Emergence of multidrug resistance among Haemophilus parainfluenzae from respiratory and urogenital samples in Barcelona, Spain

Sierra, Yanik; González-Díaz, Aida; Tubau, Fé; Imaz, Arkaitz; Cubero, Meritxell; Càmara, Jordi; Ayats, Josefina; Martí, Sara; Ardanuy, Carmen

doi:10.1007/s10096-019-03774-x

Cited by 26 publications

(13 citation statements)

References 39 publications

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“…AMR rates in Hi isolated from the respiratory tract varies between studies, with recent reports of ampicillin resistance 23.7% to 58.5%, augmentin 0% to 10.4%, cefotaxime 0% to 5.9%, co-trimoxazole 21.4% to 71.1%, and rifampicin 0% and 4.8% (49,(64)(65)(66)(67)(68)(69)(70)(71)(72). Similar rates have been reported for Hpi: ampicillin 13.2% to 50.0%, augmentin 0% to 12.5%, cefotaxime 0% to 0.3%, co-trimoxazole 14.9% to 44.2%, and rifampicin 1.5% to 26.7% (34,(73)(74)(75)(76). AMR rates detected in the present study are mostly in line with these reports, with the exception of higher rates of resistance in Hpi vs Hi.…”

Section: Discussionsupporting

confidence: 68%

Genomic diversity and antimicrobial resistance ofHaemophiluscolonising the airways of young children with cystic fibrosis

Watts

Judd

Carzino

et al. 2020

Preprint

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Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely isolated from the lungs of children with CF, however little is known about the frequency and characteristics of Haemophilus colonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing of Hi/Hpi isolated from sputum, cough swab, and bronchoalveolar lavage samples regularly collected from 147 participants aged ≤12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program. The frequency of colonisation per visit was 4.6% for Hi and 32.1% for Hpi, 80.3% of participants had Hi and/or Hpi detected on at least one visit, and using genomic data we estimate 15.6% of participants had persistent colonisation with the same strain for at least two consecutive visits. Colonising strains were genetically highly diverse and AMR was common, with 52% of Hi and 82% of Hpi displaying resistance to at least one drug. The genetic basis for AMR could be identified in most cases; novel determinants include a new plasmid encoding blaTEM-1 (ampicillin resistance), a new inhibitor-resistant blaTEM allele (augmentin resistance), and previously unreported mutations in chromosomally-encoded genes (pbp3, ampicillin resistance; folA and folP, co-trimoxazole resistance; rpoB, rifampicin resistance). Acquired AMR genes were significantly more common in Hpi than Hi (51% vs 21%, p=0.0107) and were mostly associated with the ICEHin mobile element carrying blaTEM-1, resulting in higher rates of ampicillin resistance in Hpi (73% vs 30%, p=0.0004). The genome data identified six potential instances of Haemophilus transmission between participants, three of which involved participant pairs who attended the clinic on the same day. The high prevalence of Haemophilus colonisation and high burden of antimicrobial use in children with CF likely provides a reservoir for emergence and spread of AMR as well as a source of infections.

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Section: Discussionsupporting

confidence: 68%

Genomic diversity and antimicrobial resistance ofHaemophiluscolonising the airways of young children with cystic fibrosis

Watts

Judd

Carzino

et al. 2020

Preprint

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“…Human (Smith et al, 1976;Minerbi et al, 2019) Present Humans Opportunistic urogenital pathogen (Sierra et al, 2020), digestive and biliary tract infections (Frankard et al, 2004)…”

Section: Haemophilus Parainfluenzaementioning

confidence: 99%

Microbial community origin and fate through a rural wastewater treatment plant

Newton

González

Pitre

et al. 2022

Environmental Microbiology

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Summary Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterized. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge and post‐treatment effluent were characterized. From 3163 exact sequence variants (ESVs), 860 were annotated to species‐level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially human‐associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human‐associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease‐producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human‐associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species‐level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem.

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“…Interaction nodes in the BN group showed significantly higher degrees, implying that they had more connections with other microorganisms than in the BC group ( Figures 3C, D ). Remarkably, Neisseria and Actinomyces had high degrees in the BN group, while Prevotella , Streptococcus , and Haemophilus parainfluenzae , common respiratory bacteria ( Popov et al, 2019 ; Sierra et al, 2020 ) had high degrees in the BC group. These species with high degrees are commonly considered as key taxa in the network ( Banerjee et al, 2018 ; Herren and McMahon, 2018 ).…”

Section: Resultsmentioning

confidence: 94%

“…Remarkably, Neisseria and Actinomyces had high degrees in the BN group, while Prevotella, Streptococcus, and Haemophilus parainfluenzae, common respiratory bacteria (Popov et al, 2019;Sierra et al, 2020) had high degrees in the BC group. These species with high degrees are commonly considered as key taxa in the network (Banerjee et al, 2018;Herren and McMahon, 2018).…”

Section: Microbial Interactions Exhibited Different States Between Bc and Bn Patientsmentioning

confidence: 93%

Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients

Ding

Liu

et al. 2021

Front. Cell. Infect. Microbiol.

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Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.

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Emergence of multidrug resistance among Haemophilus parainfluenzae from respiratory and urogenital samples in Barcelona, Spain

Cited by 26 publications

References 39 publications

Genomic diversity and antimicrobial resistance ofHaemophiluscolonising the airways of young children with cystic fibrosis

Genomic diversity and antimicrobial resistance ofHaemophiluscolonising the airways of young children with cystic fibrosis

Microbial community origin and fate through a rural wastewater treatment plant

Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients

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