ABSTRACT
Background: The respiratory tract microbiome is essential for human health and well-being and is determined by genetic, lifestyle, and environmental factors. Patients with Common Variable Immunodeficiency (CVID) suffer from respiratory and intestinal tract infections, leading to chronic diseases and increased mortality rates. While CVID patients' gut microbiota have been analyzed, data on the respiratory microbiome ecosystem are limited. Objective: This study aims to analyze the bacterial composition of the oropharynx of adults with CVID and its link with clinical and immunological features and risk for respiratory acute infections. Methods: Oropharyngeal samples from 72 CVID adults and 26 controls were collected in a 12-month prospective study. The samples were analyzed by metagenomic bacterial 16S ribosomal RNA sequencing and processed using the Quantitative Insights Into Microbial Ecology (QIME) pipeline. Differentially abundant species were identified and used to build a dysbiosis index. A machine learning model trained on microbial abundance data was used to test the power of microbiome alterations to distinguish between healthy individuals and CVID patients. Results: Compared to controls, the oropharyngeal microbiome of CVID patients showed lower alpha- and beta-diversity, with a relatively increased abundance of the order Lactobacillales, including the family Streptococcaceae. Intra-CVID analysis identified age >45 years, COPD, lack of IgA, and low residual IgM as associated with a reduced alpha diversity. Expansion of Haemophilus and Streptococcus genera was observed in patients with undetectable IgA and COPD, independent from recent antibiotic use. Patients receiving azithromycin as antibiotic prophylaxis had a higher dysbiosis score. Expansion of Haemophilus and Anoxybacillus was associated with acute respiratory infections within six months. Conclusions: CVID patients showed a perturbed oropharynx microbiota enriched with potentially pathogenic bacteria and decreased protective species. Low residual levels of IgA/IgM, chronic lung damage, anti antibiotic prophylaxis contributed to respiratory dysbiosis.
Subject(s)
Common Variable Immunodeficiency , Dysbiosis , Oropharynx , Respiratory Tract Infections , Humans , Common Variable Immunodeficiency/microbiology , Common Variable Immunodeficiency/immunology , Common Variable Immunodeficiency/complications , Oropharynx/microbiology , Male , Female , Middle Aged , Adult , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/immunology , Microbiota , Prospective Studies , Aged , RNA, Ribosomal, 16S/genetics , Acute Disease , Bacteria/classification , Bacteria/genetics , Case-Control StudiesABSTRACT
Ceftazidime-avibactam (CAZ-AVI) is an active antibiotic combination of a ß-lactam-ß-lactamase inhibitor against carbapenemase-producing Enterobacterales. Reports of resistance to CAZ-AVI other than metallo-ß-lactamases have increased in recent years. The aim of this study was to analyze KPC-Klebsiella pneumoniae (KP) isolates resistant to CAZ-AVI from the intestinal carriage of hospitalized elderly patients in Italy, in February 2018-January 2020. Characterization of CAZ-AVI-resistant KP isolates, including MLST, resistome, virulome and plasmid content, was performed by WGS analysis. Out of six CAZ-AVI-resistant KP isolates, three belonged to ST101 and three to ST512; two isolates produced KPC-3 (both ST512), four had mutated KPC-3 (KPC-31, in ST101 and ST512, and KPC-46, both ST101). All CAZ-AVI-resistant KP isolates were multidrug-resistant and carried several resistance genes. The yersiniabactin ybt9 gene cluster was present in all ST101 isolates, while, in ST512 isolates, no virulence genes were detected. Several plasmids were detected: IncF was present in all isolates, as well as IncR and Col440 in ST101 and IncX3 in ST512 isolates. In conclusion, it is important to monitor the circulation of K. pneumoniae resistant to CAZ-AVI to prevent the spread of clones causing difficult-to-treat infections. The presence of mutated KPC-3 in high-risk K. pneumoniae clones resistant to CAZ-AVI in hospitalized patients deserves attention.
ABSTRACT
Haemophilus influenzae invasive disease is a severe infection that needs rapid antibiotic therapy. The aim of the study was to perform and evaluate the serotype distribution, antibiotic susceptibility and molecular characteristics of 392 H. influenzae invasive isolates collected during 2017-2021 in Italy. The majority of isolates were NTHi (305/392, 77.8%), followed by Hib (49/392, 12.5%). Ampicillin resistance was frequently detected (85/392, 21.7%): 12.2% were ß-lactamase producers (all blaTEM except one blaROB), 9.4% were ß-lactamase-negative ampicillin-resistant (BLNAR), with mutations in the ftsI gene. Six isolates were resistant to ciprofloxacin, with substitutions in GyrA and ParC. An MLST analysis revealed the occurrence of international resistant clones, such as ST103 and ST14, highlighting the importance of molecular surveillance.
ABSTRACT
The spread of carbapenemase-producing (CP) Enterobacterales is currently a worldwide concern, especially in the elderly. Twelve CP-E. coli isolated from rectal swabs of colonized inpatients aged ≥65 years from four hospitals in two Italian cities (Milan and Rome) were analyzed by whole genome sequencing (WGS) to obtain multi-locus sequence typing (MLST), identification of carbapenemase-encoding genes, resistome, plasmid content, and virulence genes. MLST analysis showed the presence of 10 unrelated lineages: ST410 (three isolates from three different hospitals in two cities) and ST12, ST38, ST69, ST95, ST131, ST189, ST648, ST1288, and ST1598 (one isolate each). Most isolates (9/12, 75%) contained a serine-ß-lactamase gene (5 blaKPC-3, 2 blaKPC-2, and 2 blaOXA-181), while three isolates harbored a metallo-ß-lactamase gene (two blaNDM-5 and one blaVIM-1). In most CP-E. coli, the presence of more than one plasmid was observed, with the predominance of IncF. Several virulence genes were detected. All isolates contained genes enhancing the bacterial fitness, such as gad and terC, and all isolates but one, fimH, encoding type 1 fimbriae. In conclusion, CP-E. coli clones colonizing elderly patients showed heterogeneous genetic backgrounds. We recommend strict surveillance to monitor and prevent the spread of successful, high-risk clones in healthcare settings.
ABSTRACT
Carbapenemase-producing Enterobacterales (CPE) represent a serious threat to public health worldwide. Elderly patients are at increased risk of colonisation/infection with CPE. This study aimed to evaluate the persistence of CPE colonisation and the genotypic characteristics of persistent strains in elderly people discharged from Italian hospitals. A longitudinal study was conducted in two Italian cities (March 2018 to September 2020) enrolling 137 patients aged ≥65 years with CPE intestinal colonisation at hospital discharge. CPE colonisation was evaluated after 4, 8 and 12 months. Competing risk analysis was used to explore the association between baseline characteristics and persistence at 4 months. For all isolates, carbapenemase typing and multilocus sequence typing were performed. Persistent isolates underwent whole-genome sequencing. Of 137 patients, 91% carried carbapenemase-producing Klebsiella pneumoniae (CP-KP) and 8.8% carried carbapenemase-producing Escherichia coli. Although a large number of patients were lost to follow-up owing to death or withdrawal, 28/65 patients (43.1%) remained colonised at Month 4; 16/42 (38.1%) and 5/28 (17.9%) were found colonised up to Months 8 and 12, respectively. Colonisation persistence was more frequent in patients with bacteraemia or complicated urinary tract infection while in hospital and in those staying in long-term care facilities (LTCFs). Clonal characteristics of CP-KP isolates did not appear to influence persistence. Isolates obtained from each persistent carrier were identical or highly related by SNP phylogenetic analysis. Identification of patients at higher risk of persistent intestinal carriage after hospital discharge can prompt control measures to limit the transmission of CPE in the community, especially in LTCF settings.
Subject(s)
Carbapenem-Resistant Enterobacteriaceae , Enterobacteriaceae Infections , Aged , Bacterial Proteins/genetics , Enterobacteriaceae Infections/epidemiology , Escherichia coli , Hospitals , Humans , Klebsiella pneumoniae , Longitudinal Studies , Patient Discharge , Phylogeny , beta-Lactamases/geneticsABSTRACT
After the widespread use of Haemophilus influenzae type b (Hib) vaccine, H. influenzae invasive disease is now commonly due to non-encapsulated (NTHi), affecting mostly the youngest and the elderly. The objective of this study was to investigate H. influenzae nasopharyngeal carriage rate in adults with co-morbidities and possible associated risk factors. METHODS: Patients aged >50 years with co-morbidities attending medical centres were examined. A nasopharyngeal swab was analysed for H. influenzae presence by cultural and molecular methods (RT-PCR). Univariable and multivariable analysis of risk factors for H. influenzae carriage were performed. Serotype of isolates was determined by PCR capsular genotyping. Minimum inhibitory concentration (MIC) was determined by MIC gradient test and ß-lactamase production was detected by the nitrocephin test. Genotyping was performed by Multilocus sequence typing (MLST). Phylogenetic relationships among carriage and invasive NTHi strains were assessed. RESULTS: Among 248 enrolled patients (median age: 73 years), the carriage rate was 5.6% and 10.5% by cultural method or RT-PCR, respectively. Colonization with H. influenzae was significantly associated with the presence of acute respiratory symptoms (adjusted OR = 12.16, 95% CI: 3.05-48.58, p < 0.001). All colonizing isolates were NTHi. Three isolates (3/14, 21.4%) were resistant to ampicillin and beta-lactamase positive. MLST revealed a high degree of genetic diversity, with 11 different STs from 14 isolates. Eight out of the 11 (72.7%) STs were shared among carriage and invasive isolates. CONCLUSIONS: Adults ≥50 years old with co-morbidities are occasionally colonized by H. influenzae, even if the presence of co-morbidities is not a risk factor for colonization. The presence of acute respiratory symptoms is the only factor associated with H. influenzae colonization. Colonizing H. influenzae are all NTHi. Colonizing H. influenzae often belong to the same STs of invasive disease isolates.
Subject(s)
Haemophilus Infections , Haemophilus influenzae , Adult , Aged , Haemophilus Infections/epidemiology , Haemophilus influenzae/genetics , Humans , Infant , Middle Aged , Morbidity , Multilocus Sequence Typing , Nasopharynx , PhylogenyABSTRACT
Recently, Escherichia coli producing extended-spectrum ß-lactamases (ESBLs) have become a serious public-health problem, and food-producing animals (FPAs) have been suggested as a potential reservoir/source. This study aimed to compare ESBL-producing E. coli isolates from different sources. ESBL-producing E. coli isolates were collected from humans (n = 480) and FPAs (n = 445) in Italy (2016-2017). Isolates were screened for the presence of ESBL and carbapenemase genes and were classified according to phylogenetic group and MLST genotyping. The genes mcr-1 to -5 were searched for in colistin-resistant isolates. CTX-M was the most frequent ESBL type both in human and animal isolates. CTX-M-15 prevailed in humans (75.0%) and cattle (51.1%) but not in poultry (36.6%). CTX-M-1 was common (58.3%) in pigs. SHV-type and CMY-2-like were found in FPAs, especially in poultry (17.0% and 29.9%, respectively). Additionally, 29 isolates were mcr-1 carriers (3 from humans and 26 from FPAs). No carbapenemase genes were detected. Human isolates mostly belonged to phylogroup B2 (76.5%). Animal isolates were distributed among groups A (35.7%), B1 (26.1%) and C (12.4%). Few animal isolates (almost all from poultry) were classified into group B2 (4.3%). Most human isolates (83.4%) belonged to the pandemic ST131 clone and frequently carried CTX-M-15 (75.9%). ST131 was rarely detected in FPAs (three isolates from poultry). Nineteen STs were shared in both sources, with ST10, ST410 and ST69 being more frequently detected. Potential exchange of ESBL genes from animals to humans is feasible, underlying the need for strict monitoring based on a 'One Health' approach.
Subject(s)
Bacterial Proteins/genetics , Drug Resistance, Multiple, Bacterial/genetics , Escherichia coli Infections/veterinary , Escherichia coli/genetics , beta-Lactamases/genetics , Animals , Anti-Bacterial Agents/pharmacology , Cattle , Cross-Sectional Studies , Escherichia coli/drug effects , Escherichia coli/isolation & purification , Escherichia coli Proteins/genetics , Humans , Italy , Microbial Sensitivity Tests , Molecular Epidemiology , Multilocus Sequence Typing , Poultry/microbiology , Swine/microbiologyABSTRACT
Haemophilus influenzae serotype b (Hib) was the leading cause of bacterial meningitis in children before the implementation of infant immunization with conjugate Hib vaccines. Despite the effectiveness of the vaccine, invasive Hib disease cases (i.e. isolation of Hib from a normally sterile site) are still reported in children. All invasive Hib disease cases in children ≤ 15 years reported through the National Surveillance System of Invasive Bacterial Disease, during 2012-2018 in Italy, were analyzed. Hib PCR-confirmed isolates were subjected to MLST and PFGE analysis. The number of copies of the capb locus, a virulence factor potentially contributing to true vaccine failures (TVFs), was determined by Southern blot analysis. Vaccine effectiveness (VE) was determined using a multiple Poisson regression model. 31 cases of invasive Hib disease in children were reported. Fourteen children were vaccinated (TVFs), 14 were unvaccinated and 2 partially vaccinated (vaccination status was unknown for 1 case). The median age of children was 12 months (range 3 months-15 years). A decrease in vaccination coverage was observed in 2014-2016 (source Ministry of Health), and a rise in incidence was documented from 2016 until 2018, especially in children < 5 years. Vaccine effectiveness was estimated to be 83% (95% CI:45-95). 24 isolates were available. The predominant ST was ST6 (70.8%). Cluster analysis of ST6 isolates by PFGE identified five variants. Six isolates (25%) contained multiple copies of the capb locus distributed among TVFs (30%) and unvaccinated children (16.7%). Our data show that both failures to vaccinate and TVFs are associated with invasive Hib disease in children in Italy, during the vaccination era. Most cases in children ≤ 2 years were vaccine-preventable, since they occurred in unvaccinated subjects (13/21 cases, 62%). No host predisposing factors for TVF were recognized. TVFs were not significantly associated with either specific genotypes or amplification status of the capb locus.
Subject(s)
Haemophilus Infections , Haemophilus Vaccines , Haemophilus influenzae type b , Child , Haemophilus Infections/epidemiology , Haemophilus Infections/prevention & control , Haemophilus influenzae , Humans , Infant , Italy/epidemiology , Multilocus Sequence Typing , Vaccines, ConjugateABSTRACT
BACKGROUND: Vaccine-preventable invasive bacterial diseases (IBDs) caused by Neisseria meningitidis (Nm), Streptococcus pneumoniae (Sp), and Haemophilus influenzae (Hi) have been notified in Italy since 2007 without assessing reporting completeness. METHODS: Our study compared the number of cases of IBDs identified from the Italian Hospital Discharge Records (HDRs), using specific diagnostic ICD-9-CM codes, with those notified to the National Surveillance System (NSS) from 2007 to 2016. A multinomial logistic regression model was used to impute the aetiology of all discharges with a diagnosis of unspecified bacterial meningitis. RESULTS: Over a 10-year period, 14,243 hospital discharges with diagnosis of IBD were estimated in Italy (12,671 with specified aetiology and 1,572 with imputed aetiology). Among those, 2,513 (17.6%) were caused by Nm, 10,441 (73.3%) by Sp, and 1289 (9.1%) by Hi. Most invasive meningococcal diseases were coded as meningitis (72.3%), while Hi and Sp were more frequently coded as septicaemia (51.6% and 60.4%, respectively). The highest mean annual incidence rate was found for IBD caused by Sp (1.74 per 100,000), followed by Nm (0.42 per 100,000) and by Hi (0.21 per 100,000). Comparing NSS with HDR data, we found an initially high underreporting of all IBDs, and particularly for Hi. Data from the two systems overlapped in more recent years, due to an improved reporting completeness. The increasing IBD incidence observed in NSS data was not confirmed by HDR data trends, although with pathogen-related differences with Hi cases rising in both data sources, suggesting that is mainly due to an improved disease notification rather than to a true incidence increase. CONCLUSIONS: Comparing surveillance data with other data sources is useful to better interpret observed trends of notifiable diseases.
Subject(s)
Bacterial Infections/epidemiology , Epidemiological Monitoring , Hospital Records/statistics & numerical data , Hospitalization/statistics & numerical data , Adolescent , Adult , Child , Child, Preschool , Female , Haemophilus Infections/epidemiology , Humans , Incidence , Infant , Infant, Newborn , Italy/epidemiology , Male , Meningitis, Haemophilus/epidemiology , Meningitis, Meningococcal/epidemiology , Meningitis, Pneumococcal/epidemiology , Meningococcal Infections/epidemiology , Middle Aged , Patient Discharge/statistics & numerical data , Regression Analysis , Young AdultABSTRACT
Routine immunization of infants with conjugate vaccines against Haemophilus influenzae type b (Hib) has greatly reduced the incidence of invasive Hib disease; however changes in the epidemiology of H. influenzae disease have occurred. We describe the epidemiology of invasive H. influenzae disease and the characterization of isolates collected in Italy between 2012 and 2016. Trends in the overall incidence of invasive H. influenzae disease were calculated. Isolates were characterized by PCR capsular genotyping, antimicrobial susceptibility testing, ampicillin resistance-associated gene sequencing and MLST. Trends in incidence by serotype and serotype-specific distribution were estimated using multiple imputation of missing data. The overall incidence of invasive H. influenzae disease increased 22.5% yearly (from 0.11/100,000 in 2012 to 0.24/100,000 in 2016). Most cases (82.0%) were due to non-typeable H. influenzae (NTHi). An increasing trend in NTHi disease burden was estimated; the highest rise was among infants <12â¯months (40.8% annual increase). Invasive Hib disease showed a fluctuating trend with a clear increase in 2016, while we found an increasing trend for disease due to non-Hib capsulated serotypes in the elderly (32.9% annual increase). Ampicillin resistance mediated by either ß-lactamase or altered penicillin-binding proteins 3 (PBP3) increased. In spite of genetic diversity of NTHi, sequence types (STs) associated with ampicillin resistance status were identified (ST103/ST106 linked to ß-lactamase production and ST14 linked to a specific PBP3 substitution pattern). The increasing trend in invasive NTHi disease in infants is of concern underlying the need for the development of a future vaccine against NTHi.
Subject(s)
Haemophilus Infections/epidemiology , Adolescent , Adult , Aged , Amoxicillin/therapeutic use , Ampicillin/therapeutic use , Anti-Bacterial Agents/therapeutic use , Child , Child, Preschool , Clavulanic Acid/therapeutic use , Female , Genotype , Haemophilus Infections/drug therapy , Haemophilus Infections/prevention & control , Haemophilus Vaccines/therapeutic use , Haemophilus influenzae/drug effects , Haemophilus influenzae/pathogenicity , Humans , Infant , Infant, Newborn , Italy/epidemiology , Male , Microbial Sensitivity Tests , Middle Aged , Phylogeny , Serogroup , Young AdultSubject(s)
Common Variable Immunodeficiency , Haemophilus Infections , Haemophilus influenzae , Pneumococcal Infections , Respiratory Tract Infections , Streptococcus pneumoniae , Adolescent , Adult , Aged , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Common Variable Immunodeficiency/immunology , Common Variable Immunodeficiency/microbiology , Female , Haemophilus Infections/immunology , Haemophilus Infections/microbiology , Haemophilus influenzae/drug effects , Haemophilus influenzae/genetics , Haemophilus influenzae/growth & development , Haemophilus influenzae/isolation & purification , Humans , Immunoglobulin A/blood , Immunoglobulin G/therapeutic use , Immunoglobulin M/blood , Male , Middle Aged , Nasopharynx/microbiology , Oropharynx/microbiology , Pneumococcal Infections/immunology , Pneumococcal Infections/microbiology , Respiratory Tract Infections/immunology , Respiratory Tract Infections/microbiology , Risk Factors , Streptococcus pneumoniae/drug effects , Streptococcus pneumoniae/genetics , Streptococcus pneumoniae/growth & development , Streptococcus pneumoniae/isolation & purification , Young AdultABSTRACT
The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a critical concern worldwide. In Italy, CPE isolates are very frequent, with the KPC enzyme types strongly predominant whereas the New Delhi metallo-ß-lactamase (NDM) enzymes are extremely rare. Here we report the first detection of NDM-5-producing Escherichia coli sequence type 167 (ST167) isolates from two patients with urinary tract infection (Ec001 and Ec002 from urines), including one with colonisation (Ec003 from faeces) admitted to the same hospital 2 months apart in 2017. Minimum inhibitory concentrations (MICs) were determined by broth microdilution. The carbapenemase type was identified both by phenotypic and genotypic methods. Isolate genotypes were investigated by phylogenetic typing, multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Next-generation sequencing (NGS) was used to obtain complete sequences of plasmids. The three E. coli isolates carried the blaNDM-5 gene, shared the same resistance phenotype and belonged to ST167. By PFGE, isolates showed the same profile, suggesting that they were the same strain. NGS revealed that the blaNDM-5 gene was located on a 99-kb multireplicon plasmid (designed pNDM-5-IT) with a peculiar scaffold constituted by four replicons of the IncF type (FIA, FIB and two copies of the FII replicon). pNDM-5-IT plasmid harboured multiple resistance and virulence determinants, including the arginine deaminase (ADI) cluster never found associated with plasmids before. Since NDM-5-producing E. coli ST167 has been regarded as a successful epidemic clone in China, the emergence of such a clone carrying a plasmid associated both with multiresistance and virulence could be a public-health threat.
Subject(s)
Plasmids/genetics , Uropathogenic Escherichia coli/isolation & purification , beta-Lactamases/genetics , Aged , Drug Resistance, Multiple, Bacterial/genetics , Escherichia coli Infections/microbiology , Humans , Italy , Microbial Sensitivity Tests , Middle Aged , Urinary Tract Infections/microbiology , Uropathogenic Escherichia coli/drug effects , Uropathogenic Escherichia coli/genetics , beta-Lactamases/drug effects , beta-Lactamases/isolation & purificationABSTRACT
Infections due to multidrug-resistant (MDR) organisms in long-term care facilities (LTCFs) residents constitute a public health concern. This multicenter study investigated the frequency of ESBL-producing pathogens and MDR Clostridium difficile in clinical specimens from LTCF residents in Italy. During October 2014-March 2015, all urine and diarrheic fecal samples from LTCF residents (≥65 years) with suspected urinary tract infection or C. difficile infection, respectively, received for diagnosis by 4 hospital laboratories located in different cities were analyzed. Antibiotic susceptibility testing, characterization of resistance genes, and molecular typing of pathogens were performed. Of 806 urine cultures collected from 626 residents at 44 different LTCFs, 492 were positive for microbial infection. Of these, 158 were positive for at least an ESBL-producing Enterobacteriaceae species (32.1%), with Escherichia coli as the most frequent ESBL pathogen (23.4%) followed by Klebsiella pneumoniae (4.5%). Furthermore, 4 carbapenemase producers (0.8%) (1 E. coli with VIM-1and 3 K. pneumoniae with KPC-3) were detected. The CTX-M-15 type ESBL predominated in both E. coli (71.3%) and K. pneumoniae (77.3%). Most E. coli isolates (82.6%) belonged to the ST131/H30 clone/subclone. For K. pneumoniae, ST307 and ST15 were frequent (31.8% and 22.7%, respectively), but isolates harboring blaKPC-3 belonged to CC258. Of 136 diarrheic fecal samples collected from 111 residents at 26 different LTCFs, 21 (15.4%) were positive for toxigenic C. difficile; of these, 13 (62%) were MDR (resistant to 3 or more antimicrobial agents of different classes). The predominant C. difficile polymerase chain reaction ribotype was 356/607 (42.9%), followed by 018, 449, and 078 (14% each). Public health efforts are needed to contain the diffusion of CTX-M-producing Enterobacteriaceae and MDR C. difficile in LTCF settings.
Subject(s)
Clostridioides difficile/drug effects , Clostridium Infections/epidemiology , Drug Resistance, Multiple, Bacterial , Enterobacteriaceae Infections/epidemiology , Enterobacteriaceae/drug effects , Health Facilities , beta-Lactamases/metabolism , Aged , Aged, 80 and over , Cities/epidemiology , Clostridioides difficile/isolation & purification , Cross Infection/epidemiology , Cross Infection/microbiology , Enterobacteriaceae/isolation & purification , Enterobacteriaceae Infections/microbiology , Feces/microbiology , Female , Genes, Bacterial , Genotype , Humans , Italy/epidemiology , Long-Term Care , Male , Microbial Sensitivity Tests , Molecular Typing , Prevalence , Urine/microbiology , VirulenceABSTRACT
In the present era of conjugate vaccines against Haemophilus influenzae type b, non-vaccine-preventable strains are of concern. Here, we report the first whole-genome sequence of an invasive H. influenzae type e strain. This genomic information will enable further investigations on encapsulated non-type b H. influenzae strains.
ABSTRACT
We report on the first detection of 2 cases of invasive Haemophilus influenzae type a (Hia) disease in Italy. The cases were sustained by the same Hia "strain" belonging to the ST23 clone that has previously been reported only outside Europe. The emergence of invasive Hia disease is of concern.
Subject(s)
Communicable Diseases, Emerging/epidemiology , Communicable Diseases, Emerging/microbiology , Haemophilus Infections/epidemiology , Haemophilus influenzae/isolation & purification , Adult , Aged , Female , Genotype , Haemophilus Infections/diagnosis , Haemophilus Infections/microbiology , Haemophilus influenzae/classification , Haemophilus influenzae/genetics , Humans , Italy/epidemiology , Male , Multilocus Sequence Typing , Phenotype , SerotypingSubject(s)
Anti-Bacterial Agents/pharmacology , Colistin/pharmacology , Escherichia coli Proteins/genetics , Escherichia coli/drug effects , Escherichia coli/isolation & purification , Aged , Aged, 80 and over , Anti-Bacterial Agents/adverse effects , Anti-Bacterial Agents/therapeutic use , Colistin/adverse effects , Colistin/therapeutic use , Drug Resistance, Bacterial/genetics , Escherichia coli/genetics , Escherichia coli Infections/epidemiology , Escherichia coli Infections/microbiology , Escherichia coli Infections/transmission , Escherichia coli Proteins/isolation & purification , Female , Humans , Italy/epidemiology , Long-Term Care , Male , SymbiosisABSTRACT
Nontypeable Haemophilus influenzae (NTHi) is increasingly recognized as emerging pathogen. The routine immunization of infants with conjugated vaccines against H. influenzae type b (Hib) has greatly reduced the incidence of invasive Hib disease; however a marked change in the predominant invasive serotype from Hib to NTHi has occurred. Localized infections where the role of H. influenzae is important, such as otitis media in children and acute exacerbations in chronic obstructive pulmonary disease (COPD) in adults, are almost exclusively associated with NTHi isolates. The implementation of pneumococcal conjugate vaccines has resulted in changes in frequency of nasopharynx colonizing pathogens with an increase of NTHi, although this data is yet under debate. An effective vaccine against NTHi is not currently available. The major challenge in developing a successful vaccine is the intrinsic heterogeneity of NTHi. H. influenzae protein D is used as carrier protein in the licensed 10-valent pneumococcal conjugate vaccine (Synflorix, GlaxoSmithKline), but no robust evidences for protective efficacy against NTHi otitis have been until now obtained. Several other vaccine candidates are under investigations and we hope that significant advancements in vaccine development will be achieved in the next future. Genome-based vaccine strategy might provide an additional useful tool for discovering further vaccine antigens.
Subject(s)
Haemophilus Infections/epidemiology , Haemophilus Infections/prevention & control , Haemophilus Vaccines/immunology , Haemophilus Vaccines/isolation & purification , Haemophilus influenzae/classification , Haemophilus influenzae/immunology , Adult , Child , Child, Preschool , Female , Haemophilus Infections/microbiology , Haemophilus influenzae/isolation & purification , Humans , Infant , Infant, Newborn , Male , PregnancyABSTRACT
BACKGROUND: Haemophilus influenzae is an important pathogen able to cause a wide spectrum of diseases in children. Colonization of the upper respiratory tract is a risk factor for developing disease. This study aimed to investigate the oropharyngeal carriage rate of H. influenzae in young children in two Italian cities, 15 years after H. influenzae type b (Hib) vaccination was introduced. Antibiotic resistant traits and genotypes of the colonizing H. influenzae isolates were investigated. METHODS: Oropharyngeal swabs were obtained from 717 healthy children aged <6 years (June 2012-July 2013). Potential risk factors for H. influenzae colonization were investigated. H. influenzae isolates from carriage were characterized by PCR capsular typing, ampicillin susceptibility testing, resistance-associated gene sequencing and multilocus sequence typing (MLST). For comparison purposes, 38 non-typeable H. influenzae (NTHi) isolates from invasive disease were genotyped by MLST. RESULTS: The overall H. influenzae carriage rate was 14.1% (101/717). Age, study site, presence of young siblings, and complete Hib vaccination status were independently associated with colonization. Of 101 isolates, 98 were NTHi, 2 were type e and 1 was type f. The overall ampicillin resistance rate was 15.8% (16/101). Resistance was mediated by TEM-1 ß-lactamase production in half of isolates (n=8) or modifications in penicillin-binding protein (PBP) 3 in the other half (n=8). Several substitutions were discovered in PBP3 including the Asn526Lys change. Seventy-six different STs were identified among 98 NTHi isolates from carriage, with only 4 STs (ST12, ST57, ST238, ST1238) encompassing ≥ 3 isolates. Comparison of carriage and disease isolates found that several STs were shared between the two sources, although none of the major disease-associated STs were observed in carriage isolates. CONCLUSIONS: NTHi is the predominant serotype in carriage. The importance of monitoring both NTHi colonization rate and circulating genotypes should be emphasized in the era of the Hib conjugate vaccines.
Subject(s)
Carrier State/epidemiology , Haemophilus Infections/epidemiology , Haemophilus Infections/prevention & control , Haemophilus Vaccines/administration & dosage , Haemophilus influenzae/classification , Haemophilus influenzae/isolation & purification , Oropharynx/microbiology , Child, Preschool , Cities/epidemiology , Cross-Sectional Studies , Drug Resistance, Bacterial , Female , Genotype , Haemophilus influenzae/genetics , Humans , Infant , Infant, Newborn , Italy/epidemiology , Male , Microbial Sensitivity Tests , Molecular Epidemiology , Multilocus Sequence Typing , Polymerase Chain Reaction , Sequence Analysis, DNAABSTRACT
We report the first case of neonatal bacteremia caused by a "Haemophilus quentini" isolate in Italy. The isolate was differentiated from H. influenzae by 16S rRNA sequencing and was characterized by comparison with the wild-type "H. quentini" CCUG 36167. Both isolates carried substitutions in penicillin-binding protein 3 but were susceptible to aminopenicillins.
Subject(s)
Bacteremia/diagnosis , Bacteremia/microbiology , Haemophilus Infections/diagnosis , Haemophilus Infections/microbiology , Haemophilus/classification , Haemophilus/isolation & purification , Amino Acid Substitution , Ampicillin/pharmacology , Bacterial Proteins/genetics , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Female , Genes, rRNA , Haemophilus/genetics , Humans , Infant, Newborn , Italy , Male , Microbial Sensitivity Tests , Molecular Sequence Data , Mutation, Missense , Penicillin-Binding Proteins/genetics , Phylogeny , Pregnancy , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNAABSTRACT
Extraintestinal pathogenic Escherichia coli (ExPEC) is involved in a wide spectrum of human diseases. Chickens have been suggested as reservoirs for fluoroquinolone (FQ)-resistant ExPEC strains. Here, we report the whole-genome sequences of 4 E. coli strains sharing the same sequence type (ST) (ST410) and that were isolated from human and avian sources in Italy.