Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania.
Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania.
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DOI：
10.3390/microorganisms9112300
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发表时间：
2021-11-05
期刊：
影响因子：
4.5
通讯作者：
Denes TG
中科院分区：
文献类型：
--
作者：
Hudson LK;Andershock WE;Yan R;Golwalkar M;M'ikanatha NM;Nachamkin I;Thomas LS;Moore C;Qian X;Steece R;Garman KN;Dunn JR;Kovac J;Denes TG
弯曲杆菌病是美国最常见的细菌性食源性疾病，通常与动物源性食品有关。本研究的目的是比较田纳西州（TN）和宾夕法尼亚州（PA）的临床和非临床弯曲杆菌种群，使用系统发育相关性评估来源归因模式，并确定潜在的爆发集群。研究的弯曲杆菌分离株（n = 3080）包括收集并测序用于常规监测的TN临床分离株、从宾夕法尼亚大学卫生系统设施的患者中收集的PA临床分离株以及来自两个州的非临床分离株（测序读数可在NCBI上获得）。进行系统发育分析，将分离物分类为种组，并确定每个种的种群结构。绝大多数菌株为C.空肠（n = 2132，69.2%）和C.大肠杆菌921株，占29.9%; lari（0.4%）、C. upsaliensis（0.3%）和C.胎儿（0.1%）。梭空肠组由3个分支组成，大多数非临床分离株来自家禽（62.7%）或牛（35.8%），59.7%和16.5%的临床分离株分别来自家禽和牛的亚分支。梭大肠杆菌分离株分为两个分支;大多数非临床分离株来自家禽（61.2%）或猪（29.0%）来源，74.5%、9.2%和6.1%的临床分离株分别来自与家禽、牛或猪相关的亚分支。根据基因组相似性，我们鉴定了42个C。jejuni和C.大肠杆菌潜在爆发集群。梭空肠群中有188株临床分离株，占总分离株的19.6%;空肠临床分离株，表明更大比例的弯曲杆菌病可能与爆发比以前确定。
Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical Campylobacter populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. Campylobacter isolates studied (n = 3080) included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states for which sequencing reads were available on NCBI. Phylogenetic analyses were conducted to categorize isolates into species groups and determine the population structure of each species. Most isolates were C. jejuni (n = 2132, 69.2%) and C. coli (n = 921, 29.9%), while the remaining were C. lari (0.4%), C. upsaliensis (0.3%), and C. fetus (0.1%). The C. jejuni group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The C. coli isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 C. jejuni and one C. coli potential outbreak clusters. The C. jejuni clusters contained 188 clinical isolates, 19.6% of the total C. jejuni clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.
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