneumonia (VAP) caused by Acinetobacter baumannii (Ab), and to characterize the drug resistance of pathogenic strains and carbapenem resistance-associated genes.

Methods

Clinical data were collected from the PICU of Shengjing Hospital. Patients who met the diagnostic criteria of VAP and for whom Ab was a pathogen were selected as study participants. The patients were divided into carbapenem-resistant A. baumannii (CRAB) and carbapenem-sensitive A. baumannii (CSAB) groups. The genes closely associated with Ab resistance to carbapenems and the efflux pump-related genes were detected by real-time polymerase chain reaction, and results compared between the two groups.

Results

The total mechanical ventilation time and the administration time of antibiotics after a diagnosis of Ab infection were significantly higher in the CRAB group. And the CRAB group strains were only sensitive to amikacin, cephazolin, compound sulfamethoxazole, and tigecycline. Genetic test results indicated that IPM expression was not significantly different between two groups. The OXA-51 and OXA-23 in the CRAB group was markedly higher than that in the CSAB group, while OXA-24 expression was markedly lower. The expression of AdeABC and AdeFGH was significantly greater in the CRAB compared to CSAB group.

Conclusion

In pediatric patients with VAP caused by Ab infection, the detection rate of CRAB strains is far higher than that of CSAB strains; The abnormal expression of β-lactamase-producing genes (OXA-23, OXA-24, and OXA-51) and efflux pump-related genes (AdeABC and AdeFGH) is closely related to the production of CRAB.

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.

Accessory Genomic Epidemiology of Cocirculating Acinetobacter baumannii Clones

Acinetobacter baumannii has become one of the most important multidrug-resistant nosocomial pathogens all over the world. Nonetheless, very little is known about the diversity of A. baumannii lineages coexisting in hospital settings. Here, using whole-genome sequencing, epidemiological data, and antimicrobial susceptibility tests, we uncover the transmission dynamics of extensive and multidrug-resistant A. baumannii in a tertiary hospital over a decade. Our core genome phylogeny of almost 300 genomes suggests that there were several introductions of lineages from international clone 2 into the hospital. The molecular dating analysis shows that these introductions happened in 2006, 2007, and 2013. Furthermore, using the accessory genome, we show that these lineages were extensively disseminated across many wards in the hospital. Our results demonstrate that accessory genome variation can be a very powerful tool for conducting genomic epidemiology. We anticipate future studies employing the accessory genome along with the core genome as a powerful phylogenomic strategy to track bacterial transmissions over very short microevolutionary scales. IMPORTANCE Whole-genome sequencing for epidemiological investigations (genomic epidemiology) has been of paramount importance to understand the transmission dynamics of many bacterial (and nonbacterial) pathogens. Commonly, variation in the core genome, single nucleotide polymorphisms (SNPs), is employed to carry out genomic epidemiology. However, at very short periods of time, the core genome might not have accumulated enough variation (sufficient SNPs) to tell apart isolates. In this scenario, gene content variation in the accessory genome can be an option to conduct genomic epidemiology. Here, we used the accessory genome, as well as the core genome, to uncover the transmission dynamics of extensive and multidrug-resistant A. baumannii in a tertiary hospital for a decade. Our study shows that accessory genome variation can be a very powerful tool for conducting genomic epidemiology.

Pharmacodynamic evaluation of suppression of in vitro resistance in Acinetobacter baumannii strains using polymyxin B-based combination therapy

The emergence of polymyxin resistance in Gram-negative bacteria infections has motivated the use of combination therapy. This study determined the mutant selection window (MSW) of polymyxin B alone and in combination with meropenem and fosfomycin against A. baumannii strains belonging to clonal lineages I and III. To evaluate the inhibition of in vitro drug resistance, we investigate the MSW-derived pharmacodynamic indices associated with resistance to polymyxin B administrated regimens as monotherapy and combination therapy, such as the percentage of each dosage interval that free plasma concentration was within the MSW (%T_MSW) and the percentage of each dosage interval that free plasma concentration exceeded the mutant prevention concentration (%T_>MPC). The MSW of polymyxin B varied between 1 and 16 µg/mL for polymyxin B-susceptible strains. The triple combination of polymyxin B with meropenem and fosfomycin inhibited the polymyxin B-resistant subpopulation in meropenem-resistant isolates and polymyxin B plus meropenem as a double combination sufficiently inhibited meropenem-intermediate, and susceptible strains. T_>MPC 90% was reached for polymyxin B in these combinations, while %T_MSW was 0 against all strains. T_MSW for meropenem and fosfomycin were also reduced. Effective antimicrobial combinations significantly reduced MSW. The MSW-derived pharmacodynamic indices can be used for the selection of effective combination regimen to combat the polymyxin B-resistant strain.

Clonal change of carbapenem-resistant Acinetobacter baumannii isolates in a Korean hospital

The expansion of specific carbapenem-resistant Acinetobacter baumannii (CRAB) clones is a global concern due to its therapeutic difficulty and epidemicity. To understand the prevalence of CRAB isolates in a Korean hospital, we investigated the epidemiological characteristics of 96 CRAB isolates between 2016 and 2018, including the sequence types (STs), antimicrobial susceptibility, and genetic background of resistance to carbapenems and aminoglycosides. Six STs were identified using the Oxford multilocus sequence typing scheme; ST191 (n = 8), ST208 (n = 12), ST229 (n = 11), and ST369 (n = 21) were previously identified clones in the study hospital, whereas gpi variants of ST208, ST451 (n = 34) and ST784 (n = 10), were emerging clones. ST208 isolates exhibited higher resistance rates to minocycline than other ST isolates, whereas ST369 isolates exhibited lower resistance rates to aminoglycosides and trimethoprim/sulfamethoxazole than other ST isolates. All CRAB isolates previously isolated in the study hospital carried ISAbaI-bla_OXA-23 for carbapenem resistance, but 10 ST229 isolates carried only ISAbaI-bla_OXA-51. The carriage of armA was lower in ST369 isolates (38%) than in other ST isolates (≥83%). The frequency and diversity of aminoglycoside-modifying enzyme genes were decreased among the CRAB isolates between 2016 and 2018 compared with CRAB isolates between 2013 and 2015 at the study hospital. In conclusion, clonal complex 208 CRAB isolates are predominant in the study hospital. This study demonstrates the evolutionary change of CRAB isolates in the study hospital in relation to the emergence of new STs and selection of resistant genes.

Current situation of carbapenem-resistant Enterobacteriaceae and Acinetobacter in Japan and Southeast Asia

In the recent years, issues related to drug-resistant bacteria have evolved worldwide, and various countermeasures have been taken to control their spread. Among a wide variety of drug-resistant bacterial species, carbapenem-resistant Gram-negative bacteria, including carbapenem-resistant Enterobacteriaceae (CRE) and carbapenem-resistant Acinetobacter baumannii (CRAb), are those for which countermeasures are particularly important. Carbapenems are the last resort antibiotics for any bacterial infection; therefore, infectious diseases caused by these drug-resistant bacteria are difficult to treat. In the case of CRE, since carbapenemases responsible for carbapenem resistance are mostly encoded on transmissible plasmids, it is known that susceptible bacteria can easily become carbapenem-resistant by transfer of plasmids between Enterobacteriaceae. In addition, Enterobacteriaceae are common bacterial species found in the guts of animals, including humans. Acinetobacter is ubiquitously isolated in the environment. Due to these characteristics, it is quite difficult to prevent the intrusion of multi-drug resistant pathogens in hospitals. Therefore, effective countermeasures should be developed and utilized against such dangerous pathogens based on molecular epidemiological analyses. In this review, there are also some examples presented on how to manage to monitor and control those troublesome drug-resistant bacteria conducted in Japan and Southeast Asia.

Antibiotic Resistance and Genotypes of Nosocomial Strains of Acinetobacter baumannii in Kazakhstan

The aim of this study was to determine the prevalence of A. baumannii antibiotic-resistant strains in Kazakhstan and to characterize genotypes related to epidemic “high-risk” clones. Two hundred and twenty four A. baumannii isolates from four cities of Kazakhstan in 2011–2019 were studied. Antibiotic susceptibility testing was performed by using broth microdilutions method according to EUCAST (v 11.0) recommendations. The presence of bla_OXA-23-like, bla_{OXA-24/40-like,}bla_OXA-58-like,bla_VIM,bla_IMP, and bla_NDM genes was determined by PCR. Genotyping was performed using high-throughput real-time PCR detection of 21 SNPs at 10 chromosomal loci used in existing MLST schemes. Resistance rates to imipenem, meropenem, amikacin, gentamicin, and ciprofloxacin were 81.3%, 78.6%, 79.9%, 65.2%, and 89.3%, respectively. No colistin resistant isolates were detected. The values of the MIC 50% and the MIC 90% of tigecycline were 0.125 mg/L, only four isolates (1.8%) had the ECOFF value >0.5 mg/L. The presence of acquired carbapenemase genes was found in 82.2% strains, including bla_OXA-23-like (78.6%) or bla_OXA-58-like (3.6%) genes. The spreading of carbapenem resistant A. baumannii strains in Kazakhstan was associated with epidemic “high-risk” clonal groups, predominantly, CG208(92)^OXF/CG2^PAS (80.8%) and less often CG231(109)^OXF/CG1^PAS (1.8%).