Watts Stephen C, Judd Louise M, Carzino Rosemary, Ranganathan Sarath, Holt Kathryn E
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbournegrid.1008.9, Melbourne, Victoria, Australia.
Department of Infectious Diseases, Central Clinical School, Monash Universitygrid.1002.3, Melbourne, Victoria, Australia.
mSystems. 2021 Aug 31:e0017821. doi: 10.1128/mSystems.00178-21.
Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae and Haemophilus parainfluenzae are routinely isolated from the lungs of children with CF; however, little is known about the frequency and characteristics of Haemophilus colonization in this context. Here, we describe the detection, antimicrobial resistance (AMR), and genome sequencing of H. influenzae and isolated from airway samples of 147 participants aged ≤12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program, Melbourne, Australia. The frequency of colonization per visit was 4.6% for H. influenzae and 32.1% for , 80.3% of participants had H. influenzae and/or detected on at least one visit, and using genomic data, we estimate 15.6% of participants had persistent colonization with the same strain for at least two consecutive visits. Isolates were genetically diverse and AMR was common, with 52% of H. influenzae and 82% of displaying resistance to at least one drug. The genetic basis for AMR could be identified in most cases; putative novel determinants include a new plasmid encoding (ampicillin resistance), a new inhibitor-resistant allele (augmentin resistance), and previously unreported mutations in chromosomally carried genes (, ampicillin resistance; /, cotrimoxazole resistance; , rifampicin resistance). Acquired AMR genes were more common in than H. influenzae (51% versus 21%, = 0.0107) and were mostly associated with the ICE mobile element carrying , resulting in more ampicillin resistance in (73% versus 30%, = 0.0004). Genomic data identified six potential instances of Haemophilus transmission between participants, of which three involved participants who shared clinic visit days. Cystic fibrosis (CF) lung disease begins during infancy, and acute respiratory infections increase the risk of early disease development and progression. Microbes involved in advanced stages of CF are well characterized, but less is known about early respiratory colonizers. We report the population dynamics and genomic determinants of AMR in two early colonizer species, namely, Haemophilus influenzae and Haemophilus parainfluenzae, collected from a pediatric CF cohort. This investigation also reveals that has a high frequency of AMR carried on mobile elements that may act as a potential reservoir for the emergence and spread of AMR to H. influenzae, which has greater clinical significance as a respiratory pathogen in children. This study provides insight into the evolution of AMR and the colonization of H. influenzae and in a pediatric CF cohort, which will help inform future treatment.
儿童期呼吸道感染是早期囊性纤维化（CF）肺部疾病进展的关键风险因素。流感嗜血杆菌和副流感嗜血杆菌经常从CF患儿的肺部分离得到；然而，关于在这种情况下嗜血杆菌定植的频率和特征知之甚少。在这里，我们描述了从澳大利亚墨尔本囊性纤维化呼吸早期监测团队（AREST CF）项目中招募的147名年龄≤12岁参与者的气道样本中分离出的流感嗜血杆菌和副流感嗜血杆菌的检测、抗菌药物耐药性（AMR）及基因组测序情况。每次就诊时流感嗜血杆菌的定植频率为4.6%，副流感嗜血杆菌为32.1%，80.3%的参与者在至少一次就诊时检测到流感嗜血杆菌和/或副流感嗜血杆菌，并且利用基因组数据，我们估计15.6%的参与者同一菌株持续定植至少连续两次就诊。分离株基因多样，AMR常见，52%的流感嗜血杆菌和82%的副流感嗜血杆菌对至少一种药物耐药。在大多数情况下可以确定AMR的遗传基础；推定的新决定因素包括一个编码β-内酰胺酶（氨苄西林耐药）的新质粒、一个对抑制剂耐药的新aac(6')-Ib等位基因（阿莫西林/克拉维酸耐药）以及染色体携带基因中以前未报道的突变（blaROB-1，氨苄西林耐药；dfrA17/groEL，复方新诺明耐药；rpoB，利福平耐药）。获得性AMR基因在副流感嗜血杆菌中比在流感嗜血杆菌中更常见（51%对21%，P = 0.0107），并且大多与携带blaROB-1的ICE移动元件相关，导致副流感嗜血杆菌中氨苄西林耐药性更高（73%对30%，P = 0.0004）。基因组数据确定了参与者之间6例潜在的嗜血杆菌传播实例，其中3例涉及共享就诊日期的参与者。囊性纤维化（CF）肺部疾病始于婴儿期，急性呼吸道感染增加了早期疾病发展和进展的风险。参与CF晚期的微生物已得到充分表征，但对早期呼吸道定植菌了解较少。我们报告了从儿科CF队列中收集的两种早期定植菌，即流感嗜血杆菌和副流感嗜血杆菌的AMR群体动态和基因组决定因素。这项调查还揭示，副流感嗜血杆菌携带AMR的频率很高，这些AMR存在于移动元件上，可能成为AMR出现并传播到流感嗜血杆菌的潜在储存库，而流感嗜血杆菌作为儿童呼吸道病原体具有更大的临床意义。本研究深入了解了儿科CF队列中AMR的演变以及流感嗜血杆菌和副流感嗜血杆菌的定植情况，这将有助于为未来的治疗提供参考。
